title: SCAT, VGC, TERM, Mouse 16

description: Library name: 695_SCAT_VGC-_ISS_Term-_16_L1_1

value: 8 months


title: Liver, HGC, LAR, Mouse 3

status: Public on Dec 18 2025

type: SRA

city: Saarbrücken

first: Friederike

last: Grandke

address: Saarbrücken Campus

country: Germany

institute: Saarland University

description: Library name: 694_Liver_HC-LAR-3_L1_1

library_source: transcriptomic

data_processing:
Fastq files containing raw sequencing reads were mapped against GRCm39 and miRBase (version 22.1) 65 in order to profile miRNA counts using miRmaster (version 2.0). Information about miRNA family was obtained from mirgenedb 3.0. Detection filtering was performed by keeping only miRNAs with at least 5 raw reads in at least 10% of samples in each condition-tissue group. Expression data was normalized using rpmm normalization (reads per mapped million).
Assembly: GRCm39
Supplementary files format and content: miRNA_complete_quantification_raw.tsv: Tab-separated file of raw miRNA counts per sample.
Supplementary files format and content: lncRNA_complete_quantification_raw.tsv: Tab-separated file of raw lncRNA counts per sample.
Supplementary files format and content: piRNA_complete_quantification_raw.tsv: Tab-separated file of raw piRNA counts per sample.
Supplementary files format and content: rRNA_complete_quantification_raw.tsv: Tab-separated file of raw rRNA counts per sample.
Supplementary files format and content: scaRNA_complete_quantification_raw.tsv: Tab-separated file of raw scaRNA counts per sample.
Supplementary files format and content: snoRNA_complete_quantification_raw.tsv: Tab-separated file of raw snoRNA counts per sample.
Supplementary files format and content: snRNA_complete_quantification_raw.tsv: Tab-separated file of raw snRNA counts per sample.
Supplementary files format and content: tRNA_complete_quantification_raw.tsv: Tab-separated file of raw tRNA counts per sample.

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: For the Rodent Research Reference Mission 1 (RRR-1) / Rodent Research-8 (RR-8) 40 BALB/cAnNTac female mice were sent to the International Space Station (ISS) on 12/5/2018 (Flight mice).VGC mice were housed at NASA Kennedy Space Center in standard vivarium conditions at 4 mice per cage, 20-22.2 °C, 12hr light 12hr dark. HGC mice housing was matched to the conditions experienced by Flight mice (as closely as possible) by using double density housing (same Habitat Units and Transporters as Flight mice at launch), matched temperature, humidity, and carbon dioxide levels based on actual flight environmental monitoring. To dissect all mice together in matching conditions, VGC and HGC mice were transported to Scripps Institute just before the return of the Flight mice and were dissected in matching conditions (+/- 1 day).From each of the main experimental groups, half of the mice were assigned to the ISS Terminal (ISS Term) subgroup, which were sacrificed onboard the ISS (Flight) or on Earth (VGC, HGC) 22-24 days after launch. The other half were assigned to the Live Animal Return (LAR) group, which were returned alive to Earth on 1/14/2019 after 39.5 days on the ISS, and collected 2-4 days after splashdown following functional assays at Scripps Research Institute.

extract_protocol:
LAR mice were anesthetized with gas anesthesia and euthanized by means of cardiac puncture blood draw (exsanguination) and double thoracotomy. The liver was removed, weighed, dissected into individual lobes (1- left/right medial, 2- left lateral and 3- remaining lobes) and snap frozen on liquid nitrogen. All tissues were collected and frozen within 10-16 minutes of thoracotomy procedure. All groups were treated identically. Organ samples were maintained at -80C or lower temperatures throughout the storage, and during transportation and shipment. TERM mice were anesthetized with ketamine/xylazine/acepromazine at a dose of 120/15/3 mg/kg and euthanized by means of cardiac puncture blood draw (exsanguination) and double thoracotomy. The spleen was dissected fresh from each carcass and placed in a tube containing RNA Later. The carcass was then wrapped in foil and frozen in MELFI on board the ISS or in ground -80C freezers. Carcasses were maintained at -80C or lower temperatures throughout the storage on board the ISS, in ground freezers and during transportation and shipment. The mice were brought back to earth where dissection was held. It should be noted that carcasses frozen whole onboard the ISS were free-floating and thus in direct contact with air. This prevented them from snap freezing like samples collected on Earth which were placeddirectly in liquid nitrogen. Carcasses were thawed at room temperature one at a time (staggered)until the tissues were sufficiently pliable for dissection (approximately 60-90 minutes). Once thawed, multiple tissues were collected from each carcass within 30min of the first tissue collected. The liver was removed from each carcass, weighed, dissected into individual lobes (1-left/right medial, 2- left lateral and 3- remaining lobes) and snap frozen on liquid nitrogen.  The miRNeasy-96 protocol was followed for all samples with some modifications, as follows. Tissue Preparation: To avoid overloading the miRNeasy-96 columns, some frozen samples were trimmed to smaller sizes. All kidney, liver, and spleen samples were all trimmed to ~25mgs due to their high RNA content. Pancreas samples were trimmed to ~25mgs if they exceeded 45mgs. GAT, MAT, and SCAT samples >200mgs were trimmed to ~100mgs as samples of large size homogenize poorly in 96-well format, even though adipose tissues have relatively low RNA content. BAT and lung samples >100mgs were trimmed to ~50mgs, and thymi >50mgs were trimmed to ~25mgs. The diaphragm did not require trimming, and whole hemi-brains and whole hearts were homogenized by hand with the TissueRuptor in 1ml QIAzol per 50mgs tissue, since trimming samples in a reproducible way to capture the same organ subregion for each would be difficult. Bead homogenization: All samples, including those previously homogenized with the TissueRuptor, were randomized in 96-well format. Two 96-well plates were run simultaneously as follows. 96-well collection microtube plates were chilled on dry ice, and trimmed tissue samples were placed at the bottom of each well. One pre-chilled 5mm stainless steel bead was then placed on top of the tissue samples with bead dispenser. 700ul pre-chilled (4C) QIAzol was then added to each well, or 700ul QIAzol homogenate from the pre-homogenized heart and brain samples. Plates were immediately homogenized on the TissueLyser II for a total of four 5min runs at 25Hz, and plates were rotated and switched between the two arms of the TissueLyser II between each run. Plates were then left at room temperature for 5min before pelleting debris at 6000 x g for 1min at 4C. Phase Separation & RNA collection: Debris- and bead-free homogenate was then transferred to a new plate, to which 140ul chloroform was added to each well, and plates were shaken vigorously for 3min at room temperature before being spun at 6000 x g for 4min at 4C. 300ul aqueous phase was then transferred to a new S-Block, to which 525ul 100% EtOH was added and mixed by pipetting, followed by a room temperature spin at 6000 x g for 30s. The entire volume was then transferred to a miRNeasy-96 plate on top of an S-plate, sealed with AirPore tape sheet, and spun at 5600 x g for 4min at room temperature. Flow through was discarded, and columns washed with 800ul RWT and spun as above. This was repeated with 800ul RPE, and a final 800ul RPE wash was followed by a 10min spin. Finally, 50ul RNase-free water was added to each column and incubated at room temperature for 1min, then spun at 5600 x g for 4min at room temperature. The elution was repeated with a second volume of 50ul RNase-free water. RNA samples were stored at -80C.
All samples were processed using the MGIEasy Small RNA Library Prep Kit with the high-throughput MGI SP-960 sample prep system according to the manufacturer's protocol to generate sequencing libraries.

