title: Differentiation_biol_rep_3

status: Public on Oct 31 2025

type: SRA

city: Patras

first: Adamantia

last: Kouvela

address: Asklipiou 1

country: Greece

institute: Department of Biochemistry, School of Medicine, University of Patras

description:
limma-voom_cD-D
limma-voom_Pro-D

library_source: transcriptomic

data_processing:
Basecalling, de-multiplexing and filtering of low quality reads was performed within the Torrent Suite 5.12.3
The resulting fastq files were uploaded to the Galaxy web platform through the usegalaxy.eu public server
The differential gene expression was calculated with limma-voom (v3.50.1)
Assembly: mm10
Supplementary files format and content: limma-voom ouput in xlsx format

molecule: total RNA

organism: Mus musculus

source_name: postnatal mouse brain Neural Stem Cells

extract_protocol:
Τhe RNA isolation from cells cultured in proliferation conditions was performed with the NucleoSpin RNA Plus kit (MACHEREY-NAGEL, 740984), according to the manufacturer’s instructions. Τhe RNA isolation from cells cultured in the other two conditions was performed with the NucleoSpin RNA Plus XS kit (MACHEREY-NAGEL, 740990), according to the manufacturer’s instructions.
Total RNA libraries were prepared with the Ion Total-RNA seq kit v2 (4479789, Ion Torrent) according to the manufacturer's instructions

tag: cell type

value: postnatal mouse brain Neural Stem Cells

tag: treatment

value: differentiation conditions


title: Co-culture_biol_rep_3

description:
limma-voom_cD-D
limma-voom_cD-Pro

value: co-cultured with mouse platelets in the absence of growth factors


title: Differentiation_biol_rep_1

description:
limma-voom_cD-D
limma-voom_Pro-D


title: Proliferation_biol_rep_3

description:
limma-voom_cD-Pro
limma-voom_Pro-D

value: proliferation conditions


title: Co-culture_biol_rep_2

description:
limma-voom_cD-D
limma-voom_cD-Pro


title: Co-culture_biol_rep_1

description:
limma-voom_cD-D
limma-voom_cD-Pro


title: Proliferation_biol_rep_1

description:
limma-voom_cD-Pro
limma-voom_Pro-D


title: Differentiation_biol_rep_2

description:
limma-voom_cD-D
limma-voom_Pro-D


title: Colon digest of cycle 2 (2.5%) DSS, sample 2

city: Chicago

first: Ronen

last: Sumagin

state: Illinois

address: 303 E Chicago Ave

country: USA

institute: Northwestern University

description:
Library name: WT_cycle2_N2
10x genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were generated using Cell Ranger (v7.0.1)
Assembly: GRCh38(, GRCm38
Supplementary files format and content: tab-delimited text file includes cell and gene unique identifiers
Supplementary files format and content: mtx file contains counts for each sample

source_name: Colon tissue

extract_protocol:
Colons were excised opened longitudinally, washed of fecal content with HBSS and cut into ~5mm pieces. Epithelium was separated from the LP by placing the tissue on a shaker for 15 minutes (150RPM, 37°C) using 10% FBS and 2mM EDTA HBSS solution. Remining LP tissue was minced and digested into single cell solution by shaking (200 RPM, 10-15 minutes) in collagenase solution (5% FBS, 1.5 mg/ml, collagenase type VIII and 40μg/ml DNase in HBSS), resulting cell suspensions were washed and filtered through a 40µm filter to ensure single cell separation.  Human colonic biopsies were obtained from consented inactive UC patients (Mayo endoscopic scores of 0) during routine screening and processed into single cell suspensions in a Liberase TH (0.1WU/mL), DNase I (0.5U/mL) in HBSS solution for 3 rounds of 10 min incubations at 37°C at 800RPM. Cell suspensions were washed and passed through a 40 strainer to ensure single cell separation.
Libraries for both human and mouse samples were generated using Genomics Single Cell 3’ Reagents kit (v3) in accordance with the manufacturer’s protocols. Single cell suspensions were diluted in PBS 2%BSA targeting approximately 10,000 cells per sample. Single cells were sequenced to a read depth of ~ 20,000 reads per cell. Libraries were sequenced on an Illumina NovaSeq X Plus platform

treatment_protocol: Mice were given 2.5% DSS in drinking water for 6 days (cycle1), afterwards they were switched to regular drinking water for 14 days (recovery phase),  followed by a second administration of 2.5%DSS in drinking water for 6 days (cycle2).

tag: tissue

value: Colon tissue

tag: genotype

value: 2 cycles DSS


title: Colon digest of cycle 2 (2.5%) DSS, sample 1

description:
Library name: WT_cycle2_N1
10x genomics


title: Colon digest of cycle 1(2.5%)DSS, sample 2

description:
Library name: WT_cycle1_N2
10x genomics

value: 1 cycle DSS


title: S12h_A

city: Guiyang

first: Zhao

last: Yanchi

state: Guizhou

address: No. 9 Beijing Road

country: China

institute: Guizhou Medical University

description: Library name: SAMPLES 14

data_processing:
Hisat software was used to compare the sequencing data with the zebrafish referenced genome. To evaluate the expression level of all mRNAs, we first realized sample reads through StringTie, and then calculated the FPKM (fragments per kilobase of transcript per million mapped reads) using stringtie and edgeR software. Finally, the differentially expressed genes (DEGs) were screened by the R software package according to the following criteria: log2 (fold-change) > 1 or <−1 and at p < 0.05. These DEGs were used for further analysis of functions and signaling pathways using Gene Ontology (GO; http://geneontology.org/) and Kyoto Encyclopedia of Genes and Genomes (KEGG; https://www.genome.jp/kegg/).
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Danio rerio

source_name: Venous thrombus tissue at the injury site

extract_protocol:
Total RNA was extracted using Invitrogen TRizol reagent (California, USA). Generation of the Illumina RNA sequence library, along with paired end sequencing (300±50 bp) was conducted on an Illumina Hiseq 4000 (LC science, USA) using aliquots (5 mg) of qualified total RNA. Hisat software was used to align compare the sequencing data with the zebrafish reference genome (http://ftp.ensembl.org/pub/release-106/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.toplevel.fa.gz).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Tg (flk1:eGFP; gata1:dsRed)

value: Venous Thrombosis 12-hour Post-Injury Sample


title: S12h_C

description: Library name: SAMPLES 13

value: Venous thrombus tissue at the injury site


title: S12h_B

description: Library name: SAMPLES 15


title: S6h_B

description: Library name: SAMPLES 12

value: Venous Thrombosis 6-hour Post-Injury Sample


title: S3h_A

description: Library name: SAMPLES 8

value: Venous Thrombosis 3-hour Post-Injury Sample


title: S6h_C

description: Library name: SAMPLES 10


title: S6h_A

description: Library name: SAMPLES 11


title: S3h_B

description: Library name: SAMPLES 9


title: Proliferation_biol_rep_2

description:
limma-voom_cD-Pro
limma-voom_Pro-D


title: Control24_12022022

city: Corvallis

first: Robyn

middle: Leigh

last: Tanguay

state: OR

address: 28645 East Hwy 34

department: Environmental and Molecular Toxicology

institute: Oregon State University

description:
Library name: Sample 662
Total RNA isolated from 48 hour post fertilization zebrafish

data_processing:
STAR for genome mapping and alignment (parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate).
HTSeq for gene-level counts (parameters: -m intersection-nonempty -s yes -f bam -r pos).
DESeq2 for differential expression analysis (experiments A&B analyzed together, with sequencing runs collapsed by sample and samples contrasted to appropriate controls).
Assembly: GRCz11
Supplementary files format and content: .csv with read counts, filtered files and gene expression for all samples

source_name: 48 hpf whole embryo

growth_protocol: Animals were dechorionated at 4 hours post-fertilization (hpf) and then kept in 96-well plates in 100 µL embryo medium consisting of 15 mM NaCl, 0.5 mM KCl, 1 mM MgSO4, 0.15 mM KH2PO4, 0.05 mM Na2HPO4, and 0.7 mM NaHCO3 (Westerfield, 2000) at 28 °C in the dark.

extract_protocol:
For RNA isolation, sample tubes containing pools of 8 animals in 200 uL of 1X RNAshield were incubated at 32°C for 30 minutes to ensure complete thawing. 100 µL of 0.5 mm zirconium silicate beads were added, and samples were homogenized in the bullet blender at speed 10, for 5 minutes. Samples were then spun down for 5 minutes at 12000 xg, afterwards 250 µL of supernatant from each tube was aliquoted twice (for a total of 500 µL) into two new sample plates. These plates were then processed using the KingFisher Apex system for automated RNA extraction using Zymo Research’s Quick RNA Magbead Kit and eluted into 50 µL RNAse/DNAse free water.
The samples underwent PrepX Robotic RNA PolyA enrichment combined with NEBNext UltraII Directional RNA Library Prep/Illumina Stranded mRNA library preparation.

treatment_protocol: At 6 hours post-fertilization (hpf), animals were statically exposed to chemicals using an HP D300 digital dispenser to dispense stocks into individual wells of the 96-well plates, all normalized to 1% DMSO, and plates were sealed.

tag: age

value: 48 hour post fertilization

value: 48 hpf whole embryo


title: Cyazofamid_biological_replicate_1

description:
Library name: Sample 666
Total RNA isolated from 48 hour post fertilization zebrafish


title: Fenariml_biological_replicate_4

description:
Library name: Sample 659
Total RNA isolated from 48 hour post fertilization zebrafish


title: Fenariml_biological_replicate_1

description:
Library name: Sample 656
Total RNA isolated from 48 hour post fertilization zebrafish


title: Fenariml_biological_replicate_2

description:
Library name: Sample 657
Total RNA isolated from 48 hour post fertilization zebrafish


title: Con_C

description: Library name: SAMPLES 1

source_name: Venous Tissue

value: Venous Tissue

value: No injury and no venous thrombosis Sample


title: Cyazofamid_biological_replicate_4

description:
Library name: Sample 669
Total RNA isolated from 48 hour post fertilization zebrafish


title: S1h_C

description: Library name: SAMPLES 4

value: Venous Thrombosis 1-hour Post-Injury Sample


title: Con_A

description: Library name: SAMPLES 2


title: Con_B

description: Library name: SAMPLES 3


title: Cyazofamid_biological_replicate_3

description:
Library name: Sample 668
Total RNA isolated from 48 hour post fertilization zebrafish


title: Cyazofamid_biological_replicate_2

description:
Library name: Sample 667
Total RNA isolated from 48 hour post fertilization zebrafish


title: Colon digest of cycle 1 (2.5%) DSS, sample 1

description:
Library name: WT_cycle1_N1
10x genomics


title: Fenariml_biological_replicate_3

description:
Library name: Sample 658
Total RNA isolated from 48 hour post fertilization zebrafish


title: Forchlorfenuron-biological_replicate_3

description:
Library name: Sample 648
Total RNA isolated from 48 hour post fertilization zebrafish


title: S3h_C

description: Library name: SAMPLES 7


title: Forchlorfenuron-biological_replicate_1

description:
Library name: Sample 646
Total RNA isolated from 48 hour post fertilization zebrafish


title: Forchlorfenuron-biological_replicate_4

description:
Library name: Sample 649
Total RNA isolated from 48 hour post fertilization zebrafish


title: Endosulfan_biological_replicate_4

description:
Library name: Sample 624
Total RNA isolated from 48 hour post fertilization zebrafish


title: Endosulfan_biological_replicate_3

description:
Library name: Sample 623
Total RNA isolated from 48 hour post fertilization zebrafish


title: Thiodicarb_biological_replicate_3

description:
Library name: Sample 638
Total RNA isolated from 48 hour post fertilization zebrafish


title: S1h_A

description: Library name: SAMPLES 5


title: Thiodicarb_biological_replicate_4

description:
Library name: Sample 639
Total RNA isolated from 48 hour post fertilization zebrafish


