title: G435_TP186_HP40_B_EP6wk21

description: Library name: G435_TP186_HP40_B_EP6wk21


title: G409_TP186_GB06_B_EP6d024h1

status: Public on Sep 02 2025

type: SRA

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

country: USA

institute: Northwestern University

description: Library name: G409_TP186_GB06_B_EP6d024h1

library_source: transcriptomic

data_processing:
Raw reads were aligned to Mmul_10 using the STAR aligner (version 2.7.0e)
Assembly: Mmul_10
Supplementary files format and content: comma-seperated file containing the raw couts of all samples

molecule: polyA RNA

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
RNA was extracted from whole blood. The quality of the recovered RNA was determined using a LabChip GX (PerkinElmer) instrument.
Sequencing libraries were generating following globin depletion (KAPPA).

tag: tissue

value: Whole blood

tag: treatment

value: DNA+gp120 protein

tag: animal id

tag: timepoint

tag: vaccine route

value: Both legs, SubQ

tag: number of_challenges_to_infection


title: G408_TP186_FG06_B_EP6d024h1

description: Library name: G408_TP186_FG06_B_EP6d024h1

value: ND


title: G406_TP186_JC52_B_EP6d04h1

description: Library name: G406_TP186_JC52_B_EP6d04h1

value: Separate legs, SubQ


title: G402_TP186_GM52_B_EP6d04h1

description: Library name: G402_TP186_GM52_B_EP6d04h1


title: G400_TP186_GJ04_B_EP6d04h1

description: Library name: G400_TP186_GJ04_B_EP6d04h1


title: G424_TP186_IJ26_B_EP6d024h1

description: Library name: G424_TP186_IJ26_B_EP6d024h1


title: G398_TP186_GC03_B_EP6d04h1

description: Library name: G398_TP186_GC03_B_EP6d04h1


title: G405_TP186_JC12_B_EP6d04h1

description: Library name: G405_TP186_JC12_B_EP6d04h1


title: G393_TP186_GI46_B_EP6d04h1

description: Library name: G393_TP186_GI46_B_EP6d04h1


title: G394_TP186_IA21_B_EP6d04h1

description: Library name: G394_TP186_IA21_B_EP6d04h1


title: G396_TP186_JC25_B_EP6d04h1

description: Library name: G396_TP186_JC25_B_EP6d04h1


title: G403_TP186_GN03_B_EP6d04h1

description: Library name: G403_TP186_GN03_B_EP6d04h1


title: G401_TP186_GM41_B_EP6d04h1

description: Library name: G401_TP186_GM41_B_EP6d04h1


title: G399_TP186_GH35_B_EP6d04h1

description: Library name: G399_TP186_GH35_B_EP6d04h1


title: G397_TP186_JE99_B_EP6d04h1

description: Library name: G397_TP186_JE99_B_EP6d04h1


title: G392_TP186_GI36_B_EP6d04h1

description: Library name: G392_TP186_GI36_B_EP6d04h1


title: G395_TP186_IA36_B_EP6d04h1

description: Library name: G395_TP186_IA36_B_EP6d04h1


title: G417_TP186_JE99_B_EP6d024h1

description: Library name: G417_TP186_JE99_B_EP6d024h1


title: G414_TP186_IA21_B_EP6d024h1

description: Library name: G414_TP186_IA21_B_EP6d024h1


title: G389_TP186_GB06_B_EP6d04h1

description: Library name: G389_TP186_GB06_B_EP6d04h1


title: G391_TP186_GI29_B_EP6d04h1

description: Library name: G391_TP186_GI29_B_EP6d04h1


title: G388_TP186_FG06_B_EP6d04h1

description: Library name: G388_TP186_FG06_B_EP6d04h1


title: G390_TP186_GH90_B_EP6d04h1

description: Library name: G390_TP186_GH90_B_EP6d04h1


title: G385_TP186_JC12_B_EP6d0c

description: Library name: G385_TP186_JC12_B_EP6d0c


title: G413_TP186_GI46_B_EP6d024h1

description: Library name: G413_TP186_GI46_B_EP6d024h1


title: G386_TP186_JC52_B_EP6d01

description: Library name: G386_TP186_JC52_B_EP6d01


title: G383_TP186_GN03_B_EP6d01

description: Library name: G383_TP186_GN03_B_EP6d01


title: G382_TP186_GM52_B_EP6d01

description: Library name: G382_TP186_GM52_B_EP6d01


title: G378_TP186_GC03_B_EP6d01

description: Library name: G378_TP186_GC03_B_EP6d01


title: G379_TP186_GH35_B_EP6d01

description: Library name: G379_TP186_GH35_B_EP6d01


title: G377_TP186_JE99_B_EP6d01

description: Library name: G377_TP186_JE99_B_EP6d01


title: G384_TP186_IJ26_B_EP6d0c

description: Library name: G384_TP186_IJ26_B_EP6d0c


title: G381_TP186_GM41_B_EP6d01

description: Library name: G381_TP186_GM41_B_EP6d01


title: G404_TP186_IJ26_B_EP6d04h1_mRNA

description: Library name: G404_TP186_IJ26_B_EP6d04h1_mRNA


title: G373_TP186_GI46_B_EP6d01

description: Library name: G373_TP186_GI46_B_EP6d01


title: G374_TP186_IA21_B_EP6d01

description: Library name: G374_TP186_IA21_B_EP6d01


title: G368_TP186_FG06_B_EP6d01

description: Library name: G368_TP186_FG06_B_EP6d01


title: G369_TP186_GB06_B_EP6d02

description: Library name: G369_TP186_GB06_B_EP6d02


title: G371_TP186_GI29_B_EP6d01

description: Library name: G371_TP186_GI29_B_EP6d01


title: G372_TP186_GI36_B_EP6d01

description: Library name: G372_TP186_GI36_B_EP6d01


title: G366_TP186_IV92_B_EP6d024h1

description: Library name: G366_TP186_IV92_B_EP6d024h1


title: G387_TP186_JF94_B_EP6d01

description: Library name: G387_TP186_JF94_B_EP6d01


title: G365_TP186_IC95_B_EP6d024h1

description: Library name: G365_TP186_IC95_B_EP6d024h1


title: G364_TP186_HV65_B_EP6d024h1

description: Library name: G364_TP186_HV65_B_EP6d024h1


title: G363_TP186_HE88_B_EP6d024h1

description: Library name: G363_TP186_HE88_B_EP6d024h1


title: G362_TP186_GM62_B_EP6d024h1

description: Library name: G362_TP186_GM62_B_EP6d024h1


title: G380_TP186_GJ04_B_EP6d01_mRNA

description: Library name: G380_TP186_GJ04_B_EP6d01_mRNA


title: G359_TP186_EE71_B_EP6d024h1

description: Library name: G359_TP186_EE71_B_EP6d024h1


title: G360_TP186_GH91_B_EP6d024h1

description: Library name: G360_TP186_GH91_B_EP6d024h1


title: G376_TP186_JC25_B_EP6d01

description: Library name: G376_TP186_JC25_B_EP6d01


title: G357_TP186_IN66_B_EP6d024h1

description: Library name: G357_TP186_IN66_B_EP6d024h1


title: G375_TP186_IA36_B_EP6d01

description: Library name: G375_TP186_IA36_B_EP6d01


title: G356_TP186_HP40_B_EP6d024h1

description: Library name: G356_TP186_HP40_B_EP6d024h1


title: G355_TP186_HF57_B_EP6d024hc

description: Library name: G355_TP186_HF57_B_EP6d024hc


title: G354_TP186_GM40_B_EP6d024h1

description: Library name: G354_TP186_GM40_B_EP6d024h1


title: G358_TP186_JE14_B_EP6d024h1

description: Library name: G358_TP186_JE14_B_EP6d024h1


title: G353_TP186_GM22_B_EP6d024h1

description: Library name: G353_TP186_GM22_B_EP6d024h1


title: G370_TP186_GH90_B_EP6d01

description: Library name: G370_TP186_GH90_B_EP6d01


title: G367_TP186_JB44_B_EP6d024h1

description: Library name: G367_TP186_JB44_B_EP6d024h1


title: G352_TP186_GM16_B_EP6d024h1_mRNA

description: Library name: G352_TP186_GM16_B_EP6d024h1_mRNA


title: G350_TP186_EI94_B_EP6d024h1

description: Library name: G350_TP186_EI94_B_EP6d024h1


title: G348_TP186_JB44_B_EP6d04h1

description: Library name: G348_TP186_JB44_B_EP6d04h1


title: G351_TP186_GI26_B_EP6d024h1

description: Library name: G351_TP186_GI26_B_EP6d024h1


title: G349_TP186_EE32_B_EP6d024h1

description: Library name: G349_TP186_EE32_B_EP6d024h1


title: G347_TP186_IV92_B_EP6d04h1

description: Library name: G347_TP186_IV92_B_EP6d04h1


title: G343_TP186_GM62_B_EP6d04h1

description: Library name: G343_TP186_GM62_B_EP6d04h1


title: G344_TP186_HE88_B_EP6d04h1

description: Library name: G344_TP186_HE88_B_EP6d04h1


title: G345_TP186_HV65_B_EP6d04h1

description: Library name: G345_TP186_HV65_B_EP6d04h1


title: G346_TP186_IC95_B_EP6d04h1

description: Library name: G346_TP186_IC95_B_EP6d04h1


title: Br2720_V12J03-002_A1 (ST)

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

description: Library name: Br2720_V12J03-002_A1

data_processing:
FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline
Reads were aligned to reference genome GRCh38
Assembly: GRCh38
Supplementary files format and content: FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline with Aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, tissue_positions_list.csv, barcode, feature, and matrix files for each donor.
Library strategy: spatial transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: brain (dACC)

extract_protocol:
dACC was dissected from fresh frozen postmortem human tissue. 10 micron coronal sections were obtained by cryosectioning. Tissue was permeabilized and cDNA was synthesized to incorporate positional barcode.
Libraries were prepared using the Visium Spatial Gene Expression slides & kit according to manufacturer's instructions

value: brain (dACC)


