title: ORG-0109_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 5_ORG-109_02.RCC; Selected renamed RCC file: ORG-0109_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 5; Lane: 2; MD5: 447db8cd92b3110a99e975c1fd67d855

value: breast

value: not specified

value: NHB

value: Black

value: Pre

value: Nulliparous

value: Unknown


title: ORG-0095_BC360_20210917 histologically normal breast tissue

status: Public on Mar 17 2026

type: RNA

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

country: USA

institute: Mayo Clinic

description: Original RCC file: 20210917_Radisky 52 samples BC360 4_ORG-95_09.RCC; Selected renamed RCC file: ORG-0095_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 4; Lane: 9; MD5: 988da883d7e054babf1a045a537bc3c9

hyb_protocol: RNA was hybridized for 18 h at 65°C to the NanoString BC360 or IO360 CodeSet. Cartridges were processed on the nCounter Prep Station.

scan_protocol: Cartridges were scanned at 555 fields of view on the nCounter Digital Analyzer. All samples passed manufacturer QC thresholds used in the manuscript: imaging QC score > 0.85, binding density 0.1–2.25 spots/µm², and positive-control linearity R² > 0.95.

data_processing: The BC360_Raw_Matrix.xlsx values are complete raw NanoString counts extracted directly from the selected BC360 RCC files. This BC360 matrix contains 790 probes/features across 74 specimens (758 endogenous genes, 18 housekeeping probes, 8 negative controls, 6 positive controls). Raw RCC files were matched to specimens by exact specimen ID; when multiple candidate raw RCC files existed for the same specimen and panel, the latest RCC date was selected. The processed workbook sample ORG-0098 was matched to raw IO360 specimen ORG-0098 R per submitter instruction. Supplementary file BC360_processed_matrix.tsv retains the analyzed normalized values supplied in Combined IO360 and BC360.xlsx.

label: nanostring

molecule: total RNA

organism: Homo sapiens

source_name: histologically normal breast tissue

label_protocol: NanoString nCounter direct digital counting with panel-specific reporter and capture probes according to the manufacturer protocol; no separate external labeling step was performed.

growth_protocol: Not applicable. These are human surgical FFPE specimens and were not grown or cultured before RNA extraction.

extract_protocol: From each FFPE block, three consecutive 10 µm scrolls (approximately 50 mm² total tissue area) were deparaffinized in xylene and rehydrated through graded ethanol. RNA was extracted using the Qiagen RNeasy FFPE Kit (Cat. 73504) according to the manufacturer instructions. RNA integrity was assessed by spectrophotometry (A260/280 > 1.8) and DV200 (>40% required for inclusion). One hundred nanograms of RNA were used per hybridization.

treatment_protocol: Not applicable. Tissue was collected at surgery with no experimental ex vivo treatment before NanoString profiling.

tag: tissue

value: FFPE surgical specimen

tag: panel

tag: ethnicity

value: Not Hispanic/Latino

tag: parity

value: Parous

tag: breastfed

value: Yes

tag: density

value: HD

tag: involution

value: Partial

value: Right Mastectomy, Left Prophylactic Mastectomy

tag: diagnosis

value: R DCIS

value: unknown

value: no


title: ORG-0090_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 4_ORG-90 _04.RCC; Selected renamed RCC file: ORG-0090_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 4; Lane: 4; MD5: 09e83687ce8a0e06a9d3c3516ef62125

value: breast

value: NHW

value: White

value: Post

value: No

value: Complete

value: Bilateral Prophylactic Mastectomies

value: No (prophy)


title: ORG-0091_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 4_ORG-91_05.RCC; Selected renamed RCC file: ORG-0091_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 4; Lane: 5; MD5: 12395b8b6500d1c2b61f4180e92f089d

value: FFPE surgical specimen

value: not specified

value: Not Hispanic/Latino

value: IDC


title: ORG-0092_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 4_ORG-92_06.RCC; Selected renamed RCC file: ORG-0092_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 4; Lane: 6; MD5: 940bf2fec5105c0ba7b740f02c04ee56

value: Pre

value: Parous

value: Yes

value: HD

value: Partial

value: Left Mastectomy, Right Prophylactic Mastectomy

value: L IDC


title: ORG-0070_BC360_20210921 histologically normal breast tissue

description: Original RCC file: 20210921_Radisky 52 samples BC360 6_ORG-70_04.RCC; Selected renamed RCC file: ORG-0070_BC360_20210921.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210921; Cartridge: Radisky 52 samples BC360 6; Lane: 4; MD5: 462418940bcd202c205093259e4e9c02; Selection rule: latest RCC date chosen from 2 candidate raw RCC files for this specimen/panel.

value: breast

value: NHW

value: White

value: Nulliparous

value: unknown

value: Unknown

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R IDC

value: no


title: ORG-0093_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 4_ORG-93_07.RCC; Selected renamed RCC file: ORG-0093_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 4; Lane: 7; MD5: 5bd29ceba72ce637dc4b8f3ee0542bd9

value: FFPE surgical specimen

value: not specified

value: NHB

value: Black

value: Not Hispanic/Latino


title: ORG-0062_BC360_20211015 histologically normal breast tissue

description: Original RCC file: 20211015_Radisky 11 samples BC360 7_ORG-0062_08.RCC; Selected renamed RCC file: ORG-0062_BC360_20211015.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20211015; Cartridge: Radisky 11 samples BC360 7; Lane: 8; MD5: 0b27536e4a5ed2e327f9c1d95c5d96cf

value: Pre

value: Parous

value: Yes

value: HD

value: Partial

value: L DCIS


title: ORG-0103_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 5_ORG-103_01.RCC; Selected renamed RCC file: ORG-0103_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 5; Lane: 1; MD5: b2b8e5659e55b4d26f140c3852092d6d

value: breast

value: NHW

value: White

value: Left Mastectomy, Right Prophylactic Mastectomy

value: IDC


title: ORG-0101_L2_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run1_ORG-0101 L2_08.RCC; Selected renamed RCC file: ORG-0101_L2_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run1; Lane: 8; MD5: 13d5dceb48fe9213b4e2e132575af3de

value: Post

value: Nulliparous

value: unknown

value: Unknown

value: no


title: ORG-0125_L_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run2_ORG-0125 L_05.RCC; Selected renamed RCC file: ORG-0125_L_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run2; Lane: 5; MD5: 7492ca690b81cb6ba47e3de91a4f954a

value: FFPE surgical specimen

value: L

value: Breast Reduction

value: No


title: ORG-0130_R1_BC360_20220614 histologically normal breast tissue

description: Original RCC file: 20220614_Radisky BC360 IO360 rerun_ORG-0130 R1_09.RCC; Selected renamed RCC file: ORG-0130_R1_BC360_20220614.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20220614; Cartridge: Radisky BC360 IO360 rerun; Lane: 9; MD5: 8ac7957e48de465d6d49ecfbab0a2c17

value: Not Hispanic/Latino

value: Pre

value: Parous

value: Yes

value: HD


title: ORG-0073_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 3_ORG-73_08.RCC; Selected renamed RCC file: ORG-0073_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 3; Lane: 8; MD5: a345e9e4923e313d9ba72f6cf01ac9e1

value: breast

value: not specified

value: NHW

value: White

value: Partial

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R DCIS


title: ORG-0097_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 4_ORG-97_10.RCC; Selected renamed RCC file: ORG-0097_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 4; Lane: 10; MD5: 3194ed7620790b839d58a2efe8f6754f

value: NHB

value: Black

value: unknown

value: no


title: ORG-0100_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 4_ORG-100 _11.RCC; Selected renamed RCC file: ORG-0100_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 4; Lane: 11; MD5: c05dbb8b1fd2ac3d7d7f8e90c1677a58

value: FFPE surgical specimen

value: Post

value: Left Mastectomy, Right Prophylactic Mastectomy

value: DCIS


title: ORG-0042_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 2_ORG-42_08.RCC; Selected renamed RCC file: ORG-0042_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 2; Lane: 8; MD5: 8d4d1f136a5ce98575d6e8c2ce30729e