title: S1h_4

description: Library name: SAMPLES 6


title: Control23_08032022

description:
Library name: Sample 631
Total RNA isolated from 48 hour post fertilization zebrafish


title: Endosulfan_biological_replicate_1

description:
Library name: Sample 621
Total RNA isolated from 48 hour post fertilization zebrafish


title: Fenpropathrin_biological_replicate_4

description:
Library name: Sample 594
Total RNA isolated from 48 hour post fertilization zebrafish


title: Fenpropathrin_biological_replicate_2

description:
Library name: Sample 592
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control22_07282022

description:
Library name: Sample 603
Total RNA isolated from 48 hour post fertilization zebrafish


title: Forchlorfenuron-biological_replicate_2

description:
Library name: Sample 647
Total RNA isolated from 48 hour post fertilization zebrafish


title: Endrin_biological_replicate_3

description:
Library name: Sample 583
Total RNA isolated from 48 hour post fertilization zebrafish


title: Endrin_biological_replicate_2

description:
Library name: Sample 582
Total RNA isolated from 48 hour post fertilization zebrafish


title: Isoxaben_biological_replicate_3

description:
Library name: Sample 563
Total RNA isolated from 48 hour post fertilization zebrafish


title: Isoxaben_biological_replicate_4

description:
Library name: Sample 564
Total RNA isolated from 48 hour post fertilization zebrafish


title: Isoxaben_biological_replicate_2

description:
Library name: Sample 562
Total RNA isolated from 48 hour post fertilization zebrafish


title: Fenpropathrin_biological_replicate_1

description:
Library name: Sample 591
Total RNA isolated from 48 hour post fertilization zebrafish


title: Flumetralin_biological_replicate_4

description:
Library name: Sample 534
Total RNA isolated from 48 hour post fertilization zebrafish


title: Endrin_biological_replicate_1

description:
Library name: Sample 581
Total RNA isolated from 48 hour post fertilization zebrafish


title: Isoxaben_biological_replicate_1

description:
Library name: Sample 561
Total RNA isolated from 48 hour post fertilization zebrafish


title: Thiodicarb_biological_replicate_1

description:
Library name: Sample 636
Total RNA isolated from 48 hour post fertilization zebrafish


title: Flumetralin_biological_replicate_2

description:
Library name: Sample 532
Total RNA isolated from 48 hour post fertilization zebrafish


title: Thiodicarb_biological_replicate_2

description:
Library name: Sample 637
Total RNA isolated from 48 hour post fertilization zebrafish


title: Endosulfan_biological_replicate_2

description:
Library name: Sample 622
Total RNA isolated from 48 hour post fertilization zebrafish


title: Nitrofen_biological_replicate_4

description:
Library name: Sample 514
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control19_07202022

description:
Library name: Sample 518
Total RNA isolated from 48 hour post fertilization zebrafish


title: Nitrofen_biological_replicate_3

description:
Library name: Sample 513
Total RNA isolated from 48 hour post fertilization zebrafish


title: Nitrofen_biological_replicate_1

description:
Library name: Sample 511
Total RNA isolated from 48 hour post fertilization zebrafish


title: Chlordane_biological_replicate_3

description:
Library name: Sample 503
Total RNA isolated from 48 hour post fertilization zebrafish


title: Chlordane_biological_replicate_4

description:
Library name: Sample 504
Total RNA isolated from 48 hour post fertilization zebrafish


title: Fenpropathrin_biological_replicate_3

description:
Library name: Sample 593
Total RNA isolated from 48 hour post fertilization zebrafish


title: Endrin_biological_replicate_4

description:
Library name: Sample 584
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control21_07272022

description:
Library name: Sample 577
Total RNA isolated from 48 hour post fertilization zebrafish


title: Chlordane_biological_replicate_1

description:
Library name: Sample 501
Total RNA isolated from 48 hour post fertilization zebrafish


title: 1-Amino-2,6-dichloro-4-nitrobenzene_biological_replicate_3

description:
Library name: Sample 498
Total RNA isolated from 48 hour post fertilization zebrafish


title: Chlordane_biological_replicate_2

description:
Library name: Sample 502
Total RNA isolated from 48 hour post fertilization zebrafish


title: 1-Amino-2,6-dichloro-4-nitrobenzene_biological_replicate_4

description:
Library name: Sample 499
Total RNA isolated from 48 hour post fertilization zebrafish


title: 1-Amino-2,6-dichloro-4-nitrobenzene_biological_replicate_2

description:
Library name: Sample 497
Total RNA isolated from 48 hour post fertilization zebrafish


title: Carbosulfan_biological_replicate_4

description:
Library name: Sample 494
Total RNA isolated from 48 hour post fertilization zebrafish


title: 1-Amino-2,6-dichloro-4-nitrobenzene_biological_replicate_1

description:
Library name: Sample 496
Total RNA isolated from 48 hour post fertilization zebrafish


title: Carbosulfan_biological_replicate_3

description:
Library name: Sample 493
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control20_07272022

description:
Library name: Sample 549
Total RNA isolated from 48 hour post fertilization zebrafish


title: Flumetralin_biological_replicate_3

description:
Library name: Sample 533
Total RNA isolated from 48 hour post fertilization zebrafish


title: Ethoxyquin_biological_replicate_4

description:
Library name: Sample 484
Total RNA isolated from 48 hour post fertilization zebrafish


title: Carbosulfan_biological_replicate_2

description:
Library name: Sample 492
Total RNA isolated from 48 hour post fertilization zebrafish


title: Ethoxyquin_biological_replicate_3

description:
Library name: Sample 483
Total RNA isolated from 48 hour post fertilization zebrafish


title: Flumetralin_biological_replicate_1

description:
Library name: Sample 531
Total RNA isolated from 48 hour post fertilization zebrafish


title: Ethoxyquin_biological_replicate_1

description:
Library name: Sample 481
Total RNA isolated from 48 hour post fertilization zebrafish


title: Cyfluthrin_biological_replicate_4

description:
Library name: Sample 475
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control18_07142022

description:
Library name: Sample 486
Total RNA isolated from 48 hour post fertilization zebrafish


title: Carbosulfan_biological_replicate_1

description:
Library name: Sample 491
Total RNA isolated from 48 hour post fertilization zebrafish


title: Ethoxyquin_biological_replicate_2

description:
Library name: Sample 482
Total RNA isolated from 48 hour post fertilization zebrafish


title: Nitrofen_biological_replicate_2

description:
Library name: Sample 512
Total RNA isolated from 48 hour post fertilization zebrafish


title: Cyfluthrin_biological_replicate_3

description:
Library name: Sample 474
Total RNA isolated from 48 hour post fertilization zebrafish


title: Cyfluthrin_biological_replicate_2

description:
Library name: Sample 473
Total RNA isolated from 48 hour post fertilization zebrafish


title: Cyfluthrin_biological_replicate_1

description:
Library name: Sample 472
Total RNA isolated from 48 hour post fertilization zebrafish


title: Pendimethalin_biological_replicate_3

description:
Library name: Sample 458
Total RNA isolated from 48 hour post fertilization zebrafish


title: Pendimethalin_biological_replicate_4

description:
Library name: Sample 459
Total RNA isolated from 48 hour post fertilization zebrafish


title: Pendimethalin_biological_replicate_1

description:
Library name: Sample 456
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control17_07132022

description:
Library name: Sample 463
Total RNA isolated from 48 hour post fertilization zebrafish


title: Pendimethalin_biological_replicate_2

description:
Library name: Sample 457
Total RNA isolated from 48 hour post fertilization zebrafish


title: Butafenacil_biological_replicate_1

description:
Library name: Sample 446
Total RNA isolated from 48 hour post fertilization zebrafish


title: Butafenacil_biological_replicate_3

description:
Library name: Sample 448
Total RNA isolated from 48 hour post fertilization zebrafish


title: Butafenacil_biological_replicate_4

description:
Library name: Sample 449
Total RNA isolated from 48 hour post fertilization zebrafish


title: Butafenacil_biological_replicate_2

description:
Library name: Sample 447
Total RNA isolated from 48 hour post fertilization zebrafish


title: Trichlorfon_biological_replicate_4

description:
Library name: Sample 434
Total RNA isolated from 48 hour post fertilization zebrafish


title: Trichlorfon_biological_replicate_3

description:
Library name: Sample 433
Total RNA isolated from 48 hour post fertilization zebrafish


title: Trichlorfon_biological_replicate_1

description:
Library name: Sample 431
Total RNA isolated from 48 hour post fertilization zebrafish


title: Trichlorfon_biological_replicate_2

description:
Library name: Sample 432
Total RNA isolated from 48 hour post fertilization zebrafish


title: Dipropyl 2,5-pyridinedicarboxylate_biological_replicate_2

description:
Library name: Sample 417
Total RNA isolated from 48 hour post fertilization zebrafish


title: Tributyltin methacrylate_biological_replicate_4

description:
Library name: Sample 414
Total RNA isolated from 48 hour post fertilization zebrafish


title: Dipropyl 2,5-pyridinedicarboxylate_biological_replicate_3

description:
Library name: Sample 418
Total RNA isolated from 48 hour post fertilization zebrafish


title: Tributyltin methacrylate_biological_replicate_1

description:
Library name: Sample 411
Total RNA isolated from 48 hour post fertilization zebrafish


title: Dipropyl 2,5-pyridinedicarboxylate_biological_replicate_4

description:
Library name: Sample 419
Total RNA isolated from 48 hour post fertilization zebrafish


title: Tributyltin methacrylate_biological_replicate_2

description:
Library name: Sample 412
Total RNA isolated from 48 hour post fertilization zebrafish


title: Triadimenol_biological_replicate_3

description:
Library name: Sample 403
Total RNA isolated from 48 hour post fertilization zebrafish


title: Triadimenol_biological_replicate_4

description:
Library name: Sample 404
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control15_04222022

description:
Library name: Sample 407
Total RNA isolated from 48 hour post fertilization zebrafish


title: Dipropyl 2,5-pyridinedicarboxylate_biological_replicate_1

description:
Library name: Sample 416
Total RNA isolated from 48 hour post fertilization zebrafish


title: Tributyltin methacrylate_biological_replicate_3

description:
Library name: Sample 413
Total RNA isolated from 48 hour post fertilization zebrafish


title: Triadimenol_biological_replicate_2

description:
Library name: Sample 402
Total RNA isolated from 48 hour post fertilization zebrafish


title: Triadimenol_biological_replicate_1

description:
Library name: Sample 401
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control14_04082022

description:
Library name: Sample 384
Total RNA isolated from 48 hour post fertilization zebrafish


title: 4,6-Dinitro-o-cresol_biological_replicate_4

description:
Library name: Sample 390
Total RNA isolated from 48 hour post fertilization zebrafish


title: Piperonyl butoxide_biological_replicate_4

description:
Library name: Sample 374
Total RNA isolated from 48 hour post fertilization zebrafish


title: 4,6-Dinitro-o-cresol_biological_replicate_1

description:
Library name: Sample 386
Total RNA isolated from 48 hour post fertilization zebrafish


title: 4,6-Dinitro-o-cresol_biological_replicate_2

description:
Library name: Sample 387
Total RNA isolated from 48 hour post fertilization zebrafish


title: Piperonyl butoxide_biological_replicate_3

description:
Library name: Sample 373
Total RNA isolated from 48 hour post fertilization zebrafish


title: Chlorpyrifos oxon_biological_replicate_4

description:
Library name: Sample 354
Total RNA isolated from 48 hour post fertilization zebrafish


title: Piperonyl butoxide_biological_replicate_1

description:
Library name: Sample 371
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control13_04072022

description:
Library name: Sample 357
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control16_06092022

description:
Library name: Sample 437
Total RNA isolated from 48 hour post fertilization zebrafish


