title: G245F_5A28_V2_Epigenetics

value: DELAYED D7


title: G243C_4M66_V2_Epigenetics

status: Public on Aug 05 2024

type: genomic

city: Boston

first: Ofer

last: Levy

state: MA

address: 300 Longwood Avenue

department: Infectious Disease

country: USA

institute: Boston Children's Hospital

hyb_protocol: Samples were normalised to ~250ng DNA in 45uL and bisulfite converted using Zymo EZ-96 DNA Methylation Kit..  Used Illumina Human Methylation EPIC BeadChip following the Illumina Infinium HD Methylation Assay

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and the standard recommended Illumina scanner setting.

data_processing: Raw .idat files were read into an R statistical environment using the minfi package. Using the minfi package in R, Sample QC was performed, and failed samples were removed from analysis.  Probe level QC was performed, and poorly performing probes and known blacklist probes were removed.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: standard Illumina Protocol

extract_protocol: Extration method used the Chemagic low volume blood kit, Bead based, Chemagic DNA 400 kit H96 (Cat# CMG-1491), where 1.5ug DNA was extracted from whole blood and send to AGRF Genotyping Service.

tag: Sex

value: Male

tag: race

value: African

tag: ethnicity

value: Wollof

tag: tissue

value: Blood

tag: cell type

value: Whole blood

tag: treatment

value: HBV + BCG D1


title: G244B_6Q84_V1_Epigenetics

value: Female

value: Mandinka

value: HBV + BCG D3


title: G243C_5D65_V1_Epigenetics


title: G242K_7C26_V2_Epigenetics

value: Jola

value: HBV + BCG D7


title: G242K_9P50_V1_Epigenetics


title: G241A_9Q93_V2_Epigenetics

value: Fula

value: BCG D7


title: G241A_4P07_V1_Epigenetics


title: G240H_2C72_V2_Epigenetics


title: G238F_9G46_V1_Epigenetics

value: Others

value: DELAYED D3


title: G240H_5B31_V1_Epigenetics


title: G238F_3B28_2_V2_Epigenetics


title: G237D_7F98_V2_Epigenetics


title: G238F_3B28_1_V2_Epigenetics


title: G237D_6H93_V1_Epigenetics


title: G235H_8D51_V1_Epigenetics


title: G234J_2C38_V1_Epigenetics

value: DELAYED D1


title: G236B_1L19_V2_Epigenetics


title: G236B_8P26_V1_Epigenetics


title: G235H_3P62_V2_Epigenetics


title: G233G_4B89_V2_Epigenetics

value: HBV D3


title: G233G_6D75_V1_Epigenetics


title: G232A_1A99_V2_Epigenetics

value: Male

value: HBV D7


title: G228K_2K47_V2_Epigenetics

value: African


title: G234J_3P66_V2_Epigenetics

value: Blood


title: G228K_1A18_V1_Epigenetics

value: Whole blood


title: G239K_4G91_V2_Epigenetics

value: Wollof


title: G246E_1U18_V1_Epigenetics

value: BCG D3


title: G229A_1C07_V1_Epigenetics


title: G227H_8K62_V2_Epigenetics

value: Female


title: G229A_8J63_V2_Epigenetics


title: G230E_8F22_V1_Epigenetics


title: G225D_3B53_V1_Epigenetics


title: G232A_5Q76_V1_Epigenetics

value: Mandinka


title: G230E_5F88_V2_Epigenetics

value: Jola


title: G223B_8C51_V2_Epigenetics


title: G227H_9B00_V1_Epigenetics


title: G222J_4L47_V2_Epigenetics

value: HBV + BCG D1


title: G221F_7U13_V1_Epigenetics

value: Serahule

value: HBV + BCG D3


title: G226G_5K55_V2_Epigenetics


title: G226G_4U02_V1_Epigenetics


title: G220C_3J16_1_V1_Epigenetics

value: BCG D1


title: G219C_3H36_V2_Epigenetics

value: HBV + BCG D7


title: G225D_3B56_V2_Epigenetics

value: Fula


title: G224E_4R86_V2_Epigenetics

value: DELAYED D3


title: G220C_3J16_2_V1_Epigenetics

value: Male


title: G224E_9K89_V1_Epigenetics


title: G217G_6B32_V2_Epigenetics

value: HBV D3


title: G223B_1P72_V1_Epigenetics

value: African


title: G709B_5M07_V2_Epigenetics

value: Blood


title: G711E_4A49_V2_Epigenetics

value: Whole blood


title: G192G_5K44_V1_Epigenetics

value: Wollof

value: DELAYED D7


title: G709B_3F07_V1_Epigenetics

value: Female

value: BCG D3


title: G221F_3S01_V2_Epigenetics


title: G218E_2U49_V1_Epigenetics

value: Others

value: BCG D7


title: G219C_4J27_V1_Epigenetics


title: G192G_1K30_V2_Epigenetics


title: G024B_5C14_V1_Epigenetics


title: G217G_5G24_V1_Epigenetics


title: G190F_5U21_V2_Epigenetics


title: G024B_2U68_V2_Epigenetics


title: G022K_2R06_V2_Epigenetics

value: Serahule


title: G218E_4T41_V2_Epigenetics


title: G711E_2L52_V1_Epigenetics


title: G187D_4P35_V2_Epigenetics

value: Jola


title: G186B_8U33_1_V1_Epigenetics


title: G191J_1H21_V1_Epigenetics


title: G222J_6R00_V1_Epigenetics

value: Mandinka

value: HBV + BCG D1


title: G191J_5T26_V2_Epigenetics


title: G189K_3U19_V2_Epigenetics

value: BCG D1


title: G190F_4F11_V1_Epigenetics

value: Fula

value: HBV + BCG D3


title: G022K_8A11_V1_Epigenetics


title: G189K_5B01_V1_Epigenetics

value: Male


title: G183G_1B71_V2_Epigenetics

value: African


title: G181C_3U65_V1_Epigenetics

value: Blood


title: G181C_7D02_V2_Epigenetics

value: Whole blood


title: G188F_1S76_V1_Epigenetics


title: G186B_8U33_2_V1_Epigenetics

value: DELAYED D3


title: G185H_1H01_V2_Epigenetics

value: HBV + BCG D7


title: G187D_5A73_V1_Epigenetics

value: Female


title: G179J_3A00_V2_Epigenetics

value: DELAYED D7


title: G177K_8B84_V2_Epigenetics


title: G178H_4B52_V2_Epigenetics

value: HBV D1


title: G183G_6R43_V1_Epigenetics


title: G180E_6A16_V1_Epigenetics


title: G185H_1S58_V1_Epigenetics


title: G184J_8A32_V2_Epigenetics


title: G184J_9U47_V1_Epigenetics


title: G176F_1C62_V2_Epigenetics

value: BCG D3


title: G175E_8J83_V2_Epigenetics


title: G174A_6H31_V1_Epigenetics


title: G182A_5A49_V1_Epigenetics


title: G173D_7B58_V2_Epigenetics

value: Serahule


title: G173D_7L16_V1_Epigenetics


title: G180E_4K73_V2_Epigenetics


title: G169G_7L67_V2_Epigenetics

value: HBV D3


title: G168C_5T87_V2_Epigenetics

value: Mandinka


title: G178H_8A70_V1_Epigenetics

value: Jola


title: G169G_3Q06_V1_Epigenetics


title: G166D_8S69_V2_Epigenetics

value: Wollof

value: HBV + BCG D1


title: G177K_9S68_V1_Epigenetics

value: HBV + BCG D3


title: G164K_2M22_V2_Epigenetics

value: BCG D7


title: G162F_4D76_V1_Epigenetics

value: Male

value: African

value: DELAYED D1


title: G161H_1T61_V1_Epigenetics

value: Fula

value: Blood

value: Whole blood


title: G176F_8M19_V1_Epigenetics


title: G159F_6G49_V1_Epigenetics

value: Others


title: G175E_7S75_V1_Epigenetics

value: Female


title: G172C_1A26_V1_Epigenetics

value: DELAYED D3


title: G157C_3C16_V1_Epigenetics

value: HBV D7


title: G172C_4A53_V2_Epigenetics


title: G158A_5A32_V2_Epigenetics

value: BCG D1


title: G179J_8Q82_V1_Epigenetics

value: Mandinka

value: DELAYED D7


title: G171B_2Q83_V2_Epigenetics


title: G156H_2U20_V1_Epigenetics


title: G171B_2J32_V1_Epigenetics


title: G156H_7C12_V2_Epigenetics


title: G170G_6G33_V1_Epigenetics


title: G170G_3A88_V2_Epigenetics


title: G167E_2U72_V1_Epigenetics

value: Wollof


title: G168C_3H86_V1_Epigenetics


title: G167E_2A74_V2_Epigenetics


title: G154G_8U50_V1_Epigenetics

value: Jola

value: HBV D3


title: G154G_1G18_V2_Epigenetics


title: G153J_6H41_V1_Epigenetics


title: G153J_4A34_V2_Epigenetics


title: G152D_2S62_V2_Epigenetics

value: HBV + BCG D7


title: G166D_6H72_V1_Epigenetics

value: Male

value: HBV + BCG D1


title: G152D_3L09_V1_Epigenetics

value: African


title: G165J_5Q07_V2_Epigenetics

value: Fula


title: G151E_9Q23_V1_Epigenetics

value: Blood

value: BCG D7


title: G150K_9D01_V2_Epigenetics

value: Whole blood


title: G151E_8S07_V2_Epigenetics

value: Female


title: G150K_1F88_V1_Epigenetics


title: G165J_8M34_V1_Epigenetics


title: G149A_9T77_1_V2_Epigenetics


title: G148K_6T44_V2_Epigenetics

value: HBV D1


title: G164K_2Q44_V1_Epigenetics


title: G145D_4B37_V1_Epigenetics


title: G147H_4A00_V1_Epigenetics

value: Others

value: HBV D7


title: G145D_6B01_V2_Epigenetics


title: G144E_1A47_V1_Epigenetics

value: Mandinka


title: G143B_7T08_V1_Epigenetics

value: DELAYED D3


title: G163A_8H83_V2_Epigenetics


title: G142J_1F43_V1_Epigenetics

value: Wollof

value: DELAYED D1


title: G163A_8T09_V1_Epigenetics


title: G141F_9Q43_V2_Epigenetics

value: BCG D3


title: G142J_8C97_V2_Epigenetics


title: G140C_9L31_V1_Epigenetics


title: G161H_4P32_V2_Epigenetics


title: G162F_6P31_V2_Epigenetics

value: Jola


title: G147H_4R92_V2_Epigenetics

value: Male


title: G160B_1S52_V2_Epigenetics


title: G160B_3U82_V1_Epigenetics


title: G159F_9G11_V2_Epigenetics

value: HBV D3


title: G138E_4R41_V2_Epigenetics

value: African


title: G158A_8T96_V1_Epigenetics

value: BCG D1


title: G136J_5C69_V2_Epigenetics

value: Blood

value: HBV + BCG D3


title: G134F_6H57_V2_Epigenetics

value: Whole blood

value: HBV + BCG D1


title: G135K_3C72_V2_Epigenetics


title: G140C_7A99_V2_Epigenetics

value: Female

value: BCG D7


title: G155B_2J20_V2_Epigenetics

value: DELAYED D7


title: G155B_8B94_V1_Epigenetics


title: G133H_5U79_V1_Epigenetics

value: Mandinka


title: G133H_9B34_V2_Epigenetics

value: DELAYED D3


title: G132B_9D75_V2_Epigenetics

value: Others


title: G149A_9T77_2_V2_Epigenetics


title: G130A_6S97_V2_Epigenetics


title: G130A_2U38_V1_Epigenetics


title: G148K_1F57_V1_Epigenetics

value: HBV D1


title: G146G_3F17_V2_Epigenetics


title: G146G_8R58_V1_Epigenetics


title: G144E_9P95_V2_Epigenetics


title: G143B_7A05_V2_Epigenetics

value: Fula


title: G128J_1A51_V1_Epigenetics


title: G141F_7J49_V1_Epigenetics

value: BCG D3


title: G127F_8H25_V2_Epigenetics


title: G127F_3S70_V1_Epigenetics


title: G126K_5C39_1_V2_Epigenetics

value: Wollof

value: DELAYED D1


title: G126K_5C39_2_V2_Epigenetics

value: African


title: G125A_7T83_V2_Epigenetics

value: Male

value: HBV D3


title: G137G_3F01_V1_Epigenetics

value: Blood


title: G139C_1D31_V2_Epigenetics

value: Whole blood


title: G139C_3G91_V1_Epigenetics


title: G138E_9T55_V1_Epigenetics

value: HBV D7


title: G136J_4L37_V1_Epigenetics

value: Female

value: Jola

value: HBV + BCG D3


title: G137G_5D49_V2_Epigenetics


title: G124C_7F96_V2_Epigenetics

value: Mandinka

value: BCG D1


title: G135K_2A08_V1_Epigenetics


title: G134F_8A58_V1_Epigenetics

value: HBV + BCG D1


title: G122H_3T13_1_V1_Epigenetics

value: HBV + BCG D7


title: G131D_4P84_V1_Epigenetics

value: BCG D7


title: G131D_4G94_V2_Epigenetics


title: G129B_5J77_V1_Epigenetics

value: Others


title: G129B_4B80_V2_Epigenetics


title: G128J_3H72_V2_Epigenetics


title: G132B_9H53_V1_Epigenetics

value: DELAYED D7


title: G119H_3C93_1_V1_Epigenetics

value: DELAYED D1


title: G118B_7L38_V1_Epigenetics

value: African


title: G125A_9J41_V1_Epigenetics

value: Male

value: Fula


title: G115G_7G82_V1_Epigenetics

value: Blood


title: G124C_7A78_V1_Epigenetics

value: Whole blood


title: G123E_1C83_V1_Epigenetics


title: G121G_9R94_V1_Epigenetics

value: HBV D1