title: G342_TP186_GK91_B_EP6d04h1

description: Library name: G342_TP186_GK91_B_EP6d04h1


title: G361_TP186_GK91_B_EP6d024h1

description: Library name: G361_TP186_GK91_B_EP6d024h1


title: G341_TP186_GH91_B_EP6d04h1

description: Library name: G341_TP186_GH91_B_EP6d04h1


title: G339_TP186_JE14_B_EP6d04h1

description: Library name: G339_TP186_JE14_B_EP6d04h1


title: G336_TP186_HF57_B_EP6d04h1

description: Library name: G336_TP186_HF57_B_EP6d04h1


title: G340_TP186_EE71_B_EP6d04h1

description: Library name: G340_TP186_EE71_B_EP6d04h1


title: G337_TP186_HP40_B_EP6d04h1

description: Library name: G337_TP186_HP40_B_EP6d04h1


title: G338_TP186_IN66_B_EP6d04h1

description: Library name: G338_TP186_IN66_B_EP6d04h1


title: G335_TP186_GM40_B_EP6d04h1

description: Library name: G335_TP186_GM40_B_EP6d04h1


title: G334_TP186_GM22_B_EP6d04h1

description: Library name: G334_TP186_GM22_B_EP6d04h1


title: G332_TP186_GI26_B_EP6d04h1

description: Library name: G332_TP186_GI26_B_EP6d04h1


title: G329_TP186_JB44_B_EP6d01

description: Library name: G329_TP186_JB44_B_EP6d01


title: G327_TP186_IC95_B_EP6d01

description: Library name: G327_TP186_IC95_B_EP6d01


title: G328_TP186_IV92_B_EP6d01

description: Library name: G328_TP186_IV92_B_EP6d01


title: G326_TP186_HV65_B_EP6d01

description: Library name: G326_TP186_HV65_B_EP6d01


title: G325_TP186_HE88_B_EP6d01

description: Library name: G325_TP186_HE88_B_EP6d01


title: G330_TP186_EE32_B_EP6d04h1

description: Library name: G330_TP186_EE32_B_EP6d04h1


title: G324_TP186_GM62_B_EP6d01

description: Library name: G324_TP186_GM62_B_EP6d01


title: G321_TP186_EE71_B_EP6d01

description: Library name: G321_TP186_EE71_B_EP6d01


title: G322_TP186_GH91_B_EP6d01

description: Library name: G322_TP186_GH91_B_EP6d01


title: G323_TP186_GK91_B_EP6d01

description: Library name: G323_TP186_GK91_B_EP6d01


title: G316_TP186_GM40_B_EP6d01

description: Library name: G316_TP186_GM40_B_EP6d01


title: G317_TP186_HF57_B_EP6d01

description: Library name: G317_TP186_HF57_B_EP6d01


title: G319_TP186_IN66_B_EP6d01_mRNA

description: Library name: G319_TP186_IN66_B_EP6d01_mRNA


title: G314_TP186_GM16_B_EP6d01

description: Library name: G314_TP186_GM16_B_EP6d01


title: G315_TP186_GM22_B_EP6d01

description: Library name: G315_TP186_GM22_B_EP6d01


title: G318_TP186_HP40_B_EP6d01

description: Library name: G318_TP186_HP40_B_EP6d01


title: G320_TP186_JE14_B_EP6d01

description: Library name: G320_TP186_JE14_B_EP6d01


title: G312_TP186_EI94_B_EP6d01

description: Library name: G312_TP186_EI94_B_EP6d01


title: G311_TP186_EE32_B_EP6d01

description: Library name: G311_TP186_EE32_B_EP6d01


title: G309_TP186_JF94_B_EP2d024h_mRNA

description: Library name: G309_TP186_JF94_B_EP2d024h_mRNA


title: G307_TP186_JF94_B_EP2d0

description: Library name: G307_TP186_JF94_B_EP2d0


title: G333_TP186_GM16_B_EP6d04h1

description: Library name: G333_TP186_GM16_B_EP6d04h1


title: G306_TP186_JF94_B_EP1wk2

description: Library name: G306_TP186_JF94_B_EP1wk2


title: G313_TP186_GI26_B_EP6d01

description: Library name: G313_TP186_GI26_B_EP6d01


title: G331_TP186_EI94_B_EP6d04h1

description: Library name: G331_TP186_EI94_B_EP6d04h1


title: G310_TP186_JF94_B_EP2wk2

description: Library name: G310_TP186_JF94_B_EP2wk2


title: G308_TP186_JF94_B_EP2d04h_2

description: Library name: G308_TP186_JF94_B_EP2d04h_2


title: G305_TP186_JF94_B_EP1d024h

description: Library name: G305_TP186_JF94_B_EP1d024h


title: G304_TP186_JF94_B_EP1d04h

description: Library name: G304_TP186_JF94_B_EP1d04h


title: G303_TP186_JF94_B_EP1d01

description: Library name: G303_TP186_JF94_B_EP1d01


title: G300_TP186_JC52_B_EP2d04h

description: Library name: G300_TP186_JC52_B_EP2d04h


title: G303_TP186_JF94_B_EP1d0

description: Library name: G303_TP186_JF94_B_EP1d0


title: G302_TP186_JC52_B_EP2wk2

description: Library name: G302_TP186_JC52_B_EP2wk2


title: G298_TP186_JC52_B_EP1wk2

description: Library name: G298_TP186_JC52_B_EP1wk2


title: G299_TP186_JC52_B_EP2d0

description: Library name: G299_TP186_JC52_B_EP2d0


title: G296_TP186_JC52_B_EP1d04h

description: Library name: G296_TP186_JC52_B_EP1d04h


title: G297_TP186_JC52_B_EP1d024h

description: Library name: G297_TP186_JC52_B_EP1d024h


title: G295_TP186_JC52_B_EP1d01

description: Library name: G295_TP186_JC52_B_EP1d01


title: G294_TP186_JC12_B_EP2wk2

description: Library name: G294_TP186_JC12_B_EP2wk2


title: G292_TP186_JC12_B_EP2d04h_mRNA

description: Library name: G292_TP186_JC12_B_EP2d04h_mRNA


title: G291_TP186_JC12_B_EP2d0

description: Library name: G291_TP186_JC12_B_EP2d0


title: G288_TP186_JC12_B_EP1d04h

description: Library name: G288_TP186_JC12_B_EP1d04h


title: G289_TP186_JC12_B_EP1d024h

description: Library name: G289_TP186_JC12_B_EP1d024h


title: G295_TP186_JC52_B_EP1d0

description: Library name: G295_TP186_JC52_B_EP1d0


title: G290_TP186_JC12_B_EP1wk2_mRNA

description: Library name: G290_TP186_JC12_B_EP1wk2_mRNA


title: G287_TP186_JC12_B_EP1d0

description: Library name: G287_TP186_JC12_B_EP1d0


title: G286_TP186_JB44_B_EP2wk2

description: Library name: G286_TP186_JB44_B_EP2wk2


title: G282_TP186_JB44_B_EP1wk2_mRNA

description: Library name: G282_TP186_JB44_B_EP1wk2_mRNA


title: G283_TP186_JB44_B_EP2d0

description: Library name: G283_TP186_JB44_B_EP2d0


title: G280_TP186_JB44_B_EP1d04h

description: Library name: G280_TP186_JB44_B_EP1d04h


title: G281_TP186_JB44_B_EP1d024h

description: Library name: G281_TP186_JB44_B_EP1d024h


title: G279_TP186_JB44_B_EP1d01

description: Library name: G279_TP186_JB44_B_EP1d01


title: G285_TP186_JB44_B_EP2d024h

description: Library name: G285_TP186_JB44_B_EP2d024h


title: G278_TP186_IV92_B_EP2wk2

description: Library name: G278_TP186_IV92_B_EP2wk2


title: G301_TP186_JC52_B_EP2d024h

description: Library name: G301_TP186_JC52_B_EP2d024h


title: G279_TP186_JB44_B_EP1d0

description: Library name: G279_TP186_JB44_B_EP1d0


title: G276_TP186_IV92_B_EP2d04h

description: Library name: G276_TP186_IV92_B_EP2d04h


title: G277_TP186_IV92_B_EP2d024h

description: Library name: G277_TP186_IV92_B_EP2d024h


title: G275_TP186_IV92_B_EP2d0

description: Library name: G275_TP186_IV92_B_EP2d0


title: G273_TP186_IV92_B_EP1d024h

description: Library name: G273_TP186_IV92_B_EP1d024h


title: G293_TP186_JC12_B_EP2d024h

description: Library name: G293_TP186_JC12_B_EP2d024h


title: G272_TP186_IV92_B_EP1d04h_mRNA

description: Library name: G272_TP186_IV92_B_EP1d04h_mRNA


title: G270_TP186_IJ26_B_EP2wk2_mRNA

description: Library name: G270_TP186_IJ26_B_EP2wk2_mRNA


title: G287_TP186_JC12_B_EP1d01

description: Library name: G287_TP186_JC12_B_EP1d01


title: G271_TP186_IV92_B_EP1d0

description: Library name: G271_TP186_IV92_B_EP1d0


title: G274_TP186_IV92_B_EP1wk2_mRNA

description: Library name: G274_TP186_IV92_B_EP1wk2_mRNA


title: G268_TP186_IJ26_B_EP2d04h

description: Library name: G268_TP186_IJ26_B_EP2d04h


title: G269_TP186_IJ26_B_EP2d024h

description: Library name: G269_TP186_IJ26_B_EP2d024h


title: G267_TP186_IJ26_B_EP2d0

description: Library name: G267_TP186_IJ26_B_EP2d0


title: G263_TP186_IJ26_B_EP1d02

description: Library name: G263_TP186_IJ26_B_EP1d02


title: G264_TP186_IJ26_B_EP1d04h

description: Library name: G264_TP186_IJ26_B_EP1d04h


title: G284_TP186_JB44_B_EP2d04h

description: Library name: G284_TP186_JB44_B_EP2d04h


title: G265_TP186_IJ26_B_EP1d024h_mRNA

description: Library name: G265_TP186_IJ26_B_EP1d024h_mRNA


title: G261_TP186_IC95_B_EP2d024h

description: Library name: G261_TP186_IC95_B_EP2d024h


title: G262_TP186_IC95_B_EP2wk2

description: Library name: G262_TP186_IC95_B_EP2wk2


title: G263_TP186_IJ26_B_EP1d0

description: Library name: G263_TP186_IJ26_B_EP1d0


title: G257_TP186_IC95_B_EP1d024h

description: Library name: G257_TP186_IC95_B_EP1d024h


title: G260_TP186_IC95_B_EP2d04h

description: Library name: G260_TP186_IC95_B_EP2d04h


title: G259_TP186_IC95_B_EP2d0

description: Library name: G259_TP186_IC95_B_EP2d0


title: G256_TP186_IC95_B_EP1d04h

description: Library name: G256_TP186_IC95_B_EP1d04h


title: G258_TP186_IC95_B_EP1wk2

description: Library name: G258_TP186_IC95_B_EP1wk2


title: G254_TP186_HV65_B_EP2wk2

description: Library name: G254_TP186_HV65_B_EP2wk2


title: G255_TP186_IC95_B_EP1d02

description: Library name: G255_TP186_IC95_B_EP1d02


title: G252_TP186_HV65_B_EP2d04h

description: Library name: G252_TP186_HV65_B_EP2d04h


title: G253_TP186_HV65_B_EP2d024h

description: Library name: G253_TP186_HV65_B_EP2d024h


title: G255_TP186_IC95_B_EP1d0

description: Library name: G255_TP186_IC95_B_EP1d0


title: G271_TP186_IV92_B_EP1d01

description: Library name: G271_TP186_IV92_B_EP1d01


title: G250_TP186_HV65_B_EP1wk2

description: Library name: G250_TP186_HV65_B_EP1wk2


title: G249_TP186_HV65_B_EP1d024h

description: Library name: G249_TP186_HV65_B_EP1d024h


title: G247_TP186_HV65_B_EP1d01

description: Library name: G247_TP186_HV65_B_EP1d01


title: G248_TP186_HV65_B_EP1d04h

description: Library name: G248_TP186_HV65_B_EP1d04h


title: G251_TP186_HV65_B_EP2d0_mRNA

description: Library name: G251_TP186_HV65_B_EP2d0_mRNA


title: G246_TP186_HE88_B_EP2wk2_mRNA

description: Library name: G246_TP186_HE88_B_EP2wk2_mRNA


title: G266_TP186_IJ26_B_EP1wk2

description: Library name: G266_TP186_IJ26_B_EP1wk2


title: G245_TP186_HE88_B_EP2d024h

description: Library name: G245_TP186_HE88_B_EP2d024h


title: G247_TP186_HV65_B_EP1d0

description: Library name: G247_TP186_HV65_B_EP1d0


title: G244_TP186_HE88_B_EP2d04h

description: Library name: G244_TP186_HE88_B_EP2d04h


title: G240_TP186_HE88_B_EP1d04h_mRNA

description: Library name: G240_TP186_HE88_B_EP1d04h_mRNA


title: G243_TP186_HE88_B_EP2d0

description: Library name: G243_TP186_HE88_B_EP2d0


title: G236_TP186_GN03_B_EP2d04h

description: Library name: G236_TP186_GN03_B_EP2d04h


title: G235_TP186_GN03_B_EP2d0

description: Library name: G235_TP186_GN03_B_EP2d0


title: G237_TP186_GN03_B_EP2d024h

description: Library name: G237_TP186_GN03_B_EP2d024h


title: G239_TP186_HE88_B_EP1d01

description: Library name: G239_TP186_HE88_B_EP1d01


title: G239_TP186_HE88_B_EP1d0

description: Library name: G239_TP186_HE88_B_EP1d0


title: G234_TP186_GN03_B_EP1wk2_mRNA

description: Library name: G234_TP186_GN03_B_EP1wk2_mRNA


title: G241_TP186_HE88_B_EP1d024h_mRNA

description: Library name: G241_TP186_HE88_B_EP1d024h_mRNA


title: G242_TP186_HE88_B_EP1wk2

description: Library name: G242_TP186_HE88_B_EP1wk2


title: G231_TP186_GN03_B_EP1d01

description: Library name: G231_TP186_GN03_B_EP1d01


title: G231_TP186_GN03_B_EP1d0_mRNA

description: Library name: G231_TP186_GN03_B_EP1d0_mRNA


title: G230_TP186_GM62_B_EP2wk2_mRNA

description: Library name: G230_TP186_GM62_B_EP2wk2_mRNA


title: G233_TP186_GN03_B_EP1d024h

description: Library name: G233_TP186_GN03_B_EP1d024h


title: G232_TP186_GN03_B_EP1d04h_mRNA

description: Library name: G232_TP186_GN03_B_EP1d04h_mRNA


title: G238_TP186_GN03_B_EP2wk2_mRNA

description: Library name: G238_TP186_GN03_B_EP2wk2_mRNA


title: G229_TP186_GM62_B_EP2d024h

description: Library name: G229_TP186_GM62_B_EP2d024h


title: G227_TP186_GM62_B_EP2d0

description: Library name: G227_TP186_GM62_B_EP2d0


title: G226_TP186_GM62_B_EP1wk2_mRNA

description: Library name: G226_TP186_GM62_B_EP1wk2_mRNA


title: G223_TP186_GM62_B_EP1d01

description: Library name: G223_TP186_GM62_B_EP1d01