title: Chlorpyrifos oxon_biological_replicate_3

description:
Library name: Sample 353
Total RNA isolated from 48 hour post fertilization zebrafish


title: Piperonyl butoxide_biological_replicate_2

description:
Library name: Sample 372
Total RNA isolated from 48 hour post fertilization zebrafish


title: Chlorpyrifos oxon_biological_replicate_2

description:
Library name: Sample 352
Total RNA isolated from 48 hour post fertilization zebrafish


title: Chlorpyrifos oxon_biological_replicate_1

description:
Library name: Sample 351
Total RNA isolated from 48 hour post fertilization zebrafish


title: HUVECs,PHB1, CUT&Tag

city: Jinan

first: Hanlin

last: Lu

address: Wenhuaxi Road

institute: Qilu Hospital of Shandong University

description: Library name: CUT_TAG_PHB1

library_source: genomic

data_processing:
For CUT&TAG, the raw sequence data (50.9 million) were initially processed by Trimmomatic (v 0.36) to obtain clean reads. Then, the clean reads were aligned to the homo sapiens genome UCSC_hg19. MACS2 (v 2.1.2) was used for peak calling (q-value < 0.05) based on the alignment in the BAM file format and peaks were annotated by R package ChIPseeker (v 1.26.0).
Assembly: UCSC_hg19
Supplementary files format and content: text files include FXR or PHB1 target genes
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

source_name: human umbilical vein endothelial cells

extract_protocol:
CUT&Tag assay was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Cat#TD904, Vazyme, China) according to manufacturer's instructions.
For CUT&TAG, DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. The libraries were amplified by PCR with a universal i5 and a uniquely barcoded i7 primer. Size analysis of the finished library was conducted using the Agilent 4200 TapeStation system (Agilent Technologies, Santa Clara, CA, USA). Finally, sequencing was performed with the Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated for the subsequent analysis.

value: human umbilical vein endothelial cells


title: HUVECs, FXR, CUT&Tag

description: Library name: CUT_TAG_FXR


title: Napropamide_biological_replicate_4

description:
Library name: Sample 335
Total RNA isolated from 48 hour post fertilization zebrafish


title: Napropamide_biological_replicate_3

description:
Library name: Sample 334
Total RNA isolated from 48 hour post fertilization zebrafish


title: Napropamide_biological_replicate_2

description:
Library name: Sample 333
Total RNA isolated from 48 hour post fertilization zebrafish


title: Napropamide_biological_replicate_1

description:
Library name: Sample 331
Total RNA isolated from 48 hour post fertilization zebrafish


title: 4,6-Dinitro-o-cresol_biological_replicate_3

description:
Library name: Sample 389
Total RNA isolated from 48 hour post fertilization zebrafish


title: HUVECs, DMSO, rep1

description: Library name: DMSO_1

data_processing:
For RNA-seq, fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens UCSC_hg19. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: UCSC_hg19
Supplementary files format and content: csv file include FPKM values.

extract_protocol:
TRIzol reagent (Cat#15596018, Thermo Fisher, USA) was used to isolate and purify total RNA from HUVECs.
For RNA-seq, the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat#1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, Cat#m0209, USA), RNase H (NEB, Cat#m0297, USA) and dUTP Solution (Thermo Fisher, Cat#R0133, USA). An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, Cat#m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 ± 50 bp.


title: HUVECs, GW4064, rep3

description: Library name: GW4064_3


title: HUVECs, GW4064, rep1

description: Library name: GW4064_1


title: HUVECs, DMSO, rep3

description: Library name: DMSO_3


title: HUVECs, GW4064, rep2

description: Library name: GW4064_2


title: Control12_04062022

description:
Library name: Sample 342
Total RNA isolated from 48 hour post fertilization zebrafish


title: Emamectin benzoate_biological_replicate_4

description:
Library name: Sample 325
Total RNA isolated from 48 hour post fertilization zebrafish


title: HUVECs, DMSO, rep2

description: Library name: DMSO_2


title: HUVECs,TCDCA, rep4

description: Library name: T_4


title: HUVECs,TCDCA, rep3

description: Library name: T_3


title: Emamectin benzoate_biological_replicate_2

description:
Library name: Sample 323
Total RNA isolated from 48 hour post fertilization zebrafish


title: Emamectin benzoate_biological_replicate_3

description:
Library name: Sample 324
Total RNA isolated from 48 hour post fertilization zebrafish


title: HUVECs,TCDCA, rep2

description: Library name: T_2


title: Emamectin benzoate_biological_replicate_1

description:
Library name: Sample 322
Total RNA isolated from 48 hour post fertilization zebrafish


title: HUVECs,TCDCA, rep1

description: Library name: T_1


title: Control11_03142022

description:
Library name: Sample 314
Total RNA isolated from 48 hour post fertilization zebrafish


title: HUVECs, vehicle, rep4

description: Library name: V_4


title: Picoxystrobin_biological_replicate_4

description:
Library name: Sample 264
Total RNA isolated from 48 hour post fertilization zebrafish


title: HUVECs, vehicle, rep3

description: Library name: V_3


title: HUVECs, vehicle, rep2

description: Library name: V_2


title: HUVECs, vehicle, rep1

description: Library name: V_1


title: Picoxystrobin_biological_replicate_3

description:
Library name: Sample 263
Total RNA isolated from 48 hour post fertilization zebrafish


title: Picoxystrobin_biological_replicate_1

description:
Library name: Sample 261
Total RNA isolated from 48 hour post fertilization zebrafish


title: Picoxystrobin_biological_replicate_2

description:
Library name: Sample 262
Total RNA isolated from 48 hour post fertilization zebrafish


title: Methomyl_biological_replicate_4

description:
Library name: Sample 259
Total RNA isolated from 48 hour post fertilization zebrafish


title: Methomyl_biological_replicate_2

description:
Library name: Sample 257
Total RNA isolated from 48 hour post fertilization zebrafish


title: Methomyl_biological_replicate_3

description:
Library name: Sample 258
Total RNA isolated from 48 hour post fertilization zebrafish


title: Difenoconazole__biological_replicate_4

description:
Library name: Sample 239
Total RNA isolated from 48 hour post fertilization zebrafish


title: Carbofuran_biological_replicate_4

description:
Library name: Sample 209
Total RNA isolated from 48 hour post fertilization zebrafish


title: Difenoconazole__biological_replicate_1

description:
Library name: Sample 236
Total RNA isolated from 48 hour post fertilization zebrafish


title: Methomyl_biological_replicate_1

description:
Library name: Sample 256
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control9_02252022

description:
Library name: Sample 217
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control10_02272022

description:
Library name: Sample 247
Total RNA isolated from 48 hour post fertilization zebrafish


title: Carbofuran_biological_replicate_2

description:
Library name: Sample 207
Total RNA isolated from 48 hour post fertilization zebrafish


title: Difenoconazole__biological_replicate_3

description:
Library name: Sample 238
Total RNA isolated from 48 hour post fertilization zebrafish


title: Difenoconazole__biological_replicate_2

description:
Library name: Sample 237
Total RNA isolated from 48 hour post fertilization zebrafish


title: Carbofuran_biological_replicate_3

description:
Library name: Sample 208
Total RNA isolated from 48 hour post fertilization zebrafish


title: human chondrocyte, control 3

city: 成都市

first: Mingyang

last: Li

state: Anhui province

address: 四川省成都市高新区高朋大道17号吉泰安中心10楼1002

institute: West China Hospital, Sichuan University

description: Library name: con3

data_processing:
Raw reads were filtered to remove adaptors, poly-N sequences, and low-quality reads. Clean reads were aligned to the human genome (GRCh38) using HISAT2 v2.2.1. Gene-level read counts were obtained using FeatureCounts v2.0.2.
Assembly: GRCh38
Supplementary files format and content: The processed data file contains normalized gene expression values in FPKM format. The first column lists gene identifiers (GeneID), and each subsequent column represents an individual sample. Rows correspond to genes and columns to samples. The file is formatted as a tabular Excel spreadsheet (.xlsx) with gene expression levels for all samples.

source_name: human primary chondrocyte

growth_protocol: Human primary chondrocytes were cultured in complete chondrocyte growth medium at 37°C with 5% CO₂ in a humidified incubator.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. RNA quality and concentration were assessed using NanoDrop and Agilent 2100/4200 systems.
RNA-seq libraries were prepared using polyA-enriched, strand-specific protocols. First-strand cDNA synthesis was performed using random hexamers, followed by dUTP-based second-strand synthesis. Libraries were ligated with sequencing adaptors, PCR-amplified, and purified. Library size distribution was checked via gel electrophoresis, and concentration was quantified by Qubit and qPCR.

treatment_protocol: Cells were pretreated with 10 ng/mL IL-1β for 24 hours. After pretreatment, cells were treated with 25 μM DHA or PBS (control) for 48 hours.

tag: cell line

value: human primary chondrocyte

value: chondrocyte

value: 10 ng/mL IL-1β pretreated for 24 hours, PBS treated for 48 hours


title: human chondrocyte, DHA-treated 1

address: 四川省成都市高新区高朋大道17号吉泰安中心10楼1002

description: Library name: DHA1

value: 10 ng/mL IL-1β pretreated for 24 hours, 25μM DHA treated for 48 hours


title: human chondrocyte, DHA-treated 3

address: 四川省成都市高新区高朋大道17号吉泰安中心10楼1002

description: Library name: DHA3


title: human chondrocyte, DHA-treated 2

address: 四川省成都市高新区高朋大道17号吉泰安中心10楼1002

description: Library name: DHA2


title: human chondrocyte, control 2

address: 四川省成都市高新区高朋大道17号吉泰安中心10楼1002

description: Library name: con2


title: Benodanil_biological_replicate_4

description:
Library name: Sample 199
Total RNA isolated from 48 hour post fertilization zebrafish


title: Carbofuran_biological_replicate_1

description:
Library name: Sample 206
Total RNA isolated from 48 hour post fertilization zebrafish


title: Benodanil_biological_replicate_3

description:
Library name: Sample 198
Total RNA isolated from 48 hour post fertilization zebrafish


title: Benodanil_biological_replicate_2

description:
Library name: Sample 197
Total RNA isolated from 48 hour post fertilization zebrafish


title: human chondrocyte, control 1

address: 四川省成都市高新区高朋大道17号吉泰安中心10楼1002

description: Library name: con1


title: Benodanil_biological_replicate_1

description:
Library name: Sample 196
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 201

city: ראשון לציון

first: Iddo

last: Magen

state: Not in US

address: בן אליעזר 32, 17

country: Israel

institute: Weizmann Institute

description: Library name: BAC_9_8

library_source: other

data_processing:
Read alignment using CLC genomic workbench (Qiagen)
low-abudnant sample filtering
data imputation, batch correction and normalization by DESeq2 algorithm.
Assembly: GRCm38 for small RNA
Supplementary files format and content: tab-delimited text files include raw counts and corrected counts  for each sample

molecule: other

source_name: blood plasma

extract_protocol:
RNA extraction RNA was extracted from plasma of ALS patients by adding 5 volumes of Qiazol to one volume of plasma, followed by miRNeasy micro kit (Qiagen) according to manufacturer’s protocols and RNA yield was quantified using Qubit fluorometer Qubit fluorometer (RNA broad range assay kit; ThermoFisher Scientific).
small RNA libraries were constructed using the QIAseq miRNA library kit following manufacturer's instructions.