tag: tissue

value: Liver

tag: experiment group

value: HGC-LAR

tag: Sex

value: female

tag: strain

value: BALB/cAnNTac

tag: mouse id

tag: age


title: Thymus, HGC, LAR, Mouse 3

description: Library name: 691_Thymus_HC-LAR-3_L1_1

source_name: Thymus

value: Thymus


title: Lung, HGC, TERM, Mouse 2

description: Library name: 693_Lung_HGC-_ISS_Term-_2_L1_1

source_name: Lung

value: Lung

value: HGC-TERM

value: 3 months


title: Spleen, FL, TERM, Mouse 3

description: Library name: 692_Spleen_FL-_ISS_Term-_3_L1_1

source_name: Spleen

value: Spleen

value: FL-TERM


title: MAT, HGC, TERM, Mouse 1

description: Library name: 690_MAT_HGC-_ISS_Term-_1_L1_1

source_name: MAT

value: MAT


title: Kidney, HGC, LAR, Mouse 2

description: Library name: 689_Kidney_HC-LAR-2_L1_1

source_name: Kidney

value: Kidney


title: Spleen, VGC, TERM, Mouse 1

description: Library name: 688_Spleen_VGC-_ISS_Term-_1_L1_1

value: VGC-TERM


title: MAT, VGC, LAR, Mouse 3

description: Library name: 687_MAT_VC-LAR-3_L1_1

value: VGC-LAR


title: Lung, FL, VGC, LAR, Mouse 1

description: Library name: 686_Lung_FL-LAR-1_L1_1


title: Pancreas, VGC, LAR, Mouse 4

description: Library name: 685_Pancreas_VC-LAR-4_L1_1

source_name: Pancreas

value: Pancreas


title: Pancreas, VGC, TERM, Mouse 3

description: Library name: 710_Pancreas_VGC-_ISS_Term-_3_L1_1


title: MAT, FL, TERM, Mouse 14

description: Library name: 684_MAT_FL-_ISS_Term-_14_L1_1


title: MAT, VGC, LAR, Mouse 5

description: Library name: 683_MAT_VC-LAR-5_L1_1


title: Spleen, FL, VGC, LAR, Mouse 12

description: Library name: 681_Spleen_FL-LAR-12_L1_1


title: Liver, HGC, TERM, Mouse 5

description: Library name: 680_Liver_HGC-_ISS_Term-_5_L1_1


title: SCAT, HGC, LAR, Mouse 14

description: Library name: 699_SCAT_HC-LAR-14_L1_1

source_name: SCAT

value: SCAT


title: Diaphragm, VGC, LAR, Mouse 3

description: Library name: 678_Diaphragm_VC-LAR-3_L1_1

source_name: Diaphragm

value: Diaphragm

value: 8 months


title: Heart, HGC, TERM, Mouse 3

description: Library name: 679_Heart_HGC-_ISS_Term-_3_L1_1

source_name: Heart

value: Heart


title: Kidney, HGC, LAR, Mouse 12

description: Library name: 677_Kidney_HC-LAR-12_L1_1

value: HGC-LAR

value: female


title: Kidney, FL, VGC, LAR, Mouse 12

description: Library name: 676_Kidney_FL-LAR-12_L1_1

value: BALB/cAnNTac


title: SCAT, VGC, LAR, Mouse 5

description: Library name: 675_SCAT_VC-LAR-5_L1_1


title: SCAT, FL, TERM, Mouse 11

description: Library name: 673_SCAT_FL-_ISS_Term-_11_L1_1


title: BAT, HGC, TERM, Mouse 14

description: Library name: 670_BAT_HGC-_ISS_Term-_14_L1_1

source_name: BAT

value: BAT


title: Lung, HGC, TERM, Mouse 4

description: Library name: 669_Lung_HGC-_ISS_Term-_4_L1_1

value: Lung

value: HGC-TERM


title: Brain, HGC, TERM, Mouse 17

description: Library name: 674_Brain_HGC-_ISS_Term-_17_L1_1

source_name: Brain

value: Brain


title: Liver, FL, VGC, LAR, Mouse 11

description: Library name: 668_Liver_FL-LAR-11_L1_1

value: Liver


title: SCAT, VGC, TERM, Mouse 13

description: Library name: 667_SCAT_VGC-_ISS_Term-_13_L1_1


title: MAT, HGC, LAR, Mouse 1

description: Library name: 672_MAT_HC-LAR-1_L1_1

value: MAT

value: 3 months


title: BAT, HGC, TERM, Mouse 2

description: Library name: 665_BAT_HGC-_ISS_Term-_2_L1_1


title: Pancreas, HGC, LAR, Mouse 16

description: Library name: 663_Pancreas_HC-LAR-16_L1_1


title: Spleen, FL, VGC, LAR, Mouse 5

description: Library name: 666_Spleen_FL-LAR-5_L1_1

value: Spleen


title: MAT, VGC, TERM, Mouse 2

description: Library name: 661_MAT_VGC-_ISS_Term-_2_L1_1

value: VGC-TERM


title: Pancreas, VGC, LAR, Mouse 13

description: Library name: 660_Pancreas_VC-LAR-13_L1_1

value: Pancreas

value: VGC-LAR


title: Thymus, VGC, TERM, Mouse 3

description: Library name: 662_Thymus_VGC-_ISS_Term-_3_L1_1

value: Thymus


title: MAT, HGC, TERM, Mouse 2

description: Library name: 659_MAT_HGC-_ISS_Term-_2_L1_1


title: GAT, VGC, TERM, Mouse 5

description: Library name: 653_GAT_VGC-_ISS_Term-_5_L1_1

source_name: GAT

value: GAT


title: SCAT, VGC, LAR, Mouse 16

description: Library name: 658_SCAT_VC-LAR-16_L1_1

value: SCAT

value: 8 months


title: Thymus, FL, TERM, Mouse 16

description: Library name: 656_Thymus_FL-_ISS_Term-_16_L1_1

value: FL-TERM

value: female


title: Lung, VGC, LAR, Mouse 4

description: Library name: 657_Lung_VC-LAR-4_L1_1

value: BALB/cAnNTac


title: Lung, FL, VGC, LAR, Mouse 3

description: Library name: 655_Lung_FL-LAR-3_L1_1

value: Lung


title: GAT, VGC, TERM, Mouse 1

description: Library name: 671_GAT_VGC-_ISS_Term-_1_L1_1


title: Thymus, VGC, LAR, Mouse 16

description: Library name: 648_Thymus_VC-LAR-16_L1_1


title: Lung, VGC, LAR, Mouse 2

description: Library name: 645_Lung_VC-LAR-2_L1_1


title: Diaphragm, FL, TERM, Mouse 2

description: Library name: 647_Diaphragm_FL-_ISS_Term-_2_L1_1

value: Diaphragm


title: SCAT, FL, VGC, LAR, Mouse 14

description: Library name: 649_SCAT_FL-LAR-14_L1_1


title: MAT, HGC, LAR, Mouse 13

description: Library name: 644_MAT_HC-LAR-13_L1_1

value: HGC-LAR


title: SCAT, HGC, LAR, Mouse 16

description: Library name: 650_SCAT_HC-LAR-16_L1_1


title: Diaphragm, FL, TERM, Mouse 1

description: Library name: 646_Diaphragm_FL-_ISS_Term-_1_L1_1


title: Spleen, HGC, LAR, Mouse 13

description: Library name: 664_Spleen_HC-LAR-13_L1_1


title: BAT, VGC, LAR, Mouse 12

description: Library name: 641_BAT_VC-LAR-12_L1_1

value: BAT


title: Spleen, HGC, LAR, Mouse 16

description: Library name: 642_Spleen_HC-LAR-16_L1_1


title: BAT, HGC, TERM, Mouse 5

description: Library name: 640_BAT_HGC-_ISS_Term-_5_L1_1

value: HGC-TERM


title: Heart, HGC, LAR, Mouse 8

description: Library name: 639_Heart_HC-LAR-8_L1_1

value: Heart


title: Liver, VGC, LAR, Mouse 14

description: Library name: 637_Liver_VC-LAR-14_L1_1

value: Liver

value: 3 months


title: SCAT, VGC, LAR, Mouse 11

description: Library name: 638_SCAT_VC-LAR-11_L1_1


title: SCAT, VGC, TERM, Mouse 12

description: Library name: 635_SCAT_VGC-_ISS_Term-_12_L1_1

value: VGC-TERM


title: Thymus, FL, TERM, Mouse 2

description: Library name: 654_Thymus_FL-_ISS_Term-_2_L1_1


title: Lung, FL, TERM, Mouse 11

description: Library name: 633_Lung_FL-_ISS_Term-_11_L1_1


title: Spleen, VGC, TERM, Mouse 14

description: Library name: 651_Spleen_VGC-_ISS_Term-_14_L1_1

value: Spleen


title: GAT, VGC, LAR, Mouse 16

description: Library name: 631_GAT_VC-LAR-16_L1_1

value: VGC-LAR


title: Kidney, VGC, LAR, Mouse 5

description: Library name: 627_Kidney_VC-LAR-5_L1_1

value: Kidney


title: Diaphragm, HGC, LAR, Mouse 4

description: Library name: 632_Diaphragm_HC-LAR-4_L1_1


title: Brain, FL, TERM, Mouse 18

description: Library name: 628_Brain_FL-_ISS_Term-_18_L1_1

value: Brain


title: GAT, FL, TERM, Mouse 12

description: Library name: 652_GAT_FL-_ISS_Term-_12_L1_1

value: GAT

value: 8 months


title: BAT, FL, VGC, LAR, Mouse 5

description: Library name: 626_BAT_FL-LAR-5_L1_1

value: female


title: Pancreas, FL, TERM, Mouse 4

description: Library name: 630_Pancreas_FL-_ISS_Term-_4_L1_1

value: Pancreas

value: FL-TERM

value: BALB/cAnNTac


title: MAT, FL, VGC, LAR, Mouse 16

description: Library name: 629_MAT_FL-LAR-16_L1_1

value: MAT


title: Diaphragm, VGC, LAR, Mouse 14

description: Library name: 625_Diaphragm_VC-LAR-14_L1_1

value: Diaphragm


title: Kidney, FL, TERM, Mouse 3

description: Library name: 643_Kidney_FL-_ISS_Term-_3_L1_1


title: Diaphragm, HGC, LAR, Mouse 3

description: Library name: 620_Diaphragm_HC-LAR-3_L1_1

value: HGC-LAR


title: Thymus, VGC, TERM, Mouse 5

description: Library name: 623_Thymus_VGC-_ISS_Term-_5_L1_1

value: Thymus


title: Lung, FL, VGC, LAR, Mouse 14

description: Library name: 619_Lung_FL-LAR-14_L1_1

value: Lung


title: Diaphragm, VGC, LAR, Mouse 11

description: Library name: 624_Diaphragm_VC-LAR-11_L1_1


title: Heart, FL, VGC, LAR, Mouse 13

description: Library name: 636_Heart_FL-LAR-13_L1_1

value: Heart

value: 3 months


title: SCAT, VGC, LAR, Mouse 12

description: Library name: 622_SCAT_VC-LAR-12_L1_1

value: SCAT


title: Lung, HGC, TERM, Mouse 5

description: Library name: 617_Lung_HGC-_ISS_Term-_5_L1_1

value: HGC-TERM


title: SCAT, HGC, TERM, Mouse 11

description: Library name: 615_SCAT_HGC-_ISS_Term-_11_L1_1


title: BAT, VGC, TERM, Mouse 14

description: Library name: 612_BAT_VGC-_ISS_Term-_14_L1_1

value: BAT

value: VGC-TERM


title: Lung, VGC, TERM, Mouse 13

description: Library name: 621_Lung_VGC-_ISS_Term-_13_L1_1


title: BAT, FL, VGC, LAR, Mouse 2

description: Library name: 614_BAT_FL-LAR-2_L1_1

value: VGC-LAR


title: MAT, HGC, TERM, Mouse 4

description: Library name: 634_MAT_HGC-_ISS_Term-_4_L1_1


title: Kidney, VGC, TERM, Mouse 5

description: Library name: 616_Kidney_VGC-_ISS_Term-_5_L1_1

value: Kidney


title: BAT, FL, TERM, Mouse 14

description: Library name: 613_BAT_FL-_ISS_Term-_14_L1_1

value: female

value: 8 months


title: MAT, FL, TERM, Mouse 3

description: Library name: 618_MAT_FL-_ISS_Term-_3_L1_1

value: FL-TERM


title: Lung, FL, VGC, LAR, Mouse 13

description: Library name: 611_Lung_FL-LAR-13_L1_1

value: BALB/cAnNTac


title: Spleen, VGC, LAR, Mouse 17

description: Library name: 605_Spleen_VC-LAR-17_L1_1

value: Spleen


title: GAT, HGC, LAR, Mouse 3

description: Library name: 610_GAT_HC-LAR-3_L1_1

value: GAT


title: Thymus, HGC, TERM, Mouse 11

description: Library name: 604_Thymus_HGC-_ISS_Term-_11_L1_1


title: Lung, VGC, LAR, Mouse 16

description: Library name: 603_Lung_VC-LAR-16_L1_1


title: SCAT, HGC, LAR, Mouse 2

description: Library name: 598_SCAT_HC-LAR-2_L1_1

value: HGC-LAR


title: Kidney, FL, VGC, LAR, Mouse 3

description: Library name: 609_Kidney_FL-LAR-3_L1_1


title: BAT, FL, VGC, LAR, Mouse 12

description: Library name: 607_BAT_FL-LAR-12_L1_1


title: GAT, VGC, LAR, Mouse 1

description: Library name: 602_GAT_VC-LAR-1_L1_1


title: Lung, VGC, LAR, Mouse 12

description: Library name: 600_Lung_VC-LAR-12_L1_1


title: Diaphragm, FL, VGC, LAR, Mouse 2

description: Library name: 601_Diaphragm_FL-LAR-2_L1_1

value: Diaphragm


title: Brain, VGC, TERM, Mouse 8

description: Library name: 599_Brain_VGC-_ISS_Term-_8_L1_1

value: Brain


title: Spleen, FL, VGC, LAR, Mouse 13

description: Library name: 596_Spleen_FL-LAR-13_L1_1


title: GAT, FL, VGC, LAR, Mouse 13

description: Library name: 592_GAT_FL-LAR-13_L1_1


title: SCAT, VGC, TERM, Mouse 5

description: Library name: 591_SCAT_VGC-_ISS_Term-_5_L1_1


title: Pancreas, FL, VGC, LAR, Mouse 2

description: Library name: 589_Pancreas_FL-LAR-2_L1_1

value: Pancreas


title: Kidney, FL, VGC, LAR, Mouse 14

description: Library name: 585_Kidney_FL-LAR-14_L1_1

value: 3 months


title: GAT, HGC, LAR, Mouse 16

description: Library name: 595_GAT_HC-LAR-16_L1_1


title: Lung, VGC, TERM, Mouse 2

description: Library name: 586_Lung_VGC-_ISS_Term-_2_L1_1

value: Lung


title: Heart, VGC, LAR, Mouse 17

description: Library name: 584_Heart_VC-LAR-17_L1_1

value: Heart


title: MAT, HGC, LAR, Mouse 16

description: Library name: 590_MAT_HC-LAR-16_L1_1

value: MAT


title: GAT, FL, VGC, LAR, Mouse 14

description: Library name: 588_GAT_FL-LAR-14_L1_1


title: Heart, HGC, TERM, Mouse 11

description: Library name: 582_Heart_HGC-_ISS_Term-_11_L1_1

value: HGC-TERM


title: MAT, VGC, TERM, Mouse 4

description: Library name: 608_MAT_VGC-_ISS_Term-_4_L1_1

value: VGC-TERM


title: Old muscle - replicate 3

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

description: Library name: old_muscle_EVRNA3

data_processing:
BWA followed by featureCounts
Assembly: mm10
Supplementary files format and content: featureCounts

source_name: muscle

extract_protocol:
miRNAs were extracted exosomes that were collected from young and old mouse muscle
miRNA-seq

value: muscle

tag: time

value: old


title: Young muscle - replicate 2

description: Library name: Muscle_EV_RNA_2

value: young


title: Old muscle - replicate 2

description: Library name: old_muscle_EVRNA2


title: Old muscle - replicate 1

description: Library name: old_muscle_EVRNA1


title: Spleen, HGC, TERM, Mouse 2

description: Library name: 587_Spleen_HGC-_ISS_Term-_2_L1_1

value: female


title: Heart, FL, VGC, LAR, Mouse 17

description: Library name: 579_Heart_FL-LAR-17_L1_1

value: VGC-LAR

value: BALB/cAnNTac


title: RNA_seq_Nfkb1_KO_BMDC_Day5

city: Los Angeles

first: Benancio

last: Rodriguez

state: CA

address: 611 Charles E Young Dr.

department: MIMG

country: USA

institute: UC Los Angeles

data_processing:
Demultiplexed and trimmed reads were mapped to the NCBI37/mm9 genome using Hisat2.
After alignment, samples were processed into BAM files using Samtools.
Read counts were extracted using SeqMonk. Normalized read counts (RPKMs) were generated by normalizing for sequencing depth (per million reads) and gene length (kilobases).
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample.

molecule: polyA RNA

source_name: BMDC

growth_protocol: Grown for 3-5 days in RPMI + 10% FBS + 2-BME + Pen/Strep and 100ng/mL of Flt3L at 1x10^6 cells/mL. Media replenished on day 3

extract_protocol:
Cells were harvested in trizol and RNA was extracted using phenol-chloroform
Libraries were constructed by UCLA TCGB using the Kapa mRNA hyperprep Library Preparation Kit according to manufacturer instructions.

tag: cell type

value: BMDC

tag: genotype

tag: treatment

value: Flt3 Differentiation:Day 5


title: RNA_seq_WT_BMDC_Day5

value: Wild-type (C57/B16)


title: Young muscle - replicate 3

description: Library name: Muscle_EV_RNA_3


title: Brain, FL, VGC, LAR, Mouse 5

description: Library name: 580_Brain_FL-LAR-5_L1_1

value: Brain


title: Young muscle - replicate 1

description: Library name: Muscle_EV_RNA_1


title: BAT, HGC, LAR, Mouse 11

description: Library name: 583_BAT_HC-LAR-11_L1_1

value: BAT

value: HGC-LAR

value: 8 months


title: Fnfs-derived M1 macrophages cLIUS treated, Day 3, Biological Replicate 3

city: HUNTSVILLE

first: Anuradha

last: Subramanian

state: AL

address: 301 Sparkman Drive NW

department: Chemical Engineering

institute: University of Alabama in Huntsville

description:
Library name: M1-cLIUS-Rep 3
Fnfs-induced M1 macrophages cultured for 3 days with continuous low-intensity ultrasound (cLIUS) treatment.