title: G114D_6H17_V1_Epigenetics

value: Female

value: HBV D3


title: G121G_2U36_V2_Epigenetics


title: G120D_3Q27_V2_Epigenetics

value: BCG D3


title: G123E_8U24_V2_Epigenetics


title: G120D_1L66_V1_Epigenetics

value: Mandinka


title: G119H_3C93_2_V1_Epigenetics

value: Jola


title: G112E_9U29_V2_Epigenetics

value: BCG D1


title: G117A_1D51_V1_Epigenetics


title: G118B_2P89_V2_Epigenetics

value: HBV + BCG D7


title: G117A_4Q75_V2_Epigenetics


title: G110J_7R49_V1_Epigenetics

value: HBV + BCG D3


title: G110J_6C84_V2_Epigenetics


title: G116C_1B93_V2_Epigenetics

value: DELAYED D3


title: G115G_9B43_V2_Epigenetics

value: DELAYED D7


title: G108G_5A22_V2_Epigenetics

value: HBV D7


title: G114D_4M53_V2_Epigenetics

value: African


title: G113F_2B84_V1_Epigenetics

value: Male


title: G106E_6C80_V1_Epigenetics

value: Wollof


title: G122H_3T13_2_V1_Epigenetics

value: Blood


title: G113F_1U23_V2_Epigenetics

value: Whole blood


title: G112E_6C98_V1_Epigenetics


title: G103C_8T76_2_V1_Epigenetics

value: Fula

value: HBV D1


title: G103C_8T76_1_V1_Epigenetics

value: Female


title: G109D_4J87_V2_Epigenetics

value: BCG D7


title: G111K_8H40_2_V2_Epigenetics


title: G109D_8M57_V1_Epigenetics


title: G116C_1R36_V1_Epigenetics


title: G107J_7A91_V1_Epigenetics

value: Mandinka

value: HBV + BCG D1


title: G100H_2A95_V2_Epigenetics

value: Jola


title: G101A_3U97_V1_Epigenetics

value: BCG D3


title: G098F_6H69_2_V1_Epigenetics


title: G099K_7D39_V1_Epigenetics

value: HBV D3


title: G603B_7S03_V1_Epigenetics


title: G105F_4M36_V1_Epigenetics


title: G105F_1K29_V2_Epigenetics


title: G111K_8H40_1_V2_Epigenetics

value: BCG D1


title: G104B_7U17_V2_Epigenetics


title: G104B_2K41_V1_Epigenetics


title: G102K_9C22_V2_Epigenetics


title: G101A_2J02_V2_Epigenetics


title: G108G_9M51_V1_Epigenetics


title: G100H_6C50_V1_Epigenetics

value: HBV + BCG D3


title: G216J_4M39_V2_Epigenetics


title: G214F_8M89_V2_Epigenetics

value: DELAYED D3


title: G099K_9U07_V2_Epigenetics

value: African


title: G213H_5R36_V2_Epigenetics

value: HBV D7


title: G213H_4Q72_V1_Epigenetics

value: Wollof


title: G097D_4B31_V2_Epigenetics

value: Blood

value: DELAYED D7


title: G098F_6H69_1_V1_Epigenetics

value: Whole blood


title: G107J_5C63_V2_Epigenetics


title: G097D_6F94_V1_Epigenetics


title: G212B_1C26_V1_Epigenetics


title: G602J_9S91_V1_Epigenetics


title: G288D_8R86_V2_Epigenetics

value: Fula


title: G102K_4M93_V1_Epigenetics

value: Male


title: G216J_4L42_V1_Epigenetics

value: Female


title: G208B_3Q63_V1_Epigenetics

value: HBV + BCG D7


title: G215K_5M69_1_V1_Epigenetics

value: DELAYED D1


title: G106E_1F29_V2_Epigenetics

value: HBV D1


title: G214F_2L38_V1_Epigenetics

value: Jola


title: G211D_9J05_V2_Epigenetics

value: Mandinka

value: HBV + BCG D1


title: G206C_3U94_V1_Epigenetics

value: BCG D3


title: G211D_3D64_V1_Epigenetics


title: G210A_5S33_V1_Epigenetics

value: Others

value: BCG D7


title: G288D_7S42_V1_Epigenetics

value: African

value: HBV + BCG D3


title: G210A_7U93_V2_Epigenetics

value: Blood


title: G212B_6A40_V2_Epigenetics


title: G207A_6R93_V2_Epigenetics

value: HBV D3


title: G204D_9C82_V2_Epigenetics

value: Whole blood


title: G206C_8A83_V2_Epigenetics


title: G205G_6H71_V2_Epigenetics


title: G202E_8P74_V1_Epigenetics


title: G203F_4M00_V1_Epigenetics


title: G204D_3D95_V1_Epigenetics


title: G203F_5F81_V2_Epigenetics


title: G215K_5M69_2_V1_Epigenetics

value: Fula


title: G201K_3P73_V1_Epigenetics

value: Male

value: Wollof

value: DELAYED D3


title: G209H_5K20_V1_Epigenetics

value: Female


title: G209H_7M04_V2_Epigenetics


title: G208B_3P25_V2_Epigenetics

value: HBV + BCG D7


title: G200J_5K99_V2_Epigenetics

value: Jola


title: G199E_6F33_V2_Epigenetics

value: Mandinka

value: BCG D1


title: G200J_4C42_V1_Epigenetics


title: G199E_6L17_V1_Epigenetics


title: G207A_2T57_V1_Epigenetics


title: G198D_3A25_V1_Epigenetics

value: DELAYED D1


title: G196A_5T74_V2_Epigenetics


title: G197B_2A19_V2_Epigenetics

value: HBV D7


title: G198D_8M03_V2_Epigenetics


title: G197B_8F89_V1_Epigenetics


title: G195C_6T55_V2_Epigenetics

value: HBV D1


title: G194H_9S33_V2_Epigenetics

value: African

value: DELAYED D7


title: G195C_3A21_V1_Epigenetics

value: Blood


title: G205G_2B21_V1_Epigenetics

value: Others


title: G193K_5S31_V2_Epigenetics

value: Whole blood

value: BCG D7


title: G096B_4C06_V2_Epigenetics

value: Male


title: G201K_2G32_V2_Epigenetics

value: Wollof


title: G096B_8H92_V1_Epigenetics


title: G094J_3L07_V2_Epigenetics

value: Fula


title: G093G_5R15_V2_Epigenetics

value: HBV + BCG D1


title: G095H_4D07_V2_Epigenetics

value: Female


title: G092A_5P14_V1_Epigenetics


title: G092A_6F58_V2_Epigenetics


title: G090E_3B05_V2_Epigenetics

value: Jola


title: G091C_8T50_V2_Epigenetics

value: Mandinka

value: HBV + BCG D3


title: G089J_6K88_2_V1_Epigenetics


title: G091C_4U50_V1_Epigenetics


title: G089J_6K88_1_V1_Epigenetics


title: G090E_7Q62_V1_Epigenetics

value: DELAYED D1


title: G196A_1P78_V1_Epigenetics

value: BCG D1


title: G088H_8G53_V1_Epigenetics


title: G086F_6G04_V2_Epigenetics


title: G194H_5G09_V1_Epigenetics


title: G087K_5M79_V1_Epigenetics


title: G085E_8M88_V2_Epigenetics

value: HBV D3


title: G086F_9F17_V1_Epigenetics

value: African


title: G088H_8J10_V2_Epigenetics

value: DELAYED D7


title: G193K_9J88_V1_Epigenetics

value: Blood


title: G083D_6F71_V2_Epigenetics

value: HBV D1


title: G087K_8H24_V2_Epigenetics

value: Whole blood


title: G084A_6S02_V1_Epigenetics

value: HBV + BCG D7


title: G084A_8R14_V2_Epigenetics


title: G085E_9K92_V1_Epigenetics


title: G082C_4R52_V2_Epigenetics

value: Male


title: G094J_4K88_V1_Epigenetics

value: BCG D7


title: G082C_6U40_V1_Epigenetics


title: G095H_7G49_V1_Epigenetics


title: G080G_9P52_V1_Epigenetics

value: Fula


title: G080G_2G52_V2_Epigenetics


title: G079E_2R28_V1_Epigenetics


title: G078D_5Q16_2_V2_Epigenetics


title: G079E_3C80_V2_Epigenetics


title: G078D_5Q16_1_V2_Epigenetics


title: G072G_1P90_V2_Epigenetics

value: Serahule

value: HBV + BCG D1


title: G077B_1R22_V1_Epigenetics

value: Jola

value: BCG D3


title: G072G_4U68_V1_Epigenetics

value: Female


title: G071J_3A94_V1_Epigenetics

value: Mandinka


title: G070F_6C69_V1_Epigenetics

value: DELAYED D3


title: G070F_6G37_V2_Epigenetics


title: G067C_1D97_V1_Epigenetics


title: G068A_3F55_V1_Epigenetics

value: HBV D7


title: G068A_9J58_V2_Epigenetics

value: African


title: G067C_3U88_V2_Epigenetics


title: G069F_5J83_V1_Epigenetics

value: HBV D3


title: G069F_2P97_V2_Epigenetics

value: Blood


title: G065B_9Q06_V2_Epigenetics

value: Wollof

value: DELAYED D1


title: G066H_1G36_2_V1_Epigenetics

value: Whole blood


title: G083D_1F07_V1_Epigenetics

value: HBV D1


title: G081B_1K14_V1_Epigenetics

value: Male

value: Others


title: G063J_7A07_V1_Epigenetics


title: G064G_8S18_V1_Epigenetics

value: Fula

value: DELAYED D7


title: G064G_5J49_V2_Epigenetics


title: G063J_4C85_V2_Epigenetics

value: Jola


title: G081B_3Q52_V2_Epigenetics


title: G061E_2M45_V1_Epigenetics


title: G062D_8T92_V1_Epigenetics


title: G061E_9J60_V2_Epigenetics


title: G077B_8A98_V2_Epigenetics

value: BCG D3


title: G065B_5R70_V1_Epigenetics


title: G059A_4D59_V1_Epigenetics

value: BCG D1


title: G060K_9P85_V2_Epigenetics

value: Female

value: Mandinka


title: G059A_7G85_V2_Epigenetics


title: G057H_9C50_V1_Epigenetics


title: G058K_8K82_V1_Epigenetics

value: HBV + BCG D1


title: G060K_3M90_V1_Epigenetics

value: African

value: HBV D7


title: G066H_1G36_1_V1_Epigenetics

value: Blood


title: G057H_6L00_V2_Epigenetics


title: G055D_7H64_V2_Epigenetics

value: HBV + BCG D7


title: G056G_4J23_V1_Epigenetics

value: HBV + BCG D3


title: G056G_2R85_V2_Epigenetics

value: Whole blood


title: G054E_4D38_2_V1_Epigenetics


title: G052J_9M19_V2_Epigenetics

value: HBV D1


title: G054E_4D38_1_V1_Epigenetics


title: G051F_1F04_V2_Epigenetics


title: G053B_2R93_V2_Epigenetics


title: G050C_6K91_V1_Epigenetics


title: G050C_7S58_V2_Epigenetics


title: G051F_9D38_V1_Epigenetics


title: G052J_5U51_V1_Epigenetics

value: Male


title: G049B_4R51_2_V2_Epigenetics


title: G055D_5J65_V1_Epigenetics

value: Others


title: G053B_2C43_V1_Epigenetics


title: G048J_2K08_V1_Epigenetics


title: G058K_4U28_V2_Epigenetics


title: G048J_6J33_V2_Epigenetics


title: G046K_8M76_V2_Epigenetics


title: G047F_8S59_V2_Epigenetics

value: DELAYED D3


title: G049B_4R51_1_V2_Epigenetics


title: G046K_3G58_V1_Epigenetics

value: DELAYED D7


title: G045A_4F24_V2_Epigenetics

value: BCG D7


title: G043E_3F91_V2_Epigenetics

value: HBV D3


title: G045A_2B09_V1_Epigenetics


title: G047F_1J32_V1_Epigenetics


title: G044C_8R11_V2_Epigenetics


title: G044C_4H71_V1_Epigenetics


title: G042H_6L41_V1_Epigenetics


title: G042H_7D99_V2_Epigenetics


title: G043E_9D30_V1_Epigenetics


title: G041G_7G69_V1_Epigenetics

value: Fula


title: G041G_6R14_V2_Epigenetics


title: G040D_7S36_V2_Epigenetics

value: Female

value: BCG D3


title: G038B_3K37_2_V1_Epigenetics

value: Mandinka


title: G039H_3C97_V2_Epigenetics

value: African


title: G039H_6K61_V1_Epigenetics

value: HBV D7


title: G038B_3K37_1_V1_Epigenetics

value: Blood


title: G037A_6L48_V2_Epigenetics


title: G037A_5J88_V1_Epigenetics


title: G036C_2M30_V2_Epigenetics

value: Wollof

value: DELAYED D1


title: G040D_7T15_V1_Epigenetics

value: Whole blood


title: G035G_8U17_V2_Epigenetics

value: HBV + BCG D3


title: G036C_9S26_V1_Epigenetics


title: G034D_9T70_V1_Epigenetics


title: G033F_3K45_V1_Epigenetics

value: Male

value: Serahule

value: HBV D1


title: G033F_5R14_V2_Epigenetics


title: G032E_5D03_V2_Epigenetics


title: G034D_3D35_V2_Epigenetics


title: G032E_8F29_V1_Epigenetics


title: G031K_3U37_V1_Epigenetics

value: HBV + BCG D7


title: G031K_2H06_V2_Epigenetics


title: G028G_4A81_V2_Epigenetics

value: Jola

value: BCG D7


title: G030J_7B28_2_V1_Epigenetics


title: G030J_7B28_1_V1_Epigenetics


title: G029D_2U73_V2_Epigenetics

value: Others

value: BCG D1


title: G028G_8P52_V1_Epigenetics


title: G029D_1S61_V1_Epigenetics


title: G027J_9K82_V2_Epigenetics

value: Female

value: BCG D3


title: G027J_8Q80_V1_Epigenetics

value: African

value: Mandinka


title: G026E_4Q07_V2_Epigenetics

value: Blood

value: HBV + BCG D1


title: G026E_8U98_V1_Epigenetics

value: Wollof


title: G025F_5R35_V1_Epigenetics

value: Fula

value: Whole blood


title: G035G_1C96_V1_Epigenetics

value: Male

value: HBV + BCG D3


title: G025F_9F48_V2_Epigenetics


title: Swi6_snf22Δ_rsc1Δ_Rep2

type: SRA

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