title: G224_TP186_GM62_B_EP1d04h

description: Library name: G224_TP186_GM62_B_EP1d04h


title: G223_TP186_GM62_B_EP1d0

description: Library name: G223_TP186_GM62_B_EP1d0


title: G218_TP186_GM52_B_EP1wk2

description: Library name: G218_TP186_GM52_B_EP1wk2


title: G217_TP186_GM52_B_EP1d024h_mRNA

description: Library name: G217_TP186_GM52_B_EP1d024h_mRNA


title: G220_TP186_GM52_B_EP2d04h_mRNA

description: Library name: G220_TP186_GM52_B_EP2d04h_mRNA


title: G221_TP186_GM52_B_EP2d024h

description: Library name: G221_TP186_GM52_B_EP2d024h


title: G216_TP186_GM52_B_EP1d04h

description: Library name: G216_TP186_GM52_B_EP1d04h


title: G215_TP186_GM52_B_EP1d01

description: Library name: G215_TP186_GM52_B_EP1d01


title: G228_TP186_GM62_B_EP2d04h_mRNA

description: Library name: G228_TP186_GM62_B_EP2d04h_mRNA


title: G210_TP186_GM41_B_EP1wk2

description: Library name: G210_TP186_GM41_B_EP1wk2


title: G213_TP186_GM41_B_EP2d024h

description: Library name: G213_TP186_GM41_B_EP2d024h


title: G225_TP186_GM62_B_EP1d024h

description: Library name: G225_TP186_GM62_B_EP1d024h


title: G215_TP186_GM52_B_EP1d0

description: Library name: G215_TP186_GM52_B_EP1d0


title: G212_TP186_GM41_B_EP2d04h

description: Library name: G212_TP186_GM41_B_EP2d04h


title: G209_TP186_GM41_B_EP1d024h

description: Library name: G209_TP186_GM41_B_EP1d024h


title: G211_TP186_GM41_B_EP2d0

description: Library name: G211_TP186_GM41_B_EP2d0


title: G204_TP186_GK91_B_EP2d04h

description: Library name: G204_TP186_GK91_B_EP2d04h


title: G214_TP186_GM41_B_EP2wk2_mRNA

description: Library name: G214_TP186_GM41_B_EP2wk2_mRNA


title: G203_TP186_GK91_B_EP2d0

description: Library name: G203_TP186_GK91_B_EP2d0


title: G207_TP186_GM41_B_EP1d01

description: Library name: G207_TP186_GM41_B_EP1d01


title: G205_TP186_GK91_B_EP2d024h

description: Library name: G205_TP186_GK91_B_EP2d024h


title: G206_TP186_GK91_B_EP2wk2

description: Library name: G206_TP186_GK91_B_EP2wk2


title: G202_TP186_GK91_B_EP1wk2

description: Library name: G202_TP186_GK91_B_EP1wk2


title: G200_TP186_GK91_B_EP1d04h

description: Library name: G200_TP186_GK91_B_EP1d04h


title: G207_TP186_GM41_B_EP1d0

description: Library name: G207_TP186_GM41_B_EP1d0


title: G222_TP186_GM52_B_EP2wk2

description: Library name: G222_TP186_GM52_B_EP2wk2


title: G208_TP186_GM41_B_EP1d04h_mRNA

description: Library name: G208_TP186_GM41_B_EP1d04h_mRNA


title: G198_TP186_GJ04_B_EP2wk2

description: Library name: G198_TP186_GJ04_B_EP2wk2


title: G199_TP186_GK91_B_EP1d0_mRNA

description: Library name: G199_TP186_GK91_B_EP1d0_mRNA


title: G201_TP186_GK91_B_EP1d024h

description: Library name: G201_TP186_GK91_B_EP1d024h


title: G219_TP186_GM52_B_EP2d0

description: Library name: G219_TP186_GM52_B_EP2d0


title: G197_TP186_GJ04_B_EP2d024h

description: Library name: G197_TP186_GJ04_B_EP2d024h


title: G195_TP186_GJ04_B_EP2d0_mRNA

description: Library name: G195_TP186_GJ04_B_EP2d0_mRNA


title: G196_TP186_GJ04_B_EP2d04h

description: Library name: G196_TP186_GJ04_B_EP2d04h


title: G194_TP186_GJ04_B_EP1wk2_mRNA

description: Library name: G194_TP186_GJ04_B_EP1wk2_mRNA


title: G193_TP186_GJ04_B_EP1d024h

description: Library name: G193_TP186_GJ04_B_EP1d024h


title: G191_TP186_GJ04_B_EP1d01

description: Library name: G191_TP186_GJ04_B_EP1d01


title: G191_TP186_GJ04_B_EP1d0

description: Library name: G191_TP186_GJ04_B_EP1d0


title: G190_TP186_GH91_B_EP2wk2

description: Library name: G190_TP186_GH91_B_EP2wk2


title: G189_TP186_GH91_B_EP2d024h

description: Library name: G189_TP186_GH91_B_EP2d024h


title: G188_TP186_GH91_B_EP2d04h

description: Library name: G188_TP186_GH91_B_EP2d04h


title: G187_TP186_GH91_B_EP2d0

description: Library name: G187_TP186_GH91_B_EP2d0


title: G186_TP186_GH91_B_EP1wk2_mRNA

description: Library name: G186_TP186_GH91_B_EP1wk2_mRNA


title: G185_TP186_GH91_B_EP1d024h_mRNA

description: Library name: G185_TP186_GH91_B_EP1d024h_mRNA


title: G184_TP186_GH91_B_EP1d04h

description: Library name: G184_TP186_GH91_B_EP1d04h


title: G183_TP186_GH91_B_EP1d01

description: Library name: G183_TP186_GH91_B_EP1d01


title: G183_TP186_GH91_B_EP1d0

description: Library name: G183_TP186_GH91_B_EP1d0


title: G180_TP186_GH35_B_EP2d04h

description: Library name: G180_TP186_GH35_B_EP2d04h


title: G182_TP186_GH35_B_EP2wk2

description: Library name: G182_TP186_GH35_B_EP2wk2


title: G178_TP186_GH35_B_EP1wk2

description: Library name: G178_TP186_GH35_B_EP1wk2


title: G199_TP186_GK91_B_EP1d01

description: Library name: G199_TP186_GK91_B_EP1d01


title: G181_TP186_GH35_B_EP2d024h

description: Library name: G181_TP186_GH35_B_EP2d024h


title: G179_TP186_GH35_B_EP2d0

description: Library name: G179_TP186_GH35_B_EP2d0


title: G174_TP186_GC03_B_EP2wk2

description: Library name: G174_TP186_GC03_B_EP2wk2


title: G175_TP186_GH35_B_EP1d0_mRNA

description: Library name: G175_TP186_GH35_B_EP1d0_mRNA


title: G168_TP186_GC03_B_EP1d04h

description: Library name: G168_TP186_GC03_B_EP1d04h


title: G170_TP186_GC03_B_EP1wk2

description: Library name: G170_TP186_GC03_B_EP1wk2


title: G177_TP186_GH35_B_EP1d024h

description: Library name: G177_TP186_GH35_B_EP1d024h


title: G167_TP186_GC03_B_EP1d01

description: Library name: G167_TP186_GC03_B_EP1d01


title: G192_TP186_GJ04_B_EP1d04h

description: Library name: G192_TP186_GJ04_B_EP1d04h


title: G176_TP186_GH35_B_EP1d04h_mRNA

description: Library name: G176_TP186_GH35_B_EP1d04h_mRNA


title: G175_TP186_GH35_B_EP1d01

description: Library name: G175_TP186_GH35_B_EP1d01


title: G173_TP186_GC03_B_EP2d024h

description: Library name: G173_TP186_GC03_B_EP2d024h


title: G172_TP186_GC03_B_EP2d04h_mRNA

description: Library name: G172_TP186_GC03_B_EP2d04h_mRNA


title: G171_TP186_GC03_B_EP2d0

description: Library name: G171_TP186_GC03_B_EP2d0


title: G167_TP186_GC03_B_EP1d0_mRNA

description: Library name: G167_TP186_GC03_B_EP1d0_mRNA


title: G163_TP186_EE71_B_EP2d0

description: Library name: G163_TP186_EE71_B_EP2d0


title: G165_TP186_EE71_B_EP2d024h_mRNA

description: Library name: G165_TP186_EE71_B_EP2d024h_mRNA


title: G164_TP186_EE71_B_EP2d04h

description: Library name: G164_TP186_EE71_B_EP2d04h


title: G161_TP186_EE71_B_EP1d024h

description: Library name: G161_TP186_EE71_B_EP1d024h


title: G162_TP186_EE71_B_EP1wk2_mRNA

description: Library name: G162_TP186_EE71_B_EP1wk2_mRNA


title: G158_TP186_JE99_B_EP2wk2_mRNA

description: Library name: G158_TP186_JE99_B_EP2wk2_mRNA


title: G159_TP186_EE71_B_EP1d0_mRNA

description: Library name: G159_TP186_EE71_B_EP1d0_mRNA


title: G159_TP186_EE71_B_EP1d01

description: Library name: G159_TP186_EE71_B_EP1d01


title: G160_TP186_EE71_B_EP1d04h

description: Library name: G160_TP186_EE71_B_EP1d04h


title: G157_TP186_JE99_B_EP2d024h

description: Library name: G157_TP186_JE99_B_EP2d024h


title: G155_TP186_JE99_B_EP2d0

description: Library name: G155_TP186_JE99_B_EP2d0


title: G154_TP186_JE99_B_EP1wk2

description: Library name: G154_TP186_JE99_B_EP1wk2


title: G151_TP186_JE99_B_EP1d01

description: Library name: G151_TP186_JE99_B_EP1d01


title: G169_TP186_GC03_B_EP1d024h

description: Library name: G169_TP186_GC03_B_EP1d024h


title: G156_TP186_JE99_B_EP2d04h

description: Library name: G156_TP186_JE99_B_EP2d04h


title: G152_TP186_JE99_B_EP1d04h_mRNA

description: Library name: G152_TP186_JE99_B_EP1d04h_mRNA


title: G147_TP186_JE14_B_EP2d0

description: Library name: G147_TP186_JE14_B_EP2d0


title: G150_TP186_JE14_B_EP2wk2_mRNA

description: Library name: G150_TP186_JE14_B_EP2wk2_mRNA


title: G146_TP186_JE14_B_EP1wk2_mRNA

description: Library name: G146_TP186_JE14_B_EP1wk2_mRNA


title: G149_TP186_JE14_B_EP2d024h_2

description: Library name: G149_TP186_JE14_B_EP2d024h_2


title: G151_TP186_JE99_B_EP1d0

description: Library name: G151_TP186_JE99_B_EP1d0


title: G145_TP186_JE14_B_EP1d024h

description: Library name: G145_TP186_JE14_B_EP1d024h


title: G144_TP186_JE14_B_EP1d04h

description: Library name: G144_TP186_JE14_B_EP1d04h


title: G166_TP186_EE71_B_EP2wk2

description: Library name: G166_TP186_EE71_B_EP2wk2


title: G141_TP186_JC25_B_EP2d024h

description: Library name: G141_TP186_JC25_B_EP2d024h


title: G142_TP186_JC25_B_EP2wk2

description: Library name: G142_TP186_JC25_B_EP2wk2


title: G143_TP186_JE14_B_EP1d02

description: Library name: G143_TP186_JE14_B_EP1d02


title: G143_TP186_JE14_B_EP1d0

description: Library name: G143_TP186_JE14_B_EP1d0


title: G140_TP186_JC25_B_EP2d04h

description: Library name: G140_TP186_JC25_B_EP2d04h


title: G139_TP186_JC25_B_EP2d0

description: Library name: G139_TP186_JC25_B_EP2d0


title: G153_TP186_JE99_B_EP1d024h

description: Library name: G153_TP186_JE99_B_EP1d024h


title: G138_TP186_JC25_B_EP1wk2

description: Library name: G138_TP186_JC25_B_EP1wk2


title: G135_TP186_JC25_B_EP1d01

description: Library name: G135_TP186_JC25_B_EP1d01


title: G134_TP186_IN66_B_EP2d024h

description: Library name: G134_TP186_IN66_B_EP2d024h


title: G136_TP186_JC25_B_EP1d04h

description: Library name: G136_TP186_JC25_B_EP1d04h


title: G132_TP186_IN66_B_EP2d0_2

description: Library name: G132_TP186_IN66_B_EP2d0_2


title: G131_TP186_IN66_B_EP1wk2

description: Library name: G131_TP186_IN66_B_EP1wk2


title: G130_TP186_IN66_B_EP1d024h

description: Library name: G130_TP186_IN66_B_EP1d024h


title: G129_TP186_IN66_B_EP1d04h_mRNA

description: Library name: G129_TP186_IN66_B_EP1d04h_mRNA


title: G148_TP186_JE14_B_EP2d04h

description: Library name: G148_TP186_JE14_B_EP2d04h


title: G133_TP186_IN66_B_EP2d04h

description: Library name: G133_TP186_IN66_B_EP2d04h


title: G128_TP186_IN66_B_EP1d0_mRNA

description: Library name: G128_TP186_IN66_B_EP1d0_mRNA


title: G128_TP186_IN66_B_EP1d02

description: Library name: G128_TP186_IN66_B_EP1d02


title: G126_TP186_IA36_B_EP2d024h

description: Library name: G126_TP186_IA36_B_EP2d024h


title: G124_TP186_IA36_B_EP2d0_mRNA

description: Library name: G124_TP186_IA36_B_EP2d0_mRNA


title: G127_TP186_IA36_B_EP2wk2

description: Library name: G127_TP186_IA36_B_EP2wk2


title: G122_TP186_IA36_B_EP1d024h

description: Library name: G122_TP186_IA36_B_EP1d024h


title: G123_TP186_IA36_B_EP1wk2

description: Library name: G123_TP186_IA36_B_EP1wk2


title: G120_TP186_IA36_B_EP1d0

description: Library name: G120_TP186_IA36_B_EP1d0


title: G121_TP186_IA36_B_EP1d04h

description: Library name: G121_TP186_IA36_B_EP1d04h


title: G119_TP186_IA21_B_EP2wk2

description: Library name: G119_TP186_IA21_B_EP2wk2


title: G118_TP186_IA21_B_EP2d024h

description: Library name: G118_TP186_IA21_B_EP2d024h


title: G117_TP186_IA21_B_EP2d04h

description: Library name: G117_TP186_IA21_B_EP2d04h


title: G116_TP186_IA21_B_EP2d0

description: Library name: G116_TP186_IA21_B_EP2d0


title: G137_TP186_JC25_B_EP1d024h_mRNA

description: Library name: G137_TP186_JC25_B_EP1d024h_mRNA


title: G113_TP186_IA21_B_EP1d04h_mRNA

description: Library name: G113_TP186_IA21_B_EP1d04h_mRNA


title: G135_TP186_JC25_B_EP1d0_mRNA

description: Library name: G135_TP186_JC25_B_EP1d0_mRNA


title: G112_TP186_IA21_B_EP1d0

description: Library name: G112_TP186_IA21_B_EP1d0


title: G111_TP186_HP40_B_EP2wk2_mRNA

description: Library name: G111_TP186_HP40_B_EP2wk2_mRNA


title: G110_TP186_HP40_B_EP2d024h_mRNA

description: Library name: G110_TP186_HP40_B_EP2d024h_mRNA


title: G109_TP186_HP40_B_EP2d04h_mRNA

description: Library name: G109_TP186_HP40_B_EP2d04h_mRNA