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38.p14 (GCF_000001405.40) using the DRAGEN RNA-seq pipeline (Illumina), which is based on the STAR aligner. Gene-level read counts were generated using featureCounts, and transcript-level quantifications were obtained using the DRAGEN RNA-seq workflow.
Assembly: Homo sapiens GRCh38.p14 (GCF_000001405.40)
Supplementary files format and content: Plain text, tab-delimited (.sf) files containing transcript-level (*.quant.sf) and gene-level (*.quant.genes.sf) quantifications; columns include transcript or gene ID, length, effective length (for transcripts), TPM, and estimated counts.

organism: Homo sapiens

source_name: Peripheral blood

growth_protocol: THP1 cells were treated with 200 nM of PMA to generate M0 macrophages which were further treated with 25 µg/mL fibronectin fragments to generate Fnfs-derived M1 macrophages. The encapulated cell hydrogel constructs were maintained in RPMI medium throught the differentiation process. The hydrogel constructs were formed of 1.2% sodium alginate.

extract_protocol:
Cells were released from hydrogels (each replicate had 10 hydrogels) using dissolution buffer (55 mM sodium citrate, 50 mM EDTA, 90 mM NaCl, pH 6.9) and homogenized in TRIzol.RNA was isolated using the miRNeasy Micro Kit.
Total RNA was extracted from TRIzol lysates and assessed for integrity (RIN ≥ 9.0). Poly(A)+ RNA was enriched using oligo-dT magnetic beads (NEBNext Poly(A) Magnetic Isolation Module). Strand-specific libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs), following the manufacturer’s protocol. Libraries were quantified using KAPA qPCR and quality-checked on BioAnalyzer or TapeStation (RIN cutoff ≥ 7.0). Libraries were multiplexed and sequenced on Illumina NextSeq 6000 (paired-end 101 bp reads, 101-8-8-101 structure) or NovaSeq 6000 (~25 million paired-end reads per sample).

treatment_protocol: Fnfs-derived M1 macrophages received no treatment and were maintained for 72 hours in RPMI media for control group and were treated with cLIUS (2.5 Vpp, 5 MHz, 20 minutes per application, four applications per day) for 72 hours.

value: Peripheral blood

tag: cell line

value: THP1; TIB-202

value: monocyte

value: cLIUS derived macrophage polarization


title: Fnfs-derived M1 macrophages cLIUS treated, Day 3, Biological Replicate 2

description:
Library name: M1-cLIUS-Rep 2
Fnfs-induced M1 macrophages cultured for 3 days with continuous low-intensity ultrasound (cLIUS) treatment.


title: Fnfs-derived M1 macrophages cLIUS treated, Day 3, Biological Replicate 1

description:
Library name: M1-cLIUS-Rep 1
Fnfs-induced M1 macrophages cultured for 3 days with continuous low-intensity ultrasound (cLIUS) treatment.


title: Pancreas, HGC, LAR, Mouse 1

description: Library name: 574_Pancreas_HC-LAR-1_L1_1

value: Pancreas

value: 3 months


title: Lung, FL, TERM, Mouse 3

description: Library name: 581_Lung_FL-_ISS_Term-_3_L1_1

value: Lung

value: FL-TERM


title: Lung, HGC, TERM, Mouse 14

description: Library name: 571_Lung_HGC-_ISS_Term-_14_L1_1

value: HGC-TERM

value: female


title: Fnfs-derived M1 macrophages untreated, Day 3, Biological Replicate 1

description:
Library name: M1-Control-Rep 1
Fnfs-induced M1 macrophages cultured for 3 days without continuous low-intensity ultrasound (cLIUS) treatment.

value: untreated


title: Diaphragm, HGC, LAR, Mouse 13

description: Library name: 577_Diaphragm_HC-LAR-13_L1_1

value: Diaphragm

value: BALB/cAnNTac


title: RNA_seq_Nfkb1_KO_BMDC_Day3

value: BMDC

value: Flt3 Differentiation:Day 3


title: MAT, FL, VGC, LAR, Mouse 2

description: Library name: 594_MAT_FL-LAR-2_L1_1

value: MAT

value: VGC-LAR


title: Heart, HGC, LAR, Mouse 16

description: Library name: 593_Heart_HC-LAR-16_L1_1

value: Heart

value: HGC-LAR

value: 8 months


title: Pancreas, FL, VGC, LAR, Mouse 11

description: Library name: 576_Pancreas_FL-LAR-11_L1_1


title: BAT, FL, VGC, LAR, Mouse 3

description: Library name: 567_BAT_FL-LAR-3_L1_1

value: BAT


title: HKI-even-ChIRP-seq

city: Tianjin

first: Yuyang

last: Qian

state: Tianjin

address: 94 Weijin Road

department: cell and genetic department

country: China

institute: Nankai university

description: Library name: HKI-ChIRP-seq,even

library_source: genomic

data_processing:
Clean reads of ChIRP-seq were mapped to hg38 using STAR. Normalized bigwigs of even, odd, and merged files were generated using the ChIRP-seq processing scripts . Peaks of merged bigwig were called using MACS2, and called peaks were filtered to exclude blacklist regions from ENCODE. Peaks with correlation of even and odd > 0.8, FDR < 0.05, and read coverage > 2-fold of the input were kept as confident HOTAIR target regions.
Assembly: hg38
Supplementary files format and content: xls file  include genes counts values include ChIRP signal peaks for each Sample
Library strategy: ChIRP-seq

molecule: genomic DNA

source_name: 22Rv1_Cell line

growth_protocol: 22Rv1 cell line was cultured in 1640 medium supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
ChIRP-seq: Cells were fixed with glutaraldehyde  for 10 min and nucleus was isolated and sheared to 100-500 bp fragments by sonication, then hybridized with DNA probes. Libraries were prepared using the NEBNext DNA library kit according to the manufacturer's instructions (New England BioLabs), using Illumina novaseq6000.
ChIRP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HKI cell lines were acquired by Crispr/Cas9 mediated HOTAIR poly-A knock in.

value: 22Rv1_Cell line

value: Human prostate cancer

value: HOTAIR poly-A Knock-in


title: RNA_seq_WT_BMDC_Day3

value: Wild-type (C57/B16)


title: 22Rv1-WT-HOTAIR-odd-ChIRP-seq-2

description: Library name: 22Rv1-WT-HOTAIR-ChIP-seq-2, odd

value: WT


title: Thymus, HGC, TERM, Mouse 12

description: Library name: 565_Thymus_HGC-_ISS_Term-_12_L1_1

value: Thymus

value: HGC-TERM

value: female


title: Kidney, HGC, LAR, Mouse 4

description: Library name: 575_Kidney_HC-LAR-4_L1_1

value: Kidney

value: BALB/cAnNTac


title: GAT, HGC, TERM, Mouse 13

description: Library name: 563_GAT_HGC-_ISS_Term-_13_L1_1

value: GAT


title: Pancreas, FL, VGC, LAR, Mouse 1

description: Library name: 572_Pancreas_FL-LAR-1_L1_1

value: Pancreas

value: 3 months


title: Diaphragm, HGC, LAR, Mouse 14

description: Library name: 573_Diaphragm_HC-LAR-14_L1_1

value: Diaphragm


title: Fnfs-derived M1 macrophages untreated, Day 3, Biological Replicate 3

description:
Library name: M1-Control-Rep 3
Fnfs-induced M1 macrophages cultured for 3 days without continuous low-intensity ultrasound (cLIUS) treatment.

value: Peripheral blood

value: THP1; TIB-202

value: monocyte

value: untreated


title: Fnfs-derived M1 macrophages untreated, Day 3, Biological Replicate 2

description:
Library name: M1-Control-Rep 2
Fnfs-induced M1 macrophages cultured for 3 days without continuous low-intensity ultrasound (cLIUS) treatment.


title: SCAT, FL, TERM, Mouse 13

description: Library name: 570_SCAT_FL-_ISS_Term-_13_L1_1

value: SCAT

value: FL-TERM

value: 8 months


title: IHA, Control, Biol Rep 2

city: Notre Dame

first: Christopher

last: Patzke

state: IN

address: 109A Galvin Life Sciences Building

department: Department of Biological Sciences

institute: University of Notre Dame

description:
Library name: UC2
v1.5 S4 200 cycle

data_processing:
Raw sequencing reads were aligned to the reference genome and counted using STAR (v. 2.7.2).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw counts for each sample

source_name: IHA, Creative Bioarray

extract_protocol:
Zymo Research, Direct-zol RNA Miniprep Kit (R2051)
NEBNext Ultra II Directional RNA Library Prep kit

value: IHA, Creative Bioarray

value: control


title: IHA, Compressed, Biol Rep 1

description:
Library name: C1
v1.5 S4 200 cycle

value: mechanical compression


title: Diaphragm, FL, VGC, LAR, Mouse 3

description: Library name: 578_Diaphragm_FL-LAR-3_L1_1

value: VGC-LAR

value: female


title: HKI-odd-ChIRP-seq

description: Library name: HKI-ChIRP-seq, odd

value: 22Rv1_Cell line

value: Human prostate cancer

value: HOTAIR poly-A Knock-in


title: Pancreas, VGC, LAR, Mouse 16

description: Library name: 568_Pancreas_VC-LAR-16_L1_1

value: Pancreas

value: BALB/cAnNTac


title: 22Rv1-WT-HOTAIR-even-ChIRP-seq-2

description: Library name: 22Rv1-WT-HOTAIR-ChIRP-seq-2, even

value: WT


title: CX-1 cells, Combination, 2Day, rep1

city: Ganzhou

first: zhou

last: dongdong

address: hexie avenue

institute: Gannan Medical University

description: Library name: X_10

data_processing:
Illumina NovaSeq 6000
The clustering of the index-coded samples was performed on a cBotCluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia)according to the manufacturer’s instructions
After cluster generation, the librarypreparations were sequenced on an Illumina Novaseq platform and 150 bppaired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through fastpsoftware.
Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean reads were aligned to the referencegenome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped toeach gene.
Differential expression analysis oftwo conditions/groups (two biological replicates per condition) was performedusing the DESeq2 R package (1.20.0), Genes with an adjusted P-value <=0.05 found by DESeq2 wereassigned as differentially expressed
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm counts for each sample

source_name: cell line

growth_protocol: CX-1 cell were cultured in a medium containing DMEM and F12 medium  in a 1:1 ratio with 1% glutamine at 37 °C under 5% CO2

extract_protocol:
TRIzol(Thermo Fisher)
AMPure XP system and Agilent Bioanalyzer2100 system

treatment_protocol: CX-1 cells were treated with 3μg/ml IMMU132 、3μM GSK2606414 and combanition for 48 h

value: cell line

value: CRC

value: Combination


title: Kidney, FL, TERM, Mouse 2

description: Library name: 569_Kidney_FL-_ISS_Term-_2_L1_1

value: Kidney

value: 3 months


title: MAT, FL, TERM, Mouse 13

description: Library name: 564_MAT_FL-_ISS_Term-_13_L1_1

value: MAT

value: FL-TERM

value: 8 months


title: Pancreas, VGC, LAR, Mouse 2

description: Library name: 555_Pancreas_VC-LAR-2_L1_1


title: MAT, HGC, TERM, Mouse 14

description: Library name: 554_MAT_HGC-_ISS_Term-_14_L1_1

value: HGC-TERM


title: IHA, Compressed, Biol Rep 3

description:
Library name: C3
v1.5 S4 200 cycle

value: IHA, Creative Bioarray

value: mechanical compression


title: IHA, Compressed, Biol Rep 2

description:
Library name: C2
v1.5 S4 200 cycle


title: Kidney, VGC, TERM, Mouse 4

description: Library name: 561_Kidney_VGC-_ISS_Term-_4_L1_1

value: VGC-TERM

value: female


title: BAT, VGC, TERM, Mouse 2

description: Library name: 562_BAT_VGC-_ISS_Term-_2_L1_1

value: BAT


title: CX-1 cells, GSK2606414, 2Day, rep1

description: Library name: X_7


title: Diaphragm, VGC, LAR, Mouse 13

description: Library name: 559_Diaphragm_VC-LAR-13_L1_1

value: Diaphragm

value: VGC-LAR


title: SCAT, FL, TERM, Mouse 1

description: Library name: 560_SCAT_FL-_ISS_Term-_1_L1_1

value: SCAT

value: BALB/cAnNTac


title: BAT, HGC, TERM, Mouse 1

description: Library name: 552_BAT_HGC-_ISS_Term-_1_L1_1


title: CX-1 cells, Combination, 2Day, rep3

description: Library name: X_12

value: cell line

value: CRC


title: Pancreas, HGC, LAR, Mouse 5

description: Library name: 558_Pancreas_HC-LAR-5_L1_1

value: Pancreas

value: HGC-LAR


title: Heart, FL, TERM, Mouse 13

description: Library name: 566_Heart_FL-_ISS_Term-_13_L1_1

value: Heart


title: Heart, VGC, TERM, Mouse 13

description: Library name: 557_Heart_VGC-_ISS_Term-_13_L1_1


title: IHA, Control, Biol Rep 3

description:
Library name: UC3
v1.5 S4 200 cycle

value: control


title: SCAT, FL, VGC, LAR, Mouse 4

description: Library name: 556_SCAT_FL-LAR-4_L1_1

value: 8 months


title: CX-1 cells, GSK2606414, 2Day, rep3

description: Library name: X_9


title: IHA, Control, Biol Rep 1

description:
Library name: UC1
v1.5 S4 200 cycle


title: MAT, VGC, LAR, Mouse 13

description: Library name: 549_MAT_VC-LAR-13_L1_1

value: MAT

value: 3 months


title: CX-1 cells, GSK2606414, 2Day, rep2

description: Library name: X_8


title: Spleen, FL, TERM, Mouse 16

description: Library name: 548_Spleen_FL-_ISS_Term-_16_L1_1

value: Spleen

value: FL-TERM


title: CX-1 cells, Control, 2Day, rep1

description: Library name: X_1

value: Control


title: GAT, HGC, LAR, Mouse 1

description: Library name: 553_GAT_HC-LAR-1_L1_1

value: GAT

value: female


title: Pancreas, HGC, LAR, Mouse 12

description: Library name: 546_Pancreas_HC-LAR-12_L1_1


title: CX-1 cells, Combination, 2Day, rep2

description: Library name: X_11

value: Combination


title: CX-1 cells, IMMU132, 2Day, rep2

description: Library name: X_5


title: Liver, HGC, TERM, Mouse 3

description: Library name: 544_Liver_HGC-_ISS_Term-_3_L1_1

source_name: Liver

value: Liver

value: HGC-TERM


title: Heart, FL, TERM, Mouse 11

description: Library name: 551_Heart_FL-_ISS_Term-_11_L1_1

value: BALB/cAnNTac


title: CX-1 cells, IMMU132, 2Day, rep1

description: Library name: X_4

value: cell line

value: CRC


title: Liver, HGC, TERM, Mouse 13

description: Library name: 543_Liver_HGC-_ISS_Term-_13_L1_1


title: Liver, VGC, TERM, Mouse 16

description: Library name: 550_Liver_VGC-_ISS_Term-_16_L1_1

value: VGC-TERM


title: CX-1 cells, Control, 2Day, rep2

description: Library name: X_2


title: PDX-196, Control, 29Day, rep5

description: Library name: C_196_1

source_name: tumor

growth_protocol: Tumor tissue from Patient-derived xenograft (PDX) model grown subcutaneously in NSG mice.