library_source: genomic

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs from ChIPseq were aligned to the S. pombe reference (Wood et al. 2002) using the BWA aligner (Li, H. & Durbin, 2009). Macs2 (Zhang, Y. et al. 2008) was used to process the resulting BAM files to product bedgraphs normalized to input and untagged controls.  Deeptools (Ramirez et al. 2016) bamCoverage was used to generate CPM normalized bedgraphs for input and untagged BAMS.
Assembly: S. pombeV2 reference with the sequence of the full 40 kbmatregion provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM).

organism: Schizosaccharomyces pombe

growth_protocol: Growth in YEA at 30°C

extract_protocol:
Cells were crosslinked using 3% PFA at room temperature or 18°C for 30 min. Cells were spun at 3000rpm for 5 min washed and pellets were lysed using glass beads and lysis buffer (50mM Hepes/KOH, 140mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% DOC plus protease inhibitors). Cell lysates were sheared using a Bioruptor-300 (Diagenode) to an approximate size of 200–700 bp.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

tag: strain

tag: genotype

value: mat1Msmt0 leu1-32 ade6-216 ura4  mat2P(Bg-Bs)::ura4+  snf22-delta::KanMX6  rsc1-delta::KanMX6

tag: chip antibody

tag: growth

value: Growth in YEA 30C

tag: fixation

value: 3% PFA


title: Input_Swi6_WT_Rep2

value: mat1Msmt0 leu1-32 ade6-210 ura4 mat2P(Bg-Bs)::ura4+


title: Swi6_WT_Rep2


title: Input_Swi6_snf22Δ_rsc1Δ_Rep2


title: untag_E

value: mat1Msmt0 leu1-32 ade6-210 his2 ura4DS/E  otr1R(Sph1)::ura4+

value: ANTI-FLAG M2 affinity gel A2220


title: Input_untag_E


title: untag_B

source_name: mat1Msmt0 leu1-32 ade6-210 his2 ura4DS/E  otr1R(Sph1)::ura4+


title: untag_D


title: Input_untag_D


title: Input_untag_A


title: untag_A


title: Input_untag_B


title: Snf21_clr3Δ_Rep2

source_name: mat1Msmt0 leu1-32 ade6-216 his2 ura4DS/E  clr3∆::KanMX6  snf21-3FLAG::KanMX6  otr1R(Sph1)::ura4+


title: Input_untag_C


title: untag_C


title: Snf21_WT_Rep2

source_name: mat1Msmt0 leu1-32 ade6-210 his2 ura4DS/E  snf21-3FLAG::KanMX6  otr1R(Sph1)::ura4+


title: Input_Snf21_clr3Δ_Rep2


title: Input_Snf21_WT_Rep2


title: Input_Snf22_WT_Rep3

source_name: mat1Msmt0 leu1-32 ade6-210 his2 ura4DS/E  snf22-3FLAG::KanMX6  otr1R(Sph1)::ura4+


title: Input_Snf22_clr3Δ_Rep3

source_name: mat1Msmt0 leu1-32 ade6-216 his2 ura4  clr3∆::KanMX6  snf22-3FLAG::KanMX6  otr1R(Sph1)::ura4+


title: Snf22_clr3Δ_Rep3


title: Input_Snf21_WT_Rep1


title: Snf22_clr3Δ_Rep2


title: Snf21_clr3Δ_Rep1


title: Snf21_WT_Rep1


title: Input_Snf21_clr3Δ_Rep1


title: Snf22_WT_Rep2


title: Input_Snf22_WT_Rep2


title: Input_Snf22_clr3Δ_Rep1


title: Snf22_WT_Rep3


title: ishK2_1

city: guangzhou

first: Qingyang

last: Chen

address: Zhongshan 2nd Road

country: China

institute: Sun Yat-sen University

description: infected with shRNA of knocking down FOXK2(#1)(induced with NaB+Dox)

library_source: transcriptomic

data_processing:
After get the Clean Reads, using HISAT2 will Clean Reads alignment to reference genome; Using DESeq2 analyzing differentially expressed genes;
Using NCBI, Uniprot, GO and KEGG database of differentially expressed genes
Assembly: ViralProj14158
Supplementary files format and content: tab-delimited test files include RPKM values for each sample

molecule: total RNA

source_name: iSLK Bac16

growth_protocol: iSLK-BAC16  cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics (penicillin and streptomycin) at 37℃

extract_protocol:
RNA was extracted by TRIZOL, about 1 ug RNA was used for RNA-seq
RNA Libraries for RNA-SEQ were prepared using SMARTER Mrna-seq library prep kit following manufacturer protocols

tag: cell line

value: iSLK Bac16

value: Kidney cell

value: FOXK2 knockdown

value: induced with Nab+Dox for 72 h


title: Input_Snf22_clr3Δ_Rep2


title: iC_1

description: Control(#1)induced with NaB+Dox

value: WT


title: Snf22_clr3Δ_Rep1


title: shK1_2

description: infected with shRNA of knocking down FOXK1(#2)(uninduced)

value: FOXK1 knockdown

value: uninduced


title: Input_Snf22_WT_Rep1


title: ishK2_2

description: infected with shRNA of knocking down FOXK2(#2)(induced with NaB+Dox)


title: shK1_1

description: infected with shRNA of knocking down FOXK1(#1)(uninduced)


title: ishK1_1

description: infected with shRNA of knocking down FOXK1(#1)(induced with NaB+Dox)


title: shK2_2

description: infected with shRNA of knocking down FOXK2(#2)(uninduced)


title: shK2_1

description: infected with shRNA of knocking down FOXK2(#1)(uninduced)


title: C_2


title: C_1


title: ishK1_2

description: infected with shRNA of knocking down FOXK1(#2)(induced with NaB+Dox)


title: iC_2

description: Control(#2)induced with NaB+Dox


title: UP20, lncRNA

city: beijing

first: Yumeng

last: Ren

state: Beijing

address: Xicheng District

institute: Peking university people’s hospital

data_processing:
Use Bowtie tools soft, The Clean Reads respectively with Silva database, GtRNAdb database, Rfam database and Repbase database sequence alignment, filter ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. The remaining reads were used to detect known miRNA and new miRNA predicted by comparing with known miRNAs from miRbase and Human Genome (GRCh38), respectively. Read count for each miRNA was obtained from the mapping results, and TPM was calculated.
Assembly: hg19
Supplementary files format and content: Line-separated excel files for each example

source_name: uterine fluid exosomes

extract_protocol:
Total RNA was extracted and purified from plasma exosome using miRNeasy Serum/Plasma Advanced Kit (Qiagen, cat. No. 217204) according to the kit instruction.
A total amount of 250pg—10ng RNA per sample was used as input material for sequencing libraries using the SMARTer Stranded Total RNA-Seq Kit (Takara Bio USA, Inc.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: uterine fluid exosomes

value: Unpregnant


title: shCtrl-2

city: shanghai

first: YI

last: JINGJING

state: shanghai

address: fenglin compus

institute: FuDan university

data_processing:
Alternative splicing analysis used rMATs v4.1.0 to detect differential alternative splicing events from RNA-Seq data.
Expression analysis used HTSeq (v0.6.1) to estimate gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: hg38
Supplementary files format and content: Gene Expression.xls includes raw counts and RPKM for each sample, and fold change analysis data.
Supplementary files format and content: Alternative splicing.xls includes alternative splicing events analysis data for each sample.

source_name: Peripheral blood

growth_protocol: Jurkat cells were maintained in  RPMI-1640 medium supplemented with 10% fetal bovine serum, 100 U/mL of penicillin, and 100 μg/mL of streptomycin, and the cells were cultured in a humidified incubator at 37°C in the presence of 5% CO2

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed  using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand  cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and  add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of  Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina NovaSeq instrument for sequencing using a 2x150 paired-end (PE) configuration according to  manufacturer’s instructions.

value: Peripheral blood

value: Jurkat

value: T lymphoblast

value: puromycine selection


title: DoseExperiment_A549cells_4weeks_control_rep1

city: Kanazawa

first: Alexandra

last: Lukyanchuk

state: --Not Applicable--

address: 13-1 Takara-machi

country: Japan

institute: Kanazawa University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: The labeled beads were visualized using the iScan system (Illumina, San Diego, CA, USA)

data_processing: minfi R package

label: Cy5 and Cy3

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, control, 4 weeks, rep1

label_protocol: Standard Illumina Protocol

growth_protocol: A549 cells and DMEM/F12 medium with 10% fetal bovine solution (10 μg/mL gentamicin) were used. Cells adhering to the bottom of the flasks were removed with 0.25% trypsin/1 mM EDTA solution (Invitrogen, Carlsbad, CA, USA), and the cells were subcultured periodically.

extract_protocol: The genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany). The concentration of the extracted genomic DNA was measured using a Qubit fluorometer (Thermo Fisher Scientific, Waltham, MA, USA).

treatment_protocol: DEP-suspended culture medium was added to 2.5 × 10^5 A549 cells seeded in T-25 tissue culture bottles. The medium was replaced every 4 days after seeding, and the cells were subcultured. Four exposure concentrations of DEP were prepared: 0, 3, 10 and 30 μg/ml. The exposure period spanned 4 weeks

tag: gender

value: Male

value: cancerous lung tissue

value: 0 μg/ml of DEP for 4 weeks


title: Snf22_WT_Rep1

value: ANTI-FLAG M2 affinity gel A2220

value: Growth in YEA 30C

value: 3% PFA


title: UP18, lncRNA


title: DoseExperiment_A549cells_4weeks_DEP3_rep1

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, 3 μg/ml of DEP, 4 weeks, rep1

value: 3 μg/ml of DEP for 4 weeks


title: UP15, lncRNA


title: MainExperiment_Methylation_A549cells_4weeks_DEP30_rep1

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, 30 μg/ml of DEP, 4 weeks, rep1

treatment_protocol: DEP-suspended culture medium was added to 2.5 × 10^5 A549 cells seeded in T-25 tissue culture bottles. The medium was replaced every 4 days after seeding, and the cells were subcultured.  0 μg/ml and 30 μg/ml concentrations of DEP were prepared. The exposure period spanned 4 weeks

value: 30 μg/ml of DEP for 4 weeks


title: UP13, lncRNA


title: MainExperiment_Methylation_A549cells_4weeks_DEP30_rep3

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, 30 μg/ml of DEP, 4 weeks, rep3


title: UP16, lncRNA


title: DoseExperiment_A549cells_4weeks_DEP30_rep2

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, 30 μg/ml of DEP, 4 weeks, rep2


title: UP11, lncRNA


title: UP14, lncRNA


title: UP9, lncRNA


title: shCWF19L1-2

value: CWF19L1 knockdown


title: shCWF19L1-1


title: shCtrl-1

value: WT


title: MainExperiment_Methylation_A549cells_4weeks_control_rep2

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, control, 4 weeks, rep2


title: MainExperiment_Methylation_A549cells_4weeks_control_rep3

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, control, 4 weeks, rep3


title: UP7, lncRNA


title: DoseExperiment_A549cells_4weeks_control_rep3


title: MainExperiment_Methylation_A549cells_4weeks_DEP30_rep2


title: UP5, lncRNA


title: DoseExperiment_A549cells_4weeks_DEP3_rep2

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, 3 μg/ml of DEP, 4 weeks, rep2