value: Hispanic/Latino

value: Pre

value: Nulliparous

value: Unknown

value: Bilateral Prophylactic Mastectomies

value: R Papilloma w/ atypia


title: ORG-0047_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 2_ORG-47_09.RCC; Selected renamed RCC file: ORG-0047_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 2; Lane: 9; MD5: 3434669162d11d9a1640d1c5d8f17ca7

value: breast

value: not specified

value: NHW

value: White

value: Not Hispanic/Latino

value: Parous

value: Yes

value: ED

value: Partial

value: R IDC


title: ORG-0081_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 3_ORG-81_10.RCC; Selected renamed RCC file: ORG-0081_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 3; Lane: 10; MD5: 377cbdebe9ed277852e9c249e2f2b45d

value: FFPE surgical specimen

value: NHB

value: Black

value: unknown

value: Breast Reduction

value: No

value: no


title: ORG-0098_BC360_20211015 histologically normal breast tissue

description: Original RCC file: 20211015_Radisky 11 samples BC360 7_ORG-0098_12.RCC; Selected renamed RCC file: ORG-0098_BC360_20211015.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20211015; Cartridge: Radisky 11 samples BC360 7; Lane: 12; MD5: 325a20b599aa39c556daced36fbdff63

value: breast

value: Pre

value: Nulliparous

value: Unknown

value: Complete


title: ORG-0067_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 3_ORG-67_05.RCC; Selected renamed RCC file: ORG-0067_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 3; Lane: 5; MD5: e07127399af25a06952e5549671ad991

value: not specified

value: NHW

value: White


title: ORG-0087_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 4_ORG-87_01.RCC; Selected renamed RCC file: ORG-0087_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 4; Lane: 1; MD5: 240a98db99074f6342191b3c3b3ac8eb

value: Not Hispanic/Latino

value: HD

value: Partial

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R ILC


title: ORG-0105_R1_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run1_ORG-0105 R1_10.RCC; Selected renamed RCC file: ORG-0105_R1_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run1; Lane: 10; MD5: 819fbc5decd164430f123ec314bec7ef

value: FFPE surgical specimen

value: Parous

value: Yes

value: ED

value: IDC

value: unknown


title: ORG-0102_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 4_ORG-102 _12.RCC; Selected renamed RCC file: ORG-0102_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 4; Lane: 12; MD5: 8c91bb28d77759b45845c30549925d10

value: breast

value: Pre

value: DCIS

value: no


title: ORG-0055_R_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run1_ORG-0055 R_04.RCC; Selected renamed RCC file: ORG-0055_R_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run1; Lane: 4; MD5: d4ea84d2d5739fbce847532e881606af

value: R

value: NHW

value: Nulliparous

value: Unknown

value: Complete

value: Breast Reduction

value: No


title: ORG-0059_L_BC360_20220608 histologically normal breast tissue

description: Original RCC file: 20220608_Radisky BC360 IO360 run2_ORG-0059 L_08.RCC; Selected renamed RCC file: ORG-0059_L_BC360_20220608.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20220608; Cartridge: Radisky BC360 IO360 run2; Lane: 8; MD5: e2aa74f001ff3431d150002f93dc20bc

value: FFPE surgical specimen

value: L

value: White

value: Hispanic/Latino

value: Other

value: L IDC


title: ORG-0046_BC360_20211015 histologically normal breast tissue

description: Original RCC file: 20211015_Radisky 11 samples BC360 7_ORG-0046_06.RCC; Selected renamed RCC file: ORG-0046_BC360_20211015.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20211015; Cartridge: Radisky 11 samples BC360 7; Lane: 6; MD5: 3de6b96bba5f4270ff05c2c58ff03eec

value: breast

value: not specified

value: Not Hispanic/Latino

value: unknown


title: ORG-0063_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 3_ORG-63_03.RCC; Selected renamed RCC file: ORG-0063_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 3; Lane: 3; MD5: 2dafcd03778da30f2ddad744ebc55f59

value: Pre

value: Partial

value: no


title: ORG-0021_BC360_20210915 histologically normal breast tissue

description: Original RCC file: 20210915_Radisky 52 samples BC360 1_ORG-21_11.RCC; Selected renamed RCC file: ORG-0021_BC360_20210915.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210915; Cartridge: Radisky 52 samples BC360 1; Lane: 11; MD5: 3920b19ac49408d0ece0dfc325741797

value: NHW

value: Parous

value: Yes

value: ED

value: Bilateral Prophylactic Mastectomies

value: Atypia

value: Left DCIS 2019


title: ORG-0058_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 3_ORG-58_02.RCC; Selected renamed RCC file: ORG-0058_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 3; Lane: 2; MD5: 90eec2e4b6b7421131b6dfc8e84e6b48

value: FFPE surgical specimen

value: White

value: Post

value: Fg

value: No


title: ORG-0064_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 3_ORG-64_04.RCC; Selected renamed RCC file: ORG-0064_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 3; Lane: 4; MD5: f126025e91cb50446ff8f753b6db8c7e

value: breast

value: not specified

value: NHB

value: Black

value: Not Hispanic/Latino

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R IDC


title: ORG-0050_L_BC360_20220608 histologically normal breast tissue

description: Original RCC file: 20220608_Radisky BC360 IO360 run2_ORG-0050 L_07.RCC; Selected renamed RCC file: ORG-0050_L_BC360_20220608.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20220608; Cartridge: Radisky BC360 IO360 run2; Lane: 7; MD5: 8d0e6ab4351b6832a7d8dd568d95aba3

value: L

value: Unknown

value: Hispanic or Latino

value: Pre

value: Parous

value: Yes

value: HD

value: R DCIS

value: unknown

value: no


title: ORG-0054_BC360_20211015 histologically normal breast tissue

description: Original RCC file: 20211015_Radisky 11 samples BC360 7_ORG-0054_07.RCC; Selected renamed RCC file: ORG-0054_BC360_20211015.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20211015; Cartridge: Radisky 11 samples BC360 7; Lane: 7; MD5: 5faf844c775661db54ec21842744d699

value: breast

value: FFPE surgical specimen

value: NHW

value: White

value: Nulliparous

value: Partial

value: Breast Reduction

value: No


title: ORG-0068_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 3_ORG-68_06.RCC; Selected renamed RCC file: ORG-0068_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 3; Lane: 6; MD5: 033dce53f1b3d9da7d587c89534cc2b5

value: not specified


title: ORG-0049_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 2_ORG-49_10.RCC; Selected renamed RCC file: ORG-0049_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 2; Lane: 10; MD5: e9a95d65f1b162a7f53b54febfb40769

value: Not Hispanic/Latino

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R IDC


title: ORG-0011_BC360_20210915 histologically normal breast tissue

description: Original RCC file: 20210915_Radisky 52 samples BC360 1_ORG-11_06.RCC; Selected renamed RCC file: ORG-0011_BC360_20210915.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210915; Cartridge: Radisky 52 samples BC360 1; Lane: 6; MD5: e596917a40f7f24351ae63d86e55ec47

value: NHB

value: Black

value: Post

value: Unknown

value: Fg


title: ORG-0012_BC360_20210915 histologically normal breast tissue

description: Original RCC file: 20210915_Radisky 52 samples BC360 1_ORG-12_07.RCC; Selected renamed RCC file: ORG-0012_BC360_20210915.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210915; Cartridge: Radisky 52 samples BC360 1; Lane: 7; MD5: a1c73df4aed833b32a9b86c29d644f03

value: breast

value: Pre

value: unknown

value: HD

value: Left Mastectomy, Right Prophylactic Mastectomy

value: L ILC

value: no


title: ORG-0051_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 2_ORG-51_11.RCC; Selected renamed RCC file: ORG-0051_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 2; Lane: 11; MD5: 5328077e4ca8d5b0b7bf3977b56a477d

value: FFPE surgical specimen

value: Parous

value: Yes

value: Partial

value: Breast Reduction

value: No


title: ORG-0022_BC360_20210921 histologically normal breast tissue

description: Original RCC file: 20210921_Radisky 52 samples BC360 6_ORG-22_03.RCC; Selected renamed RCC file: ORG-0022_BC360_20210921.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210921; Cartridge: Radisky 52 samples BC360 6; Lane: 3; MD5: 547076b214b7d3277297d6b2bc4b0ee5; Selection rule: latest RCC date chosen from 2 candidate raw RCC files for this specimen/panel.