treatment_protocol: Mice harboring CRC patient-derived xenograft (PDX) tumors were administered IMMU132 at a dose of 10 mg/kg via intravenous injection once per week for three weeks

value: tumor


title: Heart, FL, TERM, Mouse 14

description: Library name: 541_Heart_FL-_ISS_Term-_14_L1_1

value: Heart


title: CX-1 cells, IMMU132, 2Day, rep3

description: Library name: X_6


title: CX-1 cells, Control, 2Day, rep3

description: Library name: X_3


title: Thymus, FL, VGC, LAR, Mouse 5

description: Library name: 545_Thymus_FL-LAR-5_L1_1

source_name: Thymus

value: Thymus

value: VGC-LAR


title: PDX-196, IMMU132, 29Day, rep5

description: Library name: T_196_1


title: PDX-82, IMMU132, 29Day, rep2

description: Library name: T_82_1


title: PDX-83, IMMU132, 29Day, rep3

description: Library name: T_83_1


title: Pancreas, FL, VGC, LAR, Mouse 5

description: Library name: 538_Pancreas_FL-LAR-5_L1_1

value: Pancreas

value: 3 months


title: PDX-36, IMMU132, 29Day, rep1

description: Library name: T_36_1


title: GAT, FL, VGC, LAR, Mouse 12

description: Library name: 542_GAT_FL-LAR-12_L1_1

value: 8 months


title: PDX-114, IMMU132, 29Day, rep4

description: Library name: T_114_1


title: Kidney, FL, VGC, LAR, Mouse 5

description: Library name: 537_Kidney_FL-LAR-5_L1_1

source_name: Kidney

value: Kidney


title: PDAC, Human Tumor, sample129

city: Chapel Hill

first: Jen Jen

last: Yeh

state: North Carolina

address: 450 West drive

institute: The University of North Carolina at Chapel Hill

description: Library name: Bulk129

data_processing:
Raw base call (BCL) files were converted to fastq files using bcl2fastq2 (v2.19.0).
RefSeq assembly (GCF_000001405.40) of the human reference genome GRCh38.p14 was used as the reference for gene quantification by Salmon 1.9.064 ("-- gcBias -- seqBias").
The total expected read counts per gene were normalized to transcripts per million (TPM).
Assembly: GENCODE Release 38 (GrCh38.p14)
Supplementary files format and content: comma-separated file containing Bulk RNAseq gene expression normalized TPM for all samples

source_name: Primary PDAC

extract_protocol:
Total RNA was extracted from tissues using the AllPrep DNA/RNA Kit (Qiagen, 80204). RNA was quantified using the Qubit RNA HS Assay Kit (Invitrogen, Q32852) and quality assessed with the 4150 TapeStation System (Agilent) and RNA ScreenTape Analysis Kit (Agilent, 5067-5576).
RNA expression libraries were generated for flash frozen samples or FFPE samples, with TruSeq Stranded mRNA kits or with KAPA RNA HyperPrep Kit with RiboErase (HMR) according to the manufacturer’s instructions.

value: Primary PDAC

value: Gemcitabine


title: PDX-114, Control, 29Day, rep4

description: Library name: C_114_1

value: Control


title: PDX-83, Control, 29Day, rep3

description: Library name: C_83_1


title: Kidney, VGC, LAR, Mouse 13

description: Library name: 540_Kidney_VC-LAR-13_L1_1

value: female


title: BAT, VGC, TERM, Mouse 16

description: Library name: 547_BAT_VGC-_ISS_Term-_16_L1_1

value: BAT


title: Heart, HGC, TERM, Mouse 14

description: Library name: 539_Heart_HGC-_ISS_Term-_14_L1_1

value: HGC-TERM

value: BALB/cAnNTac


title: PDX-82, Control, 29Day, rep2

description: Library name: C_82_1

value: CRC


title: PDAC, Human Tumor, sample126

description: Library name: Bulk126

value: FOLFIRINOX


title: Kidney, HGC, LAR, Mouse 13

description: Library name: 536_Kidney_HC-LAR-13_L1_1

value: HGC-LAR


title: PDAC, Human Tumor, sample124

description: Library name: Bulk124


title: PDAC, Human Tumor, sample123

description: Library name: Bulk123


title: PDAC, Human Tumor, sample128

description: Library name: Bulk128


title: Brain, FL, VGC, LAR, Mouse 1

description: Library name: 532_Brain_FL-LAR-1_L1_1

value: Brain


title: Thymus, FL, TERM, Mouse 4

description: Library name: 531_Thymus_FL-_ISS_Term-_4_L1_1

value: Thymus

value: FL-TERM


title: PDAC, Human Tumor, sample121

description: Library name: Bulk121


title: Brain, FL, TERM, Mouse 8

description: Library name: 535_Brain_FL-_ISS_Term-_8_L1_1


title: Kidney, HGC, TERM, Mouse 12

description: Library name: 530_Kidney_HGC-_ISS_Term-_12_L1_1


title: PDAC, Human Tumor, sample127

description: Library name: Bulk127


title: Thymus, FL, VGC, LAR, Mouse 13

description: Library name: 526_Thymus_FL-LAR-13_L1_1

value: VGC-LAR


title: Diaphragm, VGC, TERM, Mouse 5

description: Library name: 529_Diaphragm_VGC-_ISS_Term-_5_L1_1

value: Diaphragm

value: VGC-TERM

value: 3 months


title: PDX-36, Control, 29Day, rep1

description: Library name: C_36_1

value: tumor


title: PDAC, Human Tumor, sample11

description: Library name: Bulk011

value: Primary PDAC

value: Untreated


title: BAT, HGC, TERM, Mouse 12

description: Library name: 527_BAT_HGC-_ISS_Term-_12_L1_1

value: female

value: 8 months


title: PDAC, Human Tumor, sample122

description: Library name: Bulk122


title: MAT, VGC, TERM, Mouse 16

description: Library name: 528_MAT_VGC-_ISS_Term-_16_L1_1

source_name: MAT

value: MAT


title: BAT, HGC, TERM, Mouse 4

description: Library name: 534_BAT_HGC-_ISS_Term-_4_L1_1

value: BAT

value: HGC-TERM

value: BALB/cAnNTac


title: Diaphragm, VGC, TERM, Mouse 14

description: Library name: 523_Diaphragm_VGC-_ISS_Term-_14_L1_1

source_name: Diaphragm


title: PDAC, Human Tumor, sample120

description: Library name: Bulk120

value: FOLFIRINOX


title: PDAC, Human Tumor, sample119

description: Library name: Bulk119


title: PDAC, Human Tumor, sample53

description: Library name: Bulk053


title: CDpat6, SILP, non-inflamed, scRNAseq, mononuclear phagocytes, GEX

city: Copenhagen

first: William

middle: Winston

last: Agace

address: Blegdamsvej 3B

department: Skin Immunology Research Center

country: Denmark

institute: Copenhagen University

description: Library name: CDpat6_SILP_Hea_GEX

library_source: transcriptomic single cell

data_processing:
scRNAseq: raw reads were processed with 10x Genomics Cell Ranger (version 2.2.0, 3.1.0, and 8.0.0). CITEseq: Sequencing data from samples stained with TotalSeq antibodies was processed with CITE-seq count.
Assembly: GRCh38
Supplementary files format and content: GEX_matrix.mtx.gz: RNA expression as sparse count matrix, cell barcodes as columns, gene features as rows
Supplementary files format and content: GEX_features.tsv.gz: gene features, consist of three columns 1) unique gene identifier from the gtf file, 2) human readable gene name 3) feature type, for GEX these are all gene expression
Supplementary files format and content: GEX_barcodes.tsv.gz: list of barcodes for the sample
Supplementary files format and content: GEX_unspliced.csv.gz: count matrix of unspliced gene information based on velocyto calculation
Supplementary files format and content: GEX_spliced.csv.gz:  count matrix of spliced gene information based on velocyto calculation
Supplementary files format and content: ADT_matrix.mtx.gz: CITEseq protein expression as sparse count matrix, cell barcodes as columns, CITEseq antibodies as rows
Supplementary files format and content: ADT_barcodes.tsv.gz: list of barcodes for the sample
Supplementary files format and content: ADT_features.tsv.gz: consist of two columns, 1) name or dentifier for each antibody or tag that was quantified, 2) feature type, for ADT this is all ADT/CITEseq data

source_name: small intestinal lamina propria

extract_protocol:
Patient samples are from resection material of patients undergoing surgery for colorectal cancer (healthy controls, samples were taken away from the cancer site) or IBD resections. The sample material underwent protocol from Jørgensen et al. (DOI: 10.1038/s41596-020-00482-1) to isolate lamina propria. Mononuclear phagocytes were sorted based on being single, live, CD45+ CD3- CD19- HLADR+ cells and using the 10x platform submitted to sc-omics analysis.
Freshly isolated sorted single cells were subjected to droplet-based massively parallel scRNA-seq using the Chromium Single Cell 3’ Reagent Kits v2, the Chromium Single Cell 3′ Reagent Kit v3.1 with Feature Cell 5’ Reagent Kits v2 (Dual Index) with Feature Barcode technology for Cell Surface Protein & Barcoding technology for Cell Surface Protein or the Chromium Next GEM Single Immune Receptor Mapping (10x Genomics) following the manufacturer’s instructions. For CITEseq analysis, 5 μl of the purified smaller cDNA product was used as template for antibody-derived tag (ADT) sequencing and ADT sequencing libraries were constructed and indexed following the manufacturer's instructions.

value: small intestinal lamina propria

value: mononuclear phagocytes

tag: disease state

value: crohn's disease


title: CDpat4, SILP, inflamed, scRNAseq, mononuclear phagocytes, ADT

description: Library name: CDpat4_SILP_INF_ADT

library_source: other

data_processing:
scRNAseq: raw reads were processed with 10x Genomics Cell Ranger (version 2.2.0, 3.1.0, and 8.0.0). CITEseq: Sequencing data from samples stained with TotalSeq antibodies was processed with CITE-seq count.
Assembly: GRCh38
Supplementary files format and content: GEX_matrix.mtx.gz: RNA expression as sparse count matrix, cell barcodes as columns, gene features as rows
Supplementary files format and content: GEX_features.tsv.gz: gene features, consist of three columns 1) unique gene identifier from the gtf file, 2) human readable gene name 3) feature type, for GEX these are all gene expression
Supplementary files format and content: GEX_barcodes.tsv.gz: list of barcodes for the sample
Supplementary files format and content: GEX_unspliced.csv.gz: count matrix of unspliced gene information based on velocyto calculation
Supplementary files format and content: GEX_spliced.csv.gz:  count matrix of spliced gene information based on velocyto calculation
Supplementary files format and content: ADT_matrix.mtx.gz: CITEseq protein expression as sparse count matrix, cell barcodes as columns, CITEseq antibodies as rows
Supplementary files format and content: ADT_barcodes.tsv.gz: list of barcodes for the sample
Supplementary files format and content: ADT_features.tsv.gz: consist of two columns, 1) name or dentifier for each antibody or tag that was quantified, 2) feature type, for ADT this is all ADT/CITEseq data
Library strategy: CITE-seq