title: G108_TP186_HP40_B_EP2d0

description: Library name: G108_TP186_HP40_B_EP2d0


title: G106_TP186_HP40_B_EP1d024h

description: Library name: G106_TP186_HP40_B_EP1d024h


title: G107_TP186_HP40_B_EP1wk2

description: Library name: G107_TP186_HP40_B_EP1wk2


title: G125_TP186_IA36_B_EP2d04h_mRNA

description: Library name: G125_TP186_IA36_B_EP2d04h_mRNA


title: G104_TP186_HP40_B_EP1d0_mRNA

description: Library name: G104_TP186_HP40_B_EP1d0_mRNA


title: G105_TP186_HP40_B_EP1d04h

description: Library name: G105_TP186_HP40_B_EP1d04h


title: G103_TP186_HF57_B_EP2wk2

description: Library name: G103_TP186_HF57_B_EP2wk2


title: G120_TP186_IA36_B_EP1d01

description: Library name: G120_TP186_IA36_B_EP1d01


title: G101_TP186_HF57_B_EP2d04h

description: Library name: G101_TP186_HF57_B_EP2d04h


title: G100_TP186_HF57_B_EP2d0

description: Library name: G100_TP186_HF57_B_EP2d0


title: G099_TP186_HF57_B_EP1wk2_mRNA

description: Library name: G099_TP186_HF57_B_EP1wk2_mRNA


title: G098_TP186_HF57_B_EP1d024h

description: Library name: G098_TP186_HF57_B_EP1d024h


title: G096_TP186_HF57_B_EP1d01

description: Library name: G096_TP186_HF57_B_EP1d01


title: G097_TP186_HF57_B_EP1d04h

description: Library name: G097_TP186_HF57_B_EP1d04h


title: G115_TP186_IA21_B_EP1wk2

description: Library name: G115_TP186_IA21_B_EP1wk2


title: G114_TP186_IA21_B_EP1d024h

description: Library name: G114_TP186_IA21_B_EP1d024h


title: G112_TP186_IA21_B_EP1d02

description: Library name: G112_TP186_IA21_B_EP1d02


title: G096_TP186_HF57_B_EP1d0

description: Library name: G096_TP186_HF57_B_EP1d0


title: G095_TP186_GM40_B_EP2wk2_mRNA

description: Library name: G095_TP186_GM40_B_EP2wk2_mRNA


title: G094_TP186_GM40_B_EP2d024h

description: Library name: G094_TP186_GM40_B_EP2d024h


title: G092_TP186_GM40_B_EP2d0

description: Library name: G092_TP186_GM40_B_EP2d0


title: G093_TP186_GM40_B_EP2d04h

description: Library name: G093_TP186_GM40_B_EP2d04h


title: G091_TP186_GM40_B_EP1wk2

description: Library name: G091_TP186_GM40_B_EP1wk2


title: G090_TP186_GM40_B_EP1d024h

description: Library name: G090_TP186_GM40_B_EP1d024h


title: G104_TP186_HP40_B_EP1d01

description: Library name: G104_TP186_HP40_B_EP1d01


title: G088_TP186_GM40_B_EP1d0

description: Library name: G088_TP186_GM40_B_EP1d0


title: G102_TP186_HF57_B_EP2d024h

description: Library name: G102_TP186_HF57_B_EP2d024h


title: G081_TP186_GM22_B_EP1d04h

description: Library name: G081_TP186_GM22_B_EP1d04h


title: G084_TP186_GM22_B_EP2d0

description: Library name: G084_TP186_GM22_B_EP2d0


title: G080_TP186_GM22_B_EP1d0

description: Library name: G080_TP186_GM22_B_EP1d0


title: G075_TP186_GM16_B_EP1wk2

description: Library name: G075_TP186_GM16_B_EP1wk2


title: G086_TP186_GM22_B_EP2d024h

description: Library name: G086_TP186_GM22_B_EP2d024h


title: G083_TP186_GM22_B_EP1wk2_mRNA

description: Library name: G083_TP186_GM22_B_EP1wk2_mRNA


title: G076_TP186_GM16_B_EP2d0

description: Library name: G076_TP186_GM16_B_EP2d0


title: G080_TP186_GM22_B_EP1d01

description: Library name: G080_TP186_GM22_B_EP1d01


title: G073_TP186_GM16_B_EP1d04h_mRNA

description: Library name: G073_TP186_GM16_B_EP1d04h_mRNA


title: G070_TP186_GI46_B_EP2d024h

description: Library name: G070_TP186_GI46_B_EP2d024h


title: G072_TP186_GM16_B_EP1d0

description: Library name: G072_TP186_GM16_B_EP1d0


title: G069_TP186_GI46_B_EP2d04h_mRNA

description: Library name: G069_TP186_GI46_B_EP2d04h_mRNA


title: G085_TP186_GM22_B_EP2d04h

description: Library name: G085_TP186_GM22_B_EP2d04h


title: G079_TP186_GM16_B_EP2wk2_mRNA

description: Library name: G079_TP186_GM16_B_EP2wk2_mRNA


title: G082_TP186_GM22_B_EP1d024h

description: Library name: G082_TP186_GM22_B_EP1d024h


title: G074_TP186_GM16_B_EP1d024h

description: Library name: G074_TP186_GM16_B_EP1d024h


title: G068_TP186_GI46_B_EP2d0

description: Library name: G068_TP186_GI46_B_EP2d0


title: G072_TP186_GM16_B_EP1d01

description: Library name: G072_TP186_GM16_B_EP1d01


title: G089_TP186_GM40_B_EP1d04h

description: Library name: G089_TP186_GM40_B_EP1d04h


title: G088_TP186_GM40_B_EP1d01

description: Library name: G088_TP186_GM40_B_EP1d01


title: G064_TP186_GI46_B_EP1d0

description: Library name: G064_TP186_GI46_B_EP1d0


title: G066_TP186_GI46_B_EP1d024h_mRNA

description: Library name: G066_TP186_GI46_B_EP1d024h_mRNA


title: G064_TP186_GI46_B_EP1d01

description: Library name: G064_TP186_GI46_B_EP1d01


title: G065_TP186_GI46_B_EP1d04h

description: Library name: G065_TP186_GI46_B_EP1d04h


title: G067_TP186_GI46_B_EP1wk2

description: Library name: G067_TP186_GI46_B_EP1wk2


title: G087_TP186_GM22_B_EP2wk2

description: Library name: G087_TP186_GM22_B_EP2wk2


title: G078_TP186_GM16_B_EP2d024h

description: Library name: G078_TP186_GM16_B_EP2d024h


title: G077_TP186_GM16_B_EP2d04h

description: Library name: G077_TP186_GM16_B_EP2d04h


title: G071_TP186_GI46_B_EP2wk2

description: Library name: G071_TP186_GI46_B_EP2wk2


title: G063_TP186_GI36_B_EP2wk2

description: Library name: G063_TP186_GI36_B_EP2wk2


title: G059_TP186_GI36_B_EP1wk2

description: Library name: G059_TP186_GI36_B_EP1wk2


title: G058_TP186_GI36_B_EP1d024h

description: Library name: G058_TP186_GI36_B_EP1d024h


title: G054_TP186_GI29_B_EP2d024h

description: Library name: G054_TP186_GI29_B_EP2d024h


title: G051_TP186_GI29_B_EP1wk2

description: Library name: G051_TP186_GI29_B_EP1wk2


title: G060_TP186_GI36_B_EP2d0

description: Library name: G060_TP186_GI36_B_EP2d0


title: G061_TP186_GI36_B_EP2d04h

description: Library name: G061_TP186_GI36_B_EP2d04h


title: G050_TP186_GI29_B_EP1d024h

description: Library name: G050_TP186_GI29_B_EP1d024h


title: G052_TP186_GI29_B_EP2d0

description: Library name: G052_TP186_GI29_B_EP2d0


title: G057_TP186_GI36_B_EP1d04h

description: Library name: G057_TP186_GI36_B_EP1d04h


title: G056_TP186_GI36_B_EP1d0_mRNA

description: Library name: G056_TP186_GI36_B_EP1d0_mRNA


title: G056_TP186_GI36_B_EP1d02

description: Library name: G056_TP186_GI36_B_EP1d02


title: G055_TP186_GI29_B_EP2wk2

description: Library name: G055_TP186_GI29_B_EP2wk2


title: G053_TP186_GI29_B_EP2d04h

description: Library name: G053_TP186_GI29_B_EP2d04h


title: G046_TP186_GI26_B_EP2d024h

description: Library name: G046_TP186_GI26_B_EP2d024h


title: G045_TP186_GI26_B_EP2d04h_mRNA

description: Library name: G045_TP186_GI26_B_EP2d04h_mRNA


title: G043_TP186_GI26_B_EP1wk2_mRNA

description: Library name: G043_TP186_GI26_B_EP1wk2_mRNA


title: G048_TP186_GI29_B_EP1d01

description: Library name: G048_TP186_GI29_B_EP1d01


title: G048_TP186_GI29_B_EP1d0

description: Library name: G048_TP186_GI29_B_EP1d0


title: G040_TP186_GI26_B_EP1d01

description: Library name: G040_TP186_GI26_B_EP1d01


title: G042_TP186_GI26_B_EP1d024h

description: Library name: G042_TP186_GI26_B_EP1d024h


title: G047_TP186_GI26_B_EP2wk2

description: Library name: G047_TP186_GI26_B_EP2wk2


title: G044_TP186_GI26_B_EP2d0

description: Library name: G044_TP186_GI26_B_EP2d0


title: G041_TP186_GI26_B_EP1d04h

description: Library name: G041_TP186_GI26_B_EP1d04h


title: G040_TP186_GI26_B_EP1d0_mRNA

description: Library name: G040_TP186_GI26_B_EP1d0_mRNA


title: G038_TP186_GH90_B_EP2d024h

description: Library name: G038_TP186_GH90_B_EP2d024h


title: G039_TP186_GH90_B_EP2wk2

description: Library name: G039_TP186_GH90_B_EP2wk2


title: G037_TP186_GH90_B_EP2d04h

description: Library name: G037_TP186_GH90_B_EP2d04h


title: G062_TP186_GI36_B_EP2d024h

description: Library name: G062_TP186_GI36_B_EP2d024h


title: G036_TP186_GH90_B_EP2d0

description: Library name: G036_TP186_GH90_B_EP2d0


title: G035_TP186_GH90_B_EP1wk2

description: Library name: G035_TP186_GH90_B_EP1wk2


title: G033_TP186_GH90_B_EP1d04h

description: Library name: G033_TP186_GH90_B_EP1d04h


title: G031_TP186_GB06_B_EP2wk2

description: Library name: G031_TP186_GB06_B_EP2wk2


title: G032_TP186_GH90_B_EP1d01

description: Library name: G032_TP186_GH90_B_EP1d01


title: G028_TP186_GB06_B_EP2d0

description: Library name: G028_TP186_GB06_B_EP2d0


title: G034_TP186_GH90_B_EP1d024h_mRNA

description: Library name: G034_TP186_GH90_B_EP1d024h_mRNA


title: G032_TP186_GH90_B_EP1d0

description: Library name: G032_TP186_GH90_B_EP1d0


title: G027_TP186_GB06_B_EP1wk2

description: Library name: G027_TP186_GB06_B_EP1wk2


title: G025_TP186_GB06_B_EP1d01

description: Library name: G025_TP186_GB06_B_EP1d01


title: G029_TP186_GB06_B_EP2d04h

description: Library name: G029_TP186_GB06_B_EP2d04h


title: G023_TP186_FG06_B_EP2d024h

description: Library name: G023_TP186_FG06_B_EP2d024h


title: G024_TP186_FG06_B_EP2wk2_mRNA

description: Library name: G024_TP186_FG06_B_EP2wk2_mRNA


title: G026_TP186_GB06_B_EP1d024h_mRNA

description: Library name: G026_TP186_GB06_B_EP1d024h_mRNA


title: G030_TP186_GB06_B_EP2d024h

description: Library name: G030_TP186_GB06_B_EP2d024h


title: G022_TP186_FG06_B_EP2d04h

description: Library name: G022_TP186_FG06_B_EP2d04h


title: G021_TP186_FG06_B_EP2d0

description: Library name: G021_TP186_FG06_B_EP2d0


title: G025_TP186_GB06_B_EP1d0_mRNA

description: Library name: G025_TP186_GB06_B_EP1d0_mRNA


title: G020_TP186_FG06_B_EP1wk2

description: Library name: G020_TP186_FG06_B_EP1wk2


title: G019_TP186_FG06_B_EP1d024h

description: Library name: G019_TP186_FG06_B_EP1d024h


title: G018_TP186_FG06_B_EP1d04h_mRNA

description: Library name: G018_TP186_FG06_B_EP1d04h_mRNA


title: G016_TP186_EI94_B_EP2wk2

description: Library name: G016_TP186_EI94_B_EP2wk2


title: G017_TP186_FG06_B_EP1d01

description: Library name: G017_TP186_FG06_B_EP1d01


title: G015_TP186_EI94_B_EP2d024h

description: Library name: G015_TP186_EI94_B_EP2d024h


title: G014_TP186_EI94_B_EP2d04h

description: Library name: G014_TP186_EI94_B_EP2d04h


title: G013_TP186_EI94_B_EP2d0

description: Library name: G013_TP186_EI94_B_EP2d0


title: G049_TP186_GI29_B_EP1d04h_mRNA

description: Library name: G049_TP186_GI29_B_EP1d04h_mRNA


title: G012_TP186_EI94_B_EP1wk2

description: Library name: G012_TP186_EI94_B_EP1wk2


title: G011_TP186_EI94_B_EP1d024h_mRNA

description: Library name: G011_TP186_EI94_B_EP1d024h_mRNA


title: G009_TP186_EI94_B_EP1d01

description: Library name: G009_TP186_EI94_B_EP1d01


title: G010_TP186_EI94_B_EP1d04h_mRNA_2

description: Library name: G010_TP186_EI94_B_EP1d04h_mRNA_2


title: G008_TP186_EE32_B_EP2wk2_mRNA_2

description: Library name: G008_TP186_EE32_B_EP2wk2_mRNA_2


title: G006_TP186_EE32_B_EP2d04h

description: Library name: G006_TP186_EE32_B_EP2d04h


title: G005_TP186_EE32_B_EP2d0

description: Library name: G005_TP186_EE32_B_EP2d0


title: G003_TP186_EE32_B_EP1d024h

description: Library name: G003_TP186_EE32_B_EP1d024h


title: G004_TP186_EE32_B_EP1wk2

description: Library name: G004_TP186_EE32_B_EP1wk2


title: G002_TP186_EE32_B_EP1d04h

description: Library name: G002_TP186_EE32_B_EP1d04h


title: G017_TP186_FG06_B_EP1d0

description: Library name: G017_TP186_FG06_B_EP1d0


title: Br6423-7c_dACC (snRNA-seq)

description: Library name: 7c_dACC

library_source: transcriptomic single cell

data_processing:
FASTQ files were pre-processed with the 10x CellRanger pipeline
Reads were aligned to reference genome GRCh38
Assembly: GRCh38
Supplementary files format and content: Raw FASTQ files and data processed with the 10x CellRanger pipeline with barcode, feature, and matrix files for each donor.