value: not specified

value: NHW

value: White

value: Not Hispanic/Latino

value: Right Mastectomy, Left Prophylactic Mastectomy

value: IDC


title: ORG-0027_L_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run1_ORG-0027 L_02.RCC; Selected renamed RCC file: ORG-0027_L_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run1; Lane: 2; MD5: de3bc5dd7d03ea17cd74feffb7fd45ad

value: breast

value: L

value: Pre

value: Unknown

value: ED

value: R DCIS

value: unknown


title: TeloHAEC D5 ERG siRNA treated RNA-seq rep 7

type: SRA

city: Toronto

first: Kai

middle: Howson

last: Ellis

state: ON

address: 686 Bay St

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description: Library name: CC063_recovery_2025

library_source: transcriptomic

data_processing:
Preprocessing and Differential expression: Raw RNA-seq reads were processed with Trimmomatic (v0.32; using recommended parameters) to remove adaptor sequences and preserve high quality reads. The trimmed reads were then aligned to the human genome reference assembly (GRCh37/hg38) using STAR (v2.5.1b; default parameters). Quality control metrics for raw and aligned RNA-seq reads were analyzed using FastQC, MultiQC (v1.3) and Picard. After validating sample quality, feature quantification for each sample was performed using salmon against a transcriptome derived from Hg38.
Assembly: Hg38
Supplementary files format and content: Counts matrix

molecule: polyA RNA

source_name: TeloHAEC

growth_protocol: All experiments were performed in telomerase immortalized human aortic endothelial cells (TeloHAECs) grown in at 37 °C and 5% CO2 in Endothelial Cell Growth Media MV2 (PromoCell Catalogue number: C-22221) on rat tail collagen type 1-coated plates (Sigma-Aldrich REF C3867). ECGM-MV2 media was supplemented with 5% fetal calf serum, 5-ng/ml recombinant human epidermal growth factor, 0.5-ng/ml recombinant human vascular endothelial growth factor 165, 10-ng/ml recombinant human basic fibroblast growth factor, 20-ng/ml long R3 insulin-like growth factor-1, 1-μg/ml ascorbic acid, and 0.2-μg/ml hydrocortisone (from Supplement Pack Endothelial Cell Growth Medium MV2; PromoCell Catalogue number: C- 39221). Experiments using CRISPR/Cas9-edited cells were performed on cells between passage 20 and 30. Experiments using unedited TeloHAECs were performed on cells between passage 11 and 15.

extract_protocol:
Total RNA was extracted using a Qiagen Rneasy micro kit, according to manufacturer’s recommendations.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification

treatment_protocol: ERG knockdown was performed in telomerase immortalized human aortic endothelial cells (TeloHAECs. At 60-70% confluence, cells were serum starved for 1 hour in Opti-MEM reduced serum medium (ThermoFisher REF 31985-070) and transfected in ECGM-MV2. Lipofectamine RNAiMAX (Invitrogen REF 56532) was used to transfect cells. A final concentration of 40nM ambion silencer select ERG siRNA (ThermoFisher Catalogue number 4392421) or negative control siRNA (ThermoFisher Catalogue number 4390844 – s4813) was used. Media was changed 4-hours following transfection. 24- and 72-hours post-transfection, cells were harvested for ATAC-seq, RNA-seq, and cell lysates. Knock down was confirmed by western blot using collected cell lysates. Within each replicate, all three outputs were collected from different wells of a 12-well plate of cells treated identically. Cell lysate was collected as described below, using 100uL of 2x RIPA lysis buffer (Millipore Sigma REF 20-188) and 1x Protease inhibitor (Sigma Aldrich REF 11836170001). To collect cells for ATAC-seq, cells in each well were lifted with TrypLE, quenched in media , and counted. 50-70,000 cells from each well were aliquoted and spun down for 5 minutes at 500g. Cell pellet was resuspended in 100uL BAM Banker and frozen in the Mr. Frosty at -80C. Cell lysates for RNA-seq were prepared as follows: cells were washed three time with room temperature PBS, 350uL of room temperature Buffer RLT was added, cells were then scraped with and the lysates transferred to a 1.5mL tube.

tag: cell line

value: TeloHAEC

tag: cell type

value: Aortic Endothelial cells

tag: treatment

tag: batch


title: ORG-0016_BC360_20211015 histologically normal breast tissue

description: Original RCC file: 20211015_Radisky 11 samples BC360 7_ORG-0016_02.RCC; Selected renamed RCC file: ORG-0016_BC360_20211015.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20211015; Cartridge: Radisky 11 samples BC360 7; Lane: 2; MD5: a9cc59c3e247d68736dfc2dbd79bfac9

value: FFPE surgical specimen

value: Fg

value: Partial

value: R IDC

value: no


title: TeloHAEC D7 Ctrl siRNA treated RNA-seq rep 7

description: Library name: CC060_recovery_2025


title: ORG-0048_BC360_20220614 histologically normal breast tissue

description: Original RCC file: 20220614_Radisky BC360 IO360 rerun_ORG-0048_08.RCC; Selected renamed RCC file: ORG-0048_BC360_20220614.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20220614; Cartridge: Radisky BC360 IO360 rerun; Lane: 8; MD5: c4546f81c73314428a025d05dc3a1d44

value: not specified

value: NHW

value: White

value: Hispanic/Latino

value: Parous

value: Yes

value: Left Mastectomy, Right Prophylactic Mastectomy

value: L DCIS


title: ORG-0017_BC360_20211015 histologically normal breast tissue

description: Original RCC file: 20211015_Radisky 11 samples BC360 7_ORG-0017_03.RCC; Selected renamed RCC file: ORG-0017_BC360_20211015.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20211015; Cartridge: Radisky 11 samples BC360 7; Lane: 3; MD5: 13d03ead81533b0bdc275bbb657bc58e

value: breast

value: Not Hispanic/Latino

value: Pre

value: Nulliparous

value: Unknown

value: ED

value: Right Mastectomy, Left Prophylactic Mastectomy


title: TeloHAEC D3 Ctrl siRNA treated RNA-seq rep 7

description: Library name: CC058_recovery_2025

value: TeloHAEC

value: Aortic Endothelial cells


title: TeloHAEC D5 Ctrl siRNA treated RNA-seq rep 7

description: Library name: CC059_recovery_2025


title: TeloHAEC 72hr ERG siRNA treated RNA-seq rep 7

description: Library name: CC061_recovery_2025


title: TeloHAEC 72hr Ctrl siRNA treated RNA-seq rep 7

description: Library name: CC057_recovery_2025


title: TeloHAEC 72hr ERG siRNA treated RNA-seq rep 6

description: Library name: CC053_recovery_2025


title: TeloHAEC D3 ERG siRNA treated RNA-seq rep 6

description: Library name: CC054_recovery_2025


title: ORG-0018_BC360_20210915 histologically normal breast tissue

description: Original RCC file: 20210915_Radisky 52 samples BC360 1_ORG-18_09.RCC; Selected renamed RCC file: ORG-0018_BC360_20210915.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210915; Cartridge: Radisky 52 samples BC360 1; Lane: 9; MD5: 1c08a950bdecfcf725bd6c86c1900092