value: blood plasma

tag: batch


title: Control8_02202022

description:
Library name: Sample 188
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 200

address: בן אליעזר 32, 17

description: Library name: BAC_9_7


title: Tefluthrin_biological_replicate_4

description:
Library name: Sample 179
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 199

address: בן אליעזר 32, 17

description: Library name: BAC_9_6


title: Human ALS, rep 198

address: בן אליעזר 32, 17

description: Library name: BAC_9_5


title: Tefluthrin_biological_replicate_3

description:
Library name: Sample 178
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 197

address: בן אליעזר 32, 17

description: Library name: BAC_9_4


title: Tefluthrin_biological_replicate_2

description:
Library name: Sample 177
Total RNA isolated from 48 hour post fertilization zebrafish


title: Tefluthrin_biological_replicate_1

description:
Library name: Sample 176
Total RNA isolated from 48 hour post fertilization zebrafish


title: Chlorpropham_biological_replicate_4

description:
Library name: Sample 154
Total RNA isolated from 48 hour post fertilization zebrafish


title: Chlorpropham_biological_replicate_3

description:
Library name: Sample 153
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control7_02172022

description:
Library name: Sample 163
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 195

address: בן אליעזר 32, 17

description: Library name: BAC_9_24


title: Human ALS, rep 194

address: בן אליעזר 32, 17

description: Library name: BAC_9_23


title: Human ALS, rep 193

address: בן אליעזר 32, 17

description: Library name: BAC_9_22


title: Chlorpropham_biological_replicate_2

description:
Library name: Sample 152
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control6_02092022

description:
Library name: Sample 148
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 188

address: בן אליעזר 32, 17

description: Library name: BAC_9_18


title: Human ALS, rep 189

address: בן אליעזר 32, 17

description: Library name: BAC_9_19


title: Chlorpropham_biological_replicate_1

description:
Library name: Sample 151
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 191

address: בן אליעזר 32, 17

description: Library name: BAC_9_20


title: Flusilazole_biological_replicate_3

description:
Library name: Sample 138
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 190

address: בן אליעזר 32, 17

description: Library name: BAC_9_2


title: Flusilazole_biological_replicate_4

description:
Library name: Sample 139
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 192

address: בן אליעזר 32, 17

description: Library name: BAC_9_21


title: Human ALS, rep 196

address: בן אליעזר 32, 17

description: Library name: BAC_9_3


title: Flusilazole_biological_replicate_1

description:
Library name: Sample 136
Total RNA isolated from 48 hour post fertilization zebrafish


title: Flusilazole_biological_replicate_2

description:
Library name: Sample 137
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 187

address: בן אליעזר 32, 17

description: Library name: BAC_9_17


title: Human ALS, rep 186

address: בן אליעזר 32, 17

description: Library name: BAC_9_16


title: Cyproconazole_biological_replicate_4

description:
Library name: Sample 134
Total RNA isolated from 48 hour post fertilization zebrafish


title: Cyproconazole_biological_replicate_3

description:
Library name: Sample 133
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 185

address: בן אליעזר 32, 17

description: Library name: BAC_9_15


title: Human ALS, rep 184

address: בן אליעזר 32, 17

description: Library name: BAC_9_14


title: Human ALS, rep 183

address: בן אליעזר 32, 17

description: Library name: BAC_9_13


title: Cyproconazole_biological_replicate_2

description:
Library name: Sample 132
Total RNA isolated from 48 hour post fertilization zebrafish


title: Cyproconazole_biological_replicate_1

description:
Library name: Sample 131
Total RNA isolated from 48 hour post fertilization zebrafish


title: Control5_02032022

description:
Library name: Sample 129
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 181

address: בן אליעזר 32, 17

description: Library name: BAC_9_1


title: Human ALS, rep 180

address: בן אליעזר 32, 17

description: Library name: BAC_8_9


title: Human ALS, rep 182

address: בן אליעזר 32, 17

description: Library name: BAC_9_12


title: Control4_01272022

description:
Library name: Sample 102
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 177

address: בן אליעזר 32, 17

description: Library name: BAC_8_5


title: Aldicarb_biological_replicate_3

description:
Library name: Sample 124
Total RNA isolated from 48 hour post fertilization zebrafish


title: Aldicarb_biological_replicate_1

description:
Library name: Sample 121
Total RNA isolated from 48 hour post fertilization zebrafish


title: Aldicarb_biological_replicate_4

description:
Library name: Sample 125
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 175

address: בן אליעזר 32, 17

description: Library name: BAC_8_3


title: Human ALS, rep 178

address: בן אליעזר 32, 17

description: Library name: BAC_8_6


title: Sodium_dimethyldithiocarbamate_biological_replicate_2

description:
Library name: Sample 88
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 179

address: בן אליעזר 32, 17

description: Library name: BAC_8_7


title: Sodium_dimethyldithiocarbamate_biological_replicate_4

description:
Library name: Sample 90
Total RNA isolated from 48 hour post fertilization zebrafish


title: Sodium_dimethyldithiocarbamate_biological_replicate_1

description:
Library name: Sample 86
Total RNA isolated from 48 hour post fertilization zebrafish


title: Sodium_dimethyldithiocarbamate_biological_replicate_3

description:
Library name: Sample 89
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 172

address: בן אליעזר 32, 17

description: Library name: BAC_8_22


title: Abamectin_biological_replicate_3

description:
Library name: Sample 79
Total RNA isolated from 48 hour post fertilization zebrafish


title: Abamectin_biological_replicate_4

description:
Library name: Sample 80
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 173

address: בן אליעזר 32, 17

description: Library name: BAC_8_23


title: Aldicarb_biological_replicate_2

description:
Library name: Sample 122
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 174

address: בן אליעזר 32, 17

description: Library name: BAC_8_24


title: Abamectin_biological_replicate_2

description:
Library name: Sample 78
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 176

address: בן אליעזר 32, 17

description: Library name: BAC_8_4


title: Human ALS, rep 169

address: בן אליעזר 32, 17

description: Library name: BAC_8_2


title: Human ALS, rep 171

address: בן אליעזר 32, 17

description: Library name: BAC_8_21


title: Kepone_biological_replicate_4

description:
Library name: Sample 70
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 168

address: בן אליעזר 32, 17

description: Library name: BAC_8_19


title: Human ALS, rep 167

address: בן אליעזר 32, 17

description: Library name: BAC_8_18


title: Kepone_biological_replicate_3

description:
Library name: Sample 69
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 166

address: בן אליעזר 32, 17

description: Library name: BAC_8_17


title: Kepone_biological_replicate_2

description:
Library name: Sample 68
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 165

address: בן אליעזר 32, 17

description: Library name: BAC_8_16


title: Control3_04152022

description:
Library name: Sample 65
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 164

address: בן אליעזר 32, 17

description: Library name: BAC_8_15


title: Fipronil_biological_replciate_4

description:
Library name: Sample 55
Total RNA isolated from 48 hour post fertilization zebrafish


title: Kepone_biological_replicate_1

description:
Library name: Sample 66
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 163

address: בן אליעזר 32, 17

description: Library name: BAC_8_14


title: Human ALS, rep 162

address: בן אליעזר 32, 17

description: Library name: BAC_8_13


title: Fipronil_biological_replciate_2

description:
Library name: Sample 53
Total RNA isolated from 48 hour post fertilization zebrafish


title: Fipronil_biological_replciate_3

description:
Library name: Sample 54
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 159

address: בן אליעזר 32, 17

description: Library name: BAC_8_10


title: Fipronil_biological_replciate_1

description:
Library name: Sample 51
Total RNA isolated from 48 hour post fertilization zebrafish


title: Esfenvalerate_biological_replicate_4

description:
Library name: Sample 50
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 158

address: בן אליעזר 32, 17

description: Library name: BAC_8_1


title: Human ALS, rep 161

address: בן אליעזר 32, 17

description: Library name: BAC_8_12


title: Human ALS, rep 160

address: בן אליעזר 32, 17

description: Library name: BAC_8_11


title: Human ALS, rep 170

address: בן אליעזר 32, 17

description: Library name: BAC_8_20


title: Esfenvalerate_biological_replicate_2

description:
Library name: Sample 48
Total RNA isolated from 48 hour post fertilization zebrafish


title: Esfenvalerate_biological_replicate_3

description:
Library name: Sample 49
Total RNA isolated from 48 hour post fertilization zebrafish


title: Esfenvalerate_biological_replicate_1

description:
Library name: Sample 46
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 157

address: בן אליעזר 32, 17

description: Library name: BAC_7_9


title: Diniconazole_biological_replicate_4

description:
Library name: Sample 45
Total RNA isolated from 48 hour post fertilization zebrafish


title: Abamectin_biological_replicate_1

description:
Library name: Sample 76
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 153

address: בן אליעזר 32, 17

description: Library name: BAC_7_5


title: Human ALS, rep 154

address: בן אליעזר 32, 17

description: Library name: BAC_7_6


title: Diniconazole_biological_replicate_2

description:
Library name: Sample 43
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 152

address: בן אליעזר 32, 17

description: Library name: BAC_7_4


title: Diniconazole_biological_replicate_1

description:
Library name: Sample 41
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 156

address: בן אליעזר 32, 17

description: Library name: BAC_7_8


title: Human ALS, rep 151

address: בן אליעזר 32, 17

description: Library name: BAC_7_24


title: Difpas-pyrazole_biolofical_replicate_4

description:
Library name: Sample 40
Total RNA isolated from 48 hour post fertilization zebrafish


title: Difpas-pyrazole_biolofical_replicate_3

description:
Library name: Sample 39
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 148

address: בן אליעזר 32, 17

description: Library name: BAC_7_21


title: Difpas-pyrazole_biolofical_replicate_2

description:
Library name: Sample 38
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 150

address: בן אליעזר 32, 17

description: Library name: BAC_7_23


title: Difpas-pyrazole_biolofical_replicate_1

description:
Library name: Sample 36
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 147

address: בן אליעזר 32, 17

description: Library name: BAC_7_20


title: Diniconazole_biological_replicate_3

description:
Library name: Sample 44
Total RNA isolated from 48 hour post fertilization zebrafish


title: Dazomet_biological_replicate_3

description:
Library name: Sample 29
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 145

address: בן אליעזר 32, 17

description: Library name: BAC_7_19


title: Human ALS, rep 144

address: בן אליעזר 32, 17

description: Library name: BAC_7_18


title: Human ALS, rep 155

address: בן אליעזר 32, 17

description: Library name: BAC_7_7


title: Human ALS, rep 143

address: בן אליעזר 32, 17

description: Library name: BAC_7_17


title: Control2_04142022

description:
Library name: Sample 31
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 146

address: בן אליעזר 32, 17

description: Library name: BAC_7_2


title: Fenamidone_biological_replicate_4

description:
Library name: Sample 9
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 142

address: בן אליעזר 32, 17

description: Library name: BAC_7_16


title: Dazomet_biological_replicate_1

description:
Library name: Sample 26
Total RNA isolated from 48 hour post fertilization zebrafish


title: Dazomet_biological_replicate_2

description:
Library name: Sample 28
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 141

address: בן אליעזר 32, 17

description: Library name: BAC_7_15


title: Fenamidone_biological_replicate_3

description:
Library name: Sample 8
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 140

address: בן אליעזר 32, 17

description: Library name: BAC_7_14


title: Human ALS, rep 138

address: בן אליעזר 32, 17

description: Library name: BAC_7_12


title: Human ALS, rep 149

address: בן אליעזר 32, 17

description: Library name: BAC_7_22


title: Control1_04132022

description:
Library name: Sample 5
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 137

address: בן אליעזר 32, 17

description: Library name: BAC_7_11


title: Dazomet_biological_replicate_4

description:
Library name: Sample 30
Total RNA isolated from 48 hour post fertilization zebrafish


title: ATG_24hr_3

city: Kamakura

first: Shuntaro

last: Kawamura

state: Kanagawa

address: Tamanawa 1-6-42, Oak Tree Kamakura 103

country: Japan

institute: Institute of Science Tokyo

description: Library name: ATG_24hr_3

data_processing:
From the sequencing output, quality control, and alignment reads on hg19 (hg19_AmpliSeq_Transcriptome_21K_v1.bed), read counts for each gene were obtained using the Torrent ampliSeqRNA plugin (hg19 AmpliSeq Transcriptome ERCC v1) in Torrent Suite Software v5.2.1.
In the count data, genes whose total counts across all samples were less than 3 were excluded. Data scaling of the filtered count data was performed by the median of ratios method using DESeq2 (version 1.44.0).
Assembly: h19
Supplementary files format and content: The csv file contents raw count values of each Sample

source_name: 625-A4 iPSC line

growth_protocol: After the growth of iPSC colonies, cells were differentiated to LSEC progenitors. On day 8, progenitors were sorted by CD34+ MACS and reseeded. Cells were differentiated to iLSECs by culture in sinusoidal differentiation medium containing 5 ng/mL VEGF and 10 ng/mL Oncostatin M for additional 7 days.