extract_protocol:
dACC was dissected from fresh frozen postmortem human tissue. 100 micron coronal sections of dACC from fresh frozen postmortem human tissue were obtained by cryosectioning. Nuclei were isolated and barcoded with 10x Genomics Chromium.
Libraries were prepared using 10x Chromium Next GEM Single Cell 3’ v3.1 (dual-index) kit according to manufacturer's instructions.


title: G001_TP186_EE32_B_EP1d0

description: Library name: G001_TP186_EE32_B_EP1d0


title: Br3942-6c_dACC (snRNA-seq)

description: Library name: 6c_dACC


title: Br6471-3c_dACC (snRNA-seq)

description: Library name: 3c_dACC


title: Br6522-4c_dACC (snRNA-seq)

description: Library name: 4c_dACC


title: Br6432-2c_dACC (snRNA-seq)

description: Library name: 2c_dACC


title: Br2743-5c_dACC (snRNA-seq)

description: Library name: 5c_dACC


title: Br2720-1c_dACC (snRNA-seq)

description: Library name: 1c_dACC


title: U87MG_8Aza_rep1

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

description: Library name: Sample9

data_processing:
Reads were quality-checked by FastQC. Transcript quantification was performed using kallisto58  and the human hg38 (GRCh38.111) reference coding transcriptome (kallisto compatible indexes and quantifications were generated with the kallisto index and kallisto quant functions, respectively).
Transcript-level quantifications were collapsed into gene quantifications using the R package tximport and an RNA transcript to gene mapping table containing mappings for all protein-coding genes. A normalized count matrix (transcripts per million, TPM) was subsequently produced.
Assembly: GRCh38
Supplementary files format and content: tab-separated text file with TPM and log normalized count matrix

source_name: Brain tumor

growth_protocol: LN18, LN215, LN229, LN382 and U87MG human glioblastoma cell lines were kindly provided by Dr. Monika Hegi, CHUV Hospital Lausanne, and cultured in DMEM containing 10% fetal bovine serum (FBS, Gibco) and 1% penicillin/streptomycin (Gibco) in a cell incubator at 37ºC and 5% CO2.

extract_protocol:
Cells were harvested and RNA was purified from pellets of 1-2x106 cells using RNAEast MiniKit (Qiagen) following manufacturer instructions. RNAs were quantified using a NanoDrop spectrophotometer (Thermo Fisher) and quality-checked on a Fragment Analyzer (Agilent Technologies). All samples had a RIN >= 8 and 260/280 and 260/230 ratios of approximately 2.
RNA-Seq libraries were prepared from 250ng of total RNA with the Illumina Stranded mRNA Prep Kit (Illumina), using a dual indexing strategy and following the manufacturer’s protocol automated by a Sciclone liquid handling robot (PerkinElmer). Libraries were quantified using a Qubit fluorometer (Thermo Fisher) and quality checked in a Fragment Analyzer (Agilent Technologies). Single-end 100 base-pair (1x100) sequencing of the libraries was performed using a NovaSeq 6000 sequencer (Illumina). Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software version 2.20 (Illumina). RNA quality check, library preparation and sequencing were performed at the Lausanne Genomic Technologies Facility (GTF), UNIL, Switzerland.

treatment_protocol: LN18, LN215, LN229, LN382 and U87MG human glioblastoma cell lines were treated with 2μM 8-Azaadenosine or vehicle control for 72h.

value: Brain tumor

tag: cell type

value: Glioblastoma

tag: cell line

tag: replicate


title: LN382_Veh_rep1

description: Library name: Sample8

value: Vehicle


title: LN382_8Aza_rep1

description: Library name: Sample7


title: U87MG_Veh_rep1

description: Library name: Sample10


title: LN215_Veh_rep1

description: Library name: Sample4


title: LN229_Veh_rep1

description: Library name: Sample6


title: LN229_8Aza_rep1

description: Library name: Sample5


title: LN18_Veh_rep1

description: Library name: Sample2


title: LN18_8Aza_rep1

description: Library name: Sample1


title: G009_TP186_EI94_B_EP1d0

description: Library name: G009_TP186_EI94_B_EP1d0


title: G007_TP186_EE32_B_EP2d024h_mRNA

description: Library name: G007_TP186_EE32_B_EP2d024h_mRNA


title: UCMSC03

city: Klong Luang

first: Pornprapa

last: Srimorkun

state: Pathumthani

country: Thailand

institute: Thammasat University

description:
Library name: Sample 7
Column name in raw_counts_all_Samples.txt : UCMSC03

data_processing:
Illumina CASAVA v1.8 was used for base-calling
Sequencing reads were trimmed for adaptor sequence. Uncertain nucleotides constitute more than 10 percent of either read and low-quality sequences were removed
Trimmed sequence reads were mapped to GRCh38 human reference genome using HISAT2 v 2.0.5
Sequencing reads fell onto each trasncripts were counted using featureCounts v 1.5.0-p3 and normalized abundance measurements by fragment per kilibase per million reads (FPKM)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes gene ID, raw counts, gene name, chromosome, start position, end position, strand, and length for each Sample
Supplementary files format and content: csv files includes gene ID, FPKM values, gene name, chromosome, start position, end position, strand, and length for each Sample

source_name: umbilical cord tissue

growth_protocol: Human mesenchymal stromal cells were seeded in 6-well plate and maintained in alpha-MEM supplemented with 10% Fetal bovine serum (FBS) and glutaMAX until reaching 80% cell confluent.

extract_protocol:
Using RNeasy mini kit (QIAGEN). Cells were directly lyzed within the vessel and homogenized by pipetting several times.
Libraries were constructed according to NEBNext® Ultra™ RNA library prep kit for Illumina®

treatment_protocol: Human mesenchymal stromal cells were ovelayered with umbilical cord blood-derived CD34+ cells

value: umbilical cord tissue

value: primary human cell

value: mesenchymal stromal cells

tag: genotype

value: WT

value: culture in medium alone


title: G001_TP186_EE32_B_EP1d01

description: Library name: G001_TP186_EE32_B_EP1d01


title: UCMSC04

description:
Library name: Sample 8
Column name in raw_counts_all_Samples.txt : UCMSC04


title: UCMSC02

description:
Library name: Sample 6
Column name in raw_counts_all_Samples.txt : UCMSC02


title: UCMSC01

description:
Library name: Sample 5
Column name in raw_counts_all_Samples.txt : UCMSC01


title: UCMSC03_CD34

description:
Library name: Sample 3
Column name in raw_counts_all_Samples.txt : UCMSC03_CD34

value: co-culture with UCB-CD34+ cells


title: UCMSC01_CD34

description:
Library name: Sample 1
Column name in raw_counts_all_Samples.txt : UCMSC01_CD34


title: UCMSC02_CD34

description:
Library name: Sample 2
Column name in raw_counts_all_Samples.txt : UCMSC02_CD34


title: Fetal Testis, XY, Leuprolide, EH4438

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description: Library name: Leuprolide_EH4438

data_processing:
Quality control and preprocessing of data were performed by SciLicium (Rennes, France).
The first read contains 16 bases that must have a quality score higher than 10. The first 6 bp correspond to a unique sample-specific barcode and the following 10 bp to a unique molecular identifier (UMI).
The second reads were aligned to the human reference transcriptome from the UCSC website (release hg38) using BWA version 0.7.4.4 with the parameter “−l 24”
Assembly: hg38
Supplementary files format and content: Expression file and nomalized expression file are procided in tsv (tabulation-separated values) format. They contain for each sample (columns, named with the library name), the (nomalized) number of unique umis (unique molecular identifier) associated with the 28,307 genes detected.

source_name: Testis

growth_protocol: Pairs of testes from N=10 individuals aged 5-6 PCW were collected, dissected free of mesonephros and cut into two explants each. For each experimental condition, the two explants from one testis were used and cultured under a petri dish lid in agreement with a previously established hanging drop culture model of human fetal tissue explants (Melau et al., 2021 ), with minor modifications. Briefly, each testicular explant was put in a 35 µL a drop of M199 medium, no phenol red (Invitrogen Life Technologies), containing 50 μg/mL gentamycin and 2.5 μg/mL amphotericin B (Fungizone, Sigma Aldrich Chemicals).

extract_protocol:
Total RNAs were extracted from cultured explants or uncultured tissues using the RNeasy Mini Kit (Qiagen) and quantified using a NanoDropTM 8000 spectrophotometer (Thermo Fisher Scientific).
The sequencing libraries were built by tagmentation using 50 ng of ds cDNA with the Illumina Nextera XT Kit (Illumina, #FC-131-1024) following the manufacturer’s recommendations.

treatment_protocol: Exposures consisted in the addition of 0.04 % v/v dimethyl sulfoxide (DMSO) for controls, or of Leuprolide 20 ng/mL (L0399-1MG, Sigma-Aldrich Chemicals) together with 0.04 % v/v DMSO for treated samples. Explants were cultured in a humidified petri dish for 24 hours at 37°C, 5% CO2. At the end of the cultures, explants were collected, rinsed in PBS and stored at -80°C.

value: Testis

tag: batch

tag: developmental stage

value: Fetal

tag: age

value: 6 PCW

tag: Sex

value: male

value: Leuprolide


title: primary human hepatocyte, 211, rep1

city: Shanghai

first: Xinyang

last: Jia

address: haike street 501

country: China

institute: Shanghai Institute of Materia Medica

description: Library name: Sample2

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: liver

extract_protocol:
Cell suspensions (300-600 living cells per microliter determined by Count Star) were loaded on a Chromium Single Cell Controller (10× Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 3 Library and Gel Bead Kit V2 (10× Genomics, 120237) and Chromium Single Cell A Chip Kit (10× Genomics, 120236) according to the manufacturer’s protocol. Briefly, single cells were suspended in 0.04 % BSA-PBS. About 8,700 cells were added to each channel with a targeted cell recovery estimate of 5,000 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. GEMs were reverse transcribed in a C1000 Touch Thermal Cycler (Bio Rad) programed at 53 °C for 45 min, 85 °C for 5 min, and hold at 4 °C. After reverse transcription, single-cell droplets were broken and the single-strand cDNA was isolated and cleaned with Cleanup Mix containing DynaBeads (Thermo Fisher Scientific). cDNA was generated and amplified, and quality was assessed using the Agilent 4200.
After the expansion of the material passes quality inspection, the construction of a sequencing library is carried out. First, cDNA is fragmented into fragments of about 200-300 base pairs (bp) using chemical methods. The cDNA fragments are then subjected to end repair and adenylation, followed by cDNA fragment selection. P7 Adapters are ligated to connect the fragments, and PCR amplification is used to introduce sample indices. Finally, fragment selection is performed to obtain the cDNA library. After the library is completed and passes quality inspection, sequencing is carried out using the Illumina NovaSeq sequencing platform to obtain sequencing data, which is then followed by subsequent data analysis. Illumina basecall files (*.bcl) were converted to fastqs using the Cell Ranger pipeline with recommended parameters.

value: liver

value: primary human hepatocyte


title: primary human hepatocyte, 409, rep1

description: Library name: Sample5


title: primary human hepatocyte, 330, rep1

description: Library name: Sample4


title: primary human hepatocyte, 025, rep1

description: Library name: Sample1


title: Fetal Testis, XY, Leuprolide, EH4497

description: Library name: Leuprolide_EH4497


title: Fetal Testis, XY, Leuprolide, EH4436

description: Library name: Leuprolide_EH4436


title: Fetal Testis, XY, Leuprolide, EH4410

description: Library name: Leuprolide_EH4410


title: Fetal Testis, XY, Leuprolide, EH4344

description: Library name: Leuprolide_EH4344


title: Fetal Testis, XY, Leuprolide, EH4363

description: Library name: Leuprolide_EH4363


title: LN215_8Aza_rep1

description: Library name: Sample3


title: Fetal Testis, XY, Leuprolide, EH4365

description: Library name: Leuprolide_EH4365


title: Fetal Testis, XY, Leuprolide, EH3906

description: Library name: Leuprolide_EH3906


title: Fetal Testis, XY, Leuprolide, EH3959

description: Library name: Leuprolide_EH3959

value: 5 PCW


title: Fetal Testis, XY, Leuprolide, EH3880

description: Library name: Leuprolide_EH3880


title: Fetal Testis, XY, DMSO, EH4497

description: Library name: DMSO_EH4497

value: DMSO


title: Fetal Testis, XY, DMSO, EH4436

description: Library name: DMSO_EH4436


title: Fetal Testis, XY, DMSO, EH4438

description: Library name: DMSO_EH4438


title: Fetal Testis, XY, DMSO, EH4410

description: Library name: DMSO_EH4410


title: Fetal Testis, XY, DMSO, EH3959

description: Library name: DMSO_EH3959


title: Fetal Testis, XY, DMSO, EH4365

description: Library name: DMSO_EH4365


title: Fetal Testis, XY, DMSO, EH4363

description: Library name: DMSO_EH4363


title: Fetal Testis, XY, DMSO, EH4344

description: Library name: DMSO_EH4344


title: UCMSC04_CD34

description:
Library name: Sample 4
Column name in raw_counts_all_Samples.txt : UCMSC04_CD34


title: Fetal Testis, XY, DMSO, EH3906

description: Library name: DMSO_EH3906


title: primary human hepatocyte, 789, rep1

description: Library name: Sample3


title: Fetal Testis, XY, DMSO, EH3880

description: Library name: DMSO_EH3880


title: primary human hepatocyte, 416, rep1

description: Library name: Sample6


title: SMS-CTR, MTX (48 h), rep1

city: New York

first: Lydia

last: Finley

state: NY

address: 430 E 67th St

department: Cell Biology Program

institute: Memorial Sloan Kettering Cancer Center

description: Library name: SMSCTR_MTX_1

data_processing:
FASTQ files were aligned to the reference genome using DRAGEN v3.10 (Illumina) to generate BAM files.
Raw counts matrix was generated using featureCounts/subread.
Assembly: hg38
Supplementary files format and content: Processed data files include raw counts for each sample in CSV format.