value: FFPE surgical specimen

value: not specified

value: NHB

value: Black

value: unknown

value: HD

value: Partial

value: L IDC

value: no


title: TeloHAEC D7 ERG siRNA treated RNA-seq rep 6

description: Library name: CC056_recovery_2025


title: TeloHAEC D7 ERG siRNA treated RNA-seq rep 7

description: Library name: CC064_recovery_2025


title: ORG-0047_R3_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run1_ORG-0047 R3_03.RCC; Selected renamed RCC file: ORG-0047_R3_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run1; Lane: 3; MD5: 40515f3f4c969a29a87981f19e5431e1

value: breast

value: NHW

value: White

value: Not Hispanic/Latino

value: Parous

value: Yes

value: R IDC


title: TeloHAEC D3 ERG siRNA treated RNA-seq rep 7

description: Library name: CC062_recovery_2025

value: TeloHAEC

value: Aortic Endothelial cells


title: TeloHAEC D7 Ctrl siRNA treated RNA-seq rep 6

description: Library name: CC052_recovery_2025


title: TeloHAEC D5 Ctrl siRNA treated RNA-seq rep 6

description: Library name: CC051_recovery_2025


title: TeloHAEC D3 ERG siRNA treated RNA-seq rep 5

description: Library name: CC030_recovery_2025


title: TeloHAEC 72hr Ctrl siRNA treated RNA-seq rep 6

description: Library name: CC049_recovery_2025


title: TeloHAEC D7 ERG siRNA treated RNA-seq rep 5

description: Library name: CC032_recovery_2025


title: TeloHAEC D3 Ctrl siRNA treated RNA-seq rep 6

description: Library name: CC050_recovery_2025


title: TeloHAEC D3 Ctrl siRNA treated RNA-seq rep 5

description: Library name: CC026_recovery_2025


title: TeloHAEC D7 Ctrl siRNA treated RNA-seq rep 5

description: Library name: CC028_recovery_2025


title: TeloHAEC D5 ERG siRNA treated RNA-seq rep 6

description: Library name: CC055_recovery_2025


title: TeloHAEC 72hr ERG siRNA treated RNA-seq rep 5

description: Library name: CC029_recovery_2025


title: TeloHAEC D5 ERG siRNA treated RNA-seq rep 5

description: Library name: CC031_recovery_2025


title: TeloHAEC D3 Ctrl siRNA treated RNA-seq rep 4

description: Library name: CC018_recovery_2025


title: TeloHAEC D7 Ctrl siRNA treated RNA-seq rep 4

description: Library name: CC020_recovery_2025


title: TeloHAEC 72hr ERG siRNA treated RNA-seq rep 4.

description: Library name: CC021_recovery_2025


title: TeloHAEC D3 ERG siRNA treated RNA-seq rep 4

description: Library name: CC022_recovery_2025


title: TeloHAEC 5d-Ctrl-siRNA rep 9

description: Library name: WL3778

library_source: genomic

data_processing:
The quality of raw ATAC-seq sequencing data was assessed with FastQC (v0.11.8) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were trimmed of adapter sequences using Trimmomatic (v0.32; using recommended parameters). Burrows-Wheeler Aligner (BWA) (v0.7.8, default parameters) was used to align the trimmed reads to the hg38 (GRCh38) genome reference assembly. Further QC, including assessments of the library complexity, read size distribution, and read density at the TSS were performed using ATACseqQC. Peaks were called using Genrich (https://github.com/jsh58/Genrich) using its multiple replicates, deduplication and ATAC-sequencing modes.
Assembly: Hg38
Supplementary files format and content: narrowPeak files

molecule: genomic DNA

extract_protocol:
Approximately 250,000 cells were harvested from each biological replicate of TeloHAECs treated with ERG or Control SiRNA for 24 or 72 hours and cryopreserved in BAMbanker freezing media using a Mr. Frosty. On the day of ATAC-sequencing, cells were washed with 1 Ml of 37°C endothelial cell growth media (link) and pelleted at 500xg. Free DNA from cells lysed during the cryopreservation process was removed through a 30 minute incubation in endothelial cell growth media supplemented with 200 units of DNAse at 37°C. Approximately 50,000 live cells were isolated from the recovered population, and lysed in non-ionic detergent lysis buffer (10-mM Tris-HCl, pH 7.4, 3-mM MgCl2, 10-mM NaCl, 0.1% NP-40).
Nuclei were pelleted and resuspended in 50 μl transposition reaction solution containing 2.5 μl Tn5 transposase attached to sequencing adapters (Illumina Nextera Tagment DNA enzyme TDE1, Nextera® DNA Sample Preparation Kit cat# FC-121-1030), 25 μl Tagment DNA buffer (20-mM Tris-HCl Ph7.6, 10-Mm MgCl2, 20% Dimethyl Formamide), 16.5 ul PBS, 5 ul NFH2O, 0.1% tween, and 0.01% Digitonin. Samples resuspended in Tn5 mixture were incubated at 37 °C for 30 min under gentle mixing conditions (300 rpm) using a thermomixer (Eppendorf, Hamburg, Germany). The transposed and adapter-ligated DNA fragments were purified using the Zymo Research DNA Clean and Concentrator purification kit and PCR amplified using barcoded primers (Nextera Index Kit, FC-121-1011), using cycle numbers determined by qPCR. A SageSciences PippinPrep was used to size select DNA between 125 and 600 basepairs using a 2% agarose gel. The final ATAC-seq libraries were sequenced with a 2 × 126-bp paired-end run in Illumina HiSeq2500 to obtain ~50 million, paired-end reads per sample.

value: Aortic endothelial cell


title: TeloHAEC D5 ERG siRNA treated RNA-seq rep 4

description: Library name: CC023_recovery_2025


title: TeloHAEC 3d-ERG-siRNA rep 9

description: Library name: WL3773


title: TeloHAEC 72hr-ERG-siRNA rep 9

description: Library name: WL3772


title: TeloHAEC D7 ERG siRNA treated RNA-seq rep 4

description: Library name: CC024_recovery_2025


title: TeloHAEC D5 Ctrl siRNA treated RNA-seq rep 5

description: Library name: CC027_recovery_2025


title: TeloHAEC 5d-ERG-siRNA rep 9

description: Library name: WL3774


title: TeloHAEC D5 Ctrl siRNA treated RNA-seq rep 4

description: Library name: CC019_recovery_2025


title: TeloHAEC 72hr Ctrl siRNA treated RNA-seq rep 5

description: Library name: CC025_recovery_2025


title: TeloHAEC 3d-Ctrl-siRNA rep 8

description: Library name: WL3769


title: TeloHAEC 7d-Ctrl-siRNA rep 9

description: Library name: WL3779


title: TeloHAEC 7d-ERG-siRNA rep 8

description: Library name: WL3767


title: TeloHAEC 3d-Ctrl-siRNA rep 9

description: Library name: WL3777


title: TeloHAEC 5d-Ctrl-siRNA rep y

description: Library name: WL3762

value: y


title: TeloHAEC 7d-Ctrl-siRNA rep y

description: Library name: WL3763


title: TeloHAEC 72hr-ERG-siRNA rep 8

description: Library name: WL3764


title: TeloHAEC 72hr-Ctrl-siRNA rep 9

description: Library name: WL3776


title: TeloHAEC 72hr-Ctrl-siRNA rep y

description: Library name: WL3760


title: TeloHAEC 7d-ERG-siRNA rep 9

description: Library name: WL3775


title: TeloHAEC 72hr Ctrl siRNA treated RNA-seq rep 4.