molecule: protein


title: BAT, HGC, LAR, Mouse 16

description: Library name: 519_BAT_HC-LAR-16_L1_1

source_name: BAT

value: HGC-LAR


title: Liver, HGC, TERM, Mouse 12

description: Library name: 533_Liver_HGC-_ISS_Term-_12_L1_1

value: Liver


title: CDpat4, SILP, inflamed, scRNAseq, mononuclear phagocytes, GEX

description: Library name: CDpat4_SILP_INF_GEX


title: CDpat6, SILP, inflamed, scRNAseq, mononuclear phagocytes, GEX

description: Library name: CDpat6_SILP_INF_GEX


title: SCAT, VGC, LAR, Mouse 4

description: Library name: 518_SCAT_VC-LAR-4_L1_1

source_name: SCAT

value: SCAT

value: VGC-LAR


title: Brain, VGC, LAR, Mouse 13

description: Library name: 517_Brain_VC-LAR-13_L1_1

source_name: Brain

value: Brain

value: 3 months


title: Lung, FL, VGC, LAR, Mouse 4

description: Library name: 522_Lung_FL-LAR-4_L1_1

source_name: Lung

value: Lung


title: Pancreas, VGC, LAR, Mouse 5

description: Library name: 525_Pancreas_VC-LAR-5_L1_1

source_name: Pancreas

value: Pancreas

value: female


title: PDAC, Human Tumor, sample7

description: Library name: Bulk007

value: Primary PDAC

value: Untreated


title: CDpat5, SILP, inflamed, scRNAseq, mononuclear phagocytes, GEX

description: Library name: CDpat5_SILP_INF_GEX


title: CDpat4, SILP, non-inflamed, scRNAseq, mononuclear phagocytes, ADT

description: Library name: CDpat4_SILP_Hea_ADT


title: MAT, HGC, TERM, Mouse 11

description: Library name: 520_MAT_HGC-_ISS_Term-_11_L1_1

value: MAT

value: HGC-TERM

value: 8 months


title: Kidney, HGC, TERM, Mouse 14

description: Library name: 521_Kidney_HGC-_ISS_Term-_14_L1_1

value: Kidney

value: BALB/cAnNTac


title: CDpat4, SILP, non-inflamed, scRNAseq, mononuclear phagocytes, GEX

description: Library name: CDpat4_SILP_Hea_GEX

value: small intestinal lamina propria

value: mononuclear phagocytes

value: crohn's disease


title: Kidney, HGC, TERM, Mouse 1

description: Library name: 524_Kidney_HGC-_ISS_Term-_1_L1_1


title: CDpat2, SILP, inflamed, scRNAseq, mononuclear phagocytes, GEX

description: Library name: CDpat2_SILP_INF_GEX


title: MAT, FL, VGC, LAR, Mouse 4

description: Library name: 515_MAT_FL-LAR-4_L1_1


title: CDpat2, SILP, non-inflamed, scRNAseq, mononuclear phagocytes, GEX

description: Library name: CDpat2_SILP_Hea_GEX


title: CDpat3, SILP, inflamed, scRNAseq, mononuclear phagocytes, GEX

description: Library name: CDpat3_SILP_INF_GEX


title: GAT, HGC, TERM, Mouse 16

description: Library name: 516_GAT_HGC-_ISS_Term-_16_L1_1

source_name: GAT

value: GAT


title: CDpat3, SILP, non-inflamed, scRNAseq, mononuclear phagocytes, GEX

description: Library name: CDpat3_SILP_Hea_GEX


title: CDpat1, SILP, inflamed, scRNAseq, mononuclear phagocytes, GEX

description: Library name: CDpat1_SILP_INF_GEX


title: SCAT, FL, VGC, LAR, Mouse 16

description: Library name: 513_SCAT_FL-LAR-16_L1_1

value: SCAT

value: VGC-LAR


title: SCAT, FL, TERM, Mouse 12

description: Library name: 512_SCAT_FL-_ISS_Term-_12_L1_1

value: FL-TERM


title: CDpat5, SILP, non-inflamed, scRNAseq, mononuclear phagocytes, GEX

description: Library name: CDpat5_SILP_Hea_GEX


title: P6, cLP, multiome, mononuclear phagocytes, ADT

description: Library name: P6_cLP_ADT

source_name: colonic lamina propria

value: colonic lamina propria

value: healthy


title: Spleen, HGC, LAR, Mouse 17

description: Library name: 514_Spleen_HC-LAR-17_L1_1

source_name: Spleen

value: Spleen

value: HGC-LAR

value: female

value: 3 months


title: Liver, FL, TERM, Mouse 4

description: Library name: 509_Liver_FL-_ISS_Term-_4_L1_1

value: Liver


title: CDpat1, SILP, non-inflamed, scRNAseq, mononuclear phagocytes, GEX

description: Library name: CDpat1_SILP_Hea_GEX


title: Pancreas, FL, TERM, Mouse 2

description: Library name: 511_Pancreas_FL-_ISS_Term-_2_L1_1

value: Pancreas


title: Diaphragm, FL, VGC, LAR, Mouse 14

description: Library name: 510_Diaphragm_FL-LAR-14_L1_1

value: Diaphragm


title: P5, cLP, multiome, mononuclear phagocytes, ADT

description: Library name: P5_cLP_ADT


title: Diaphragm, FL, VGC, LAR, Mouse 4

description: Library name: 508_Diaphragm_FL-LAR-4_L1_1

value: BALB/cAnNTac

value: 8 months


title: P6, cLP, multiome, mononuclear phagocytes, GEX

description: Library name: P6_cLP_GEX

value: mononuclear phagocytes


title: P5, cLP, multiome, mononuclear phagocytes, GEX

description: Library name: P5_cLP_GEX


title: Liver, FL, TERM, Mouse 2

description: Library name: 507_Liver_FL-_ISS_Term-_2_L1_1


title: Heart, FL, TERM, Mouse 16

description: Library name: 505_Heart_FL-_ISS_Term-_16_L1_1

source_name: Heart

value: Heart


title: P4, SILP, multiome, mononuclear phagocytes, ADT

description: Library name: P4_SILP_ADT

value: small intestinal lamina propria


title: P4, cLP, multiome, mononuclear phagocytes, ADT

description: Library name: P4_cLP_ADT


title: P4, SILP, multiome, mononuclear phagocytes, GEX

description: Library name: P4_SILP_GEX


title: Diaphragm, VGC, LAR, Mouse 5

description: Library name: 503_Diaphragm_VC-LAR-5_L1_1


title: Diaphragm, HGC, LAR, Mouse 12

description: Library name: 504_Diaphragm_HC-LAR-12_L1_1


title: P4, cLP, multiome, mononuclear phagocytes, GEX

description: Library name: P4_cLP_GEX


title: SCAT, FL, TERM, Mouse 5

description: Library name: 502_SCAT_FL-_ISS_Term-_5_L1_1

value: SCAT


title: P3, cLP, scRNAseq, mononuclear phagocytes, GEX

description: Library name: P3_cLP_GEX


title: P3, SILP, scRNAseq, mononuclear phagocytes, GEX

description: Library name: P3_SILP_GEX


title: Thymus, VGC, TERM, Mouse 12

description: Library name: 501_Thymus_VGC-_ISS_Term-_12_L1_1

value: Thymus

value: VGC-TERM


title: SLC25A48KO_2

city: Nedlands

first: Danielle

middle: Louise

last: Rudler

state: WA

address: 6 Verdun Street

department: Mitochondrial Medicine and Biology

country: Australia

institute: The Kids Research Institute

description: Library name: SLC25A48KO_2

data_processing:
Sequencing reads were trimmed of adapter sequences using Trim Galore  using cutadapt (with parameters: --paired --fastqc --illumina, corresponding to cutadapt parameters: -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA)
Trimmed reads were aligned to the human genome downloaded from GENCODE masked for nuclear mitochondrial sequences with STAR (--quantMode TranscriptomeSAM).
The transcriptome alignments produced by STAR were quantified with Salmon (-l ISR --seqBias --gcBias) against a transcriptome fasta produced from the GENCODE gene annotation and genome sequence with gffread.
The output files were imported into R with tximport and knockouts were analysed for differential expression against wild types with DESeq2. Effect size shrinkage was performed with the apeglm algorithm with a threshold of log2(1.5) and false-sign-or-small (FSOS) rate s-values were output.
Assembly: GRCh38
Supplementary files format and content: differential expression results;  read counts (*.sf) prior to differential expression analysis

extract_protocol:
RNA was isolated from cell pellets using miRNeasy mini kit (QIAGEN).
RNA sequencing libraries were constructed with the Illumina TruSeq Sample Prep Kit. Paired end deep sequencing of RNAs was performed on an Illumina NovaSeq according to the manufacturer's instructions.


title: SCAT, FL, VGC, LAR, Mouse 1

description: Library name: 499_SCAT_FL-LAR-1_L1_1

value: VGC-LAR


title: Kidney, FL, VGC, LAR, Mouse 13

description: Library name: 500_Kidney_FL-LAR-13_L1_1

value: Kidney


title: SLC25A48KO_3

description: Library name: SLC25A48KO_3


title: Lung, HGC, LAR, Mouse 11

description: Library name: 498_Lung_HC-LAR-11_L1_1

value: Lung


title: Diaphragm, FL, TERM, Mouse 12

description: Library name: 497_Diaphragm_FL-_ISS_Term-_12_L1_1

value: FL-TERM


title: MAT, VGC, LAR, Mouse 14

description: Library name: 506_MAT_VC-LAR-14_L1_1

value: MAT

value: female


title: Diaphragm, VGC, LAR, Mouse 12

description: Library name: 494_Diaphragm_VC-LAR-12_L1_1


title: Pancreas, HGC, TERM, Mouse 3

description: Library name: 496_Pancreas_HGC-_ISS_Term-_3_L1_1

value: HGC-TERM

value: 3 months


title: Thymus, HGC, LAR, Mouse 12

description: Library name: 491_Thymus_HC-LAR-12_L1_1

value: HGC-LAR


title: SLC25A45KO_1

description: Library name: SLC25A45KO_1


title: SLC25A45KO_2

description: Library name: SLC25A45KO_2


title: SLC25A44KO_2

description: Library name: SLC25A44KO_2


title: SLC25A45KO_3

description: Library name: SLC25A45KO_3


title: SLC25A44KO_1

description: Library name: SLC25A44KO_1


title: Lung, FL, TERM, Mouse 1

description: Library name: 493_Lung_FL-_ISS_Term-_1_L1_1

value: BALB/cAnNTac


title: WT_3

description: Library name: WT_3

value: WT


title: SCAT, FL, VGC, LAR, Mouse 2

description: Library name: 490_SCAT_FL-LAR-2_L1_1


title: SCAT, HGC, TERM, Mouse 1

description: Library name: 492_SCAT_HGC-_ISS_Term-_1_L1_1


title: WT_2

description: Library name: WT_2


title: BAT, HGC, LAR, Mouse 4

description: Library name: 489_BAT_HC-LAR-4_L1_1

value: BAT

value: 8 months


title: SCAT, VGC, LAR, Mouse 14

description: Library name: 488_SCAT_VC-LAR-14_L1_1


title: WT_1

description: Library name: WT_1


title: Sample SBM1271

city: Boston

first: Ksenia

last: Safina

address: 4 Blackfan St

institute: Brigham and Women's Hospital

description:
Library name: SBM1271
10X Genomics, 10x 3' v4

data_processing:
Count matrices were generated using CellRanger v.7.1.0 with default settings.
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz contains the transcript count per cell
Supplementary files format and content: barcodes.tsv.gz contains the list of cell barcodes
Supplementary files format and content: features.tsv.gz contains the list of features (genes)

source_name: Sternum bone marrow

extract_protocol:
mRNA was extracted and hybridized to polyT oligos on 10x Genomics beads.
10x Genomics 3' single-cell RNA-sequencing protocols (v3, v3.1, or v4) were used to construct libraries.

value: Sternum bone marrow

value: Bone marrow mononuclear cells

value: M

tag: batch


title: SLC25A48KO_1

description: Library name: SLC25A48KO_1


title: GAT, VGC, TERM, Mouse 16

description: Library name: 487_GAT_VGC-_ISS_Term-_16_L1_1

value: GAT

value: VGC-TERM


title: Sample SBM1237

description:
Library name: SBM1237
10X Genomics, 10x 3' v4


title: Liver, FL, VGC, LAR, Mouse 14

description: Library name: 486_Liver_FL-LAR-14_L1_1

source_name: Liver

value: Liver

value: VGC-LAR


title: Technical replicate 2 of sample SBM1307

description:
Library name: SBM1307_rep2
10X Genomics, 10x 3' v3.1

value: F


title: SLC25A44KO_3

description: Library name: SLC25A44KO_3


title: Spleen, VGC, TERM, Mouse 16

description: Library name: 485_Spleen_VGC-_ISS_Term-_16_L1_1

value: Spleen


title: Pancreas, FL, VGC, LAR, Mouse 14

description: Library name: 483_Pancreas_FL-LAR-14_L1_1

value: Pancreas

value: female


title: Technical replicate 1 of sample SBM1307

description:
Library name: SBM1307_rep1
10X Genomics, 10x 3' v3.1


title: Technical replicate 2 of sample SBM1264

description:
Library name: SBM1264_rep2
10X Genomics, 10x 3' v3.1


title: Lung, VGC, TERM, Mouse 12

description: Library name: 484_Lung_VGC-_ISS_Term-_12_L1_1

value: Lung


title: Technical replicate 1 of sample SBM1264

description:
Library name: SBM1264_rep1
10X Genomics, 10x 3' v3.1


title: BAT, HGC, LAR, Mouse 3

description: Library name: 495_BAT_HC-LAR-3_L1_1

value: HGC-LAR


title: GAT, VGC, TERM, Mouse 13

description: Library name: 482_GAT_VGC-_ISS_Term-_13_L1_1

value: BALB/cAnNTac


title: Technical replicate 2 of sample SBM1096

description:
Library name: SBM1096_rep2
10X Genomics, 10x 3' v3.1

value: WT


title: Kidney, FL, VGC, LAR, Mouse 2

description: Library name: 481_Kidney_FL-LAR-2_L1_1

value: Kidney

value: 3 months


title: Lung, FL, TERM, Mouse 5

description: Library name: 480_Lung_FL-_ISS_Term-_5_L1_1

value: FL-TERM


title: Technical replicate 1 of sample SBM1073

description:
Library name: SBM1073_rep1
10X Genomics, 10x 3' v3.1

value: Sternum bone marrow

value: Bone marrow mononuclear cells


title: Spleen, FL, VGC, LAR, Mouse 16

description: Library name: 477_Spleen_FL-LAR-16_L1_1

value: 8 months


title: Technical replicate 2 of sample SBM1073

description:
Library name: SBM1073_rep2
10X Genomics, 10x 3' v3.1


title: Technical replicate 1 of sample SBM1096

description:
Library name: SBM1096_rep1
10X Genomics, 10x 3' v3.1

value: M


title: BAT, VGC, LAR, Mouse 14

description: Library name: 476_BAT_VC-LAR-14_L1_1

value: BAT


title: Diaphragm, VGC, LAR, Mouse 1

description: Library name: 479_Diaphragm_VC-LAR-1_L1_1

value: Diaphragm

value: VGC-LAR


title: Technical replicate 2 of sample BM2

description:
Library name: BM2_rep2
10X Genomics, 10x 3' v3

source_name: Bone marrow

value: Bone marrow

value: F


title: Technical replicate 1 of sample BM2

description:
Library name: BM2_rep1
10X Genomics, 10x 3' v3


title: Technical replicate 3 of sample BM1

description:
Library name: BM1_rep3
10X Genomics, 10x 3' v3.1


title: Spleen, HGC, TERM, Mouse 11

description: Library name: 474_Spleen_HGC-_ISS_Term-_11_L1_1

value: Spleen

value: HGC-TERM

value: female


title: MAT, HGC, LAR, Mouse 5

description: Library name: 475_MAT_HC-LAR-5_L1_1

value: MAT

value: HGC-LAR

value: BALB/cAnNTac


title: Sample SBM1177

description:
Library name: SBM1177
10X Genomics, 10x 3' v4

value: WT


title: Liver, FL, VGC, LAR, Mouse 1

description: Library name: 473_Liver_FL-LAR-1_L1_1

value: Liver

value: 3 months


title: Technical replicate 2 of sample BM1

description:
Library name: BM1_rep2
10X Genomics, 10x 3' v3.1

value: Bone marrow mononuclear cells


title: BAT, FL, TERM, Mouse 5

description: Library name: 472_BAT_FL-_ISS_Term-_5_L1_1

value: FL-TERM


title: Technical replicate 1 of sample BM1

description:
Library name: BM1_rep1
10X Genomics, 10x 3' v3.1

value: M


title: Thymus, VGC, LAR, Mouse 3

description: Library name: 471_Thymus_VC-LAR-3_L1_1

source_name: Thymus

value: Thymus

value: 8 months


title: Spleen, VGC, LAR, Mouse 9

description: Library name: 470_Spleen_VC-LAR-9_L1_1

value: VGC-LAR


title: HEK293T_Oxsr1 KO_2_R1

city: Xiamen

first: Xiawei

last: Huang

state: Fujian

address: Xiang an nan lu 4221

institute: Xiamen university

description: Library name: HEK293T_Oxsr1 KO_2

data_processing:
Raw sequencing data in FASTQ format were first processed using fastp (v0.20.1) to remove adapters and low-quality reads with parameters: fastp -i sample.R1.fastq -I sample.R2.fastq -o out.R1.fastq -O out.R2.fastq -q 20 -u 10 -n 10 -l 100 -p. Clean reads were then aligned to the human reference genome (Homo sapiens, Ensembl v96, hg38) using HISAT2 (v2.0.4) with parameters: hisat2 -1 R1.fastq.gz -2 R2.fastq.gz -S sample_mapped.sam. The resulting BAM files were assembled into transcripts using StringTie (v1.3.4d) with the reference GTF file and parameters: stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam. Transcript assemblies from all samples were merged using StringTie --merge. Transcript annotation comparison was performed using gffcompare (v0.9.8). Transcript abundance was then estimated using StringTie with parameters: stringtie -e -B -p 4 -G merged.gtf -o sample.gtf sample.bam. FPKM values were extracted using the Ballgown package. Differential gene expression analysis was conducted using DESeq2 (v1.26.0).
Assembly: Homo sapiens genome assembly hg38 (UCSC).
Supplementary files format and content: Processed data files include gene-level read counts  and gene-level FPKM values  for each sample. Differential expression results are provided  containing gene identifiers, log2 fold change, adjusted P-values, and statistical significance indicators.