title: UP4, lncRNA


title: UP8, lncRNA


title: UP3, lncRNA


title: DoseExperiment_A549cells_4weeks_DEP3_rep3

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, 3 μg/ml of DEP, 4 weeks, rep3


title: UP2, lncRNA


title: DoseExperiment_A549cells_4weeks_DEP10_rep2

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, 10 μg/ml of DEP, 4 weeks, rep2

value: 10 μg/ml of DEP for 4 weeks


title: UP1, lncRNA

value: uterine fluid exosomes


title: MainExperiment_Methylation_A549cells_4weeks_control_rep4

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, control, 4 weeks, rep4


title: DoseExperiment_A549cells_4weeks_DEP10_rep1

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, 10 μg/ml of DEP, 4 weeks, rep1


title: UP12, lncRNA

value: Unpregnant


title: P18, lncRNA

value: Pregnant


title: P16, lncRNA


title: DoseExperiment_A549cells_4weeks_control_rep2


title: P15, lncRNA


title: P11, lncRNA


title: P12, lncRNA


title: P14, lncRNA


title: P10, lncRNA


title: P9, lncRNA


title: P6, lncRNA


title: P4, lncRNA


title: P8, lncRNA


title: P13, lncRNA


title: P7, lncRNA


title: P5, lncRNA


title: P3, lncRNA


title: P2, lncRNA


title: P1, lncRNA


title: P17, lncRNA


title: UP18, miRNA


title: MainExperiment_Methylation_A549cells_4weeks_DEP30_rep4

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, 30 μg/ml of DEP, 4 weeks, rep4


title: UP17, miRNA


title: DoseExperiment_A549cells_4weeks_DEP30_rep1


title: UP16, miRNA


title: UP15, miRNA


title: UP14, miRNA


title: UP19, miRNA


title: UP9, miRNA


title: UP11, miRNA


title: UP17, lncRNA


title: UP20, miRNA


title: UP5, miRNA


title: UP6, miRNA


title: UP8, miRNA


title: UP7, miRNA


title: UP2, miRNA


title: UP3, miRNA


title: UP1, miRNA


title: UP4, miRNA


title: P17, miRNA


title: P16, miRNA


title: UP19, lncRNA


title: P15, miRNA


title: P18, miRNA


title: P12, miRNA


title: P13, miRNA


title: P11, miRNA


title: P14, miRNA


title: UP13, miRNA


title: P10, miRNA


title: UP12, miRNA


title: P9, miRNA


title: UP10, miRNA


title: P7, miRNA


title: P8, miRNA


title: P6, miRNA


title: P5, miRNA


title: Cicer arietinum lateral roots inoculated with Phytophthora medicaginis, scrambled_C, 24hpi

city: Sydney

first: Jonathan

middle: Michael

last: Plett

state: New South Wales

address: 50 Bourke street

department: Soil Biology and Genomics

country: Australia

institute: Western Sydney University

description:
processed data_Cicerari.txt
processed_data_Phytmed.txt

data_processing:
CLC Genomics Workbench v21.0.0
The raw RNA-seq reads were trimmed to remove low quality sequences and adapters using CLC genomic workbench
Trimmed sequence reads were mapped to Cicer arietinum and Phytophthora medicaginis genomes using CLC genomic workbench (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic workbench
Assembly: Cicer arietnum Desi genome and Phytophthora medicaginis isolate 7831 genome, respectively
Supplementary files format and content: tab-delimited text files include unique count values for each sample

organism:
Cicer arietinum
Phytophthora medicaginis

source_name: lateral roots.hyphae

growth_protocol: Cicer arietinum were maintained on full strnegth MS media supplemented with 3% CaCO3 and Gamborg's vitamins in a reach in growth chamber at 15 h light/ 9 h dark cycle at 18˚C, 70% relative humidity and 500 μmol m-2 s-1 light intensity. Fifteen-day old seedlings were used for inoculation. P. medicaginis was maintained on V8 juice agar plates (containing 200 mL L-1 V8TM bottled juice; 3.0 g L-1 CaCO3, 15.0 g L-1 agar) supplemented with ampicillin (100 μg mL-1) at 25˚C in the dark. Fifteen-day old seedlings were used for inoculation. P. medicaginis was maintained on V8 juice agar plates (containing 200 mL L-1 V8TM bottled juice; 3.0 g L-1 CaCO3, 15.0 g L-1 agar) supplemented with ampicillin (100 μg mL-1) at 25˚C in the dark. P. medicaginis was always passaged through the host prior to inoculations. P. medicaginis inoculum was prepared one day before inoculations by aseptically transferring mycelial agar blocks taken from the edge of an actively growing culture onto 0.5 x 0.5 mm2 sterile membranes overlaid on V8 juice agar plates. For inoculations, membranes carrying P. medicaginis mycelium were placed directly on the root at a distance of 1.5 cm from the tip of roots of fifteen-day old seedlings. After inoculation, seedlings were placed back into the growth chamber with 15 h light/ 9 h dark cycle at 18˚C, 70% relative humidity and 200-500 μmol light intensity.

extract_protocol:
RNA was extracted from three samples per treatment with each sample containing two root pieces of 1.5 cm in length containing the infected site at the centre of each root using the Bioline Plant II RNA extraction kit according to the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using Illumina Library Prep Kit following manufacturer's protocols.

treatment_protocol: Two hours after inoculation , we treated the P. medicaginis inoculation site with nebulized dsiRNA mixtures. The treatment group consisted of a dsiRNA mix of two dsiRNAs targeting two different sites of the small secreted protein Phytmed_10271 mRNA. The control group consisted of scrambled dsiRNA.  The dsiRNA spray application process was repeated every 12 hours to maintain repression of the target gene for the duration of the experiment. Root tissue was harvested at 24 hpi from three replicates each for treatment and control groups, and snap frozen in liquid nitrogen before freezing at -80 °C.

value: lateral roots.hyphae

value: Variety "Sonali"/ isolate 7836

value: scrambled dsiRNA (control)


title: P4, miRNA


title: P3, miRNA


title: P1, miRNA


title: Cicer arietinum lateral roots inoculated with Phytophthora medicaginis, phytmed 10271_kd_C, 24hpi

value: Variety "Sonali"/ isolate 7833

value: dsiRNA targeting Phytmed_10271 small secreted protein


title: Cicer arietinum lateral roots inoculated with Phytophthora medicaginis, scrambled_B, 24hpi

value: Variety "Sonali"/ isolate 7835


title: Cicer arietinum lateral roots inoculated with Phytophthora medicaginis, phytmed 10271_kd_B, 24hpi

value: Variety "Sonali"/ isolate 7832


title: Cicer arietinum lateral roots inoculated with Phytophthora medicaginis, phytmed 10271_kd_A, 24hpi

value: Variety "Sonali"/ isolate 7831


title: A549, TS-KO co-culture, R1

city: Odense - M

first: Paolo

last: Ceppi

address: Campusej, 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Quality control analysis of Fastq files were done using FastQC package.
Reads were then aligned to human reference genome with GRCh38 build (release 105) with the respective Ensembl GTF annotation file using STAR v2.7.9a aligner in a two-pass mode.
Read counts were measured with featureCounts function in Rsubread package using R 4.2.1
Differential gene expression analysis was performed using DESeq2 v1.36.0 pipeline.
Assembly: hg38; GRCh38 (release 105)
Supplementary files format and content: tab-delimited text file includes Raw count values from featureCounts for all samples

source_name: TYMS knockout co-culture, R1

growth_protocol: A549 cell line was maintained in DMEM high glucose medium (Gibco) with 10% fetal bovine serum (FBS) and maintained at 37oC with 5% CO2 in a humidified incubator

extract_protocol:
Total RNA was isolated using miRNeasy kit (Qiagen) as per manufacturer's protocol. 500 ng of Total RNA was used for the library construction.
Sequencing libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol (NEB).

value: Lung adenocarcinoma

value: NSCLC cell line

value: TYMS KO

value: No treatment

tag: time

value: 14 days post transduction


title: HDF, SSc serum 2, L524-0367

city: Xi'an

first: Mei

last: Lu

address: No. 157, West 5th Road, Xincheng District

institute: The Second Affiliated Hospital of Xi'an Jiaotong University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.The expression levels of genes and transcripts were quantified through the utilization of the RSEM software.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files

source_name: Human dermal fibroblasts

extract_protocol:
RNA was harvested using RNAiso Plus (Takara).1ug of total RNA was used for the constraction of sequencing libraries.
RNA libraries for RNA-seq were prepared for sequencing using standard illumina protocols.

tag: agent

value: stimulated with L524-0366 and serum

tag: disease

value: Human dermal fibroblasts

value: systemic sclerosis patient


title: A549, TS.KO co-culture, R2

source_name: TYMS knockout co-culture, R2


title: P2, miRNA

source_name: uterine fluid exosomes

value: uterine fluid exosomes

value: Pregnant


title: HDF, SSc serum 3, L524-0368


title: A549, TS-KO, R2

source_name: TYMS knockout, R2


title: HDF, SSc serum 1, L524-0366


title: A549, TS-KO co-culture, R3

source_name: TYMS knockout co-culture, R3


title: MainExperiment_Methylation_A549cells_4weeks_control_rep1

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, control, 4 weeks, rep1

value: Male

value: cancerous lung tissue

value: 0 μg/ml of DEP for 4 weeks


title: A549, TS-KO, R3

source_name: TYMS knockout, R3


title: HDF, SSc serum 3, control

value: stimulated with serum


title: HDF, SSc serum 2, control


title: A549, gNTC1 co-culture, R3

source_name: Non-targeting control co-culture R3

value: NTC KO


title: A549, TS-KO, R1

source_name: TYMS knockout, R1


title: HDF, SSc serum 1, control


title: Cicer arietinum lateral roots inoculated with Phytophthora medicaginis, scrambled_A, 24hpi

value: lateral roots.hyphae

value: Variety "Sonali"/ isolate 7834

value: scrambled dsiRNA (control)


title: A549, gNTC1 co-culture, R1

source_name: Non-targeting control co-culture R1

value: Lung adenocarcinoma

value: NSCLC cell line


title: p53 WT 3

city: Irvine

first: Fiona

last: Law

state: CA

address: 839 Health Sciences Road

institute: UCI

data_processing:
Sequencing reads were quantified and aligned to 252 the human genome GRCh38 using kallisto v0.48.0. Estimated counts of transcripts from the 253 same Ensembl gene ID were added together and the sums were converted to integers. Differential 254 expression analysis was performed using DESeq2 v1.38.3.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file includes raw counts

extract_protocol:
Rneasy kit (Qiagen)
Novogene Corporation Inc

value: WT

value: 16 hr induction


title: A549, gNTC1, R3

source_name: Non-targeting control, R3

value: No treatment

value: 14 days post transduction


title: p53 WT 1


title: p53 WT 2


title: A549, gNTC1, R2

source_name: Non-targeting control, R2


title: p53 null 3


title: A549, gNTC1, R1

source_name: Non-targeting control, R1


title: p53 null 2


title: p53 null 1


title: SC354_SC271-2

city: Houston

first: Carl

last: Gay

state: TX

address: 1515 Holcombe Blvd

department: Thoracic-Head & Neck Med Onc

institute: The University of Texas MD Anderson Cancer Center

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software v2.1.1
Assembly: hg38
Supplementary files format and content: gzip compressed tab delimited value files and matrix files

source_name: PDX tumor

extract_protocol:
Fresh tumors or biopsies were dissociated overnight to obtain single cell suspension.
Chromium Next GEM Single Cell 3' v3.1 (CG000204)

value: PDX tumor

value: LCNEC

value: untreated


title: SC342_SC288A

description: 10X Genomics


title: SC324_SC369A

description: 10X Genomics

source_name: patient biopsy

value: patient biopsy

value: relapsed


title: UP10, lncRNA

value: uterine fluid exosomes

value: Unpregnant


title: p53 R175H, UCI-1001 2

value: UCI-1001, 3 hr induction


title: SC332_SC378A

description: 10X Genomics


title: p53 R175H, DMSO 2

value: DMSO, 3 hr induction


title: p53 R175H, UCI-1014 2

value: UCI-1014, 3 hr induction


title: SC277_288A

description: 10X Genomics


title: p53 R175H, DMSO 1


title: A549, gNTC1 co-culture, R2

source_name: Non-targeting control co-culture R2

value: NTC KO


title: SC267_SC194-3P

description: 10X Genomics


title: SC324_SC279A

description: 10X Genomics


title: SC307_SC297-1

description: 10X Genomics


title: SC267_262A

description: 10X Genomics


title: Hyperoxia_Female_3

city: Philadelphia

first: Abiud

last: Cantu

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

data_processing:
Trimgalore 0.6.7 was used for adapter trimming using default parameters.
STAR 2.7.9 was used for alignment. Using parameters: --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend --outSAMstrandField intronMotif
Salmon 1.10.1 was used for quantification with default parameters.
Salmon output was loaded to R 4.3.2 using Tximeta 1.20.3 and DESeq2 1.42 collapseReplicates() was used to sum technical replicates.
DESeq2 was used to perform differential expression and clusterProfiler 4.10.0 for pathway enrichment and over representation.
Assembly: mm39
Supplementary files format and content: Tab separated plain text file containing raw counts. Each column is a sample and each row is a gene.