description: Library name: CC017_recovery_2025


title: TeloHAEC 5d-ERG-siRNA rep 8

description: Library name: WL3766


title: TeloHAEC 3d-ERG-siRNA rep 8

description: Library name: WL3765


title: TeloHAEC 5d-Ctrl-siRNA rep 8

description: Library name: WL3770


title: TeloHAEC 3d-Ctrl-siRNA rep x

description: Library name: WL3753

value: x


title: TeloHAEC 72hr-Ctrl-siRNA rep 8

description: Library name: WL3768


title: TeloHAEC 5d-ERG-siRNA rep y

description: Library name: WL3758


title: TeloHAEC 72hr Ctrl siRNA treated RNA-seq rep 4

description: Library name: CC015

value: 72hr Ctrl siRNA


title: TeloHAEC 24hr ERG siRNA treated RNA-seq rep 4

description: Library name: CC014

value: 24hr ERG siRNA


title: TeloHAEC 7d-ERG-siRNA rep y

description: Library name: WL3759


title: TeloHAEC 24hr ERG siRNA treated RNA-seq rep 3

description: Library name: CC010


title: TeloHAEC 72hr Ctrl siRNA treated RNA-seq rep 3

description: Library name: CC011


title: TeloHAEC 72hr-ERG-siRNA rep y

description: Library name: WL3756


title: TeloHAEC 5d-ERG-siRNA rep x

description: Library name: WL3750


title: TeloHAEC 24hr Ctrl siRNA treated RNA-seq rep 3

description: Library name: CC009

value: 24hr Ctrl siRNA


title: TeloHAEC 3d-Ctrl-siRNA rep y

description: Library name: WL3761


title: TeloHAEC 3d-ERG-siRNA rep y

description: Library name: WL3757


title: TeloHAEC 72hr-Ctrl-siRNA rep x

description: Library name: WL3752


title: TeloHAEC 7d-Ctrl-siRNA rep 8

description: Library name: WL3771


title: TeloHAEC 3d-ERG-siRNA rep x

description: Library name: WL3749


title: TeloHAEC 24hr ERG siRNA treated RNA-seq rep 1

description: Library name: CC002


title: TeloHAEC 5d-Ctrl-siRNA rep x

description: Library name: WL3754


title: TeloHAEC 7d-ERG-siRNA rep x

description: Library name: WL3751


title: TeloHAEC 24hr Ctrl siRNA treated RNA-seq rep 2

description: Library name: CC005


title: TeloHAEC 72hr Ctrl siRNA treated RNA-seq rep 2

description: Library name: CC007


title: dERG1(clone9)-exp4

description: Library name: WL1697

data_processing:
Preprocessing and Differential expression: Raw RNA-seq reads were processed with Trimmomatic (v0.32; using recommended parameters) to remove adaptor sequences and preserve high quality reads. The trimmed reads were then aligned to the human genome reference assembly (GRCh37/hg38) using STAR (v2.5.1b; default parameters). Quality control metrics for raw and aligned RNA-seq reads were analyzed using FastQC, MultiQC (v1.3) and Picard. After validating sample quality, feature quantification for each sample was performed using featureCounts against a transcriptome derived from Hg19.
Assembly: Hg19
Supplementary files format and content: Counts matrix

extract_protocol:
Total RNA was extracted using a Qiagen Rneasy micro kit, according to manufacturer’s recommendations.
CATseq (RNA-seq on CRISPR cells) collection and analysis: RNA-seq libraries were prepared using CATS mRNA-seq kit v2 (with poly(A) selection) with dual indexing (Diagenode, Belgium) as per the manufacturer’s protocol. Briefly, 250 ng of total RNA was spiked-in with SIRV Set 3 (Lexogen GmbH, Austria) calculated based on 1% mRNA and 1% spike-in as per the manufacturer’s protocol was used to generate cDNA. The resulting libraries were quantified with Qubit DNA High Sensitivity assay (ThermoFisher). Fragment sizes were analyzed on the Agilent Bioanalyzer using the High Sensitivity DNA assay prior to sequencing. Paired-end 50-bp sequencing was performed at The Centre for Applied Genomics (TCAG, Canada) on an Illumina HiSeq2500 Rapid Run (Illumina, USA) with cycles extended to 68 bp using a custom paired-end sequencing primer for read 2 (Diagenode) and the following dark cycle recipe 5DC+58(R1)+8(Index1)+8(Index2)+5DC+58(R2).

treatment_protocol: For the CRISPR/Cas9 deletion experiment, gRNAs targeting the 5′ and 3′ boundaries of ERG exon 6 were designed using the MIT CRISPR design tool (http://crispr.mit.edu/). The gRNAs were purchased from Integrated DNA Technologies (IDT) as standard DNA oligomers. The gRNA oligomers were then annealed, phosphorylated, and cloned into pSpCas9(BB)-2A-GFP (PX458) under the U6 promoter (Addgene Plasmid ID 48138). TeloHAECs were transfected with 2.5 µg of each 5′ and 3′ gRNA-PX458 plasmids or two scramble control gRNA-PX458 plasmids using Lipofectamine 2000 (2 µl/1-µg DNA, Invitrogen) in 100-mm dishes. The GFP+ cell populations, representing cells transfected with the GFP-tagged Cas9 construct, were isolated using FACS with a Becton Dickinson FACSAria sorter after 48 h (SickKids-UHN Flow Cytometry Facility). Non- transfected cells were utilized to set the sorting gates. After recovery, single cells were seeded in 96-well plates and inspected for colonies after 1–2 weeks. Upon 60% confluency, the colonies were split into replicate 96-well plates. Genomic DNA was isolated from one of the replicate plates by lysing cells in 96-well plates for 3 h at 65 °C in a lysis buffer (100-mM NaCl, 10-mM Tris-HCl pH 8, 25-mM EDTA pH 8, 0.5% SDS, 0.2 mg/mL) followed by 15-min inactivation at 95 °C. Genotyping was performed using Taq Polymerase (Invitrogen) with primers flanking the deletion sites or the motif mutation sites. The PCR products were run-on gel electrophoresis, visualized using MiniBIS Pro (DNR Bio-Imaging Systems), gel extracted and sent for Sanger sequencing. Sanger sequencing was confirmed by aligning to the human genome (hg19) using the Blat function in the UCSC Genome Browser. Given the potential of generating undesired large deletions using CRISPR/Cas9, up to three wild type and homozygous clones were tested as that would diminish the likelihood of basing our conclusions on one clone with spurious off target deletions.