extract_protocol:
Total RNA from mouse livers was isolated using TRIzol™ Plus RNA Purification Kit (Cat# 12183555, Thermo Fisher) and DNA was removed by treatment with TURBO DNA-free™ Kit (Cat# AM1907, Thermo Fisher).
Total RNA was extracted using a standard TRIzol-based protocol. RNA integrity was assessed using an Agilent Bioanalyzer 2100. Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions, which includes poly(A) mRNA enrichment, fragmentation, cDNA synthesis, adapter ligation, and PCR amplification. Libraries were quantified and quality-controlled before sequencing.

value: Oxsr1 KO


title: Liver, VGC, TERM, Mouse 12

description: Library name: 469_Liver_VGC-_ISS_Term-_12_L1_1

value: VGC-TERM


title: HEK293T_Oxsr1 KO_1_R1

description: Library name: HEK293T_Oxsr1 KO_1


title: HEK293T_WT3_R1

description: Library name: HEK293T_WT3


title: Kidney, VGC, TERM, Mouse 3

description: Library name: 468_Kidney_VGC-_ISS_Term-_3_L1_1

source_name: Kidney

value: Kidney


title: Technical replicate 3 of sample BM2

description:
Library name: BM2_rep3
10X Genomics, 10x 3' v3

value: Bone marrow

value: F


title: GAT, VGC, LAR, Mouse 14

description: Library name: 478_GAT_VC-LAR-14_L1_1

value: GAT

value: female


title: SCAT, VGC, LAR, Mouse 2

description: Library name: 467_SCAT_VC-LAR-2_L1_1

value: SCAT

value: BALB/cAnNTac


title: HEK293T_WT2_R1

description: Library name: HEK293T_WT2

value: WT


title: Brain, VGC, TERM, Mouse 7

description: Library name: 465_Brain_VGC-_ISS_Term-_7_L1_1

value: Brain

value: 3 months


title: GAT, VGC, TERM, Mouse 11

description: Library name: 466_GAT_VGC-_ISS_Term-_11_L1_1


title: Thymus, HGC, TERM, Mouse 5

description: Library name: 464_Thymus_HGC-_ISS_Term-_5_L1_1

value: HGC-TERM


title: Heart, HGC, LAR, Mouse 12

description: Library name: 463_Heart_HC-LAR-12_L1_1

value: Heart

value: HGC-LAR


title: HEK293T_WT1_R1

description: Library name: HEK293T_WT1


title: Highlander20

city: Delhi

first: Aastha

last: Mishra

state: Delhi

address: Mall Road, Delhi-110 007

department: Genomics and genome biology

country: India

institute: Council Of Scientific And Industrial Research–Institute Of Genomics And Integrative Biology (CSIR–IGIB)

description: Library name: HL20

data_processing:
The CBCL files from the NovaSeq 6000 platform was demultiplexed to generate FASTQ files using the bcl2fastq tool v2.20.0.422
The low quality bases and adapters were removed using fastp tool v0.23.4
The reads were  mapped to reference genome  using a splice-aware tool, STAR aligner v2.7.11b and PCR duplicates were removed using GATK's v4.5.0.0 MarkDuplicates
Read summarization was carried out with the FeatureCounts tool based on the GENCODE v45 GTF file.
The read count matrix was imported into R v4.4.1 and DESeq2 package was used for DEG analysis.
Assembly: GRCh38.p14
Supplementary files format and content: csv text file includes raw counts for each sample

source_name: Blood

extract_protocol:
RNA was extracted using PAXgene blood RNA kit (PreAnalytiX, switzerland). 500ng of total RNA was used for the construction of libraries.
The library construction process included ribosomal RNA (rRNA) removal, RNA fragmentation, complementary DNA (cDNA) synthesis, adapter ligation, library enrichment,normalisation and quantification. Ribosomal RNA, including 5S, 16S, and 23S rRNA, was removed from the samples using the QIAseq FastSelect Epidemiology Kit (Qiagen, Germany). First- and second-strand cDNA synthesis was performed via reverse transcription of the RNA insert. Following library preparation, PCR enrichment was carried out to amplify the target library using the QIAseq Stranded RNA Library Kit (Qiagen, Germany). The library concentrations were normalized with the QIAseq Normalizer Kit (Qiagen, Germany)