organism: Mus musculus

source_name: Lung

extract_protocol:
Total RNA from sorted alveolar macrophage cells were isolated using the RNeasy Plus Micro Kit (74034, QIAGEN). Sample concentration and quality checks were done using the Agilent Bioanalyzer.
The libraries were prepped using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing 634894, TAKARABIO. The first 8 nt were UMIs followed by the Pico v3 SMART UMI Adapter, both of which were trimmed. Novg libraries were purified further to remove fragments with less than 250bp and resequenced.

value: Lung

tag: age

value: PND 7

value: Female

value: Alveolar Macrophages

value: C57BL/6 WT

value: Hyperoxia


title: Hyperoxia_Female_1

tag: Sex


title: SC211_210A

description: 10X Genomics


title: Hyperoxia_Female_2


title: SC157_TC821

description: 10X Genomics

value: PDX tumor


title: Hyperoxia_Male_3

value: Male


title: ADAD42 3

city: St. Louis

first: Zhao

last: Sun

state: MO

address: 4523 Clayton Ave

department: Developmental Biology

institute: Washington University in St. Louis

description: g4fad-sp ucl803-3

data_processing:
Basecalling: Illumina's bcl2fastq
Custom python demultiplexing
Alignment: STAR version 2.5.1a
Gene counts: Subread:featureCount 1.4.6-p5
Sequencing performance assessment: RSeQC 2.6.2
Assembly: hg38
Supplementary files format and content: TXT containing ensembl ID, entrezgene ID, gene name, type, source of name, transcript count, description, and CPM for each sample per gene.

source_name: spheroids

extract_protocol:
RNA was isolated using Qiashredder columns into Qiagen Rneasy plus mini.
Samples were prepared according to library kit manufacturer’s protocol

value: spheroids

value: neurons

value: ADAD


title: Normoxia_Female_3

value: Normoxia


title: Hyperoxia_Male_2


title: Normoxia_Female_2


title: ADAD42 1

description: g4fad-sp ucl803-1


title: ADAD42 2

description: g4fad-sp ucl803-2


title: Normoxia_Female_1


title: p53 R175H, UCI-1001 1


title: HC36 2

description: g4ct-sp 5838-2

value: HC


title: HC36 3

description: g4ct-sp 5838-3


title: HC36 1

description: g4ct-sp 5838-1


title: Normoxia_Male_2


title: ADAD38 3

description: g3fad-sp ucl53-3


title: ADAD38 2

description: g3fad-sp ucl53-2


title: ADAD38 1

description: g3fad-sp ucl53-1


title: HC44 3

description: g3ct-sp 4060-3


title: SC157_TC684

description: 10X Genomics

value: LCNEC

value: untreated


title: H11_12276 B3s

type: RNA

city: Vizela

first: Marta

middle: Patrícia

last: Ferreira

state: Braga

address: Rua da junuqeira, Santo Adrião

country: Portugal

hyb_protocol: NOT PROVIDED

scan_protocol: NOT PROVIDED

data_processing: The data analysis was conducted using ROSALIND®, which utilizes a HyperScale architecture developed by ROSALIND, Inc. in San Diego, CA.

label: not provided

source_name: ileal surgical specimens

label_protocol: NOT PROVIDED

extract_protocol: Formalin-fixed and paraffin-embedded (FFPE) total RNA from each sample was isolated at IPATIMUP Diagnostics from three independent extractions, each containing three sections of 20m thick, using automated extraction – Maxwell RSC 16 equipment with RCS RNA FFPE Kit (Promega, USA) - in accordance to the manufacturer’s instructions. After isolation, the three independent extractions were pooled and column concentration was performed using Amicon Ultra centrifugal filters 3K (Merck Millipore, Germany) to increase the final concentration of RNA.   RNA concentrations were quantified by using Qubit 3.0 Fluorimeter (Invitrogen, USA) and fragmentation was evaluated through Agilent 2100 Bioanalyzer. A minimum of 400 ng of total RNA was used for each sample. In order to detect any procedural error during the material processing (thus making possible not to repeat it forward), three separated batches were runed (batch 1, batch 2 and batch 3) in different dates.

tag: group

tag: batch


title: H14_27400 B3s


title: HC44 2

description: g3ct-sp 4060-2

tag: tissue


title: HC44 1

description: g3ct-sp 4060-1

tag: cell type


title: ADAD58 3

description: g2fad-sp ucl33-3


title: ADAD58 2

description: g2fad-sp ucl33-2


title: ADAD58 1

description: g2fad-sp ucl33-1


title: H08_15530 B3o


title: H08_6046 B3o


title: Normoxia_Male_3

tag: treatment


title: HC61 2

description: g2ct-sp 8260-2


title: HC61 3

description: g2ct-sp 8260-3


title: Normoxia_Male_1


title: H07_15709 B3o


title: HC61 1

description: g2ct-sp 8260-1


title: ADAD56 3

description: g1fad-sp 6840-3


title: H11_15263 B3s


title: ADAD56 2

description: g1fad-sp 6840-2


title: H04_4351 B2


title: H06_8412 B2


title: H07_132 B3o


title: H03_4660 B2


title: H10_7298 B2


title: ADAD56 1

description: g1fad-sp 6840-1


title: H07_80 B2


title: H06_15811 B2


title: H06_6159 B2


title: HC52 3

description: g1ct-sp 4453-3


title: HC52 2

description: g1ct-sp 4453-2


title: MainExperiment_GE_A549cells_4weeks_DEP30_rep4

data_processing:
The raw fastq files obtained from RNA-seq were trimmed to remove adapters and bases with < 20 quality using FastQC software
STAR aligner was used with the Ensembl_Homo_sapiens.GRCh37 reference genome to align the filtered reads
Read count extraction was performed using HT-seq-union counting
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: cancerous lung tissue

extract_protocol:
RNA was isolated from the cells using the RNeasy Mini Kit (Qiagen, Hilden, Germany); The concentration and integrity of the isolated RNA was quantified using the NanoDrop (Thermo Fisher Scientific) and Agilent TapeStation. A total of 500 ng RNA for each sample with RNA integrity number (RIN) values > 8 was used for sequencing library construction.
PolyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). The polyA RNA was employed as the input for the preparation of the library for RNA-seq, which was conducted using the NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs). The approach uses dUTP-based method to preserve strand information. After indexing via PCR (10 cycles) enrichment, resulting transcriptome libraries were quantified by Qubit DNA Assay (Thermo Fisher Scientific) and their fragment size distribution was estimated by TapeStation D1000 ScreenTape (Agilent). The libraries were then pooled/multiplexed at an equimolar amount each and loaded onto Illumina NovaSeq 6000 paired-end sequencing (2 × 150 bp), yielding approximately 20M PE reads per sample. Library preparation and sequencing were conducted by Azenta Life Sciences (Tokyo, Japan).

value: cancerous lung tissue

value: WT

value: 30 ug/ml of DEP for 4 weeks


title: HC52 1

description: g1ct-sp 4453-1


title: H06_1834 B3o


title: UP6, lncRNA

source_name: uterine fluid exosomes

value: uterine fluid exosomes

value: Unpregnant


title: MainExperiment_GE_A549cells_4weeks_DEP30_rep3


title: H07_10582 B3s


title: MainExperiment_GE_A549cells_4weeks_DEP30_rep1


title: H07_1438 B3o

value: Female


title: H05_4115 B2


title: MainExperiment_GE_A549cells_4weeks_DEP30_rep2


title: H04_13492 B3s


title: H04_12642 B2


title: RNA_KK_CB_3

city: Hefei

first: Caoling

last: Xu

state: Anhui

address: 96 Jinzhai Road

department: Department of Life Sciences and Medicine

institute: University of Science and Technology of China

data_processing:
Trim_galore removes adapters and low-quality reads
Mapping to the mouse genome(mm10)
Genes, transcripts or PiRNA quantification
Assembly: mm10
Supplementary files format and content: Txt files of genes, transcripts or PiRNA quantification

source_name: Testis

extract_protocol:
The total RNA was isolated from testicular enriched fractions of pachytene spermatocytes and round spermatids using Trizol (Invitrogen) following manufacturers’ protocol.1 ug of total RNA was used for the construction of RNA sequencing libraries.25 ng CB RNA was used for the construction of sequencing librarie.200 ng total RNA was used for the construction of small RNA sequencing libraries.
RNA libraries for RNA-seq were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina®  in accordance with the manufacturer's recommendations. The total RNA from CB was utilized for strand-specific library preparation without polyA selection or ribosome depletion using the Hieff NGS ®Ultima Dual-mode RNA Library Prep Kit for Illumina®.The small RNA libraries were prepared using the MGIEasy Small RNA Library Prep Kit.

value: Testis

value: Germ cells

value: DDX4 homozygous knock-in

value: The cells from the testes used two-step digestion method.


title: H04_14290 B3o

value: Male


title: RNA_KK_CB_2


title: MainExperiment_GE_A549cells_4weeks_control_rep4

value: 0 ug/ml of DEP for 4 weeks


title: MainExperiment_GE_A549cells_4weeks_control_rep3


title: H03_2612 B3o


title: H01_639 B2


title: H15_25230 B3s


title: H03_7683 B2


title: RNA_KK_CB_1


title: H14_14419 B3s


title: MainExperiment_GE_A549cells_4weeks_control_rep2


title: p53 R175H, UCI-1014 1

value: UCI-1014, 3 hr induction


title: RNA_WK_CB_3

value: DDX4 heterozygous knock-in


title: H13_23723 B3s


title: MainExperiment_GE_A549cells_4weeks_control_rep1


title: RNA_WK_CB_1


title: P5_scRNAseq

city: Chengdu

first: Long

middle: Qian

last: Kang

state: Sichuan Province

address: 新川路2222号

department: Biotherapeutics

institute: Sichuan University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.2.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/piplines/latest/what-is-cell-ranger).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Human cardiac myxoma

extract_protocol:
An appropriate amount of human cardiac septal tissue was taken and placed into the serum-free medium with sterile forceps, and the tissue was minced with sterile scissors and filtered through a 40 μm filter to obtain the cell suspension. Subsequently, an appropriate amount of type II collagenase was added, and digestion was carried out in a 37 ℃ water bath for 20 min to terminate the enzyme digestion, and the residual collagenase was washed away by centrifugation-discarding the supernatant and resuspending with culture medium. 300g-500g for 5 min-8 min to remove the cellular debris. Finally, erythrocyte lysis was performed using erythrocyte lysis solution.
Library was performed according to the manufacturer's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, CM cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-n-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single was retrotranscripted cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UM) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIseclect reagent for subsequent library construction. During the library construction Illumina R2 primer R2 sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Human cardiac myxoma


title: H11_14693 B3o


title: RNA_KK_2

value: Round spermatids


title: H10_13031 B3s


title: P4_scRNAseq

description: 10x Genomics


title: H13_12694 B3o


title: H09_18585 B3o


title: H09_20929 B3s


title: H08_13248 B2


title: P3_scRNAseq

description: 10x Genomics


title: P2_scRNAseq

description: 10x Genomics


title: H07_11018 B3o


title: Lesion M3-1, ROI 2260-5079

city: Groningen

first: Astrid

last: Alsema

address: Antonius Deusinglaan 1

department: Biomedical Sciences of Cells and Systems

country: Netherlands

institute: University Medical Center Groningen

description: NanoString GeoMx

data_processing:
Fastq files were converted to .dcc files using the GeoMx NGS Pipeline according to the GeoMx DSP NGS Readout User Manual (MAN-10153-01) Option 1: Standard Standalone Pipeline.
DCC files can be loaded into R for data processing with the GeomxTools open software package.
Assembly: GRCh38
Supplementary files format and content: DCC files
Supplementary files format and content: One .ini file for NanoString's NGS Pipeline software, one .xlsx metadata file with sample information, one .pkc file with probe information for loading into R, and five .png image files of the five samples.
Library strategy: Spatial Transcriptomics

source_name: Brain white matter

extract_protocol:
FFPE brain samples were sectioned at 5 µm thickness. Sections were treated with Nanostring Whole Transcriptome Atlas probes according to the GeoMx® DSP Manual Slide Preparation User Manual (MAN-10150-03), and stained for IBA1. Whole transcriptome probes were collected from IBA1+ segments as according to the GeoMx® DSP Instrument User Manual (MAN-10152-03).
Libraries were made from these probes according the GeoMx® DSP NGS Readout User Manual (MAN-10153-03).
NanoString GeoMx® Digital Spatial Profiling libraries were loaded at 650 pM molarity on the Illumina NextSeq 2000 and sequenced with a P1 v3 100 bp reagent kit.