extract_protocol:
Total RNA was extracted from cultured cells using NucleoSpin RNA Plus XS (MACHEREY-NAGEL).
A cDNA library was generated from 10 ng of total RNA, using a SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific). Amplification, primer digestion, and adapter ligation were performed using an Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific). The cDNA library was purified using Agencourt AMPure XP Reagent (Beckman Coulter) and quantified using Ion Library TaqMan Quantitation Kit (Thermo Fisher Scientific), followed by dilution to 75 pM with water and pooled equally.

treatment_protocol: Day 14 iLSECs were treated with 100 µg/mL of rIgG or ATG for either 4 or 24 hours in sinusoidal endothelial differentiation media.

value: 625-A4 iPSC line

value: iPSC-derived liver sinusoidal endothelial cell (iLSEC)

value: ATG

tag: time


title: Human ALS, rep 136

address: בן אליעזר 32, 17

description: Library name: BAC_7_10


title: Human ALS, rep 135

address: בן אליעזר 32, 17

description: Library name: BAC_7_1


title: ATG_24hr_1

description: Library name: ATG_24hr_1


title: ATG_4hr_3

description: Library name: ATG_4hr_3

value: 4 h


title: Human ALS, rep 132

address: בן אליעזר 32, 17

description: Library name: BAC_6_7


title: Human ALS, rep 133

address: בן אליעזר 32, 17

description: Library name: BAC_6_8


title: ATG_4hr_1

description: Library name: ATG_4hr_1


title: Human ALS, rep 130

address: בן אליעזר 32, 17

description: Library name: BAC_6_5


title: rIgG_24hr_3

description: Library name: rIgG_24hr_3

value: rIgG


title: rIgG_24hr_2

description: Library name: rIgG_24hr_2


title: Human ALS, rep 128

address: בן אליעזר 32, 17

description: Library name: BAC_6_3


title: rIgG_4hr_3

description: Library name: rIgG_4hr_3


title: Human ALS, rep 127

address: בן אליעזר 32, 17

description: Library name: BAC_6_24


title: ATG_24hr_2

description: Library name: ATG_24hr_2


title: Human ALS, rep 134

address: בן אליעזר 32, 17

description: Library name: BAC_6_9


title: rIgG_4hr_2

description: Library name: rIgG_4hr_2


title: Human ALS, rep 126

address: בן אליעזר 32, 17

description: Library name: BAC_6_23


title: Fenamidone_biological_replicate_2

description:
Library name: Sample 7
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 139

address: בן אליעזר 32, 17

description: Library name: BAC_7_13


title: Fenamidone_biological_replicate_1

description:
Library name: Sample 6
Total RNA isolated from 48 hour post fertilization zebrafish


title: Human ALS, rep 131

address: בן אליעזר 32, 17

description: Library name: BAC_6_6


title: rIgG_4hr_1

description: Library name: rIgG_4hr_1


title: Human ALS, rep 125

address: בן אליעזר 32, 17

description: Library name: BAC_6_22


title: Vehicle_0hr_4

description: Library name: Vehicle_0hr_4

value: Vehicle

value: 0 h


title: Human ALS, rep 123

address: בן אליעזר 32, 17

description: Library name: BAC_6_20


title: Vehicle_0hr_3

description: Library name: Vehicle_0hr_3


title: Human ALS, rep 122

address: בן אליעזר 32, 17

description: Library name: BAC_6_2


title: Vehicle_0hr_2

description: Library name: Vehicle_0hr_2


title: ATG_4hr_2

description: Library name: ATG_4hr_2


title: rIgG_24hr_1

description: Library name: rIgG_24hr_1


title: Human ALS, rep 129

address: בן אליעזר 32, 17

description: Library name: BAC_6_4


title: iAEC_2

description: Library name: iAEC_2

data_processing:
From the sequencing output, quality control, and alignment reads on hg19 (hg19_AmpliSeq_Transcriptome_21K_v1.bed), read counts for each gene were obtained using the Torrent ampliSeqRNA plugin (hg19 AmpliSeq Transcriptome ERCC v1) in Torrent Suite Software v5.2.1.
Assembly: h19
Supplementary files format and content: The csv file contents raw count values of each Sample

growth_protocol: For iLSEC induction, cells were differentiated to LSEC progenitors after the growth of iPSC colonies. On day 8, progenitors were sorted by CD34+ MACS and reseeded. Cells were differentiated to iLSECs by culture in sinusoidal differentiation medium containing 5 ng/ml VEGF and 10 ng/ml Oncostatin M for additional 7 days. iPSCs are differentiated to iAECs by culture in mesoderm induction medium for 3 days. On day 4, the medium was changed to endothelial induction medium containing 200 ng/mL VEGF. On day 7, endothelial cells were reseeded and cultured in arterial endothelial expansion medium containing 50 ng/mL VEGF.

value: iPSC-derived liver arterial endothelial cell (iAEC)


title: Human ALS, rep 120

address: בן אליעזר 32, 17

description: Library name: BAC_6_17


title: Human ALS, rep 119

address: בן אליעזר 32, 17

description: Library name: BAC_6_16


title: iLSEC_3

description: Library name: iLSEC_3


title: Human ALS, rep 118

address: בן אליעזר 32, 17

description: Library name: BAC_6_13


title: Human ALS, rep 117

address: בן אליעזר 32, 17

description: Library name: BAC_6_12


title: iLSEC_2

description: Library name: iLSEC_2


title: iLSEC_1

description: Library name: iLSEC_1


title: Human ALS, rep 116

address: בן אליעזר 32, 17

description: Library name: BAC_6_11


title: Human ALS, rep 115

address: בן אליעזר 32, 17

description: Library name: BAC_6_1


title: Human ALS, rep 114

address: בן אליעזר 32, 17

description: Library name: BAC_5_9


title: Human ALS, rep 113

address: בן אליעזר 32, 17

description: Library name: BAC_5_8


title: wtlate-nof5

city: Calgary

first: Jennifer

last: Corcoran

state: AB

address: 3230 Hospotal Drive NW

department: Microbiology, Immunology, and Infectious Diseases

country: Canada

institute: University of Calgary

description: wt-latency

data_processing:
Pseudoalignment with Salmon (v1.10.2) with --libType ISR
Count tables were generated using tximport (v1.28.0). Transcript-level counts used parameters ‘type = salmon, dropInfReps = TRUE, txOut = TRUE, countsFromAbundance = dtuScaledTPM’. Gene-level counts used parameters ‘type = salmon, dropInfReps = TRUE, txOut = FALSE, countsFromAbundance = lengthScaledTPM’.
Differential expression testing using limma (v3.54) with voom transformation and Benjamini-Hochberg correction applied to the p-values.
Differential transcript utilization using IsoformSwitchAnalyzeR (v2.0.1). The function ‘preFilter’ was used with parameters ‘geneExpressionCutoff = 1, isoformExpressionCutoff = 0, IFcutoff = 0.01, removeSingleIsoformGenes = TRUE’. The function ‘isoformSwitchTestDEXSeq’ was used with parameters ‘alpha = 0.05, dIFcutoff = 0.10, reduceToSwitchingGenes = TRUE’.
Assembly: hg38 (GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set)
Assembly: GQ994935.1 (herpesvirus 8 strain JSC-1 clone BAC16)
Supplementary files format and content: quant.sf: Tab-delimited; Salmon transcript TPM
Supplementary files format and content: htseq TSV: Tab-delimited; htseq transcript counts
Supplementary files format and content: Limma TSV: Tab-delimited; differential expression comparing the indicated samples
Supplementary files format and content: isoformSwitchAnalysis.tsv: Tab-delimited; differential isoform fractions identified by IsoformSwitchAnalyzeR

organism:
Homo sapiens
Human gammaherpesvirus 8

growth_protocol: iSLKs BAC16s were maintained in DMEM supplemented with 10% fetal bovine serum, antibiotics, and 1200 ug/mL hygromycin Band grown at 37C with 5% C02

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
NEBNext Ultra II RNA kit (NEB) with rRNA depletion (NEB)

treatment_protocol: 1ug/mL doxycycline was added for 48 hrs to induce lytic reactivation