value: Blood

tag: group

value: Highlander


title: Highlander22

description: Library name: HL22

value: male


title: Highlander21

description: Library name: HL21


title: Brain, FL, TERM, Mouse 7

description: Library name: 461_Brain_FL-_ISS_Term-_7_L1_1

value: FL-TERM


title: Highlander18

description: Library name: HL18


title: BAT, VGC, TERM, Mouse 11

description: Library name: 462_BAT_VGC-_ISS_Term-_11_L1_1

value: BAT

value: VGC-TERM

value: 8 months


title: Highlander17

description: Library name: HL17


title: Highlander19

description: Library name: HL19


title: BAT, HGC, LAR, Mouse 1

description: Library name: 460_BAT_HC-LAR-1_L1_1


title: SCAT, HGC, LAR, Mouse 1

description: Library name: 459_SCAT_HC-LAR-1_L1_1


title: Highlander16

description: Library name: HL16


title: HEK293T_Oxsr1 KO_3_R1

description: Library name: HEK293T_Oxsr1 KO_3

value: Oxsr1 KO


title: Highlander15

description: Library name: HL15


title: Liver, FL, VGC, LAR, Mouse 16

description: Library name: 457_Liver_FL-LAR-16_L1_1

value: Liver

value: VGC-LAR

value: female


title: BAT, FL, VGC, LAR, Mouse 14

description: Library name: 458_BAT_FL-LAR-14_L1_1

value: BALB/cAnNTac


title: Highlander14

description: Library name: HL14


title: Highlander13

description: Library name: HL13


title: GAT, HGC, LAR, Mouse 13

description: Library name: 455_GAT_HC-LAR-13_L1_1

value: GAT


title: Highlander12

description: Library name: HL12


title: Highlander11

description: Library name: HL11


title: Lung, FL, VGC, LAR, Mouse 2

description: Library name: 452_Lung_FL-LAR-2_L1_1

value: Lung

value: 3 months


title: Highlander10

description: Library name: HL10


title: Highlander9

description: Library name: HL09


title: GAT, FL, TERM, Mouse 5

description: Library name: 451_GAT_FL-_ISS_Term-_5_L1_1


title: GAT, VGC, TERM, Mouse 4

description: Library name: 450_GAT_VGC-_ISS_Term-_4_L1_1


title: Highlander8

description: Library name: HL08


title: Highlander7

description: Library name: HL07


title: Highlander6

description: Library name: HL06


title: Brain, FL, VGC, LAR, Mouse 13

description: Library name: 448_Brain_FL-LAR-13_L1_1

value: Brain


title: Highlander5

description: Library name: HL05


title: Spleen, HGC, TERM, Mouse 5

description: Library name: 446_Spleen_HGC-_ISS_Term-_5_L1_1

value: Spleen

value: HGC-TERM


title: Heart, VGC, LAR, Mouse 8

description: Library name: 445_Heart_VC-LAR-8_L1_1

value: Heart


title: GAT, HGC, TERM, Mouse 5

description: Library name: 444_GAT_HGC-_ISS_Term-_5_L1_1


title: Highlander2

description: Library name: HL02

value: Blood

value: Highlander

value: male


title: MAT, VGC, TERM, Mouse 13

description: Library name: 443_MAT_VGC-_ISS_Term-_13_L1_1

source_name: MAT

value: MAT

value: VGC-TERM


title: Highlander3

description: Library name: HL03


title: Highlander1

description: Library name: HL01


title: Lung, FL, TERM, Mouse 12

description: Library name: 442_Lung_FL-_ISS_Term-_12_L1_1

value: FL-TERM

value: 8 months


title: HAPE-Severe14

description: Library name: HAPE42

value: HAPE-Severe


title: Liver, FL, TERM, Mouse 16

description: Library name: 456_Liver_FL-_ISS_Term-_16_L1_1

value: Liver

value: female


title: Liver, FL, TERM, Mouse 3

description: Library name: 441_Liver_FL-_ISS_Term-_3_L1_1

value: BALB/cAnNTac


title: HAPE-Severe13

description: Library name: HAPE41


title: MAT, VGC, LAR, Mouse 1

description: Library name: 440_MAT_VC-LAR-1_L1_1

value: VGC-LAR


title: BAT, VGC, LAR, Mouse 11

description: Library name: 453_BAT_VC-LAR-11_L1_1

value: BAT


title: HAPE-Severe12

description: Library name: HAPE40


title: HAPE-Severe11

description: Library name: HAPE39


title: Diaphragm, VGC, TERM, Mouse 11

description: Library name: 437_Diaphragm_VGC-_ISS_Term-_11_L1_1

source_name: Diaphragm

value: Diaphragm


title: BAT, VGC, LAR, Mouse 4

description: Library name: 449_BAT_VC-LAR-4_L1_1

source_name: BAT


title: Diaphragm, FL, TERM, Mouse 11

description: Library name: 447_Diaphragm_FL-_ISS_Term-_11_L1_1


title: HAPE-Severe10

description: Library name: HAPE38


title: MAT, VGC, TERM, Mouse 14

description: Library name: 436_MAT_VGC-_ISS_Term-_14_L1_1


title: HAPE-Severe8

description: Library name: HAPE36


title: Liver, FL, VGC, LAR, Mouse 3

description: Library name: 434_Liver_FL-LAR-3_L1_1


title: Thymus, FL, TERM, Mouse 14

description: Library name: 435_Thymus_FL-_ISS_Term-_14_L1_1

value: Thymus


title: BAT, FL, VGC, LAR, Mouse 4

description: Library name: 433_BAT_FL-LAR-4_L1_1


title: HAPE-Severe6

description: Library name: HAPE34


title: GAT, HGC, TERM, Mouse 2

description: Library name: 432_GAT_HGC-_ISS_Term-_2_L1_1

value: GAT

value: HGC-TERM

value: 3 months


title: HAPE-Severe7

description: Library name: HAPE35

value: Blood


title: Highlander4

description: Library name: HL04

value: Highlander

value: male


title: HAPE-Severe5

description: Library name: HAPE33


title: HAPE-Severe3

description: Library name: HAPE31


title: HAPE-Severe2

description: Library name: HAPE30


title: HAPE-Severe4

description: Library name: HAPE32


title: MAT, FL, TERM, Mouse 1

description: Library name: 431_MAT_FL-_ISS_Term-_1_L1_1

value: MAT


title: BAT, FL, TERM, Mouse 16

description: Library name: 429_BAT_FL-_ISS_Term-_16_L1_1

value: FL-TERM


title: GAT, FL, VGC, LAR, Mouse 16

description: Library name: 430_GAT_FL-LAR-16_L1_1

value: 8 months


title: Spleen, HGC, TERM, Mouse 16

description: Library name: 427_Spleen_HGC-_ISS_Term-_16_L1_1

value: Spleen


title: Heart, VGC, TERM, Mouse 16

description: Library name: 428_Heart_VGC-_ISS_Term-_16_L1_1

value: Heart

value: VGC-TERM


title: GAT, VGC, TERM, Mouse 12

description: Library name: 438_GAT_VGC-_ISS_Term-_12_L1_1

value: female

value: BALB/cAnNTac


title: HAPE-Moderate13

description: Library name: HAPE28

value: HAPE-Moderate


title: HAPE-Severe1

description: Library name: HAPE29

value: HAPE-Severe


title: HAPE-Severe9

description: Library name: HAPE37


title: HAPE-Moderate11

description: Library name: HAPE26


title: Lung, HGC, TERM, Mouse 11

description: Library name: 425_Lung_HGC-_ISS_Term-_11_L1_1

value: Lung


title: Heart, VGC, TERM, Mouse 11

description: Library name: 424_Heart_VGC-_ISS_Term-_11_L1_1


title: MAT, FL, TERM, Mouse 11

description: Library name: 426_MAT_FL-_ISS_Term-_11_L1_1


title: HAPE-Moderate10

description: Library name: HAPE25


title: Pancreas, VGC, LAR, Mouse 14

description: Library name: 420_Pancreas_VC-LAR-14_L1_1

value: Pancreas

value: VGC-LAR


title: Thymus, VGC, LAR, Mouse 5

description: Library name: 419_Thymus_VC-LAR-5_L1_1

value: Thymus

value: 3 months


title: HAPE-Moderate9

description: Library name: HAPE24

value: Blood


title: GAT, FL, VGC, LAR, Mouse 1

description: Library name: 422_GAT_FL-LAR-1_L1_1

value: GAT


title: HAPE-Moderate7

description: Library name: HAPE22

value: male


title: HAPE-Moderate6

description: Library name: HAPE21


title: HAPE-Moderate5

description: Library name: HAPE20


title: SCAT, HGC, LAR, Mouse 4

description: Library name: 417_SCAT_HC-LAR-4_L1_1

source_name: SCAT

value: SCAT

value: HGC-LAR


title: HAPE-Moderate4

description: Library name: HAPE19


title: MAT, VGC, LAR, Mouse 12

description: Library name: 418_MAT_VC-LAR-12_L1_1

value: MAT

value: 8 months


title: HAPE-Moderate3

description: Library name: HAPE18


title: SCAT, HGC, LAR, Mouse 3

description: Library name: 415_SCAT_HC-LAR-3_L1_1


title: HAPE-Moderate12

description: Library name: HAPE27


title: Liver, FL, VGC, LAR, Mouse 5

description: Library name: 413_Liver_FL-LAR-5_L1_1

value: Liver


title: SCAT, HGC, TERM, Mouse 16

description: Library name: 414_SCAT_HGC-_ISS_Term-_16_L1_1

value: HGC-TERM

value: female


title: HAPE-Moderate1

description: Library name: HAPE16

value: HAPE-Moderate


title: Spleen, HGC, LAR, Mouse 5

description: Library name: 412_Spleen_HC-LAR-5_L1_1

value: Spleen

value: BALB/cAnNTac


title: HAPE-Mild15

description: Library name: HAPE15

value: HAPE-Mild


title: MAT, HGC, LAR, Mouse 12

description: Library name: 421_MAT_HC-LAR-12_L1_1


title: HAPE-Mild14

description: Library name: HAPE14


title: Kidney, FL, VGC, LAR, Mouse 4

description: Library name: 411_Kidney_FL-LAR-4_L1_1

value: Kidney

value: VGC-LAR


title: HAPE-Mild13

description: Library name: HAPE13


title: HAPE-Moderate8

description: Library name: HAPE23


title: HAPE-Mild12

description: Library name: HAPE12


title: HAPE-Mild11

description: Library name: HAPE11


title: Diaphragm, HGC, TERM, Mouse 2

description: Library name: 408_Diaphragm_HGC-_ISS_Term-_2_L1_1

value: Diaphragm

value: 3 months


title: GAT, FL, VGC, LAR, Mouse 5

description: Library name: 410_GAT_FL-LAR-5_L1_1

value: GAT


title: Liver, HGC, LAR, Mouse 4

description: Library name: 409_Liver_HC-LAR-4_L1_1


title: HAPE-Mild9

description: Library name: HAPE09

value: Blood


title: HAPE-Mild8

description: Library name: HAPE08

value: male


title: SCAT, VGC, LAR, Mouse 1

description: Library name: 416_SCAT_VC-LAR-1_L1_1

value: SCAT


title: SCAT, FL, VGC, LAR, Mouse 13

description: Library name: 404_SCAT_FL-LAR-13_L1_1


title: GAT, FL, TERM, Mouse 13

description: Library name: 407_GAT_FL-_ISS_Term-_13_L1_1

value: FL-TERM


title: Thymus, HGC, LAR, Mouse 2

description: Library name: 403_Thymus_HC-LAR-2_L1_1

value: Thymus

value: HGC-LAR


title: MAT, HGC, TERM, Mouse 3

description: Library name: 406_MAT_HGC-_ISS_Term-_3_L1_1

value: MAT

value: HGC-TERM


title: HAPE-Mild6

description: Library name: HAPE06

value: female


title: HAPE-Moderate2

description: Library name: HAPE17

value: HAPE-Moderate


title: Liver, VGC, LAR, Mouse 16

description: Library name: 405_Liver_VC-LAR-16_L1_1

value: Liver

value: BALB/cAnNTac

value: 8 months


title: MAT, HGC, LAR, Mouse 11

description: Library name: 401_MAT_HC-LAR-11_L1_1


title: HAPE-Mild3

description: Library name: HAPE03

value: HAPE-Mild


title: HAPE-Mild4

description: Library name: HAPE04


title: HAPE-Mild2

description: Library name: HAPE02


title: Liver, VGC, TERM, Mouse 1

description: Library name: 400_Liver_VGC-_ISS_Term-_1_L1_1

value: VGC-TERM


title: Lung, FL, TERM, Mouse 16

description: Library name: 398_Lung_FL-_ISS_Term-_16_L1_1

value: Lung


title: Kidney, VGC, LAR, Mouse 16

description: Library name: 399_Kidney_VC-LAR-16_L1_1

value: Kidney

value: VGC-LAR


title: GAT, FL, TERM, Mouse 16

description: Library name: 397_GAT_FL-_ISS_Term-_16_L1_1

value: GAT


title: Control18

description: Library name: CON18

value: Blood

value: control

value: male


title: HAPE-Mild1

description: Library name: HAPE01


title: Thymus, VGC, LAR, Mouse 14

description: Library name: 396_Thymus_VC-LAR-14_L1_1

value: Thymus

value: 3 months


title: Thymus, HGC, TERM, Mouse 1

description: Library name: 395_Thymus_HGC-_ISS_Term-_1_L1_1

value: HGC-TERM


title: Control19

description: Library name: CON19


title: HAPE-Mild10

description: Library name: HAPE10


title: Control16

description: Library name: CON16


title: HAPE-Mild7

description: Library name: HAPE07


title: Control17

description: Library name: CON17


title: Control15

description: Library name: CON15


title: RNAseq_panTEADKD_treated_parental_H226_cells_rep2

city: South San Francisco

first: Bence

last: Daniel

address: 1 DNA Way

department: Department Proteomic and Genomic Technologies

institute: Genentech Inc.

description: Library name: RNAseq_H226_Parental_panTEADKD_rep2

data_processing:
The analysis of RNA-seq data was conducted using HTSeqGenie (R package version 4.30.0) within the BioConductor framework in the following manner: reads characterized by low nucleotide qualities (defined as having 70% of bases with quality scores below 23) or those matching rRNA and adapter sequences were excluded. The remaining reads were aligned to the human reference genome (human: GRCh38.p10) using GSNAP (2013-10-10-v2) with a maximum allowance of two mismatches per 75-base sequence (utilizing parameters: '-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap'). The aligned reads were quantified using the `featureCounts` function from the `Rsubread` package, with the GTF annotation file `Homo_sapiens.GRCh38.104.gtf`. The count matrix was extracted for downstream analysis. The count matrix was imported into the `edgeR` package for differential expression analysis. Lowly expressed genes were filtered out using the `filterByExpr` function, when gene expression was consistently low in all conditions. The data were normalized using the `calcNormFactors` function.
Assembly: hg38
Supplementary files format and content: Normalized bigwigs.

growth_protocol:
Two established preclinical models of malignant mesothelioma were used in this study: NCI-H226 (hereafter H226), which is NF2-null, and MSTO-211H (hereafter MSTO), which carries a PSEN1-LATS1 fusion leading to loss of LATS1 kinase activity and impaired phosphorylation of YAP. MSTO also harbors a 42-bp deletion in exon 5 of LATS2, resulting in its inactivation33,53,54. Cell lines were obtained from the American Type Culture Collection (ATCC) and maintained in RPMI-1640 medium supplemented with 10% FBS (Sigma-Aldrich), 2 mM L-glutamine (Gibco Life Sciences), and Penicillin?Streptomycin, in a humidified incubator at 37 °C with 5% CO?. GNE-7883?resistant NF2-null H226 and MSTO-211H cells were generated by long-term, stepwise dose adaptation to the pan-TEAD inhibitor GNE-7883. H226 cells were gradually exposed from 0.25 µM to 2.5 µM over ~55 days, and MSTO-211H cells from 0.25 µM to 3.0 µM, with incremental increases every 1?2 weeks while maintaining at least 25% cell confluence. During escalation, transient cytostasis was followed by the emergence of proliferating persister populations under sustained drug pressure. Resistant pools were expanded from these outgrowths and maintained in medium containing 5 µM GNE-7883. Characterization of these resistant models followed previously described procedures37. For acute treatment conditions, H226 and MSTO cells were treated with 2.5 µM GNE-7883 for 48-hours before collection.
Two established preclinical models of malignant mesothelioma were used in this study: NCI-H226 (hereafter H226), which is NF2-null, and MSTO-211H (hereafter MSTO), which carries a PSEN1-LATS1 fusion leading to loss of LATS1 kinase activity and impaired phosphorylation of YAP. MSTO also harbors a 42-bp deletion in exon 5 of LATS2, resulting in its inactivation33,53,54. Cell lines were obtained from the American Type Culture Collection (ATCC) and maintained in RPMI-1640 medium supplemented with 10% FBS (Sigma-Aldrich), 2 mM L-glutamine (Gibco Life Sciences), and Penicillin–Streptomycin, in a humidified incubator at 37 °C with 5% CO₂. GNE-7883–resistant NF2-null H226 and MSTO-211H cells were generated by long-term, stepwise dose adaptation to the pan-TEAD inhibitor GNE-7883. H226 cells were gradually exposed from 0.25 µM to 2.5 µM over ~55 days, and MSTO-211H cells from 0.25 µM to 3.0 µM, with incremental increases every 1–2 weeks while maintaining at least 25% cell confluence. During escalation, transient cytostasis was followed by the emergence of proliferating persister populations under sustained drug pressure. Resistant pools were expanded from these outgrowths and maintained in medium containing 5 µM GNE-7883. Characterization of these resistant models followed previously described procedures37. For acute treatment conditions, H226 and MSTO cells were treated with 2.5 µM GNE-7883 for 48-hours before collection.

extract_protocol:
RNA was isolated from 5x105 cells by standard, TRIzol-based RNA precipitation method as follows. Cells were resuspended in 1ml TRIzol (Ambion). Chloroform was added (200ul) to this lysate and extensively vortexed to achieve a homogenous mixture; then, it was incubated for 3-minutes at room temperature before centrifugation at 14,000g (relative centrifugal force) at 4C for 15-minutes. Aqueous layer was collected from the top and transferred into a new tube (~550ul), and the RNA was precipitated with equal volume of 2-propanol for 20-minutes at room temperature. RNA precipitates were centrifuged at 16,000g for 15-minutes at 4C and supernatant was carefully discarded without disturbing the RNA pellet. RNA pellet was washed with 1ml 75% EtOH and after the wash, dissolved in 30ul nuclease-free water. RNA concentration was determined by nanodrop.
Approximately, 500 ng of RNA was used for library synthesis using the TrueSeq RNA Sample Preparation kit v2 (Illumina). Size of the libraries was confirmed using 2200 TapeStation, and the concentration was determined by a qPCR-based method using the Library Quantification Kit (KAPA).

value: Mesothelioma

value: panTEAD knockdown


title: RNAseq_YAPTAZKD_treated_parental_H226_cells_rep2

description: Library name: RNAseq_H226_Parental_YAPTAZKD_rep2

value: YAP/TAZ knockdown


title: RNAseq_YAPTAZKD_treated_parental_H226_cells_rep1

description: Library name: RNAseq_H226_Parental_YAPTAZKD_rep1


title: Control14

description: Library name: CON14


title: HAPE-Mild5

description: Library name: HAPE05


title: MAT, FL, VGC, LAR, Mouse 5

description: Library name: 402_MAT_FL-LAR-5_L1_1

value: MAT

value: female

value: BALB/cAnNTac


title: RNAseq_Cas9_treated_parental_H226_cells_rep2

description: Library name: RNAseq_H226_Parental_Cas9_rep2

value: wild type


title: Thymus, HGC, TERM, Mouse 16

description: Library name: 392_Thymus_HGC-_ISS_Term-_16_L1_1

value: 8 months


title: RNAseq_Cas9_treated_parental_H226_cells_rep1

description: Library name: RNAseq_H226_Parental_Cas9_rep1

value: Lung


title: Control13

description: Library name: CON13


title: RNAseq_G7883_resistant_MSTO_cells_rep3

description: Library name: RNAseq_MSTO_Resistant_G7883_rep3

source_name: Ascites

value: Ascites


title: BAT, FL, VGC, LAR, Mouse 1

description: Library name: 391_BAT_FL-LAR-1_L1_1

value: BAT

value: VGC-LAR


title: RNAseq_G7883_resistant_MSTO_cells_rep2

description: Library name: RNAseq_MSTO_Resistant_G7883_rep2


title: RNAseq_G7883_resistant_MSTO_cells_rep1

description: Library name: RNAseq_MSTO_Resistant_G7883_rep1


title: RNAseq_G7883_treated_parental_MSTO_cells_rep2

description: Library name: RNAseq_MSTO_Parental_G7883_rep2


title: Thymus, FL, VGC, LAR, Mouse 4

description: Library name: 390_Thymus_FL-LAR-4_L1_1


title: Control11

description: Library name: CON11

value: Blood

value: control


title: RNAseq_G7883_treated_parental_MSTO_cells_rep1

description: Library name: RNAseq_MSTO_Parental_G7883_rep1


title: Control10

description: Library name: CON10

value: male


title: RNAseq_DMSO_treated_parental_MSTO_cells_rep2

description: Library name: RNAseq_MSTO_Parental_DMSO_rep2


title: Diaphragm, HGC, TERM, Mouse 5

description: Library name: 394_Diaphragm_HGC-_ISS_Term-_5_L1_1

value: Diaphragm

value: 3 months


title: RNAseq_G7883_treated_parental_MSTO_cells_rep3

description: Library name: RNAseq_MSTO_Parental_G7883_rep3

value: Mesothelioma


title: RNAseq_DMSO_treated_parental_MSTO_cells_rep3

description: Library name: RNAseq_MSTO_Parental_DMSO_rep3


title: BAT, VGC, LAR, Mouse 13

description: Library name: 393_BAT_VC-LAR-13_L1_1


title: RNAseq_panTEADKD_treated_parental_H226_cells_rep1

description: Library name: RNAseq_H226_Parental_panTEADKD_rep1

source_name: Lung

value: panTEAD knockdown


title: Brain, HGC, LAR, Mouse 1

description: Library name: 387_Brain_HC-LAR-1_L1_1

source_name: Brain

value: Brain

value: HGC-LAR


title: G7883_resistant_H226_cells_rep2

description: Library name: H226_7883R_2

data_processing:
Adaptor sequences were trimmed from FASTQ files using TrimGalore (v0.6.10, Babraham Institute)
Reads were aligned to the reference genome hg38 using BWA mem (v0.7.18), and the resulting files were parsed to identify junction contacts using pairtools parse2 (v1.1.0).
Reads were sorted and deduplicated using pairtools sort and pairtools dedup, and converted to BED files using a custom Python script. Promoter-linked junction pairs were identified by intersecting the BED files with a reference file containing genomic regions of interest, and the results were filtered and split into different viewpoints.
Assembly: hg38
Supplementary files format and content: Normalized (CPM) bigwig files that contain gene promoter-linked (promoter-aligning) sequencing reads of all investigated promoters.
Library strategy: Micro-Capture C