tag: disease state

value: Multiple sclerosis (MS)

value: Brain white matter

value: Microglia


title: Lesion M3-1, ROI 1738-4354

description: NanoString GeoMx


title: RNA_WK_CB_2

tag: genotype


title: Lesion M3-1, ROI 1731-2419

description: NanoString GeoMx


title: Lesion M3-1, ROI 0128-4595

description: NanoString GeoMx


title: Lesion M3-1, ROI 0085-4259

description: NanoString GeoMx


title: P1_scRNAseq

description: 10x Genomics


title: Lesion M3-1, ROI 4363-0748

description: NanoString GeoMx


title: Lesion M3-1, ROI 4840-0145

description: NanoString GeoMx


title: RNA_WT_1

value: WT


title: RNA_WT_2


title: Lesion M3-1, ROI 4367-0782

description: NanoString GeoMx


title: RNA_WK_1


title: K562 SF3B1 K666N-eltanexor_navitoclax-2-comboRNA

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

description: polyA RNA

data_processing:
All samples were trimmed with Trimmomatic (v0.32) to remove low-quality and short reads and aligned to the human genome hg19 using STAR aligner (v 2.7.9a).
For total RNA and polyA RNA, RSEM (v 1.3.1) was used to obtain expected gene counts against the human gene reference Gencode (v 41). Differential expression was determined using DESeq2 and R (v 4.2.0). A gene was considered detected if the TPM (Transcripts Per Million) >1 in at least two replicates of one sample and significantly changed if the adjusted p-value was < 0.05 and fold change >1.5<−1.5.
Alternative splicing bam files with the Gencode v41 annotation file were used as input for rMATS (v4.1.2). Events with |inclusion level difference| > 0.05, P < 0.05 and FDR < 0.05 were identified as significantly differentially expressed AS events
For small RNAseq reads were aligned against human elements in RepBase (v23.08) with STAR (v2.7.9a), and the unmapped output was then mapped against the human genome (hg19), allowing three mismatches and keeping all uniquely aligned reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes the Differentially expressed genes per comparison

growth_protocol: K562 cells were cultured in 10% fetal bovine serum and 1% pencillin/streptomycin at early passages (P1-10) and then treated with either vehicle (DMSO) or 200nM selinexor for 24 hours. After 24 hours, RNA was extracted. For the combination treatment RNA sequencing, cells were treated with either vehicle/DMSO, 200nM eltanexor, 1uM venetoclax, 1uM A1331852, 1uM navitoclax, or the combinations of eltanexor+venetoclax, eltanexor+A1331852, and eltanexor+navitoclax for 24 hours.

extract_protocol:
Total RNA for mRNA sequencing was extracted using QIAGEN RNeasy mini kit. To separate nuclear and cytoplasmic fractions, pellet the cells via centrifugation for 5 minutes at 1500RPM and discard the supernatant. The pellet was then resuspended into 300mL of ice cold 0.25x lysis buffer (Tris-Cl pH 8.0, NaCl, MgCl2, Nonidet P-40). The pellet was kept on ice for two minutes and rotate the tube every 45 seconds to ensure proper lysis followed by centrifugation at highest speed at 4°C for two minutes. After centrifugation, the supernatant was carefully removed and placed in a new tube as this was the cytoplasmic fraction. For the remaining nuclear fraction pellet, 500mL of ice-cold PBS was added and centrifuged at 1500RPM for 5 minutes. The QIAGEN RNeasy mini kit was then used for long RNAs and miRNeasy Tissue/Cells Advanced Micro Kit was used for small RNA extraction.
For mRNA sequencing was Poly(A)-selected and the Illumina libraries were prepared using the TruSeq stranded mRNA Library Preparation kit. For the nuclear cytoplasmic mRNAs, ribsomoal RNA depeletion method with the TruSeq stranded Total RNA library was used with 50 million paired end reads. For the nuclear cytoplasmic small RNAs, the size selection step with the Perkin Elmer Next Flex Small RNA library preparation kit on the Illumina sequencing platform with 50 million single end reads.

value: chronic myeloid leukemia cells

value: eltanexor+navitoclax


title: K562-eltanexor_navitoclax-2-comboRNA

description: polyA RNA


title: RNA_KK_1


title: Lesion M3-1, ROI 4372-0816

description: NanoString GeoMx


title: Lesion M3-1, ROI 4353-0646

description: NanoString GeoMx


title: K562 SF3B1 K666N-eltanexor_navitoclax-1-comboRNA

description: polyA RNA


title: RNA_WK_2


title: G93A_7

city: Rome

first: Marco

last: Rosina

state: Rome

address: Viale Regina Elena 299

department: Neuroscience

country: Italy

institute: Italian National Institute of Health

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted  in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: mm10
Supplementary files format and content: Gene expression raw count in csv format file

source_name: Brown Adipose Tissue

growth_protocol: animals were housed at standard conditions

extract_protocol:
After euthanasia, mice were rinsed with 70% ethanol and BAT was exposed, removed with sterile scissors, and weighted. RNA was isolated with RNeasy Lipid Tissue Mini Kit (Qiagen, cat. #74804). Briefly, BAT tissue was homogenized in 1 ml of QIAzol Lysis Reagent. Phase separation was performed with addition of 200 l of chloroform, vigorous shaking and centrifugation at 12000 ×g for 15 min at 4°C. Aqueous phase was extracted, and 1 vol of 70% ethanol was added to provide appropriate binding conditions. The sample is then applied to the RNeasy spin column and processed according to manufacturer’s instructions. Total RNA was eluted in 30 µl of RNase-free water.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

treatment_protocol: animals were euthanized at 120 day old with cervical dislocation

value: Brown Adipose Tissue

value: 120 days


title: Lesion M3-1, ROI 4357-0680

description: NanoString GeoMx


title: Lesion M3-1, ROI 4362-0714

description: NanoString GeoMx


title: K562 SF3B1 K666N-eltanexor_A1331852-2-comboRNA

description: polyA RNA


title: H13_13851 B3s


title: G93A_6


title: Lesion M3-1, ROI 2626-3502

description: NanoString GeoMx


title: Lesion M3-1, ROI 3616-0533

description: NanoString GeoMx


title: K562 SF3B1 K666N-eltanexor_A1331852-1-comboRNA

description: polyA RNA


title: Lesion M3-1, ROI 3590-0601

description: NanoString GeoMx


title: G93A_1


title: K562-eltanexor_A1331852-2-comboRNA

description: polyA RNA


title: Lesion M3-1, ROI 3606-0569

description: NanoString GeoMx


title: Lesion M3-1, ROI 3629-0500

description: NanoString GeoMx


title: WT_6


title: Lesion M3-1, ROI 3644-0468

description: NanoString GeoMx


title: K562-eltanexor_A1331852-1-comboRNA

description: polyA RNA


title: Lesion M3-1, ROI 1346-4826

description: NanoString GeoMx


title: WT_4


title: K562-eltanexor_navitoclax-1-comboRNA

description: polyA RNA


title: K562 SF3B1 K666N-eltanexor_venetoclax-2-comboRNA

description: polyA RNA

value: eltanexor+venetoclax


title: Lesion M3-1, ROI 1390-4787

description: NanoString GeoMx


title: Lesion M3-1, ROI 1303-4863

description: NanoString GeoMx


title: WT_3


title: G93A_3


title: K562 SF3B1 K666N-eltanexor_venetoclax-1-comboRNA

description: polyA RNA


title: WT_1


title: Lesion M3-1, ROI 1324-4844

description: NanoString GeoMx


title: Lesion M3-1, ROI 0964-4276

description: NanoString GeoMx


title: Lesion M3-1, ROI 0993-4261

description: NanoString GeoMx


title: totalRNA_sonkd_rep2

city: Nijmegen

first: Oscar

last: Garcia-Blay

state: Gelderland

address: Heyendaalseweg 135

department: Biophysical Chemistry

institute: Institute for Molecules and Materials (Radboud University)

description: raw files are reads in .fastq format. Processed data files are SPLICE-q estimation of intron-specific splicing efficiency (SE) in .tsv format.

data_processing:
total RNA-seq step 1: STAR2.7.11a was utilized to generate an indexed genome reference from GRCm39 mus musculus dna sequences per chromosome.
total RNA-seq step 2: STAR2.7.11a was utilized to align the reads from the .fastq file of each sample to the genome of reference. Output was an unsorted BAM file.
total RNA-seq step 3: BAM files were sorted with samtools
total RNA-seq step 4: SPLICE-q.py was utilized to estimate splicing efficiency of introns. NOTE:  The automatic prefix 'chr' was changed to '' (null) in the SPLICE-q.py file because the chromosome id did not have this prefix in the .bam file
long-read nanopore sequencing step 1: Raw reads were obtained from Nanopore sequencer as .fast5 files
long-read nanopore sequencing step 2: basecalling was performed during sequencing run by the tools provided by Oxford Nanopore.
long-read nanopore sequencing step 3: .fastq files from basecalling were concatenated and  minimap2 was utilized to align the basecalled reads to the transcriptome of reference Mus_musculus.GRCm39.cdna and produce a SAM file.
long-read nanopore sequencing step 4: samtools sort was utilized to produce a sorted BAM file.
long-read nanopore sequencing step 5: samtools index and idxstats were utilized to obtain the results of the alignment in terms of counts per isoform.
Assembly: For total RNA-seq: Mus_musculus.GRCm39.dna.chromosome (1 to X)
Assembly: For long-read nanopore sequencing: Mus_musculus.GRCm39.cds.all
Supplementary files format and content: For total RNA-seq: SPLICEq output (splicing efficiency per intron) in .tsv file.
Supplementary files format and content: For long-read nanopore sequencing: count table of transcripts in .txt file.

source_name: E14 mESCs (129/Ola background)

growth_protocol: Mouse embryonic stem cells (mESCs) were seeded with a density of 0.5E6 cells in a gelatinized 9.6cm2 well. mESC culture medium  consisted of Dulbecco's Modified Eagle Medium, supplemented with 0.1mM betamercaptoethanol, 1000 U/mL of Penicillin, 0.1 mg/mL of Streptomycin, 1mM of sodium pyruvate , 1000 U/mL of ESGRO recombinant Mouse Leukemia Inhibitory Factor and 15% of ES-qualified heat inactivated Fetal Bovine Serum (FBS)

extract_protocol:
24 hours post-transfection, RNA extraction was performed with TRIzol reagent following instructions of the manufacturer.
RNA amount and quality was assessed with Qubit and BioAnalizer. Rt-qPCR was performed to validate Son KD at the mRNA level. For total RNA-seq: RNA samples were delivered to sequencing company in dry ice. Depletion of rRNA was performed in sequencing location prior to library preparation. For Nanopore cDNA sequencing: library preparation was performed following the instruction provided by the manufacturer (Flow-cell:FLO-MIN106D ;Protocol: cDNA).

treatment_protocol: Mouse embryonic stem cells (mESCs) were seeded with a density of 1E6 cells in a 25cm2 well. 24 hours post-seeding, transfection of Son siRNA or control siRNA was performed in a total volume of 7 mL of transfection media. Transfection media onsisted on 70% standard complete growth media in absence of antibiotics (Penicillin, Streptomycin) and 30% lipoplex solution with the siRNA. Lipoplex solution was obtained by combining 50% of 5% Lipofectamine2000  in Opti-MEM with 50% of 1mM siRNA in Opti-MEM, and incubating at room temperature for 15 minutes.