source_name: SMS-CTR

growth_protocol: Rhabdomyosarcoma cell lines were maintained in DMEM with 10% fetal bovine serum. This medium was also used for experiments.

extract_protocol:
RNA was isolated using TRIzol (Thermo Fisher Scientific, 15596018) according to the manufacturer’s instructions.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 9.3-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR.

treatment_protocol: Cells were treated with vehicle control (DMSO) or methotrexate (0.2 uM, Sigma-Aldrich) for 48 hours.

value: SMS-CTR

value: methotrexate


title: SMS-CTR, vehicle (DMSO, 48 h), rep2

description: Library name: SMSCTR_vehicle_2

value: vehicle


title: Renal cortex, Prdm16 ko, mouse3

city: Wuhan

first: Yuting

last: Zhu

state: Hubei

address: 1277 Jiefang Avenue

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Library name: Sample 6

data_processing:
The BD Rhapsody WTA Analysis Pipeline (version 1.8) was used to create sequencing libraries from single cell transcriptomes without specifying a targeted panel. After sequencing, the analysis pipeline takes the FASTQ files, a reference genome file (mouse:mm10) and a transcriptome annotation file (mouse:GENCODE vM23/Ensembl 98) for sequence alignment. The pipeline generates a unique molecular identifier (UMI) count matrix which will be processed using python package Scanpy (version 1.8) for further analysis.
Assembly: Mouse mm10
Assembly: GENCODE vM23/Ensembl 98
Supplementary files format and content: Tab-separated values files and  matrix files

organism: Mus musculus

source_name: Renal cortex

extract_protocol:
Fresh renal cortex tissues were excised and stored in MACS Tissue Storage Solution before further processing. The samples were washed with PBS and minced into small fragments of approximately 1mm³ while maintained on ice. Subsequently, the minced samples underwent enzymatic digestion utilizing a combination of Collagenase I, Collagenase II, Hyaluronidase, Liberase and DNase I for 90 minutes at 37°C with stirring. Following digestion, the samples were filtered through 100 µm and 40 µm cell strainers and centrifuged at 300 g for 5 minutes. After removing the supernatant, the resulting cell pellets were resuspended in red blood cell lysis buffer to facilitate the lysis of red blood cells. Finally, the cell pellets were washed with Dulbecco's phosphate-buffered saline containing sample buffer, and then resuspended, stained and counted in the same buffer.
The BD Rhapsody system was utilized to capture the transcriptomic information of the single cells derived from renal cortex. Single-cell capture was achieved through the random distribution of a suspension containing single cells into over 200,000 microwells via a limited dilution method. Beads embedded with oligonucleotide barcodes were added to saturation, ensuring that each bead in the microwell was paired with a single cell. The cells underwent lysis within the microwell, allowing for the hybridization of mRNA to the barcoded capture oligos present on the beads. Subsequently, the beads were collected into a single tube for the processes of reverse transcription and ExoI digestion. During the synthesis of cDNA, each cDNA molecule was labeled at the 5’ end (corresponding to the 3’ end of its mRNA transcript) with a unique molecular identifier (UMI) and a barcode designating the cell origin of it. Whole transcriptome libraries were constructed by employing the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow, which includes random priming and extension (RPE), RPE amplification PCR, and WTA index PCR. The libraries underwent quantification using a High Sensitivity D1000 ScreenTape along with High Sensitivity D1000 Reagents on a 4150 TapeStation System and assessed via the Qubit High Sensitivity DNA assay. Sequencing was carried out using an Illumina sequencer in a paired-end run of 150 bp.

value: Renal cortex

value: Prdm16 global knockout


title: SMS-CTR, MTX (48 h), rep2

description: Library name: SMSCTR_MTX_2


title: Renal cortex, Prdm16 ko, mouse1

description: Library name: Sample 4


title: Renal cortex, Prdm16 ko, mouse2

description: Library name: Sample 5


title: Renal cortex, WT, mouse3

description: Library name: Sample 3

value: Wild type


title: SMS-CTR, vehicle (DMSO, 48 h), rep1

description: Library name: SMSCTR_vehicle_1


title: RD, MTX (48 h), rep2

description: Library name: RD_MTX_2

source_name: RD

value: RD


title: RD, MTX (48 h), rep1

description: Library name: RD_MTX_1


title: RD, vehicle (DMSO, 48 h), rep1

description: Library name: RD_vehicle_1


title: C_3

city: 苏州市

first: hongjin

last: huo

address: 江苏省苏州市工业园区仁爱路199号苏州大学独墅湖校区

institute: Suzhou Medical College of Soochow University

description: Library name: Sample 6

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38 (这边基因组信息为物种拉丁文加上基因组版本号). The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
Assembly: mm10
Supplementary files format and content: tab-delimited txt files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher) following the manufacturer's procedure.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: epithelial cells

value: 100 nM PFOS


title: RH41, MTX (48 h), rep2

description: Library name: RH41_MTX_2


title: Renal cortex, WT, mouse1

description: Library name: Sample 1


title: Renal cortex, WT, mouse2

description: Library name: Sample 2


title: RD, vehicle (DMSO, 48 h), rep2

description: Library name: RD_vehicle_2


title: C_2

address: 江苏省苏州市工业园区仁爱路199号苏州大学独墅湖校区

description: Library name: Sample 5


title: A_3

address: 江苏省苏州市工业园区仁爱路199号苏州大学独墅湖校区

description: Library name: Sample 3

value: 0 nM PFOS


title: C_1

address: 江苏省苏州市工业园区仁爱路199号苏州大学独墅湖校区

description: Library name: Sample 4


title: RH41, MTX (48 h), rep1

description: Library name: RH41_MTX_1


title: RH41, vehicle (DMSO, 48 h), rep2

description: Library name: RH41_vehicle_2


title: RH41, vehicle (DMSO, 48 h), rep1

description: Library name: RH41_vehicle_1


title: A_1

address: 江苏省苏州市工业园区仁爱路199号苏州大学独墅湖校区

description: Library name: Sample 1


title: A_2

address: 江苏省苏州市工业园区仁爱路199号苏州大学独墅湖校区

description: Library name: Sample 2


title: peritoneal immune cells, KO BCR

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

description:
Library name: KO BCR
10x Genomics

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.3.0) was used for generation of Seurat object.
The count matrix was normalized with NormalizeData function.
tSNE and UMAP were performed by R package Seurat (version 4.3.0).
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peritoneal immune cells

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

treatment_protocol: Wild-type (WT) and PTENα knockout (KO) mice were placed on a high-fat diet beginning at 4 weeks of age and maintained for three months. To obtain peritoneal immune cells, mice were intraperitoneally injected with serum-free RPMI 1640 medium, and the lavage fluid was collected. CD45⁺ immune cells were then isolated by flow cytometry and subjected to single-cell RNA sequencing to profile the peritoneal immune microenvironment.

value: peritoneal immune cells

value: KO

value: HFD


title: RH30, MTX (48 h), rep1

description: Library name: RH30_MTX_1


title: peritoneal immune cells, KO GEX

description:
Library name: KO 10x
10x Genomics


title: RH30, vehicle (DMSO, 48 h), rep2

description: Library name: RH30_vehicle_2


title: peritoneal immune cells, WT BCR

description:
Library name: WT BCR
10x Genomics

value: WT


title: RH30, vehicle (DMSO, 48 h), rep1

description: Library name: RH30_vehicle_1


title: peritoneal immune cells, WT GEX

description:
Library name: WT 10x
10x Genomics


title: 4xEnh_NPC_H3K4me2_Rep1

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

country: Spain

institute: Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria

description: Library name: Sample_72

library_source: genomic

data_processing:
ChIP-seq
ChIP-seq rads were trimmed using trommomatic (v0.39). Low-quality bases (Phred score <3) were removed from the read ends, and a sliding window of 4 bases was used to trim when the average quality dropped below 15. Reads shorter than 36 bp after trimming were discarded.
ChIP-seq pair-end reads were aligned against mm10 based custom reference genomes that included the sequence of the corresponding enhancer at the insertion site (Gata6 +100kb), using Bowtie2(v2.5.4). Bowtie2 alignment was restricted to concordant alignments, allowing up to two valid alignments per read
batch effect correction was performed by applying quantile normalization separately for each antibody across the different genotypes and replicates
Assembly: mm10 based custom refence genomes
Supplementary files format and content: Bigwig; for each sample the bigwig files show the quantile normalized signal for biological replicate

molecule: genomic DNA

source_name: Mouse ESCs (E14Tg2a)

growth_protocol: Mouse ESCs (E14Tg2a) were cultured on gelatin-coated plates at 37°C with 5% CO2 in the presence of Knock-out DMEM, supplemented with 15% FBS , 0.1 mM 2-mercaptoethanol, 1x Glutamax, 1× penicillin–streptomycin, 1× MEM non-essential amino acids and leukemia inhibitory factor (LIF).

extract_protocol:
Briefly, ~4 × 107 and ~1 × 107 cells were used for co-activators and histone marks, respectivel. Cells were crosslinked with 1% formaldehyde for 10 min at room temperature (RT) and quenched with 0.125 M glycine for 10 min. Cells were consecutively incubated with three different lysis buffers (Buffer 1_ 50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TX-100; Buffer 2_ 10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; Buffer 3_ 10 mM Tris, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) in order to isolate chromatin. Next, chromatin was sonicated for 8 minutes in Buffer 3 (20 s on, 30 s off, 25% amplitude) using an EpiShear probe sonicator (Active Motif).  The sonicated chromatin was mixed with 3 μg of H3K27ac antibody or 10 μg of Rad21 antibody and incubated overnight at 4°C. Next, 50-100 μl of Dynabeads (Thermo Fisher, 10-002-D) were aliquoted into a microtube for each ChIP reaction. The dynabeads were washed with 1 ml of cold blocking solution (0,5% BSA and 1x PBS). The antibody bound chromatin was added to the washed beads and incubated for four hours at 4ºC. Magnetic beads were washed five times with RIPA buffer (50 mM Hepes, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0,7% Na-Deoxycholate). The chromatin was eluted and incubated at 65 °C overnight to reverse the crosslinking. Next, samples were treated with 0,2 mg/ml Rnase A and 0,2 mg/ml proteinase K. DNA  purification was performed using Zymoclean Gel DNA Recovery kit (Zymo Research, D4008).
TruSeq DNA Sample prep Kit (Illumina) ; starting material 10ng

treatment_protocol: Differentiation towards Neural Progenitor cells was performed by growing mESC for six days in N2B27 medium, supplemented with FGF and XAV

value: Mouse ESCs (E14Tg2a)

value: NPC

tag: chip antibody

value: Actif Motif 39141


title: OCI-AML4 DMSO 6hr rep3 [RNA-Seq]

city: Boston

first: Travis

last: Fleming

state: MA

address: 1 Blackfan St

department: Hematology/Oncology

institute: Boston Children's Hospital

description: Library name: 6hr OCI-AML4 DMSO RNA rep3

data_processing:
FASTQ files were demultiplexed with bcl2fastq and aligned to the hg38 reference genome using bowtie2 (version 2.5.2). Sam files were sorted, indexed and converted to bam files with Samtools (version 1.18). For data visualization in a genome browser, bam files were converted to bigwig files using the bamCoverage package from deepTools (version 3.5.4) normalizing by counts per million (CPM). Count tables for genes were also generated from bam files using the featureCounts package from Subread (version 2.0.6) and differential gene expression analysis was performed using DESeq2 (version 1.40.2). Results were visualized using ggplot2 (version 3.4.4).
Assembly: hg38
Supplementary files format and content: bigWig and tab-delimited text files which includes raw counts for each sample

growth_protocol: MUTZ-3 cells (DSMZ), HNT-34 cells (Creative Bioarray), and OCI-AML4 cells (DSMZ) were cultured at 37 °C in α-MEM (Life Technologies) supplemented with 20% FBS, 20% conditioned medium from 5637 cells (ATCC) and 1% penicillin/streptomycin. Confluency for all cells was maintained between 7 × 105 and 1.5 × 106 ml−1. UCSD-AML1 cells (a gift from Dr. Kimberly Stegmaier’s lab) were cultured at 37 °C in RPMI 1640 (Life Technologies) supplemented with 20% FBS, 1% penicillin/streptomycin and 10ng/mL GM-CSF (Peprotech). Confluency was maintained between 5 × 105 and 1.5 × 106 ml−1.

extract_protocol:
Total RNA was extracted using the RNeasy Micro kit (QIAGEN, 74004) from 10,000-50,000 cells sorted or harvested in 25 µl Buffer RLT Plus with 1% BME.
RNA libraries for RNA-seq were prepared using the SmartSeq2 protocol from the reverse transcription step using 10 ng of RNA. The whole transcriptome amplification step was set at ten cycles. Bulk RNA libraries were pooled at appropriate molar ratios to obtain at least 20 million reads per library. Libraries were subject to paired-end sequencing with 150 cycles.

treatment_protocol: Cells were treated with 500nM of dTAGV-1 or DMSO for 6-24 hours.