value: renal epithelial carcinoma

value: wt


title: Human ALS, rep 112

address: בן אליעזר 32, 17

description: Library name: BAC_5_7


title: wtlate-nof3

description: wt-latency


title: wtlate-nof4

description: wt-latency


title: Human ALS, rep 124

address: בן אליעזר 32, 17

description: Library name: BAC_6_21


title: wtlate-nof2

description: wt-latency


title: Vehicle_0hr_1

description: Library name: Vehicle_0hr_1


title: Human ALS, rep 110

address: בן אליעזר 32, 17

description: Library name: BAC_5_4


title: Human ALS, rep 121

address: בן אליעזר 32, 17

description: Library name: BAC_6_18


title: iAEC_1

description: Library name: iAEC_1


title: Human ALS, rep 111

address: בן אליעזר 32, 17

description: Library name: BAC_5_5


title: iAEC_3

description: Library name: iAEC_3


title: wt48-nof3

description: wt-lytic

value: doxcycline induced reactivation


title: wt48-nof2

description: wt-lytic


title: Human ALS, rep 108

address: בן אליעזר 32, 17

description: Library name: BAC_5_24


title: wt48-nof4

description: wt-lytic


title: wt48-nof1

description: wt-lytic


title: Human ALS, rep 105

address: בן אליעזר 32, 17

description: Library name: BAC_5_21


title: delclate-nof5

description: delc-latency

value: delc


title: Human ALS, rep 104

address: בן אליעזר 32, 17

description: Library name: BAC_5_20


title: Human ALS, rep 103

address: בן אליעזר 32, 17

description: Library name: BAC_5_2


title: Human ALS, rep 102

address: בן אליעזר 32, 17

description: Library name: BAC_5_19


title: delclate-nof2

description: delc-latency


title: delclate-nof3

description: delc-latency


title: Human ALS, rep 101

address: בן אליעזר 32, 17

description: Library name: BAC_5_18


title: delc48-nof5

description: delc-lytic


title: Human ALS, rep 100

address: בן אליעזר 32, 17

description: Library name: BAC_5_17


title: Human ALS, rep 99

address: בן אליעזר 32, 17

description: Library name: BAC_5_16


title: wt48-nof5

description: wt-lytic


title: wtlate-nof1

description: wt-latency


title: Human ALS, rep 109

address: בן אליעזר 32, 17

description: Library name: BAC_5_3


title: Human ALS, rep 98

address: בן אליעזר 32, 17

description: Library name: BAC_5_15


title: delc48-nof4

description: delc-lytic


title: delc48-nof3

description: delc-lytic


title: Human ALS, rep 97

address: בן אליעזר 32, 17

description: Library name: BAC_5_14


title: Human ALS, rep 107

address: בן אליעזר 32, 17

description: Library name: BAC_5_23


title: delc48-nof1

description: delc-lytic


title: Human ALS, rep 96

address: בן אליעזר 32, 17

description: Library name: BAC_5_13


title: delc48-nof2

description: delc-lytic


title: Human ALS, rep 95

address: בן אליעזר 32, 17

description: Library name: BAC_5_12


title: Human ALS, rep 94

address: בן אליעזר 32, 17

description: Library name: BAC_5_11


title: delblate-nof4

description: delb-latency

value: delb


title: delblate-nof5

description: delb-latency


title: Human ALS, rep 106

address: בן אליעזר 32, 17

description: Library name: BAC_5_22


title: delclate-nof4

description: delc-latency


title: Human ALS, rep 92

address: בן אליעזר 32, 17

description: Library name: BAC_5_1


title: delblate-nof2

description: delb-latency


title: delclate-nof1

description: delc-latency


title: Human ALS, rep 90

address: בן אליעזר 32, 17

description: Library name: BAC_4_8


title: Human ALS, rep 89

address: בן אליעזר 32, 17

description: Library name: BAC_4_7


title: delbclate-nof5

description: delbc-latency

value: delbc


title: delblate-nof1

description: delb-latency


title: delbclate-nof4

description: delbc-latency


title: delbclate-nof3

description: delbc-latency


title: Human ALS, rep 88

address: בן אליעזר 32, 17

description: Library name: BAC_4_6


title: delbclate-nof2

description: delbc-latency


title: Human ALS, rep 87

address: בן אליעזר 32, 17

description: Library name: BAC_4_5


title: Human ALS, rep 85

address: בן אליעזר 32, 17

description: Library name: BAC_4_3


title: Human ALS, rep 86

address: בן אליעזר 32, 17

description: Library name: BAC_4_4


title: delbclate-nof1

description: delbc-latency


title: delbc48-nof5

description: delbc-lyticreactivation


title: Human ALS, rep 84

address: בן אליעזר 32, 17

description: Library name: BAC_4_24


title: delblate-nof3

description: delb-latency


title: Human ALS, rep 93

address: בן אליעזר 32, 17

description: Library name: BAC_5_10


title: Human ALS, rep 83

address: בן אליעזר 32, 17

description: Library name: BAC_4_23


title: delbc48-nof3

description: delbc-lyticreactivation


title: Human ALS, rep 82

address: בן אליעזר 32, 17

description: Library name: BAC_4_22


title: Human ALS, rep 80

address: בן אליעזר 32, 17

description: Library name: BAC_4_20


title: delbc48-nof4

description: delbc-lyticreactivation


title: Human ALS, rep 91

address: בן אליעזר 32, 17

description: Library name: BAC_4_9


title: delbc48-nof2

description: delbc-lyticreactivation


title: delbc48-nof1

description: delbc-lyticreactivation


title: Human ALS, rep 81

address: בן אליעזר 32, 17

description: Library name: BAC_4_21


title: Human ALS, rep 79

address: בן אליעזר 32, 17

description: Library name: BAC_4_2


title: delb48-nof3

description: delb-lyticreactivation


title: delb48-nof5

description: delb-lyticreactivation


title: delb48-nof4

description: delb-lyticreactivation


title: Human ALS, rep 77

address: בן אליעזר 32, 17

description: Library name: BAC_4_18


title: delb48-nof1

description: delb-lyticreactivation


title: Human ALS, rep 76

address: בן אליעזר 32, 17

description: Library name: BAC_4_17


title: Human ALS, rep 75

address: בן אליעזר 32, 17

description: Library name: BAC_4_15


title: 1xdrslate-nof5


title: Human ALS, rep 74

address: בן אליעזר 32, 17

description: Library name: BAC_4_14


title: Human ALS, rep 73

address: בן אליעזר 32, 17

description: Library name: BAC_4_13


title: 1xdrslate-nof4


title: Human ALS, rep 72

address: בן אליעזר 32, 17

description: Library name: BAC_4_12


title: 1xdrslate-nof3


title: Human ALS, rep 71

address: בן אליעזר 32, 17

description: Library name: BAC_4_11


title: 1xdrslate-nof1


title: Human ALS, rep 70

address: בן אליעזר 32, 17

description: Library name: BAC_4_10


title: 1xdrs48-nof5

description: 1xdrs-lytic reactivation


title: Human ALS, rep 69

address: בן אליעזר 32, 17

description: Library name: BAC_4_1


title: 1xdrslate-nof2


title: Human ALS, rep 68

address: בן אליעזר 32, 17

description: Library name: BAC_3_9


title: Human ALS, rep 78

address: בן אליעזר 32, 17

description: Library name: BAC_4_19


title: Human ALS, rep 67

address: בן אליעזר 32, 17

description: Library name: BAC_3_7


title: 1xdrs48-nof4

description: 1xdrs-lytic reactivation


title: 1xdrs48-nof3

description: 1xdrs-lytic reactivation


title: 1xdrs48-nof2

description: 1xdrs-lytic reactivation


title: Human ALS, rep 66

address: בן אליעזר 32, 17

description: Library name: BAC_3_6


title: 1xdrs48-nof1

description: 1xdrs-lytic reactivation


title: Human ALS, rep 64

address: בן אליעזר 32, 17

description: Library name: BAC_3_4


title: delb48-nof2

description: delb-lyticreactivation


title: Human ALS, rep 65

address: בן אליעזר 32, 17

description: Library name: BAC_3_5


title: Human ALS, rep 61

address: בן אליעזר 32, 17

description: Library name: BAC_3_22


title: Human ALS, rep 62

address: בן אליעזר 32, 17

description: Library name: BAC_3_23


title: immune cells, LCMV infected

city: Galveston

first: hui

last: wang

state: Texas

address: 301 university blvd

department: Pathology

country: Armenia

institute: UTMB

description:
Library name: CL
10x genomics

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files obtained from the 10x Genomics sequencing were processed using the Cell Ranger pipelines (version 7.1.0, 10x Genomics) to align the reads to the reference genome and generate gene expression matrices for downstream analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include DESeq2-normalized counts

source_name: lymphcytes

extract_protocol:
Half of the spleen tissues were mechanically dissociated and passed through 70 µM cell strainer for preparing single cell suspensions. Red blood cells were lysed using Red Cell Lysis Buffer (Sigma-Aldrich, St. Louis, MO) for 5 minutes at room temperature. After washing, the cells were resuspended in complete RPMI 1640 medium containing 10% FBS
2 × 10⁶ cells were incubated overnight for probe hybridization in a Bio-Rad T100 thermocycler. For single-cell encapsulation, approximately 10,000 cells were loaded onto the 10x Chromium system (10X Genomics), where Gel-Bead-in-Emulsions (GEMs) were generated. The GEM incubation reaction was carried out in the Bio-Rad T100 thermocycler to facilitate the encapsulation of individual cells with their corresponding beads for subsequent RNA capture. Probe-labeled cDNA was then recovered from GEMs by pre-amplification PCR, followed by DNA cleanup to remove any impurities. The amplified cDNA underwent 10x Genomics-specific sample indexing according to the manufacturer's protocol, followed by post-indexing cleanup with the SPRIselect reagent. Library quality was assessed by quantifying and evaluating the size distribution of the libraries using an Agilent Bioanalyzer. Libraries were then pooled in equimolar amounts for sequencing on a NovaSeq instrument (Illumina).

value: lymphcytes

value: lcmv


title: Human ALS, rep 63

address: בן אליעזר 32, 17

description: Library name: BAC_3_3

value: blood plasma


title: immune cells, uninfected

description:
Library name: C
10x genomics

value: control


title: Spleen: CM + NTCI, biol rep 2

city: Nashville

first: Jozef

last: Zienkiewicz

state: TN

address: 1161 21st Ave. South, T2220, MCN

department: Medicine

institute: Vanderbilt University

description:
Library name: Sample_10_SCN_2
controlCM_vs_comparisonPeptide.genes.*.csv
12071-HQ-0008_S1

data_processing:
DRAGEN RNA Pipeline 3.6.3 (DRAGEN Host Software Version 05.021.572.3.6.3 and Bio-IT Processor Version 0x04261818); DRAGEN Differential Expression 4.0.3; Illumina DRAGEN Secondary Analysis
Sequence reads were trimmed to remove adapter sequences and low-quality tails using DRAGEN RNA Pipeline 3.6.3
Trimmed sequences were aligned and mapped to GRCm38 using STAR2.3 and RefSeq annotations built-in DRAGEN RNA Pipeline 3.6.3
After alignment, the read counts were used as input for differential expression analysis between test (comparison) and control groups using R and DESeq2 built-in DRAGEN Differential Expression 4.0.3
The Illumina DRAGEN Secondary Analysis were used to generate processed data files.
Assembly: Mus_musculus.GRCm38.99
Supplementary files format and content: genes.res.csv - CVS file containing DESeq2 results: the mean expression, log2 (fold change), standard error of log2 (fold change), p-value, adjusted p-value, and the expression status of each gene.

source_name: Spleen

growth_protocol: Unlimited acess to regular irradiated rodent chow diet and water.

extract_protocol:
spleen was disrupted in lysis buffer on ice using a Dounce hand homogenizer. Total RNA was isolated using NucleoSpin RNA Plus kit (Macherey-Nagel, Germany) according to the manufacturer’s instructions. RNA concentration and purity were determined using a NanoDrop One spectrophotometer (Thermo Fisher Scientific, Hampton, NH). RNA integrity numbers (RIN) were measured using TapeStation system (Agilent Technologies, Santa Clara, CA)
total RNA was processed into Stranded mRNA (NEB) Library folowing manufacturer's protocols

treatment_protocol: The experimental groups (Sham (5% dextrose) + Saline, n = 5; CM + Saline, n = 5; CM + Meropenem, and CM + NTCI + Meropenem, n = 5) were comprised of randomly assigned 8 – 10-week-old female C57Bl/6J mice (The Jackson Laboratory, Bar Harbor, ME). The mice were infected by a single intraperitoneal (i.p.) injection of a cecal microbiome (CM) stock corresponding to 1.5x10^6 CFU/kg). The i.p. treatment with NTCI (cSN50.1 peptide, 33 μg/g/injection in 200 μl 0.45% NaCl) or Saline (0.45% NaCl, 200 μl) as vehicle control begun 1h after infection and was continued every 3 hrs. for the first 24h, every 6 hrs. during the 2-nd day of experiment, then every 12 hrs. until euthanasia at 168h post infection. Mice treated with NTCI also received subcutaneous antimicrobial therapy with meropenem (25 mg/kg) starting at 1h post CM challenge and every 12 hrs. until euthanasia. Mice were euthanized at 26 hrs. post CM challenge. Circulation system was washed with cold PBS (2 ml to each ventricle) and spleen was removed for total RNA extraction.