value: E14 mESCs (129/Ola background)

value: sonkd


title: K562-eltanexor_venetoclax-1-comboRNA

description: polyA RNA


title: totalRNA_sonkd_rep1


title: Lesion M3-1, ROI 3655-0432

description: NanoString GeoMx


title: totalRNA_control_rep2

value: control


title: Lesion M3-1, ROI 0936-4292

description: NanoString GeoMx


title: totalRNA_control_rep1


title: Lesion M3-1, ROI 1369-4806

description: NanoString GeoMx


title: Lesion M3-1, ROI 0881-4323

description: NanoString GeoMx


title: K562 SF3B1 K666N-navitoclax-1-comboRNA

description: polyA RNA

value: 1uM navitoclax


title: K562 SF3B1 K666N-navitoclax-2-comboRNA

description: polyA RNA


title: Lesion M2-1, ROI 4769-0428

description: NanoString GeoMx


title: Lesion M2-1, ROI 4983-0404

description: NanoString GeoMx


title: Lesion M3-1, ROI 1280-4883

description: NanoString GeoMx


title: K562-navitoclax-1-comboRNA

description: polyA RNA


title: wildtype C57BL/6J mouse 2, 2 Months

city: Shanghai

first: Howell

last: Cheng

address: 320 Yueyang Road

institute: Institute of Neuroscience, Chinese Acedemy of Sciences

description: cells from wildtype C57BL/6J mouse 2, 2 Months

data_processing:
Raw fastq sequence data were processed using Cellranger v7.1.0
A total of 19,969 cells from the thalamus region with a median of 13048 unique molecular identifiers (UMIs) and 4030 genes per cell was loaded for downstream Seurat (v5) analysis.
Assembly: mm10-2020-A
Supplementary files format and content: Tab separated values files and matrix files

source_name: Thalamus

extract_protocol:
Thalamic tissue dissected from two adult wildtype C57BL/6J mice were sequentially digested with papain, protase and dispase in choline chloride solution for preparing single-cell suspensions
single-cell libraries were generated using 10X Genomics 3’-labeling kit (V3)

value: Thalamus

value: mixed

value: wildtype

value: no treatment


title: K562-navitoclax-2-comboRNA

description: polyA RNA


title: Lesion M2-1, ROI 4769-0212

description: NanoString GeoMx

value: Multiple sclerosis (MS)


title: Lesion M2-1, ROI 4946-0191

description: NanoString GeoMx

value: Brain white matter


title: K562 SF3B1 K666N-A1331852-2-comboRNA

description: polyA RNA


title: Lesion M3-1, ROI 1020-4246

description: NanoString GeoMx

value: Microglia


title: Lesion M2-1, ROI 0264-2117

description: NanoString GeoMx


title: wildtype C57BL/6J mouse 1, 2 Months

description: cells from wildtype C57BL/6J mouse 1, 2 Months


title: K562-eltanexor_venetoclax-2-comboRNA

description: polyA RNA


title: MASH Regression 8w 3

city: La Jolla

first: Souradipta

last: Ganguly

address: 9500 Gilman Drive

institute: University of California, San Diego

description: MASH Regression 3

data_processing:
scRNA-Seq data was aligned with Cell Ranger version 3.0 and, each library was mapped to the mm10 genome.
The Seurat package (version 3.0) was used for processing and merging raw count data, normalization, and clustering.
Gene expression of each cell was normalized by total transcript counts and multiplied by 10,000.
Cells of suspected low quality were removed, which had too few genes expressed (<500), which had high mitochondrial gene expression (>5%).
Visualization was performed with Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction and the Louvain algorithm with a resolution of 0.5 was used to cluster the cells.
Assembly: GRCm38
Supplementary files format and content: .rds file

source_name: liver

extract_protocol:
For primary liver cell isolation, mice livers were perfused by cannulation through the inferior vena cava with 0.33mg/ml pronase (Roche, Indianapolis, IN), followed by 0.67mg/ml collagenase D (Roche, Indianapolis, IN), for 5-10 minutes before ex vivo digestion in a solution containing pronase, collagenase D and DNase1 (Roche, Indianapolis, IN) for 10min in a rotating incubator at 370C. The dissociated cells were strained through a 100μm mesh. The cell suspension was centrifuged at 50g for 1 minute to remove the hepatocytes, supernatant was collected and centrifuged at 800g for 7 minutes. Cell pellet washed with GBSS-B buffer at 700g for 7 minutes. Cells were finally isolated by Nycodenz gradient centrifugation at 2000g for 20 minutes. The Hepatic stellate cells (HSC) layer (upper layer) and the other non-parenchymal cells (NPC) layer (lower layer) were then collected and washed with GBSS-B at 800g for 7 minutes and processed. Total RNA was isolated using Rneasy column (Qiagen, Valencia, CA).
10X Genomics 3’ Single Cell RNA-seq (Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1) following manufactures protocol.

value: liver

value: Non Parenchymal cells (NPC)

value: Western Diet (WD)/Chow Diet


title: Lesion M2-1, ROI 1578-3922

description: NanoString GeoMx


title: Lesion M2-1, ROI 1621-2482

description: NanoString GeoMx


title: Lesion M2-1, ROI 4057-5206

description: NanoString GeoMx


title: K562 SF3B1 K666N-A1331852-1-comboRNA

description: polyA RNA

value: chronic myeloid leukemia cells


title: Lesion M2-1, ROI 4028-5194

description: NanoString GeoMx


title: K562-A1331852-2-comboRNA

description: polyA RNA


title: MASH Regression 8w 1

description: MASH Regression 1


title: Lesion M3-1, ROI 0909-4308

description: NanoString GeoMx


title: MASH Regression 8w 2

description: MASH Regression 2


title: Lesion M2-1, ROI 4086-5219

description: NanoString GeoMx


title: Lesion M2-1, ROI 4141-5236

description: NanoString GeoMx


title: Lesion M2-1, ROI 2343-2377

description: NanoString GeoMx


title: Lesion M2-1, ROI 3998-5186

description: NanoString GeoMx


title: K562 SF3B1 K666N-venetoclax-1-comboRNA

description: polyA RNA

value: 1uM venetoclax


title: Lesion M2-1, ROI 2412-2205

description: NanoString GeoMx


title: Lesion M2-1, ROI 4115-5227

description: NanoString GeoMx


title: K562-A1331852-1-comboRNA

description: polyA RNA


title: K562 SF3B1 K666N-venetoclax-2-comboRNA

description: polyA RNA


title: Lesion M2-1, ROI 2376-2296

description: NanoString GeoMx


title: Foz 12w MASH 1

description: MASH progression 1


title: Lesion M2-1, ROI 2358-2336

description: NanoString GeoMx


title: K562-venetoclax-1-comboRNA

description: polyA RNA


title: Foz 0w Control 3

description: Control  3


title: Foz 12w MASH 3

description: MASH progression 3


title: Lesion M2-1, ROI 4291-6024

description: NanoString GeoMx


title: Lesion M2-1, ROI 2433-2162

description: NanoString GeoMx


title: Foz 12w MASH 2

description: MASH progression 2


title: Lesion M2-1, ROI 2394-2249

description: NanoString GeoMx


title: Lesion M2-1, ROI 4229-6007

description: NanoString GeoMx


title: Foz 0w Control 2

description: Control  2


title: Lesion M2-1, ROI 4374-6064

description: NanoString GeoMx


title: K562-venetoclax-2-comboRNA

description: polyA RNA


title: K562 SF3B1 K666N-eltanexor-1-comboRNA

description: polyA RNA

value: 200nM eltanexor


title: mouse_EoE_HDM_CD4

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation for scRNA-seq were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10, hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: esophagitis

extract_protocol:
A FACSAria III cell sorter (BD) was used for live cell sorting.
Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3.1 according to manufacturer’s protocol (10X Genomics). The generated scRNA-seq libraries were sequenced using a 128 cycle (paired-end reads) with a NovaSeq 6000 (Illumina).

value: esophagitis

value: EoE

value: CD4+ cell

value: Wild-type

value: HDM


title: K562 SF3B1 K666N-eltanexor-2-comboRNA

description: polyA RNA


title: Lesion M2-1, ROI 4263-6009

description: NanoString GeoMx


title: Lesion M2-1, ROI 4346-6050

description: NanoString GeoMx


title: Foz 0w Control 1

description: Control  1


title: K562 SF3B1 K666N-DMSO-2-comboRNA

description: polyA RNA

value: Vehicle/DMSO


title: Lesion M2-1, ROI 4320-6034

description: NanoString GeoMx


title: K562-eltanexor-2-comboRNA

description: polyA RNA


title: mouse_EoE_Control_CD45_2

description: 10x Genomics

value: Control

value: CD45+ cell


title: mouse_EoE_HDM_CD45_2

description: 10x Genomics


title: Lesion M1-1, ROI 0846-5742

description: NanoString GeoMx

value: Multiple sclerosis (MS)


title: Lesion M2-1, ROI 1276-1083

description: NanoString GeoMx

value: Brain white matter


title: Lesion M2-1, ROI 1303-1059

description: NanoString GeoMx

value: Microglia


title: Lesion M2-1, ROI 1236-1099

description: NanoString GeoMx


title: mouse_EoE_Control_CD4

description: 10x Genomics


title: mouse_EoE_HDM_CD45_1

description: 10x Genomics


title: Lesion M2-1, ROI 1194-1113

description: NanoString GeoMx


title: Lesion M1-1, ROI 0631-6091

description: NanoString GeoMx


title: K562 SF3B1 K666N-DMSO-1-comboRNA

description: polyA RNA


title: K562-DMSO-1-comboRNA

description: polyA RNA


title: Lesion M1-1, ROI 0763-6380

description: NanoString GeoMx


title: Lesion M1-1, ROI 0154-6587

description: NanoString GeoMx


title: Lesion M2-1, ROI 1329-1030

description: NanoString GeoMx


title: K562-DMSO-2-comboRNA

description: polyA RNA


title: H11_18113 B3s

value: Female


title: K562-eltanexor-1-comboRNA

description: polyA RNA


title: Lesion M1-1, ROI 2301-0561

description: NanoString GeoMx


title: Lesion M2-1, ROI 1324-1047

description: NanoString GeoMx


title: Lesion M2-1, ROI 1869-4407

description: NanoString GeoMx


title: Lesion M1-1, ROI 2659-2095

description: NanoString GeoMx


title: K562 SF3B1 K666N-selinexor-3-cytoplasmic

description: cytoplasmic RNA

value: 200nM selinexor


title: Lesion M1-1, ROI 4689-0627

description: NanoString GeoMx


title: mouse_EoE_Control_CD45_1

description: 10x Genomics


title: K562 SF3B1 K666N-selinexor-2-cytoplasmic

description: cytoplasmic RNA


title: Lesion M1-1, ROI 4715-0621

description: NanoString GeoMx


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_144hpi_rep1

city: Sydney

first: Jonathan

last: Plett

address: 50 Bourke street

description: Cicer arietinum roots inoculated with Phytophthora medicaginis mycellium

data_processing:
Raw RNA-seq data from one replicate each for the 19 hpi timepoints, and a control sample were mapped to the coding genes of Phytophthora medicaginis and primary transcripts of the Cicer arietinum Desi genome (Jain et al., 2013) using CLC Genomics Workbench 10. The alignment stringency included a minimum length fraction of 0.8, minimum similarity fraction of 0.9 and maximum number of hits per read of 10 while all other parameters were set to default.
Unique gene reads were calculated using CLC Genomics Workbench 10.
Genome_build: Phytophthora medicaginis isolate 7831 genome primary transcripts  or Cicer arietinum Desi genome primary transcripts (Jain, M., Misra, G., Patel, R. K., Priya, P., Jhanwar, S., Khan, A. W., Shah, N., Singh, V. K., Garg, R., Jeena, G., Yadav, M., Kant, C., Sharma, P., Yadav, G., Bhatia, S., Tyagi, A. K. & Chattopadhyay, D. 2013. A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). The Plant Journal, 74, 715-729.)
Supplementary_files_format_and_content: One matrix table of the raw gene counts for every Phytophthora medicaginis gene and every sample (processed data_1.txt). A second matrix table of the raw gene counts for every Cicer arietinum gene and every sample (processed data_2.txt).

source_name: Cicer arietinum variety 'Sonali' and Phytophthora medicaginis isolate 7831

growth_protocol: Chickpea var. 'Sonali' seeds were surface sterilised (4% NaOCl solution for 15 min, 70% EtOH for ten minutes and sterile ddH2O rinse three times) before sowing on modified full strength Murashige and Skoog agar plates (4.4% MS; 3% CaCO3, pH 7, 1.1% bacto agar) supplemented with Gamborg’s vitamins. Seedlings were grown in controlled growth chambers with 15 h light/ 9 h dark cycle at 18˚C, 70% relative humidity and 500 μmol m-2 s-1 light intensity. Fifteen-day old seedlings were used for inoculation. P. medicaginis isolate TR7831 was maintained on V8 juice agar plates (containing 200 mL L-1 V8TM bottled juice; 3.0 g L-1 CaCO3, 15.0 g L-1 agar) supplemented with ampicillin (100 μg mL-1) at 25˚C in the dark. Prior to inoculations, P. medicaginis was passaged through the host to ensure pathogenicity, and after reisolating on V8 juice agar plates supplemented with ampicillin (100 ug mL-1), the 2rd generation of P. medicaginis was used to prepare inoculum. P. medicaginis inoculum (3rd generation) was prepared one day before inoculations by aseptically transferring mycelial agar blocks taken from the edge of an actively growing culture onto 0.5 x 0.5 mm2 sterile membranes overlaid on V8 juice agar plates.

extract_protocol:
Root samples flash frozen with liquen nitrogen; RNA was extracted using the Bioline Plant II RNA extraction kit according to the manufacturer’s guidelines.
Poly-A RNA libraries were prepared and sequenced using Illumina HiSeq platform with a 150bp paired-end configuration

treatment_protocol: Roots were inoculated with P. medicaginis mycellial agar blocks 1 cm from the root tip and harvested at 8, 16, 20, 28, 32, 36, 40, 44, 48, 60, 84, 96, 108, 120, 132 and 144 hpi.