title: TeloHAEC 7d-Ctrl-siRNA rep x

description: Library name: WL3755


title: TeloHAEC 72hr ERG siRNA treated RNA-seq rep 3

description: Library name: CC012

value: 72hr ERG siRNA


title: TeloHAEC 72hr ERG siRNA treated RNA-seq rep 1

description: Library name: CC004


title: TeloHAEC 24hr Ctrl siRNA treated RNA-seq rep 4

description: Library name: CC013


title: dERG3(clone67)-exp4

description: Library name: WL1701


title: WT3-exp4

description: Library name: WL1695


title: dERG1(clone9)-exp3

description: Library name: WL1685


title: TeloHAEC 72hr Ctrl siRNA treated RNA-seq rep 1

description: Library name: CC003


title: WT3-exp3

description: Library name: WL1683


title: TeloHAEC 72hr ERG siRNA treated RNA-seq rep 4

description: Library name: CC016


title: TeloHAEC 72hr-ERG-siRNA rep x

description: Library name: WL3748


title: TeloHAEC 72hr ERG siRNA treated RNA-seq rep 2

description: Library name: CC008


title: dERG2(clone15)-exp4

description: Library name: WL1699


title: TeloHAEC 24hr ERG siRNA treated RNA-seq rep 2

description: Library name: CC006


title: WT1-exp4

description: Library name: WL1691


title: dERG3(clone67)-exp3

description: Library name: WL1689


title: WT2-exp3

description: Library name: WL1681


title: dERG2(clone15)-exp3

description: Library name: WL1687


title: WT1-exp3

description: Library name: WL1679


title: TeloHAEC 72hr-ERG-SiRNA rep3

description: Library name: WL3523

tag: genotype

value: WT-ERG


title: TeloHAEC 24hr Ctrl siRNA treated RNA-seq rep 1

description: Library name: CC001


title: TeloHAEC 24hr-ERG-SiRNA rep3

description: Library name: WL3522


title: TeloHAEC 72hr-Ctrl-SiRNA rep3

description: Library name: WL3525


title: WT2-exp4

description: Library name: WL1693


title: TeloHAEC 72hr-Ctrl-SiRNA rep4

description: Library name: WL3521


title: TeloHAEC 72hr-Ctrl-SiRNA rep2

description: Library name: WL3517


title: TeloHAEC 72hr-ERG-SiRNA rep4

description: Library name: WL3519


title: TeloHAEC 24hr-Ctrl-SiRNA rep4

description: Library name: WL3520


title: TeloHAEC 72hr-ERG-SiRNA rep2

description: Library name: WL3515


title: TeloHAEC 24hr-Ctrl-SiRNA rep3

description: Library name: WL3524


title: TeloHAEC 24hr-ERG-SiRNA rep4

description: Library name: WL3518


title: TeloHAEC 24hr-ERG-SiRNA rep2

description: Library name: WL3514


title: GRF5 DAP-seq, Input control

city: Pingdingshan

first: Dongxiao

last: Liu

address: Longxiang Avenue & Yuying Road Intersection, New Urban Area

country: China

institute: Henan University of Urban Construction

description:
Library name: GRF5_1.DAP_input
Direct DNA-binding sites of GRF5

data_processing:
Raw sequencing reads were trimmed to remove adaptor sequences and low-quality bases (Q-score < 30) using Trimmomatic v0.39.
Trimmed reads were aligned to the Arabidopsis thaliana TAIR10 reference genome using Bowtie2 v2.4.6 with default parameters; only uniquely mapping reads were retained for subsequent analysis.
Peak calling was performed using MACS2 v2.2.7.1 with the input control sample to eliminate non-specific binding, applying a q-value cutoff of 0.01.
Assembly: TAIR10 (Arabidopsis thaliana reference genome)
Supplementary files format and content: BAM files: Aligned sequencing reads for DAP-seq replicates and input control; 2. narrowPeak files: GRF5-bound peak regions identified by MACS2 (including peak coordinates, signal intensity, and q-values); 3. tab-delimited text file: Peak annotation (gene overlap, promoter association) and GRF5 target gene list (e.g., NRT1.1, NRT2.1).

organism: Arabidopsis thaliana

source_name: Root tissue

growth_protocol: Arabidopsis thaliana seeds were germinated on MS medium and grown at 22°C with a 16-h light/8-h dark cycle. Seven-day-old seedlings were transferred to low nitrate medium (0.2 mM NO₃⁻) and cultured for 3 days to induce root foraging responses before root tissue collection.

extract_protocol:
Root tissues from low nitrate-treated Arabidopsis seedlings were harvested, ground into powder in liquid nitrogen, and genomic DNA was isolated using the Qiagen DNeasy Plant Mini Kit according to the manufacturer’s instructions; 2. Recombinant GRF5 protein was expressed and purified from Escherichia coli using a His-tag affinity purification system, followed by verification of protein purity via SDS-PAGE.
DAP-seq libraries were prepared as follows: 1. Purified GRF5 protein was incubated with Arabidopsis root genomic DNA fragments (200-500 bp) to form protein-DNA complexes; 2. Protein-bound DNA was enriched via immunoprecipitation with anti-GRF5 antibody; 3. Enriched DNA fragments were used as input for library construction with the KAPA HyperPlus Library Preparation Kit (Roche); 4. Libraries were amplified with 12 PCR cycles, size-selected (250-450 bp) using Agencourt AMPure XP beads, and validated by Agilent High Sensitivity DNA Analysis.

treatment_protocol: Low nitrate treatment: Seedlings were exposed to low nitrate medium (0.2 mM NO₃⁻) for 3 days to activate nitrate-responsive root growth and GRF5-mediated regulatory pathways.

value: Root tissue

value: Primary root cells

value: Wild-type (Col-0)

value: control


title: GRF5 DAP-seq, Biol rep2

description:
Library name: GRF5_1.DAP_rep2
Direct DNA-binding sites of GRF5

value: Low nitrate (0.2 mM NO₃⁻), 3 days


title: LG-Lockwood23-N4

city: Vancouver

first: Jana

last: Jajarmi

state: BC

institute: University of British Columbia

description:
Library name: LG_N4
Lockwood23_LG_data.csv

library_source: other

data_processing:
Reads were aligned to sgRNA library sequences and counted
Supplementary files format and content: csv table showing sgRNA name and average counts across sequencing replicates

molecule: other

organism: synthetic construct

source_name: plasmid

extract_protocol:
Plasmid DNA was extracted from bacterial colonies via Qiagen Maxiprep
Preliminary library sequencing was performed by setting up x4 50uL PCR reactions (PCR1) using Q5® Hot Start High-Fidelity 2X Master Mix (NEB, catalogue number M0494L) using 50ng of plasmid library per reaction. PCR was performed per manufacturer’s instructions for 12 cycles. Forward primer mix for PCR1 was an equimolar mix of 8 primers with varying numbers of degenerate bases (S1-8). Primer sequences are outlined in Supplementary Table 1 (Library-NGS-S1-8-F, Lenti-CRISPR-V2-NGS-R). PCR1 products were pooled and cleaned up using AmpureXP beads (Beckman Coulter, catalogue number A63880) at a ratio of 0.8X. Beads were washed twice with 80% ethanol before being eluted in 50uL IDTE. Eluate was cleaned up again following the same protocol with 0.8X bead ratio, and entire product was eluted into 50uL IDTE. Final product was used as a template for x4 50uL PCR reactions using Q5® Hot Start High-Fidelity 2X Master Mix for barcoding and addition of Illumina sequencing adapters (PCR2). PCRs were run according to manufacturer’s instructions for 10 cycles. PCR2 primer sequences are outlined in Supplementary Table 1. PCR2 products were cleaned up using the same bead protocol described, however only a single binding and elution was performed. Samples were sent to the UBC Sequencing Consortium (USC) for quality check, pooling, and sequencing on Illumina MiSeq using the Nano v2 kit with 20% PhiX spike in. Samples were run using a 2x150bp program, though only Read1 was utilized for sgRNA alignment. sgRNA counts were generated using R, all adapter trimming and sorting was performed by the USC.

value: plasmid

value: Bacterial

value: LG


title: TeloHAEC Del9-ERG ATAC-seq rep1

description: Library name: WL2803

value: TeloHAEC

value: PBS


title: TeloHAEC 24hr-Ctrl-SiRNA rep2

description: Library name: WL3516

value: Aortic endothelial cell


title: whole_blood_temperate_30C_d3_M [MA0050_6_47]

city: CASTANET-TOLOSAN cedex

first: Laure

last: GRESS

address: 24 chemin de Borde Rouge CS52627

department: Occitanie-Toulouse

country: France

institute: INRAE

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201314552

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Pig GE 8x60K (AMID 37880)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R for each microarray analysis serial using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 8 out of the total number of microarrays per serial. The mean signal of the different washing batches were substracted to individuals signals to correct the batch effect of the multiple serials observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has ?????  rows each corresponding to a unique ProbeName (provided as data Matrix).
log2 normalized signal

organism: Sus scrofa

source_name: whole blood,3 days at 30 degrees

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: F1 pigs were obtained from 10 F0 purebred Large White dams inseminated with 5 F0 boars of the Créole breed. Among F1 pigs, 10 were selected for back crossing 130 genetically related Large White sows in two experimental facilities (70 and 60 sows in the tropical and temperate the facility, respectively). The backcross generation resulted in herds of 664 pigs in the tropical facility and 634 pigs in the temperate facility, each composed of females and castrated males.   The temperate animals farm is located in Poitou-Charente, France (INRAE-GenESI, Poitou-Charentes, France; 46° N, 0.45° W); and the tropical farm is located in a French Indies Island (INRAE-PTEA, Guadeloupe, French West Indies; 16° N, 61° W). Data were collected from April 2013 to October 2014.   The average temperature difference between environment was about 1.1°C (25.2°C in temperate, 26.3°C in tropical, on average), the temperature-humidity index difference was 2.4°C (22.9°C in temperate, 25.3 in tropical, on average), resulting in pigs from the tropical facility growing in a heat-stress environment.   Whole blood transcriptome data were generated from a subset of 361 backcross animals: 181 pigs from the tropical facility and 180 pigs from the temperate facility.