value: Spleen

value: CM + NTCI + Meropenem


title: Human ALS, rep 60

address: בן אליעזר 32, 17

description: Library name: BAC_3_21


title: Human ALS, rep 59

address: בן אליעזר 32, 17

description: Library name: BAC_3_20


title: Spleen: CM + NTCI, biol rep 1

description:
Library name: Sample_09_SCN_1
controlCM_vs_comparisonPeptide.genes.*.csv
12071-HQ-0007_S1


title: immunce cells, PFOA treated, LCMV infected

description:
Library name: PL
10x genomics

value: pfoa+lcmv


title: Spleen: CM + NTCI, biol rep 3

description:
Library name: Sample_11_SCN_3
controlCM_vs_comparisonPeptide.genes.*.csv
12071-HQ-0009_S1


title: immune cells, PFOA treated, uninfected

description:
Library name: P
10x genomics

value: pfoa


title: Human ALS, rep 58

address: בן אליעזר 32, 17

description: Library name: BAC_3_2


title: Human ALS, rep 57

address: בן אליעזר 32, 17

description: Library name: BAC_3_19


title: Human ALS, rep 54

address: בן אליעזר 32, 17

description: Library name: BAC_3_16


title: Spleen: CM + Mero, biol rep 2

description:
Library name: Sample_08_SCM_2
CMcontrol_vs_CMMcomparison.genes.*.csv
12071-HQ-0006_S1

value: CM + Meropenem


title: Spleen: CM + Mero, biol rep 1

description:
Library name: Sample_07_SCM_1
CMcontrol_vs_CMMcomparison.genes.*.csv
12071-HQ-0004_S1


title: Human ALS, rep 53

address: בן אליעזר 32, 17

description: Library name: BAC_3_15


title: Spleen: Sham + Saline, biol rep 3

description:
Library name: Sample_03_SSS_3
12222-HQ-14R_S1

value: Sham + Saline


title: Spleen: CM + Saline, biol rep 2

description:
Library name: Sample_05_SCS_2
spShcontrol_vs_CMcomparison.genes.*.csv
12071-HQ-0002_S1

value: CM + Saline


title: Spleen: CM + Saline, biol rep 1

description:
Library name: Sample_04_SCS_1
spShcontrol_vs_CMcomparison.genes.*.csv
12071-HQ-0001_S1


title: Human ALS, rep 56

address: בן אליעזר 32, 17

description: Library name: BAC_3_18


title: Human ALS, rep 51

address: בן אליעזר 32, 17

description: Library name: BAC_3_13


title: Spleen: Sham + Saline, biol rep 1

description:
Library name: Sample_01_SSS_1
12222-HQ-12R_S1


title: Spleen: CM + Saline, biol rep 3

description:
Library name: Sample_06_SCS_3
spShcontrol_vs_CMcomparison.genes.*.csv
12071-HQ-0003_S1


title: Human ALS, rep 52

address: בן אליעזר 32, 17

description: Library name: BAC_3_14


title: Human ALS, rep 55

address: בן אליעזר 32, 17

description: Library name: BAC_3_17


title: Primary astrocytes, LPS+PBM, 24H, rep 4

city: Haikou

first: Feifan

last: Zhou

address: 58 Renmin Avenue

institute: Hainan University

description:
Library name: Sample 32
DSPM-4_fpkm

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high  quality clean reads, reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2  (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean   reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the    reference genome using HISAT2. 2.4  with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Given FPKM(A) to be the expression of gene A, C to be number of fragments mapped to gene A, N to be total number of fragments that mapped to reference genes, and L to be number of bases on gene A. The FPKM method is able to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. Therefore,    the calculated gene expression can be directly used for comparing the difference of gene expression among samples.
Assembly: mm10
Supplementary files format and content: textfile includes raw counts for each sample
Supplementary files format and content: text files include FPKM values for each sample

source_name: Primary astrocytes

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen,15596018)
The cell lysis or the extracted total RNA was mixed with 1ul of 10uM Oligo-dT primer and 1ul of 10uM dNTP reagent and then incubated at 72℃ for 3min. The reverse transcription reaction was performed in 1X Super Script II first-strand buffer system with 200U of Super Script II reverse transcriptase，0.1ul  of TSO （100uM），20U RNAse Inhibitor，0.75ul of DTT（100mM），3ul of Betaine（5M）and 0.09ul of MgCl2（1M）. The full length cDNA was synthesized at 42℃ for 90min and then with 10 cycles of 50℃ for 2min and 42℃ for 2min. Finally, the product was incubated at 70℃ for 15min to inactive the enzyme activation. After amplified the synthesized cDNA with 10 to15 cycles of PCR amplification, the product was purified and used for library construction. After analyzed by Agilent Bioanalyzer and quantified by real time PCR, the library was sequenced with Illumina Novaseq platform.

value: Primary astrocytes

value: LPS+PBM


title: Human ALS, rep 50

address: בן אליעזר 32, 17

description: Library name: BAC_3_12


title: Spleen: Sham + Saline, biol rep 2

description:
Library name: Sample_02_SSS_2
12222-HQ-13R_S1


title: Human ALS, rep 48

address: בן אליעזר 32, 17

description: Library name: BAC_3_10


title: Primary astrocytes, LPS+PBM, 24H, rep 3

description:
Library name: Sample 31
DSPM-3_fpkm


title: Human ALS, rep 47

address: בן אליעזר 32, 17

description: Library name: BAC_3_1


title: Primary astrocytes, LPS+PBM, 24H, rep 2

description:
Library name: Sample 30
DSPM-2_fpkm


title: Primary astrocytes, LPS, 24H, rep 4

description:
Library name: Sample 28
DLPS-4_fpkm

value: LPS


title: Primary astrocytes, LPS, 24H, rep 3

description:
Library name: Sample 27
DLPS-3_fpkm


title: Human ALS, rep 49

address: בן אליעזר 32, 17

description: Library name: BAC_3_11


title: Human ALS, rep 44

address: בן אליעזר 32, 17

description: Library name: BAC_2_7


title: Human ALS, rep 45

address: בן אליעזר 32, 17

description: Library name: BAC_2_8


title: Primary astrocytes, LPS+PBM, 24H, rep 1

description:
Library name: Sample 29
DSPM-1_fpkm


title: Human ALS, rep 46

address: בן אליעזר 32, 17

description: Library name: BAC_2_9


title: Primary astrocytes, LPS, 24H, rep 1

description:
Library name: Sample 25
DLPS-1_fpkm


title: Human ALS, rep 41

address: בן אליעזר 32, 17

description: Library name: BAC_2_4


title: Human ALS, rep 40

address: בן אליעזר 32, 17

description: Library name: BAC_2_3


title: Primary astrocytes, PBM, 24H, rep 3

description:
Library name: Sample 23
DPBM-3_fpkm

value: PBM


title: Human ALS, rep 43

address: בן אליעזר 32, 17

description: Library name: BAC_2_6


title: Primary astrocytes, PBM, 24H, rep 4

description:
Library name: Sample 24
DPBM-4_fpkm


title: Human ALS, rep 39

address: בן אליעזר 32, 17

description: Library name: BAC_2_24


title: Human ALS, rep 42

address: בן אליעזר 32, 17

description: Library name: BAC_2_5


title: Primary astrocytes, PBM, 24H, rep 1

description:
Library name: Sample 21
DPBM-1_fpkm


title: Primary astrocytes, PBM, 24H, rep 2

description:
Library name: Sample 22
DPBM-2_fpkm


title: Human ALS, rep 38

address: בן אליעזר 32, 17

description: Library name: BAC_2_23


title: Primary astrocytes, Control, 24H,rep 4

description:
Library name: Sample 20
DCTL-4_fpkm

value: Control


title: Human ALS, rep 37

address: בן אליעזר 32, 17

description: Library name: BAC_2_22


title: Primary astrocytes, Control, 24H,rep 3

description:
Library name: Sample 19
DCTL-3_fpkm


title: Human ALS, rep 36

address: בן אליעזר 32, 17

description: Library name: BAC_2_21


title: Primary astrocytes, LPS, 24H, rep 2

description:
Library name: Sample 26
DLPS-2_fpkm


title: Primary astrocytes, Control, 24H,rep 2

description:
Library name: Sample 18
DCTL-2_fpkm


title: Human ALS, rep 35

address: בן אליעזר 32, 17

description: Library name: BAC_2_20


title: Primary astrocytes, Control, 24H,rep 1

description:
Library name: Sample 17
DCTL-1_fpkm


title: Human ALS, rep 34

address: בן אליעזר 32, 17

description: Library name: BAC_2_2


title: Primary astrocytes, LPS+PBM, 4H, rep 4

description:
Library name: Sample 16
SPM4-4_fpkm


title: Primary astrocytes, LPS+PBM, 4H, rep 3

description:
Library name: Sample 15
SPM4-3_fpkm


title: Human ALS, rep 33

address: בן אליעזר 32, 17

description: Library name: BAC_2_19


title: Human ALS, rep 32

address: בן אליעזר 32, 17

description: Library name: BAC_2_18


title: Primary astrocytes, LPS+PBM, 4H, rep 1

description:
Library name: Sample 13
SPM4-1_fpkm


title: Primary astrocytes, LPS+PBM, 4H, rep 2

description:
Library name: Sample 14
SPM4-2_fpkm


title: Human ALS, rep 30

address: בן אליעזר 32, 17

description: Library name: BAC_2_16


title: Human ALS, rep 29

address: בן אליעזר 32, 17

description: Library name: BAC_2_15


title: Human ALS, rep 31

address: בן אליעזר 32, 17

description: Library name: BAC_2_17


title: Primary astrocytes, LPS, 4H, rep 4

description:
Library name: Sample 12
LPS4-4_fpkm


title: Primary astrocytes, LPS, 4H, rep 3

description:
Library name: Sample 11
LPS4-3_fpkm


title: Human ALS, rep 27

address: בן אליעזר 32, 17

description: Library name: BAC_2_12


title: Human ALS, rep 28

address: בן אליעזר 32, 17

description: Library name: BAC_2_14


title: Primary astrocytes, LPS, 4H, rep 2

description:
Library name: Sample 10
LPS4-2_fpkm


title: Human ALS, rep 21

address: בן אליעזר 32, 17

description: Library name: BAC_1_7


title: Primary astrocytes, Control, 4H,rep 4

description:
Library name: Sample 4
CTL4-4_fpkm


title: Human ALS, rep 26

address: בן אליעזר 32, 17

description: Library name: BAC_2_11


title: Human ALS, rep 25

address: בן אליעזר 32, 17

description: Library name: BAC_2_10


title: Human ALS, rep 23

address: בן אליעזר 32, 17

description: Library name: BAC_1_9


title: Primary astrocytes, PBM, 4H, rep 3

description:
Library name: Sample 7
PBM4-3_fpkm


title: Primary astrocytes, LPS, 4H, rep 1

description:
Library name: Sample 9
LPS4-1_fpkm


title: Primary astrocytes, PBM, 4H, rep 2

description:
Library name: Sample 6
PBM4-2_fpkm


title: Human ALS, rep 24

address: בן אליעזר 32, 17

description: Library name: BAC_2_1


title: Primary astrocytes, PBM, 4H, rep 1

description:
Library name: Sample 5
PBM4-1_fpkm


title: Human ALS, rep 22

address: בן אליעזר 32, 17

description: Library name: BAC_1_8


title: Primary astrocytes, Control, 4H,rep 2

description:
Library name: Sample 2
CTL4-2_fpkm


title: Primary astrocytes, Control, 4H,rep 3

description:
Library name: Sample 3
CTL4-3_fpkm


title: Primary astrocytes, PBM, 4H, rep 4

description:
Library name: Sample 8
PBM4-4_fpkm


title: Human ALS, rep 17

address: בן אליעזר 32, 17

description: Library name: BAC_1_3


title: Human ALS, rep 18

address: בן אליעזר 32, 17

description: Library name: BAC_1_4


title: 32_383408_OVID, oviduct, normal

city: Frederick

first: Ludmila

last: Szabova

state: MD

address: 1050 Boyles Street

department: CAPR

institute: Frederick National Laboratory for Cancer Research

description: Library name: 32_383408_OVID

data_processing:
32 mRNA-Seq samples were pooled and sequenced on NovaSeq 6000 SP using Illumina® Stranded mRNA Prep and paired-end sequencing. The samples have 37 to 56 million pass filter reads with more than 91% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (mm10) and the annotated transcripts using STAR. The average mapping rate of all samples is 93%. Unique alignment is above 83%. There are 5.13 to 7.10% unmapped reads. The mapping statistics are calculated using Picard software. The samples have 0.32% ribosomal bases. Percent coding bases are between 45-52%. Percent UTR bases are 34-37%, and mRNA bases are between 80-88% for all the samples. Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility. The samples have 77-88% non-duplicate reads.
Basecalling RTA v3.4.4 Illumina instrument run time analysis software
Illumina bcl2fastq2.20 was used to demultiplex and convert binary base calls and quality scores to fastq format
The sequencing reads were trimmed of adapters and low quality bases using Cutadapt (version 1.18).
The trimmed reads were mapped to mouse reference genome (GRCm38/mm10) and Gencode annotation M21 using  STAR aligner (version 2.7.0f) with two-pass alignment option.
RSEM (version 1.3.1) was used for gene and transcript quantification based on GENCODE annotation file.
Assembly: Mouse_mm10
Supplementary files format and content: tab-delimited text files include raw count  values for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: oviduct