value: AML cell line

value: Control


title: Enh_NPC_H3K4me2_Rep1

description: Library name: Sample_71

value: Enh


title: OCI-AML4 DMSO 6hr rep2 [RNA-Seq]

description: Library name: 6hr OCI-AML4 DMSO RNA rep2


title: OCI-AML4 dTAGV-1 6hr rep3 [RNA-Seq]

description: Library name: 6hr OCI-AML4 dTAG RNA rep3

value: MECOM degradation


title: OCI-AML4 dTAGV-1 6hr rep2 [RNA-Seq]

description: Library name: 6hr OCI-AML4 dTAG RNA rep2


title: Enh_NPC_H3K4me3_Rep2

description: Library name: Sample_67

value: Actif Motif 39159


title: 4xEnh_NPC_H3K4me3_Rep1

description: Library name: Sample_68


title: OCI-AML4 dTAGV-1 6hr rep1 [RNA-Seq]

description: Library name: 6hr OCI-AML4 dTAG RNA rep1


title: WT_NPC_H3K4me2_Rep1

description: Library name: Sample_70

value: Wild type


title: OCI-AML4 DMSO 6hr rep1 [RNA-Seq]

description: Library name: 6hr OCI-AML4 DMSO RNA rep1


title: HNT-34 DMSO 6hr rep3 [RNA-Seq]

description: Library name: 6hr HNT-34 DMSO RNA rep3


title: Enh_NPC_H3K4me3_Rep1

description: Library name: Sample_66


title: WT_NPC_H3K4me3_Rep1

description: Library name: Sample_64


title: WT_NPC_H3K4me3_Rep2

description: Library name: Sample_65


title: HNT-34 DMSO 6hr rep1 [RNA-Seq]

description: Library name: 6hr HNT-34 DMSO RNA rep1


title: 4xEnh_NPC_H3K27me3_Rep1

description: Library name: Sample_63

value: Actif Motif 39155


title: RH30, MTX (48 h), rep2

description: Library name: RH30_MTX_2

value: methotrexate


title: HNT-34 dTAGV-1 6hr rep2 [RNA-Seq]

description: Library name: 6hr HNT-34 dTAG RNA rep2


title: HNT-34 DMSO 6hr rep2 [RNA-Seq]

description: Library name: 6hr HNT-34 DMSO RNA rep2


title: HNT-34 dTAGV-1 6hr rep3 [RNA-Seq]

description: Library name: 6hr HNT-34 dTAG RNA rep3


title: WT_NPC_H3K27me3_Rep1

description: Library name: Sample_61


title: UCSD-AML1 DMSO 6hr rep2 [RNA-Seq]

description: Library name: 6hr UCSD-AML1 DMSO RNA rep2


title: 4xEnh_NPC_H3K27Ac_Rep2

description: Library name: Sample_60

value: Actif Motif 39133


title: HNT-34 dTAGV-1 6hr rep1 [RNA-Seq]

description: Library name: 6hr HNT-34 dTAG RNA rep1


title: UCSD-AML1 DMSO 6hr rep1 [RNA-Seq]

description: Library name: 6hr UCSD-AML1 DMSO RNA rep1


title: 4xEnh_NPC_H3K4me3_Rep2

description: Library name: Sample_69


title: Enh_NPC_H3K27Ac_Rep2

description: Library name: Sample_58


title: WT_NPC_H3K27Ac_Rep2

description: Library name: Sample_56


title: UCSD-AML1 dTAGV-1 6hr rep2 [RNA-Seq]

description: Library name: 6hr UCSD-AML1 dTAG RNA rep2


title: MUTZ-3 DMSO 4hr rep3

description: Library name: 4hr MUTZ-3 DMSO PRO-seq rep3

library_source: other

data_processing:
All custom scripts described herein are available on the AdelmanLab GitHub (https://github.com/AdelmanLab/NIH_scripts). Using a custom script (trim_and_filter_PE.pl), FASTQ read pairs were trimmed to 41bp per mate, and read pairs with a minimum average base quality score of 20 were retained. Read pairs were further trimmed using cutadapt (version 4.1) to remove adapter sequences and low-quality 3’ bases (–match-read-wildcards -m 20 -q 10). R1 reads, corresponding to RNA 3’ ends, were then aligned to the spiked in Drosophila genome index (dm6) using BWA, with those reads not mapping to the spike genome serving as input to the primary genome alignment step. Reads mapping to the hg38 reference genome were then sorted, via samtools (version 1.3.1 -n), and subsequently converted to bam files. The bam files are converted to bigwig files by bamCoverage of deepTools (version 3.5). For metagene plots, bigwig files of three replicates of each group and combined and averaged using WiggleTools.
Assembly: hg38
Supplementary files format and content: bedGraph for forward and reverse strands for each sample
Library strategy: PRO-Seq

molecule: other

growth_protocol: MUTZ-3 cells (DSMZ) were cultured at 37 °C in α-MEM (Life Technologies) supplemented with 20% FBS, 20% conditioned medium from 5637 cells (ATCC) and 1% penicillin/streptomycin. Confluency for all cells was maintained between 7 × 105 and 1.5 × 106 ml−1.

extract_protocol:
Aliquots of frozen (-80C) permeabilized MUTZ-3 cells were thawed on ice and pipetted gently to fully resuspend. Aliquots were removed and permeabilized cells were counted using a Luna II, Logos Biosystems instrument. For each sample, 1 million permeabilized cells were used for nuclear run-on, with 50,000 permeabilized Drosophila S2 cells added to each sample for normalization. Nuclear run on assays and library preparation were performed essentially as described in Reimer et al. 2021 with modifications noted: 2X nuclear run-on buffer consisted of (10 mM Tris (pH 8), 10 mM MgCl2, 1 mM DTT, 300mM KCl, 20uM/ea biotin-11-NTPs (Perkin Elmer), 0.8U/uL SuperaseIN (Thermo), 1% sarkosyl). Run-on reactions were performed at 37C. Adenylated 3’ adapter was prepared using the 5’ DNA adenylation kit (NEB) and ligated using T4 RNA ligase 2, truncated KQ (NEB, per manufacturers instructions with 15% PEG-8000 final) and incubated at 16C overnight. 180uL of betaine blocking buffer (1.42g of betaine brought to 10mL with binding buffer supplemented to 0.6 uM blocking oligo (TCCGACGATCCCACGTTCCCGTGG/3InvdT/)) was mixed with ligations and incubated 5 min at 65C and 2 min on ice prior to addition of streptavidin beads. After T4 polynucleotide kinase (NEB) treatment, beads were washed once each with high salt, low salt, and blocking oligo wash (0.25X T4 RNA ligase buffer (NEB), 0.3uM blocking oligo) solutions and resuspended in 5’ adapter mix (10 pmol 5’ adapter, 30 pmol blocking oligo, water). 5’ adapter ligation was per Reimer et al. 2021 but with 15% PEG-8000 final.
Eluted cDNA was amplified 5-cycles (NEBNext Ultra II Q5 master mix (NEB) with Illumina TruSeq PCR primers RP-1 and RPI-X) following the manufacturer’s suggested cycling protocol for library construction. A portion of preCR was serially diluted and for test amplification to determine optimal amplification of final libraries. Pooled libraries were sequenced using the Illumina NovaSeq 6000 platform.

treatment_protocol: Cells were treated with 500nM of dTAGV-1 or DMSO for 1-4 hours.


title: MUTZ-3 DMSO 4hr rep2

description: Library name: 4hr MUTZ-3 DMSO PRO-seq rep2


title: UCSD-AML1 dTAGV-1 6hr rep1 [RNA-Seq]

description: Library name: 6hr UCSD-AML1 dTAG RNA rep1


title: WT_NPC_H3K27Ac_Rep1

description: Library name: Sample_55


title: MUTZ-3 DMSO 4hr rep1

description: Library name: 4hr MUTZ-3 DMSO PRO-seq rep1


title: 4xEnh_NPC_Cdk9_Rep2

description: Library name: Sample_54

value: Cell signaling 2316S


title: Enh_NPC_H3K27Ac_Rep1

description: Library name: Sample_57


title: MUTZ-3 dTAGV-1 4hr rep3

description: Library name: 4hr MUTZ-3 dTAG PRO-seq rep3


title: MUTZ-3 dTAGV-1 4hr rep2

description: Library name: 4hr MUTZ-3 dTAG PRO-seq rep2


title: Enh_NPC_H3K27me3_Rep1

description: Library name: Sample_62


title: Enh_NPC_Cdk9_Rep2

description: Library name: Sample_52


title: 4xEnh_NPC_Cdk9_Rep1

description: Library name: Sample_53


title: MUTZ-3 dTAGV-1 4hr rep1

description: Library name: 4hr MUTZ-3 dTAG PRO-seq rep1


title: WT_NPC_Cdk9_Rep1

description: Library name: Sample_49


title: MUTZ-3 dTAGV-1 1hr rep1

description: Library name: 1hr MUTZ-3 dTAG PRO-seq rep1


title: Enh_NPC_Cdk9_Rep1

description: Library name: Sample_51


title: WT_NPC_Cdk9_Rep2

description: Library name: Sample_50


title: OCI-AML4 DMSO 6hr rep3

description: Library name: 6hr OCI-AML4 DMSO ATAC rep3

data_processing:
FASTQ files were demultiplexed with bcl2fastq and aligned to the hg38 reference genome using bowtie2 (version 2.5.2). Sam files were sorted, indexed and converted to bam files with Samtools (version 1.18). For data visualization in a genome browser, bam files were converted to bigwig files using the bamCoverage package from deepTools (version 3.5.4) normalizing by counts per million (CPM). Peak calling was performed using MACS2 (version 2.2.9.1) with the flags --shift -100 and --extsize 200 to generate narrowPeak files. NarrowPeak files from DMSO and dTAGV-1-treated cells were then merged and converted to SAF format to generate a consensus peak set for each cell line. This consensus peak file and corresponding bam files were then processed using the featureCounts package from Subread (version 2.0.6) to generate a count table for ATAC peaks. Differential peak accessibility analysis was performed using DESeq2 (version 1.40.2). Results were visualized using ggplot2 (version 3.4.4).
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Accessible chromatin was assessed using Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) as previously described with the Omni-ATAC protocol. Cells were treated with 500nM dTAGV-1 or DMSO for 6 hours and then 50,000 live cells were sorted into PBS with 2% BSA. Cells were washed twice in 150μL and 50μL 1xPBS, resuspended in 50μL ATAC-seq lysis buffer, incubated for 10 min on ice and centrifuged at 400g for 10 min at 4 °C.
The pellet was incubated in the transposase reaction mix (25μL 2×TD buffer (Illumina), 2.5μL transposase (Illumina Cat# FC-121-1030) and 22.5μL nuclease-free water) for 30min at 37 °C with gentle agitation. After DNA purification with the Zymo DNA Clean and Concentrator Kit (Zymo, Cat# D4033) libraries were amplified with NEBNext High-Fidelity PCR Master Mix (NEB, Cat# M0541S) using custom Nextera primers. Libraries for sequencing were size selected with Agencourt AMPure XP beads (Beckman Coulter, Cat# A63880). DNA concentration was measured with an Invitrogen Qubit fluorometer (Life Technologies) and Agilent Fragment Analyzer. Libraries were subject to paired-end sequencing with 150 cycles.


title: 4xEnh_NPC_H3K27Ac_Rep1

description: Library name: Sample_59


title: MUTZ-3 dTAGV-1 1hr rep2

description: Library name: 1hr MUTZ-3 dTAG PRO-seq rep2


title: MUTZ-3 dTAGV-1 1hr rep3

description: Library name: 1hr MUTZ-3 dTAG PRO-seq rep3


title: 4xEnh_NPC_Hypophosphorylated_RNA_polII_Rep1

description: Library name: Sample_47

value: Thermo Fisher Scientific MA110882


title: Enh_NPC_Hypophosphorylated_RNA_polII_Rep2

description: Library name: Sample_46


title: OCI-AML4 DMSO 6hr rep1

description: Library name: 6hr OCI-AML4 DMSO ATAC rep1


title: 4xEnh_NPC_Hypophosphorylated_RNA_polII_Rep2

description: Library name: Sample_48


title: OCI-AML4 dTAGV-1 6hr rep3

description: Library name: 6hr OCI-AML4 dTAG ATAC rep3


title: WT_NPC_Hypophosphorylated_RNA_polII_Rep2

description: Library name: Sample_44


title: Enh_NPC_Hypophosphorylated_RNA_polII_Rep1

description: Library name: Sample_45


title: OCI-AML4 dTAGV-1 6hr rep2

description: Library name: 6hr OCI-AML4 dTAG ATAC rep2


title: WT_NPC_Hypophosphorylated_RNA_polII_Rep1

description: Library name: Sample_43


title: OCI-AML4 dTAGV-1 6hr rep1

description: Library name: 6hr OCI-AML4 dTAG ATAC rep1


title: 4xEnh_NPC_Total_RNA_polII_Rep2

description: Library name: Sample_42

value: Actif Motif 39097


title: HNT-34 DMSO 6hr rep3

description: Library name: 6hr HNT-34 DMSO ATAC rep3


title: 4xEnh_NPC_Total_RNA_polII_Rep1

description: Library name: Sample_41


title: HNT-34 DMSO 6hr rep2

description: Library name: 6hr HNT-34 DMSO ATAC rep2


title: Enh_NPC_Total_RNA_polII_Rep1

description: Library name: Sample_39


title: WT_NPC_Total_RNA_polII_Rep2

description: Library name: Sample_38


title: HNT-34 dTAGV-1 6hr rep3

description: Library name: 6hr HNT-34 dTAG ATAC rep3


title: HNT-34 dTAGV-1 6hr rep2

description: Library name: 6hr HNT-34 dTAG ATAC rep2


title: HNT-34 dTAGV-1 6hr rep1

description: Library name: 6hr HNT-34 dTAG ATAC rep1


title: OCI-AML4 DMSO 6hr rep2

description: Library name: 6hr OCI-AML4 DMSO ATAC rep2


title: WT_NPC_Total_RNA_polII_Rep1

description: Library name: Sample_37


title: 4xEnh_NPC_Brd4_Rep2

description: Library name: Sample_36

value: Bethyl 793 A


title: UCSD-AML1 DMSO 6hr rep2

description: Library name: 6hr UCSD-AML1 DMSO ATAC rep2


title: UCSD-AML1 DMSO 6hr rep1

description: Library name: 6hr UCSD-AML1 DMSO ATAC rep1


title: UCSD-AML1 dTAGV-1 6hr rep2

description: Library name: 6hr UCSD-AML1 dTAG ATAC rep2


title: 4xEnh_NPC_Brd4_Rep1

description: Library name: Sample_35


title: Enh_NPC_Brd4_Rep2

description: Library name: Sample_34


title: UCSD-AML1 dTAGV-1 6hr rep1

description: Library name: 6hr UCSD-AML1 dTAG ATAC rep1


title: WT_NPC_Brd4_Rep2

description: Library name: Sample_32


title: Enh_NPC_Brd4_Rep1

description: Library name: Sample_33


title: WT_NPC_Brd4_Rep1

description: Library name: Sample_31


title: Input_DBC1_NHS_SM1_D1KO

city: Seoul

first: Jeong

middle: Hoon

last: Kim

address: Irwon-dong Gangnam-gu

country: South Korea

institute: Sungkyunkwan University

data_processing:
basecalling: bcl2fastq v2.20.0
Adapter trimming: Trimmomatic v0.38
Align: Bowtie 1.1.2
Deduplication: Picard 1.118 MarkDuplicates
Peak calling: MACS2 2.1.1.20160309
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: 22RV1 and SM1 cells were grown at 37°C with 5% CO2 in a humidified atmosphere in RPMI 1640 supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Chromatin preparation and ChIP were performed with the SimpleChIP Plus Enzymatic Chromatin IP kit (Cell signaling Technology) following the manufacturer’s instructions.
ChIP-seq libraries were constructed with the TruSeq ChIP Library Preparation Kit (Illumina).