extract_protocol: 800µL whole blood (with EDTA anticoagulant) was mixed with 800µL DL buffer (lysis buffer of the RNA extraction kit). Aliquots were then frozen at -20°C for 4 hours prior to freezing at -80°C.  Whole blood RNA extractions were performed using the NucleoSpin 96 RNA Blood, 96-well kit (Macherey-Nagel), following the manufacturer instructions (centrifuge processing). Minor laboratory adaptations were applied: (i) Membrane desalting steps with RB3 buffer were performed twice. (ii) Twice the amount of reconstituted rDNase was used in the rDNase reaction mixture for a 30-minute treatment. (iii) RNA was eluted in a volume of 60 µL.

treatment_protocol: Blood samples were obtained at 23 weeks of age in each facility (noted as d0). Pigs raised in the temperate facility underwent an experimental heat stress challenge. The experimental heat stress period occurred from Monday of week 24 until the end of week 26 (3 weeks), during which pigs were subject to a 30°C temperature. The animals were further sampled for blood at two timepoints: on Thursday of week 24 (noted as d3) and at the end of week 26 (noted as d18).

tag: experimental facility

value: temperate

tag: gender

value: male

tag: breeding batch

tag: condition

tag: wash batch

tag: analysis serial


title: LcV2-Lockwood23-N4

description:
Library name: LcV2_N4
Lockwood23_LcV2_data.csv


title: whole_blood_temperate_24C_d0_M [MA0050_6_43]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313852

source_name: whole blood,24 degrees


title: whole_blood_tropical_ambient_d0_M [MA0050_6_45]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331529

source_name: whole blood,ambient

value: tropical


title: whole_blood_tropical_ambient_d0_F [MA0050_6_46]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430537

value: female


title: LcV2-Lockwood23-N1

description:
Library name: LcV2_N1
Lockwood23_LcV2_data.csv


title: whole_blood_temperate_24C_d0_F [MA0050_6_44]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201411263


title: TeloHAEC Del14-ERG ATAC-seq rep2

description: Library name: WL2804


title: GRF5 DAP-seq, Biol rep1

description:
Library name: GRF5_1.DAP_rep1
Direct DNA-binding sites of GRF5

tag: tissue


title: TeloHAEC WT ATAC-seq rep1

description: Library name: WL2801


title: LcV2-Lockwood23-N2

description:
Library name: LcV2_N2
Lockwood23_LcV2_data.csv


title: LcV2-Lockwood23-N3

description:
Library name: LcV2_N3
Lockwood23_LcV2_data.csv


title: whole_blood_temperate_24C_d0_F [MA0050_6_42]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310944


title: whole_blood_temperate_30C_d3_F [MA0050_6_39]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315547


title: LG-Lockwood23-N3

description:
Library name: LG_N3
Lockwood23_LG_data.csv


title: whole_blood_tropical_ambient_d0_F [MA0050_6_40]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331301


title: whole_blood_tropical_ambient_d0_M [MA0050_6_41]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330317


title: whole_blood_tropical_ambient_d0_M [MA0050_6_38]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430531


title: whole_blood_temperate_30C_d3_M [MA0050_6_37]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313248


title: whole_blood_temperate_24C_d0_F [MA0050_6_36]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311487


title: whole_blood_temperate_24C_d0_M [MA0050_6_35]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410594


title: whole_blood_temperate_30C_d18_M [MA0050_6_34]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313234

source_name: whole blood,18 days at 30 degrees


title: whole_blood_temperate_30C_d18_F [MA0050_6_32]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410513


title: whole_blood_temperate_24C_d0_M [MA0050_6_33]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201314807


title: whole_blood_temperate_30C_d18_M [MA0050_6_31]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315283


title: whole_blood_tropical_ambient_d0_M [MA0050_6_30]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430035


title: whole_blood_temperate_30C_d18_F [MA0050_6_28]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315212


title: TeloHAEC WT ATAC-seq rep2

description: Library name: WL2802


title: whole_blood_tropical_ambient_d0_F [MA0050_6_26]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331133


title: whole_blood_temperate_30C_d3_F [MA0050_6_27]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313228


title: whole_blood_temperate_24C_d0_M [MA0050_6_25]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311730


title: whole_blood_tropical_ambient_d0_M [MA0050_6_19]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430549


title: whole_blood_temperate_30C_d18_M [MA0050_6_18]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201312476


title: whole_blood_temperate_30C_d3_M [MA0050_6_20]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315282


title: whole_blood_temperate_30C_d18_F [MA0050_6_11]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310774


title: whole_blood_temperate_30C_d3_M [MA0050_6_23]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201314563


title: whole_blood_temperate_30C_d18_M [MA0050_6_29]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201314563


title: whole_blood_tropical_ambient_d0_M [MA0050_6_24]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430575


title: whole_blood_tropical_ambient_d0_F [MA0050_6_10]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331300


title: whole_blood_tropical_ambient_d0_M [MA0050_6_16]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330733


title: whole_blood_temperate_30C_d3_F [MA0050_6_12]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313845


title: whole_blood_temperate_30C_d18_F [MA0050_6_15]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310276


title: whole_blood_temperate_30C_d3_F [MA0050_6_21]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311710


title: whole_blood_temperate_24C_d0_M [MA0050_6_17]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410523


title: whole_blood_tropical_ambient_d0_F [MA0050_6_8]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331148


title: whole_blood_temperate_30C_d18_F [MA0050_6_7]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201312442


title: whole_blood_temperate_30C_d18_F [MA0050_6_9]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201314801


title: whole_blood_tropical_ambient_d0_F [MA0050_6_14]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330979


title: whole_blood_temperate_24C_d0_F [MA0050_6_5]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315299


title: whole_blood_temperate_30C_d3_M [MA0050_6_3]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201316049


title: whole_blood_temperate_30C_d3_F [MA0050_6_4]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310894


title: whole_blood_temperate_24C_d0_F [MA0050_6_13]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410593


title: whole_blood_tropical_ambient_d0_F [MA0050_6_2]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330109


title: whole_blood_tropical_ambient_d0_F [MA0050_6_22]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330321


title: whole_blood_tropical_ambient_d0_F [MA0050_6_6]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331595


title: whole_blood_temperate_24C_d0_F [MA0050_5_94]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201411265


title: whole_blood_temperate_24C_d0_F [MA0050_6_1]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315280


title: whole_blood_tropical_ambient_d0_F [MA0050_5_96]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430589


title: whole_blood_temperate_30C_d3_F [MA0050_5_93]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310263


title: whole_blood_temperate_30C_d3_F [MA0050_5_90]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315215


title: whole_blood_temperate_30C_d18_M [MA0050_5_92]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313205


title: whole_blood_temperate_30C_d3_M [MA0050_5_89]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313232


title: whole_blood_temperate_30C_d18_F [MA0050_5_85]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201316134


title: whole_blood_temperate_30C_d18_F [MA0050_5_88]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313843


title: whole_blood_tropical_ambient_d0_M [MA0050_5_84]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331558


title: whole_blood_temperate_30C_d3_F [MA0050_5_86]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310261


title: whole_blood_temperate_30C_d3_M [MA0050_5_91]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410497


title: whole_blood_temperate_30C_d3_F [MA0050_5_83]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315301


title: whole_blood_temperate_24C_d0_M [MA0050_5_78]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201312434


title: whole_blood_tropical_ambient_d0_M [MA0050_5_74]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430130