growth_protocol: mouse ovarian tumors developed in vivo

extract_protocol:
total RNA extracted with RNAeasy mini kit Qiagen
RNAseq

value: oviduct

tag: strain

tag: model

value: normal control

value: wild type

tag: Sex

value: female


title: Human ALS, rep 19

address: בן אליעזר 32, 17

description: Library name: BAC_1_5

value: blood plasma


title: Primary astrocytes, Control, 4H,rep 1

description:
Library name: Sample 1
CTL4-1_fpkm


title: Human ALS, rep 15

address: בן אליעזר 32, 17

description: Library name: BAC_1_23


title: 31_383407_OVID, oviduct, normal

description: Library name: 31_383407_OVID


title: Human ALS, rep 14

address: בן אליעזר 32, 17

description: Library name: BAC_1_22


title: 30_383406_OVID, oviduct, normal

description: Library name: 30_383406_OVID


title: Human ALS, rep 20

address: בן אליעזר 32, 17

description: Library name: BAC_1_6


title: 28_383407_OVA, ovary, normal

description: Library name: 28_383407_OVA

source_name: ovary

value: ovary


title: Human ALS, rep 16

address: בן אליעזר 32, 17

description: Library name: BAC_1_24


title: 29_383408_OVA, ovary, normal

description: Library name: 29_383408_OVA


title: Human ALS, rep 12

address: בן אליעזר 32, 17

description: Library name: BAC_1_20


title: 27_383406_OVA, ovary, normal

description: Library name: 27_383406_OVA


title: Human ALS, rep 13

address: בן אליעזר 32, 17

description: Library name: BAC_1_21


title: 26_369206, tumor, Ovgp1-BPR allograft

description: Library name: 26_369206

source_name: tumor

value: tumor

value: Ovgp1 allograft

value: Brca1 fl/fl, Trp53 KozR172H ki/+, K18GT121 Tg/+, Ovgp1-CreERT2 Tg/+


title: 25_366185, tumor, Ovgp1-BPR allograft

description: Library name: 25_366185


title: Human ALS, rep 11

address: בן אליעזר 32, 17

description: Library name: BAC_1_19


title: 22_336453, tumor, Ovgp1-BPR GEMM

description: Library name: 22_336453

value: Ovgp1 GEMM


title: 23_346710, tumor, Ovgp1-BPR GEMM

description: Library name: 23_346710


title: Human ALS, rep 8

address: בן אליעזר 32, 17

description: Library name: BAC_1_16


title: 21_333669, tumor, Ovgp1-BPR GEMM

description: Library name: 21_333669


title: Human ALS, rep 10

address: בן אליעזר 32, 17

description: Library name: BAC_1_18


title: 24_359557, tumor, Ovgp1-BPR allograft

description: Library name: 24_359557


title: 20_376161, tumor, Pax8-BPR allograft

description: Library name: 20_376161

value: Pax8-BPR allograft

value: Brca1 fl/fl, Trp53 fl/fl, K18GT121 Tg/+, Pax8-CreERT2 Tg/+


title: Human ALS, rep 9

address: בן אליעזר 32, 17

description: Library name: BAC_1_17


title: Human ALS, rep 6

address: בן אליעזר 32, 17

description: Library name: BAC_1_14


title: Human ALS, rep 7

address: בן אליעזר 32, 17

description: Library name: BAC_1_15


title: 19_376158_2, tumor, Pax8-BPR allograft

description: Library name: 19_376158_2


title: Human ALS, rep 5

address: בן אליעזר 32, 17

description: Library name: BAC_1_13


title: Human ALS, rep 1

address: בן אליעזר 32, 17

description: Library name: BAC_1_1


title: Human ALS, rep 2

address: בן אליעזר 32, 17

description: Library name: BAC_1_10


title: 17_336495, tumor, Pax8-BPR GEMM

description: Library name: 17_336495

value: Pax8-BPR GEMM


title: Human ALS, rep 3

address: בן אליעזר 32, 17

description: Library name: BAC_1_11


title: 12_279355, tumor, Ad-BPR allograft

description: Library name: 12_279355

value: Ad-BPR allograft

value: Brca1 fl/fl, Trp53 fl/fl, K18GT121 Tg/+


title: A549 cells (input), rep2

first: Alex

last: Gao

state: Alberta

address: 3330 Hospital Dr NW

department: Physiology and Pharmacology

description: Library name: Sample 10

data_processing:
Demultiplexing was performed using bcl2fastq conversion software (v2.18.0.12) and read quality was assessed using FastQC (v0.10.1).
Good-quality reads were mapped to GRCh38 reference genome using bowtie2 (v2.4.4) and the resultant BAM files were sorted and indexed using samtools (v) prior to peak calling using MACS2 (v2.2.7.1). MACS-identified peaks for GR and RELA were assessed by DiffBind R package (v3.2) to calculate differential binding in response to each treatment compared to no stimulation.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes GR and RELA binding locations in addition to RNAP2 binding intensity
Supplementary files format and content: bigwig

growth_protocol: The human pulmonary type II cell line, A549, was grown under standard culture condition using Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 2mM L-glutamine. Cells were incubated at 37°C in 5% CO2 and were grown to confluence either in 100mm, or 6/12/24-well plates, as appropriate. Prior to experiments, cells were incubated overnight in basal media that was serum- and additive-free.

extract_protocol:
Protein-DNA cross-linking was performed by adding methanol-free formaldehyde to 1% in the culture medium and incubating for 10 min at room temperature. Formaldehyde was then quenched at room temperature for 5 min with 125mM glycine prior to washing cells for 5 min with ice-cold PBS and scraping into ice-cold lysis buffer (5mM PIPES pH 8.0, 1mM EDTA, 85mM KCl, 5% glycerol, 0.5% NP-40) supplemented with protease inhibitor cocktail (PIC). Cell suspensions were incubated at 4°C for 3 h with continuous agitation. Nuclei were collected by centrifugation (600 g, 5 min, 4°C) and resuspended in ice-cold nuclei lysis buffer (NLB) (1xPBS containing 1mM EDTA, 5% glycerol, 0.5% sodium deoxycholate, 0.1% SDS, 1% NP-40) supplemented with PIC. Samples were sonicated at 4°C using a Bioruptor set for 28 – 30 high-power bursts with 30 s on-off cycles. Lysates were cleared by centrifugation (maximum speed for 15 min at 4°C) and supernatants used for immunoprecipitation. Protein G magnetic Dynabeads were preincubated with primary antibody (2.5µl/sample) overnight at 4 °C in NLB supplemented with PIC and 5 mg/ml BSA. After washing twice with ice-cold NLB plus PIC, the Dynabeads were incubated with cleared lysates overnight at 4°C in NLB supplemented with PIC and BSA. Beads were given 4 washes with ice-cold NLB containing 500mM NaCl, followed by 4 washes with ice-cold LiCl buffer (20mM Tris at pH 8.0, 1 mM EDTA, 250mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate). Crosslinks were reversed by incubation in TE buffer (10mM Tris-HCl,1mM EDTA, pH 8.0) supplemented with 0.7% SDS and 0.2 mg/ml proteinase K for 3h at 55 °C, then 16 h at 65°C. DNA was purified with a ChIP DNA Clean & Concentrator kit.
ChIP-seq libraries were prepared using the NEB Ultra II kit.

treatment_protocol: Budesonide was dissolved in DMSO as a 10mM stock. Unless specifically indicated, budesonide was used at 300nM on cells, representing a concentration that was maximally effective/near maximal on a 2×GRE reporter and gene expression in A549 cells. Final DMSO concentrations on cells were ≤ 0.1%. Recombinant human IL1B was dissolved in phosphate-buffered saline (PBS) containing 0.1% bovine serum albumin (BSA). IL1B was previously found to be maximally or near maximally effective on NF-κB reporters and gene expression at 1ng/ml and this concentration was used in all experiments unless specifically indicated. Following overnight incubation in serum free medium, cells were changed to fresh serum free medium and either not stimulated (NS) or treated with, IL1B, budesonide (Bud) or IL1B plus budesonide (I+B) for the indicated times prior to harvesting for RNA extraction. Data are from two independent experiments.

value: lung carcinoma epithelial cells

value: WT

tag: chip antibody


title: 16_336478, tumor, Pax8-BPR GEMM

description: Library name: 16_336478


title: 15_242196, tumor, Pax8-BPR GEMM

description: Library name: 15_242196


title: 14_280772, tumor, Ad-BPR allograft

description: Library name: 14_280772


title: A549 cells (input), rep1

description: Library name: Sample 9


title: 13_280769, tumor, Ad-BPR allograft

description: Library name: 13_280769


title: Human ALS, rep 4

address: בן אליעזר 32, 17

description: Library name: BAC_1_12


title: A549 cells, RNAP2 ChIP, Bud, 1h, rep 2

description: Library name: Sample 6

value: Bud

value: RPB1 NTD (RNAP2 subunit A, Cell Signaling #14958S)


title: 11_279346, tumor, Ad-BPR allograft

description: Library name: 11_279346


title: 10_237713, tumor, Ad-BPR GEMM

description: Library name: 10_237713

value: Ad-BPR GEMM


title: 18_345390, tumor, Pax8-BPR GEMM

description: Library name: 18_345390

value: female


title: 9_237702, tumor, Ad-BPR GEMM

description: Library name: 9_237702


title: A549 cells, RNAP2 ChIP, IL1B, 1h, rep 2

description: Library name: Sample 4


title: 8_59241, tumor, OSE-BPR allograft

description: Library name: 8_59241

value: FVB

value: OSE-BPR allograft


title: A549 cells, RNAP2 ChIP, I+B, 1h, rep 2

description: Library name: Sample 8

value: I+B


title: A549 cells, RNAP2 ChIP, IL1B, 1h, rep 1

description: Library name: Sample 3


title: A549 cells, RNAP2 ChIP, I+B, 1h, rep 1

description: Library name: Sample 7


title: A549 cells, RNAP2 ChIP, NS, 1h, rep 1

description: Library name: Sample 1

value: NS


title: 6_57724, tumor, OSE-BPR allograft

description: Library name: 6_57724

value: tumor


title: 7_57725, tumor, OSE-BPR allograft

description: Library name: 7_57725


title: 5_57452, tumor, OSE-BPR allograft

description: Library name: 5_57452


title: A549 cells, RNAP2 ChIP, NS, 1h, rep 2

description: Library name: Sample 2


title: A549 (input), rep 2

description: Library name: Sample 18

data_processing:
Demultiplexing was performed using bcl2fastq conversion software (v2.18.0.12) and read quality was assessed using FastQC (v0.10.1).
Good-quality reads were mapped to GRCh38 reference genome using bowtie2 (v2.4.4) and the resultant BAM files were sorted and indexed using samtools (v) prior to peak calling using MACS2 (v2.2.7.1). MACS-identified peaks for GR and RELA were assessed by DiffBind R package (v3.2) to calculate differential binding in response to each treatment compared to no stimulation.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes peak names, locations, binding intensity, and behaviour by treatment.
Supplementary files format and content: bigwig


title: 2_36685, tumor, OSE-BPR GEMM

description: Library name: 2_36685

value: OSE-BPR GEMM


title: 4_57451, tumor, OSE-BPR allograft

description: Library name: 4_57451


title: A549 cells, RNAP2 ChIP, Bud, 1h, rep 1

description: Library name: Sample 5


title: A549 cells, RELA ChIP, Bud, 1h, rep 2

description: Library name: Sample 14

value: RELA (Cell Signaling, #8242S)


title: A549 (input), rep 1

description: Library name: Sample 17


title: 1_33641, tumor, OSE-BPR GEMM

description: Library name: 1_33641