value: Root and mycellium

value: 144 hours post inoculation

tag: diseased state

value: diseased


title: K562 SF3B1 K666N-selinexor-3-nuclear

description: nuclear RNA

value: chronic myeloid leukemia cells


title: Skin injury replicate 1

city: Clayton

first: Mikaël

last: Martino

state: Victoria

address: 15 Innovation Walk

department: Australian Regenerative Medicine Institute

institute: Monash University

description:
Processed_Endo_injured_BMS_and_healthy_Spleen_data.csv
Endo-SK1_S13_L001

data_processing:
Raw fastq files were analysed using the RNAsik pipeline (Tsyganov, K., et al., 2018, Journal of Open Source Software) using STAR aligner (Dobin, A., et al., 2013, Bioinformatics) with Mus musculus GRCm38.
Reads were quantified using featureCounts (Liao, Y., et al., 2014, Bioinformatics) producing the raw genes count matrix and various quality control metrics.
Raw counts (forward stranded reads) were then analysed with Degust web tool (Powell, D.R., et al., 2019, Zenodo) which performs normalisation using trimmed mean of M values (TMM) (Robinson, M.D. and Oshlack, A., 2010, Genome Biol) and differential gene expression analysis using limma/voom (Law, C.W., et al., 2014, Genome Biol)
Samples were batched corrected to account for variation between two different sequencing facilities across replicates. This was done within Degust by adding a covariate to the linear model for each sequencing batch which reduced the noise and improved the power of the test.
Assembly: GRCm38
Supplementary files format and content: csv, gene counts, rows represent genes and each column represents different information, starting from the chromosome, gene name, biotype, followed by read counts corresponding to the individual samples.

source_name: skin

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, #74034) according to the manufacturer’s instructions
Libraries were prepared with the Tecan/Nugen Ovation Solo Library prep kit, starting with 1 ng of input total RNA

value: skin

value: Regulatory T cells

tag: strain

value: male

value: 10 weeks

value: full thickness skin biopsy punch

value: day 7 post-injury


title: Lesion M1-1, ROI 4794-0599

description: NanoString GeoMx


title: Lesion M1-1, ROI 2071-2951

description: NanoString GeoMx


title: K562 SF3B1 K666N-selinexor-1-cytoplasmic

description: cytoplasmic RNA


title: Lesion M1-1, ROI 4768-0606

description: NanoString GeoMx


title: Lesion M1-1, ROI 4741-0613

description: NanoString GeoMx


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_132hpi_rep1

institute: Western Sydney University

value: 132 hours post inoculation


title: K562 SF3B1 K666N-selinexor-2-nuclear

description: nuclear RNA


title: Lesion M1-1, ROI 4662-0635

description: NanoString GeoMx


title: Lesion M1-1, ROI 2105-2791

description: NanoString GeoMx


title: K562 SF3B1 K666N-selinexor-1-nuclear

description: nuclear RNA


title: Lesion M1-1, ROI 3387-0933

description: NanoString GeoMx


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_120hpi_rep1

value: 120 hours post inoculation


title: Lesion M1-1, ROI 2090-2855

description: NanoString GeoMx

value: Multiple sclerosis (MS)


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_108hpi_rep1

value: 108 hours post inoculation


title: Skin injury replicate 3

description:
Processed_Endo_injured_BMS_and_healthy_Spleen_data.csv
Endo-SK3_S15_L001


title: K562-selinexor-3-cytoplasmic

description: cytoplasmic RNA


title: Lesion M1-1, ROI 2098-2824

description: NanoString GeoMx

value: Brain white matter

value: Microglia


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_96hpi_rep1

value: 96 hours post inoculation


title: Skin injury replicate 2

description:
Processed_Endo_injured_BMS_and_healthy_Spleen_data.csv
Endo-SK2_S14_L001


title: Lesion M1-1, ROI 2076-2919

description: NanoString GeoMx


title: Lesion M1-1, ROI 2084-2887

description: NanoString GeoMx


title: Lesion M1-1, ROI 1474-0497

description: NanoString GeoMx


title: K562-selinexor-2-cytoplasmic

description: cytoplasmic RNA

value: 200nM selinexor


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_84hpi_rep1

value: Root and mycellium

value: 84 hours post inoculation


title: Lesion M1-1, ROI 1442-0495

description: NanoString GeoMx


title: Lesion M1-1, ROI 1410-0492

description: NanoString GeoMx


title: Lesion M1-1, ROI 1316-0486

description: NanoString GeoMx


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_60hpi_rep1

value: 60 hours post inoculation

value: diseased


title: Lesion M1-1, ROI 1347-0489

description: NanoString GeoMx


title: K562-selinexor-2-nuclear

description: nuclear RNA

value: chronic myeloid leukemia cells


title: K562-selinexor-3-nuclear

description: nuclear RNA


title: Lesion M1-1, ROI 3749-1589

description: NanoString GeoMx


title: Lesion M1-1, ROI 1378-0491

description: NanoString GeoMx


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_48hpi_rep1

value: 48 hours post inoculation


title: Lesion M1-1, ROI 4442-2198

description: NanoString GeoMx


title: Lesion M1-1, ROI 4465-2219

description: NanoString GeoMx


title: Lesion M1-1, ROI 4486-2242

description: NanoString GeoMx


title: K562 SF3B1 K666N-DMSO-3-cytoplasmic

description: cytoplasmic RNA

value: Vehicle/DMSO


title: Lesion M1-1, ROI 4534-2287

description: NanoString GeoMx


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_40hpi_rep1

value: 40 hours post inoculation


title: Lesion M1-1, ROI 4513-2261

description: NanoString GeoMx


title: K562-selinexor-1-nuclear

description: nuclear RNA


title: Lesion M1-1, ROI 4555-2311

description: NanoString GeoMx


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_36hpi_rep1

value: 36 hours post inoculation


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_32hpi_rep1

value: 32 hours post inoculation


title: K562 SF3B1 K666N-DMSO-1-cytoplasmic

description: cytoplasmic RNA


title: No Template Control plate A

description: NanoString GeoMx


title: K562 SF3B1 K666N-DMSO-2-cytoplasmic

description: cytoplasmic RNA


title: Lesion A3-1, ROI 0863-4338

description: NanoString GeoMx


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_28hpi_rep1

value: 28 hours post inoculation

value: Onset of disease


title: K562 SF3B1 K666N-DMSO-3-nuclear

description: nuclear RNA


title: K562-selinexor-1-cytoplasmic

description: cytoplasmic RNA


title: Lesion A3-1, ROI 2419-0671

description: NanoString GeoMx

value: Multiple sclerosis (MS)


title: Lesion A3-1, ROI 2361-0764

description: NanoString GeoMx

value: Brain white matter


title: Lesion A3-1, ROI 2300-0857

description: NanoString GeoMx

value: Microglia


title: Lesion A2-1, ROI 2727-2169

description: NanoString GeoMx


title: K562 SF3B1 K666N-DMSO-2-nuclear

description: nuclear RNA


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_44hpi_rep1

value: 44 hours post inoculation


title: Lesion A2-1, ROI 0625-1130

description: NanoString GeoMx


title: Lesion A2-1, ROI 2747-2095

description: NanoString GeoMx


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_16hpi_rep1

value: 16 hours post inoculation

value: Non-diseased


title: K562 SF3B1 K666N-DMSO-1-nuclear

description: nuclear RNA


title: Lesion A2-1, ROI 0687-2032

description: NanoString GeoMx


title: K562-DMSO-3-cytoplasmic

description: cytoplasmic RNA


title: Lesion A2-1, ROI 0593-0554

description: NanoString GeoMx


title: P145_3K64_V1_Epigenetics

city: Boston

first: Ofer

last: Levy

state: MA

address: 300 Longwood Avenue

institute: Boston Children's Hospital

hyb_protocol: [not provided]

scan_protocol: [not provided]

data_processing:
Extracted DNA send to AGRF Genotyping Service
EPIC array annotation object mapping probes IDs to hg38 human reference genome (Ensembl GRCh38v98)
Quality controlled for overall sample quality based on median methylated and unmethylated signals
QC steps included checking detection P cells, raw cell distribution, sex prediction, data normalization, and checked by density and RLE plots. Relative Log Expression computed for every spot in the array as the difference between the spot intensity and the median intensity for the same feature across all the arrays. Since majority of the spots are not expected to be differentially expressed, the plot should show boxplots centered around zero and all of them having the aproximately the same dispersion. An array showing greater dispersion than the other, or being not centered at zero could have quality problems.
Probe-level QC: removed poor-performing probes, Removed unwanted SNP and non-CG methylation probes, and then extracted Final Beta and Mvals
processed data: csv; Beta = QC/QA'd Beta values, SQN normalized

label: Cy3, Cy5

source_name: Blood

label_protocol: [not provided]

extract_protocol:
Cell type: Whole blood; Extraction method:  Chemagic low volume blood kit, Bead based, Chemagic DNA 400 kit H96 (Cat# CMG-1491). ; Assay:Illumina Human Methylation EPIC v2.0. ; Extracted DNA send to AGRF Genotyping Service.
1.5ug of DNA send to AGRF for bisulphite treatment and hybridization to array

tag: geographic location

value: Papua New Guinea

value: Blood

value: Whole blood

value: Female

value: HBV


title: Lesion A2-1, ROI 0729-0211

description: NanoString GeoMx


title: Lesion A2-1, ROI 2569-1200

description: NanoString GeoMx


title: K562-DMSO-2-cytoplasmic

description: cytoplasmic RNA

tag: cell line

value: chronic myeloid leukemia cells

value: Vehicle/DMSO


title: P142_9G3A_V1_1_Epigenetics

description: Assay:Illumina Human Methylation EPIC v2.0.

value: Delayed


title: Lesion A2-1, ROI 2606-1251

description: NanoString GeoMx


title: Lesion A2-1, ROI 2588-1226

description: NanoString GeoMx


title: P141_2H1G_V2_Epigenetics

value: HBV+BCG


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_20hpi_rep1

value: Root and mycellium

value: 20 hours post inoculation


title: K562-DMSO-3-nuclear

description: nuclear RNA


title: Lesion A2-1, ROI 2624-1274

description: NanoString GeoMx

value: Multiple sclerosis (MS)


title: Lesion A2-1, ROI 3449-1820

description: NanoString GeoMx

value: Brain white matter


title: P141_5K3K_V1_Epigenetics


title: K562-DMSO-2-nuclear

description: nuclear RNA


title: K562-DMSO-1-cytoplasmic

description: cytoplasmic RNA


title: Lesion A2-1, ROI 2637-1303

description: NanoString GeoMx

value: Microglia


title: P140_9E4K_V1_Epigenetics

value: BCG


title: Lesion A2-1, ROI 3342-1651

description: NanoString GeoMx


title: K562-DMSO-1-nuclear

description: nuclear RNA


title: Cicer arietinum roots inoculated with Phytophthora medicaginis_8hpi_rep1

value: 8 hours post inoculation


title: Lesion A2-1, ROI 3427-1785

description: NanoString GeoMx


title: K562 SF3B1 K666N-selinexor-3

description: polyA RNA

value: 200nM selinexor


title: P135_9K0K_V2_Epigenetics

value: Papua New Guinea


title: P138_2A0B_V1_Epigenetics

value: Blood


title: Lesion A2-1, ROI 3404-1753

description: NanoString GeoMx


title: Lesion A2-1, ROI 3381-1722

description: NanoString GeoMx


title: Lesion A2-1, ROI 2879-1716

description: NanoString GeoMx


title: K562 SF3B1 K666N-selinexor-2

description: polyA RNA


title: P132_4E7B_V1_Epigenetics

value: Whole blood

value: Male


title: Lesion A2-1, ROI 2842-1815

description: NanoString GeoMx


title: K562-selinexor-3

description: polyA RNA


title: Lesion A2-1, ROI 2806-1913

description: NanoString GeoMx


title: K562 SF3B1 K666N-selinexor-1

description: polyA RNA


title: P128_5D9G_V2_Epigenetics

value: Female


title: Lesion A1-2, ROI 0630-0400

description: NanoString GeoMx


title: K562-selinexor-2

description: polyA RNA

value: chronic myeloid leukemia cells


title: P128_5N7G_V1_1_Epigenetics


title: Lesion A2-1, ROI 3364-1685

description: NanoString GeoMx


title: P127_7H5A_V2_Epigenetics


title: Lesion A1-1, ROI 0805-2667

description: NanoString GeoMx


title: K562-selinexor-1

description: polyA RNA


title: Lesion A2-1, ROI 2643-1342

description: NanoString GeoMx


title: P126_9J3D_V1_Epigenetics

value: HBV


title: K562 SF3B1 K666N-DMSO-3

description: polyA RNA

value: Vehicle/DMSO


title: Lesion A1-2, ROI 0481-1372

description: NanoString GeoMx


title: Lesion A1-2, ROI 0591-1458

description: NanoString GeoMx


title: P124_1G4A_V1_Epigenetics

value: Delayed


title: Lesion A1-2, ROI 0612-1568

description: NanoString GeoMx


title: Lesion A1-2, ROI 0605-1532

description: NanoString GeoMx


title: K562 SF3B1 K666N-DMSO-2

description: polyA RNA


title: Lesion A1-2, ROI 0598-1494

description: NanoString GeoMx


title: Lesion A1-2, ROI 0257-1490

description: NanoString GeoMx


title: Lesion A2-1, ROI 2793-1967

description: NanoString GeoMx


title: Lesion A2-1, ROI 2862-1766

description: NanoString GeoMx


title: P142_9G3A_V1_2_Epigenetics


title: K562-DMSO-3

description: polyA RNA


title: Lesion A1-1, ROI 1018-0495

description: NanoString GeoMx


title: P116_9M2F_V1_Epigenetics


title: Lesion A1-1, ROI 0906-2885

description: NanoString GeoMx