growth_protocol:
Cell lines used in this study were obtained from American Type Culture Collection (ATCC). Cells were maintained in RPMI 1640 supplemented with 10% FBS (Sigma-Aldrich Corporation), 2 mM L-glutamine (Gibco Life Sciences) and Penicillin-Streptomycin in a humidified incubator maintained at 37°C with 5% CO2.
Two established preclinical models of malignant mesothelioma were used in this study: NCI-H226 (hereafter H226), which is NF2-null, and MSTO-211H (hereafter MSTO), which carries a PSEN1-LATS1 fusion leading to loss of LATS1 kinase activity and impaired phosphorylation of YAP. MSTO also harbors a 42-bp deletion in exon 5 of LATS2, resulting in its inactivation33,53,54. Cell lines were obtained from the American Type Culture Collection (ATCC) and maintained in RPMI-1640 medium supplemented with 10% FBS (Sigma-Aldrich), 2 mM L-glutamine (Gibco Life Sciences), and Penicillin–Streptomycin, in a humidified incubator at 37 °C with 5% CO₂. GNE-7883–resistant NF2-null H226 and MSTO-211H cells were generated by long-term, stepwise dose adaptation to the pan-TEAD inhibitor GNE-7883. H226 cells were gradually exposed from 0.25 µM to 2.5 µM over ~55 days, and MSTO-211H cells from 0.25 µM to 3.0 µM, with incremental increases every 1–2 weeks while maintaining at least 25% cell confluence. During escalation, transient cytostasis was followed by the emergence of proliferating persister populations under sustained drug pressure. Resistant pools were expanded from these outgrowths and maintained in medium containing 5 µM GNE-7883. Characterization of these resistant models followed previously described procedures37. For acute treatment conditions, H226 and MSTO cells were treated with 2.5 µM GNE-7883 for 48-hours before collection.

extract_protocol:
Cells were scraped and crosslinked in the presence of 1% formaldehyde (in PBS) for 10-minutes in suspension followed by the addition of 1.5ml 1M Glycine and further incubation for 5-minutes at room temperature. Cells were washed in ice-cold PBS, counted, and 3-4x106 cell aliquots were prepared for nuclei isolation with the following MCC lysis buffer: 10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin and 1% BSA in nuclease-free H2O. Each cell aliquot of 3x106 was resuspended in 500ul MCC lysis buffer and incubated on ice for 5-minutes. Cells were spun down, washed in ice-cold PBS, and washed in nuclease-free H2O before proceeding to MNase digestion with 90-130U of MNase for 3x106 cells that went on for 1-hour at 37C while shaking in a thermomixer (Eppendorf) at 550rcf. MNase was stopped by the addition of EGTA. At this point, nuclei were split into two tubes, and end-repair and proximity ligation were performed overnight. On the next day, nuclei were spun and subjected to proteinase K digestion at 65C overnight. DNA was column purified (Minelute, Qiagen) and eluted in 130ul H2O for sonication with Covaris E220 model using the following settings: Fill Level – 10, Duty Cycle – 15, PIP – 300, Cycles/Bursts – 200; sonicated for 5-minutes. DNA was cleaned up with Minelute, quantified and subjected to library preparation with Ovation Ultralow V2 Library Systems (Tecan) using 100ng DNA and 8 PCR cycles. Amplified libraries were subjected to hybridization with biotinylated oligonucleotide pools that were designed by the HyperDesign Team (Roche) and synthesized by Roche. All hybridization reagents were purchased from Roche as part of the KAPA Hyper Prep kit, and hybridization, pull-down, and washes were performed per manufacturer’s instructions. Bead-bound libraries were amplified with the PCR reagents from the Ovation Ultralow Library V2 Kit (Tecan). Libraries were quantified and sequenced on a NovaSeq 6000 with 2x150bp configuration. MCC analysis was performed on two biological replicates per condition, and each biological sample was defined as a pooled total of 3 different MNase conditions (90U, 110U and 130U, 3x106 cells per MNase reaction), each split into two ligation reactions for subsequent downstream steps as described above.
Micro-Capture C (MCC)

treatment_protocol: TEAD small molecule inhibitor (SMI) resistant NF2 null NCI-H226 were generated by incubation with increasing concentrations of TEAD SMI over time (0.25 μM to 3 μM at bi-weekly with 0.1-0.5 μM increments), ensuring at least a 25% confluence at all times. The generation of the resistant cell lines was done using pooled populations of survivor cells. Resistant cells were grown in the presence of 5 μM GNE-7883. NCI-H226 cells treated with 2.5 μM GNE-7883 for 48-hours were collected for acute treatment conditions.


title: RNAseq_DMSO_treated_parental_MSTO_cells_rep1

description: Library name: RNAseq_MSTO_Parental_DMSO_rep1


title: Control9

description: Library name: CON09


title: MAT, HGC, LAR, Mouse 4

description: Library name: 388_MAT_HC-LAR-4_L1_1

value: MAT

value: female


title: G7883_treated_parental_H226_cells_rep2

description: Library name: H226_P_7883_2

value: wild type


title: Control7

description: Library name: CON07


title: DMSO_treated_parental_H226_cells_rep2

description: Library name: H226_P_DMSO_2


title: G7883_resistant_H226_cells_rep1

description: Library name: H226_7883R_1


title: Control8

description: Library name: CON08


title: Spleen, VGC, LAR, Mouse 16

description: Library name: 386_Spleen_VC-LAR-16_L1_1

value: Spleen

value: BALB/cAnNTac

value: 8 months


title: Control6

description: Library name: CON06


title: Control12

description: Library name: CON12


title: DMSO_treated_parental_H226_cells_rep1

description: Library name: H226_P_DMSO_1

value: Lung


title: Diaphragm, VGC, LAR, Mouse 2

description: Library name: 389_Diaphragm_VC-LAR-2_L1_1

value: VGC-LAR


title: G7883_resistant_MSTO_cells_rep2

description: Library name: MSTO_7883R_2

value: Ascites


title: Liver, VGC, LAR, Mouse 5

description: Library name: 384_Liver_VC-LAR-5_L1_1

value: Liver


title: Control5

description: Library name: CON05

value: Blood

value: control

value: male


title: Pancreas, VGC, TERM, Mouse 2

description: Library name: 383_Pancreas_VGC-_ISS_Term-_2_L1_1

source_name: Pancreas

value: Pancreas

value: VGC-TERM

value: 3 months


title: G7883_treated_parental_MSTO_cells_rep2

description: Library name: MSTO_P_7883_2

value: Mesothelioma


title: DMSO_treated_parental_MSTO_cells_rep2

description: Library name: MSTO_P_DMSO_2


title: MAT, FL, VGC, LAR, Mouse 14

description: Library name: 382_MAT_FL-LAR-14_L1_1

value: MAT


title: G7883_treated_parental_MSTO_cells_rep1

description: Library name: MSTO_P_7883_1


title: Control4

description: Library name: CON04


title: Control3

description: Library name: CON03


title: G7883_resistant_MSTO_cells_rep1

description: Library name: MSTO_7883R_1


title: Diaphragm, HGC, LAR, Mouse 5

description: Library name: 381_Diaphragm_HC-LAR-5_L1_1

value: Diaphragm

value: HGC-LAR

value: female


title: YAP_G7883_resistant_MSTO_cells_rep2

description: Library name: YAP_MSTO_Resistant_G7883_rep2

data_processing:
ChIP-seq results were analyzed using the ENCODE ChIP-seq pipeline (v2.2.1)61. ChIP-seq reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.4.3)63. Aligned reads were then filtered for quality and duplicates using samtools (v1.9)74 and Picard (Broad Institute - v2.20.7).
Assembly: hg38
Supplementary files format and content: Normalized bigwigs.

extract_protocol:
NCI-H226 and MSTO-211 mesothelioma cells (10 x 106) were double crosslinked with 50mM DSG (disuccinimidyl glutarate, #C1104 - ProteoChem) for 30-minutes followed by 10-minutes of 1% formaldehyde. Formaldehyde was quenched by the addition of glycine. Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0). Nuclei were sheared with Covaris sonicator using the following setup: Fill level ? 10, Duty Cycle ? 15, PIP ? 350, Cycles/Burst ? 200, Time ? 8-minutes). Sheared chromatin was immunoprecipitated overnight with the following antibodies: FOSL1 (PA5-66880 ? Invitrogen), YAP (14074S ? Cell Signaling), KLF4 (AF3158 ? R&D Systems). Antibody chromatin complexes were pulled down with Protein A magnetic beads and washed twice in IP wash buffer I. (1% Triton, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer II. (1% Triton, 0.1% SDS, 500 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer III. (0.25 M LiCl, 0.5% NP-40, 1mM EDTA, 20 mM Tris, pH 8.0, 0.5% NaDOC) and once in TE buffer (10 mM EDTA and 200 mM Tris, pH 8.0). DNA was eluted from the beads by vigorous shaking for 20-minutes in elution buffer (100mM NaHCO3, 1% SDS). DNA was de-crosslinked overnight at 65C and purified with the MinElute PCR purification kit (Qiagen).
DNA was quantified by Qubit and equal amounts (2ng) of DNA was used for sequencing library construction with the Ovation Ultralow Library System V2 (Tecan) using 15 PCR cycles according to the manufacturer?s recommendations. Libraries were sequenced with Illumina Nextseq 2000, using paired-end 50bp read configuration.

value: wild type


title: DMSO_treated_parental_MSTO_cells_rep1

description: Library name: MSTO_P_DMSO_1


title: YAP_G7883_resistant_MSTO_cells_rep1

description: Library name: YAP_MSTO_Resistant_G7883_rep1


title: Control2

description: Library name: CON02


title: Control1

description: Library name: CON01


title: YAP_G7883_treated_parental_MSTO_cells_rep1

description: Library name: YAP_MSTO_Parental_G7883_rep1


title: Diaphragm, HGC, TERM, Mouse 14

description: Library name: 385_Diaphragm_HGC-_ISS_Term-_14_L1_1

data_processing:
Fastq files containing raw sequencing reads were mapped against GRCm39 and miRBase (version 22.1) 65 in order to profile miRNA counts using miRmaster (version 2.0). Information about miRNA family was obtained from mirgenedb 3.0. Detection filtering was performed by keeping only miRNAs with at least 5 raw reads in at least 10% of samples in each condition-tissue group. Expression data was normalized using rpmm normalization (reads per mapped million).
Assembly: GRCm39
Supplementary files format and content: miRNA_complete_quantification_raw.tsv: Tab-separated file of raw miRNA counts per sample.
Supplementary files format and content: lncRNA_complete_quantification_raw.tsv: Tab-separated file of raw lncRNA counts per sample.
Supplementary files format and content: piRNA_complete_quantification_raw.tsv: Tab-separated file of raw piRNA counts per sample.
Supplementary files format and content: rRNA_complete_quantification_raw.tsv: Tab-separated file of raw rRNA counts per sample.
Supplementary files format and content: scaRNA_complete_quantification_raw.tsv: Tab-separated file of raw scaRNA counts per sample.
Supplementary files format and content: snoRNA_complete_quantification_raw.tsv: Tab-separated file of raw snoRNA counts per sample.
Supplementary files format and content: snRNA_complete_quantification_raw.tsv: Tab-separated file of raw snRNA counts per sample.
Supplementary files format and content: tRNA_complete_quantification_raw.tsv: Tab-separated file of raw tRNA counts per sample.

value: HGC-TERM

value: BALB/cAnNTac

value: 8 months


title: Lung, FL, VGC, LAR, Mouse 11

description: Library name: 380_Lung_FL-LAR-11_L1_1

value: Lung

value: VGC-LAR


title: Spleen, FL, VGC, LAR, Mouse 8

description: Library name: 379_Spleen_FL-LAR-8_L1_1

value: Spleen


title: YAP_DMSO_treated_parental_MSTO_cells_rep2

description: Library name: YAP_MSTO_Parental_DMSO_rep2

value: Ascites


title: G7883_treated_parental_H226_cells_rep1

description: Library name: H226_P_7883_1


title: YAP_G7883_treated_parental_MSTO_cells_rep2

description: Library name: YAP_MSTO_Parental_G7883_rep2


title: YAP_DMSO_treated_parental_MSTO_cells_rep1

description: Library name: YAP_MSTO_Parental_DMSO_rep1


title: KLF4_G7883_resistant_H226_cells_rep2

description: Library name: KLF4_H226_Resistant_G7883_rep2


title: BAT, VGC, LAR, Mouse 2

description: Library name: 378_BAT_VC-LAR-2_L1_1

value: BAT