treatment_protocol: The HSF1 and DBC1 genes were knocked out from 22RV1 and SM1 cells using CRISPR/Cas9 gene editing technology. Cells were treated with or without heat shock at 42℃ for 60 min (HS or NHS).

value: Metastatic castration-resistant prostate cancer cells

value: Non-heat shock (NHS)


title: DBC1_NHS_SM1

value: DBC1 (Bethyl, A300-434A)


title: Input_DBC1_NHS_SM1


title: Enh_NPC_Total_RNA_polII_Rep2

description: Library name: Sample_40

value: Mouse ESCs (E14Tg2a)

value: NPC


title: 4xEnh_NPC_p300_Rep1

description: Library name: Sample_29

value: Actif Motif 61401


title: HNT-34 DMSO 6hr rep1

description: Library name: 6hr HNT-34 DMSO ATAC rep1

value: AML cell line

value: Control


title: Enh_NPC_p300_Rep2

description: Library name: Sample_28

value: Enh


title: Input_NHS_SM1_D1KO


title: DBC1_NHS_SM1_D1KO


title: Enh_NPC_p300_Rep1

description: Library name: Sample_27


title: WT_NPC_p300_Rep2

description: Library name: Sample_26

value: Wild type


title: Input_NHS_SM1


title: WT_NPC_p300_Rep1

description: Library name: Sample_25


title: K27ac_NHS_SM1_H1KO

value: H3K27ac (Abcam, ab4729)


title: K27ac_NHS_SM1_D1KO


title: 4xEnh_NPC_Med26_Rep2

description: Library name: Sample_24

value: Cell signaling 13641


title: HSF1_NHS_SM1

value: HSF1 (Enzo, ADI-SPA-901-F)


title: 4xEnh_NPC_Med26_Rep1

description: Library name: Sample_23


title: K27ac_NHS_SM1


title: WT_NPC_Med26_Rep1

description: Library name: Sample_19


title: Input_K27ac_HS_22RV1_D1KO

value: Castration-resistant prostate cancer cells

value: Heat shock at 42℃ for 60 min (HS)


title: Enh_NPC_Med26_Rep2

description: Library name: Sample_22


title: 4xEnh_NPC_p300_Rep2

description: Library name: Sample_30


title: WT_NPC_Med26_Rep2

description: Library name: Sample_20


title: 4xEnh_NPC_Rad21_Rep2

description: Library name: Sample_18

value: Abcam ab154769


title: HSF1_NHS_SM1_H1KO


title: Enh_NPC_RAD21_Rep1

description: Library name: Sample_17


title: Input_K27ac_HS_22RV1


title: Enh-CBS_NPC_Rad21_Rep2

description: Library name: Sample_16

value: Enh-CBS


title: Input_NHS_SM1_H1KO

value: Metastatic castration-resistant prostate cancer cells


title: Input_K27ac_HS_22RV1_H1KO


title: Felis catus, retina, rep1

city: guagnzhou

first: Zhibin

last: Li

address: tianhe

institute: The Third Affiliated Hospital of Sun Yat-Sen University

description: Library name: AM3G1202

data_processing:
Raw data were filtered using a custom script in Cell Ranger v3.0.2 (10X Genomics).
Assembly: F.catus_Fca126_mat1.0, Oreochromis_mossambicus_EIV1, ASM1899790v1, bMelUnd1.mat.Z, bGalGal1.mat.broiler.GRCg7b, ZJU1.0
Supplementary files format and content: Tab-separated values files and matrix files.

organism: Felis catus

source_name: Retina

extract_protocol:
Eyeballs were excised and preserved in ice-cold, oxygenated Hanks Balanced Salt Solution (HBSS). Using fine scissors, the cornea was removed with a circular incision along the ora serrata. The lens and vitreous body were then extracted as thoroughly as possible. The detachment of the retina from the scleral cup was performed using ophthalmic forceps, followed by the careful removal of any retinal pigment epithelium (RPE) adhering to the retina. The isolated retina was washed once with fresh HBSS and immediately frozen in liquid nitrogen. For subsequent dissociation, the samples were transported on dry ice. The dissociated retinal tissue was washed with phosphate-buffered saline (PBS) and cut into smaller pieces, followed by the addition of 100 μL of precooled 0.1 × Lysis Buffer, thorough mixing, and incubation on ice for 5 min. The sample was then washed with 1 mL of precooled wash buffer, and cell debris and larger tissues were removed using 40-μm MACS Smart Strainer filtration. The sample was then centrifuged at 4 °C and 500 ×g for 5 min, after which the supernatant without nuclear particles was discarded. The sample underwent three wash cycles with wash buffer. The pellet was resuspended on ice in cooled, diluted nuclei buffer. Nuclear concentration was determined using a Countess II FL automatic cell counter, ensuring the nuclear suspension concentration was within the appropriate range.
The retinal cells underwent library construction using a 10X Chromium Single-Cell 3’ Library Kit v3 (PN-1000078) following the guidelines provided by the manufacturer.

value: Retina

value: Retinal cells


title: Enh_NPC_Med26_Rep1

description: Library name: Sample_21

value: Mouse ESCs (E14Tg2a)


title: GM12878, Cellular, 1M, Triptolide, biol rep 3

city: Copenhagen

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

description: Library name: GM12878 Trip3

data_processing:
Quality Control & Trimming: Raw reads were quality-checked with FastQC. Adapters and low-quality bases were trimmed using fastp, removing the first 3 bases and reads shorter than 30 bp.
rRNA Filtering: Reads mapping to rRNA were filtered using rRNAdust
Mapping: Filtered reads were aligned to the hg38 genome using STAR, allowing only uniquely mapping reads.
Post-processing: BAM files were sorted, indexed, and converted to strand-specific CTSS bed files. Unmatched G additions were corrected on the 5′ end, and final BigWig files were generated.
QC Metrics: Alignment complexity was assessed with Preseq, and alignment statistics were computed using samtools stats and flagstat.
Assembly: hg38
Supplementary files format and content: CTSS BigWig files: strand-specific coverage tracks with counts representing the number of 5′ ends of CAGE tags per genomic position, split into plus and minus strands.

growth_protocol: K562 were cultured in Advanced RPMI 1640 including 1 mM sodium pyruvate and 11.1 mM D-Glucose; HepG2 in DMEM medium without sodium pyruvate and 25 mM D-Glucose; A549 in Ham's F-12 Nutrient Mix including 1 mM sodium pyrivate; 1 mM L-Glutamine and 10 mM D-Glucose; HCT116 in DMEM medium including 1 mM sodium pyruvate and 5,6 mM D-Glucose; GM12878 in RPMI 1640 medium without sodium pyruvate and 11,1 mM D-Glucose. 10% v/v FCS and 1% v/v Penicillin-Streptomycin were added to all media compositions and 1% v/v L-Glutamine specifically for K562. All 5 cell lines were reared in Corning T-25 or T-75 flasks and incubated at 37°C and 5% CO₂.

extract_protocol:
Nuclei extraction was performed by employing a combination of hypotonic lysis buffer (10 mM Tris-HCl, pH 7,4; 10 mM NaCl; 3 mM MgCl2; 1% m/v BSA; 1% v/v 0,1% Tween-20; 0,1% NP-40; 0,01% Digitonin) including RNase inhibitors (4 mU/µl SUPERaseIn; 4 mU/µl Protector RNaseInh) and application of sheer forces by running the suspension through a 24 G needle for 10 times. Total RNA of nuclei or whole cell samples was extracted using the PureLink RNA Mini Kit with on-column DNase digestion. RNA quality was verified using the RNA 6000 Pico reagents and chips for automated gel electrophoresis on a 2100 Bioanalyzer.
SLIC-CAGE libraries for all samples were generated as outlined in Cvetesic N et al., 2018 (doi: 10.1101/gr.235937.118), including the addition of carrier RNA, reverse transcription, oxidation and biotinylation of capped RNA species, removal of ssRNA overhangs and incompletely transcribed RNA, cap-trapping on Streptavidin beads, release of single-stranded cDNA, adapter ligation and second-strand synthesis, digestion of carriers, size selection and PCR amplification. Libraries were pooled and single-end sequenced on an Illumina NextSeq550 sequencer using High Output v2.5 kits for 75 cycles.

treatment_protocol: 4 replicates of each 1 M GM12878 cells were treated with 10 µM triptolide for 5 h and 3 control replcates with 1 M GM12878 cells were acquired by applying DMSO as vehicle to the cells.

value: 5 h, 10 µM Triptolide


title: GM12878, Cellular, 1M, Triptolide, biol rep 4

description: Library name: GM12878 Trip4


title: WT_NPC_Rad21_Rep2

description: Library name: Sample_14

value: NPC


title: HSF1_NHS_SM1_D1KO

value: Non-heat shock (NHS)


title: GM12878, Cellular, 1M, Triptolide, biol rep 2

description: Library name: GM12878 Trip2


title: GM12878, Cellular, 1M, Triptolide, biol rep 1

description: Library name: GM12878 Trip1


title: GM12878, Cellular, 1M, DMSO, biol rep 3

description: Library name: GM12878 Ctrl3

value: DMSO


title: K27ac_HS_22RV1_D1KO


title: GM12878, Cellular, 1M, DMSO, biol rep 2

description: Library name: GM12878 Ctrl2


title: Enh-CBS_NPC_CTCF_Rep1

description: Library name: Sample_11

value: Actif Motif 61311


title: WT_NPC_Rad21_Rep1

description: Library name: Sample_13

value: Wild type


title: Enh-CBS_NPC_CTCF_Rep2

description: Library name: Sample_12


title: K27ac_HS_22RV1

value: H3K27ac (Abcam, ab4729)


title: GM12878, Cellular, 1M, DMSO, biol rep 1

description: Library name: GM12878 Ctrl1


title: GM12878, Nuclei, 10M, biol rep 3

description: Library name: GM12878 10M N3

molecule: nuclear RNA


title: WT_NPC_CTCF_Rep2

description: Library name: Sample_10


title: K27ac_NHS_22RV1_D1KO


title: shNrf3-HFD

type: RNA

city: Kyotanabe

first: Tsuyoshi

last: Waku

address: 1-3 Tatara Miyakodani

country: Japan

institute: Doshisha University

description: Gene expression data from tumor tissues derived from Renca-shNrf3 cells in HFD-fed mice

hyb_protocol: Following fragmentation, 2 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Human Gene 1.0ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000-7G.

data_processing: The data were analyzed with Expression console  (Build 1.4.1.46) using Affymetrix default analysis settings and RMA scaling as normalization method.

label: biotin

organism: Mus

source_name: Tumor tissues derived from Renca-shNrf3 cells in HFD-fed mice

label_protocol: Biotinated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Ambion WT expression kit and Gene Chip WT Terminal Labeling and Hybridization Kit Manual, Affymetrix).

growth_protocol: 4~6-week old BALB/cCrSlc male mice were purchased from Shimizu Laboratory Supplies (Kyoto, Japan), and assigned to ad libitum feeding of normal chow diet (NC) (CE-2, CREA Japan) or high-fat diet (HFD) (HFD-60, Oriental Yeast) for 17 weeks.

extract_protocol: Then, total RNA of the tumor tissue was extracted using ISOGEN II (NIPPON GENE), according to the manufacturer's instructions.

treatment_protocol: Renca-shCtrl or shNrf3 cells were subcutaneously injected into flanks of NC or HFD-fed mice. After two weeks, tumor tissues were removed, and the weights were measured.

value: renal adenocarcinoma Renca cells

value: shNrf3 expression

tag: diet

value: HFD

value: tumor


title: GM12878, Nuclei, 5M, biol rep 3

description: Library name: GM12878 5M N3


title: Input_K27ac_NHS_22RV1_D1KO

value: Castration-resistant prostate cancer cells


title: Enh-CBS_NPC_Rad21_Rep1

description: Library name: Sample_15

value: Enh-CBS

value: Abcam ab154769


title: GM12878, Nuclei, 10M, biol rep 1

description: Library name: GM12878 10M N1


title: shNrf3-NC

description: Gene expression data from tumor tissues derived from Renca-shNrf3 cells in NC-fed mice

source_name: Tumor tissues derived from Renca-shNrf3 cells in NC-fed mice

value: control


title: shCtrl-NC

description: Gene expression data from tumor tissues derived from Renca-shCtrl cells in NC-fed mice

source_name: Tumor tissues derived from Renca-shCtrl cells in NC-fed mice

value: shCtrl expression


title: shCtrl-HFD

description: Gene expression data from tumor tissues derived from Renca-shCtrl cells in HFD-fed mice

source_name: Tumor tissues derived from Renca-shCtrl cells in HFD-fed mice


title: Enh-CBS_mESC_CTCF_Rep1

description: Library name: Sample_7

value: Mouse ESCs (E14Tg2a)

value: mESC


title: Input_K27ac_NHS_22RV1


title: WT_NPC_CTCF_Rep1

description: Library name: Sample_9

value: NPC