title: whole_blood_temperate_24C_d0_M [MA0050_5_87]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201411223


title: whole_blood_temperate_24C_d0_M [MA0050_5_82]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310914


title: whole_blood_temperate_30C_d3_M [MA0050_5_76]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313874


title: whole_blood_temperate_30C_d3_M [MA0050_5_80]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313246


title: whole_blood_temperate_30C_d18_F [MA0050_5_75]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201314558


title: whole_blood_tropical_ambient_d0_M [MA0050_5_73]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330973


title: whole_blood_temperate_24C_d0_M [MA0050_5_95]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313135


title: whole_blood_tropical_ambient_d0_M [MA0050_5_72]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331338


title: whole_blood_temperate_30C_d18_F [MA0050_5_68]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315211


title: whole_blood_temperate_30C_d18_M [MA0050_5_66]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313960


title: whole_blood_temperate_30C_d3_M [MA0050_5_71]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313208


title: whole_blood_tropical_ambient_d0_F [MA0050_5_77]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331316


title: whole_blood_temperate_30C_d3_M [MA0050_5_70]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313919


title: whole_blood_temperate_30C_d3_F [MA0050_5_63]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315212


title: whole_blood_tropical_ambient_d0_M [MA0050_5_69]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430113


title: whole_blood_tropical_ambient_d0_F [MA0050_5_67]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330145


title: whole_blood_tropical_ambient_d0_F [MA0050_5_62]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430255


title: whole_blood_temperate_24C_d0_F [MA0050_5_58]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310030


title: whole_blood_temperate_30C_d3_F [MA0050_5_56]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313934


title: whole_blood_tropical_ambient_d0_F [MA0050_5_57]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330131


title: whole_blood_temperate_30C_d18_M [MA0050_5_79]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410497


title: whole_blood_tropical_ambient_d0_F [MA0050_5_65]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331342


title: whole_blood_tropical_ambient_d0_F [MA0050_5_64]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430097


title: whole_blood_tropical_ambient_d0_M [MA0050_5_60]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330962


title: whole_blood_temperate_30C_d3_M [MA0050_5_81]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311643


title: whole_blood_tropical_ambient_d0_F [MA0050_5_50]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331048


title: whole_blood_temperate_30C_d3_M [MA0050_5_59]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315557


title: whole_blood_temperate_24C_d0_F [MA0050_5_46]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313204


title: whole_blood_temperate_30C_d18_F [MA0050_5_54]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201316131


title: whole_blood_temperate_30C_d18_F [MA0050_5_55]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310261


title: whole_blood_tropical_ambient_d0_M [MA0050_5_51]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330713


title: whole_blood_temperate_30C_d3_F [MA0050_5_61]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410593


title: whole_blood_temperate_30C_d18_M [MA0050_5_45]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313852


title: whole_blood_temperate_30C_d3_M [MA0050_5_40]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410695


title: whole_blood_tropical_ambient_d0_F [MA0050_5_52]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330147


title: whole_blood_tropical_ambient_d0_M [MA0050_5_47]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330150


title: whole_blood_temperate_30C_d18_F [MA0050_5_53]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313957


title: whole_blood_temperate_30C_d3_F [MA0050_5_39]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311636


title: whole_blood_tropical_ambient_d0_F [MA0050_5_44]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330724


title: whole_blood_temperate_30C_d18_M [MA0050_5_48]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315305


title: whole_blood_temperate_30C_d3_F [MA0050_5_49]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313125


title: whole_blood_temperate_30C_d3_F [MA0050_5_35]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315297


title: whole_blood_tropical_ambient_d0_F [MA0050_5_42]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330337


title: whole_blood_tropical_ambient_d0_F [MA0050_5_43]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330685


title: Si3, Cut&Tag

city: Guangzhou

first: Zhiping

state: Guangdong

address: No. 855, East Xingye Avenue

institute: Jinan University

description: Library name: Si_rep3

data_processing:
Cutadapt was conducted for trimming raw fastq files to remove adaptors and low-quality bases.
The trimmed fastq files were then mapped to the mm10 reference genome utilizing Bowtie2
Then uniquely mapped reads were obtained using SAMtools.
Picard was used to remove duplicates and For visualization, deepTools was utilized with the “bamCoverage” function to generate normalized RPM bigWig files. Then MACS2 was utilized for peak calling.
Assembly: mm10
Supplementary files format and content: BigWig
Library strategy: CUT&Tag

organism: Mus musculus

source_name: VSMC

growth_protocol: Mouse primary VSMCs were isolated from C57BL/6J mice and grown in medium at 37°C and 5% CO2.

extract_protocol:
CUT&Tag was performed with a Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (pA/G-Tnp) (TD904, Vazyme Biotech) according to the manufacturer’s instructions. VSMCs treated with scramble or Slc1a5 siRNA were collected, incubated, and bound to concanavalin A-coated magnetic beads. Then, VSMCs were resuspended, incubated with H3K9ac antibodies overnight at 4 °C, and then incubated with secondary antibodies. The samples were incubated with pA/G-Tnp for transposition. After tagmentation, DNA was isolated, amplified, and purified to construct a library.
DNA libraries were prepared using TruePrep Index Kit V2 for Illumina following manufacturer's instructions.

treatment_protocol: VSMC cells are uniformly seeded to achieve a density of about 70% at the time of transfection. Diluted siRNA (supplied by GenePharma) is combined with Opti-MEM and Lipofectamin RNAiMAX Reagent, allowed to incubate at room temperature for 5 minutes, and then applied to the cell-plated wells. Following this, the cells are incubated at 37°C for 72 hours, with transfection efficiency subsequently evaluated through Western Blot analysis.

value: VSMC

value: Mouse Vascular Smooth Muscle Cells


title: whole_blood_temperate_24C_d0_M [MA0050_5_36]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313229


title: whole_blood_tropical_ambient_d0_F [MA0050_5_34]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430359


title: whole_blood_tropical_ambient_d0_F [MA0050_5_32]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331173


title: whole_blood_temperate_30C_d3_F [MA0050_5_30]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201314543


title: whole_blood_temperate_24C_d0_F [MA0050_5_41]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310775


title: NC, IgG, Cut&Tag

description: Library name: NC_IgG

value: Negative control

value: IgG


title: whole_blood_temperate_24C_d0_M [MA0050_5_38]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311494


title: Si, IgG, Cut&Tag

description: Library name: Si_IgG


title: whole_blood_temperate_24C_d0_F [MA0050_5_29]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311727


title: whole_blood_temperate_30C_d3_M [MA0050_5_31]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201314806


title: Si1, Cut&Tag

description: Library name: Si_rep1


title: whole_blood_temperate_24C_d0_M [MA0050_5_28]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313958


title: whole_blood_temperate_30C_d18_F [MA0050_5_26]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201316133


title: Si2, Cut&Tag

description: Library name: Si_rep2


title: whole_blood_temperate_30C_d3_M [MA0050_5_27]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313851


title: whole_blood_tropical_ambient_d0_M [MA0050_5_37]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330098


title: whole_blood_temperate_30C_d18_M [MA0050_5_18]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410594


title: whole_blood_tropical_ambient_d0_F [MA0050_5_24]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330110


title: whole_blood_temperate_30C_d18_F [MA0050_5_25]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315299


title: NC1, Cut&Tag

description: Library name: NC_rep1


title: NC2, Cut&Tag

description: Library name: NC_rep2


title: whole_blood_temperate_24C_d0_F [MA0050_5_23]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313869


title: ChIP_DKO-SL1FA_HDAC1

city: Toyonaka

first: Takamasa

last: Ito

state: Osaka

address: 1-1 Machikaneyama

department: Biological Science

country: Japan

institute: Osaka University

description: Library name: ChIP_DKO-SL1FA_HDAC1

data_processing:
Reads were trimmed using Trim Galore (v0.6.10) and aligned to the mm10 genome using Bowtie2 (v2.5.4) with --very-sensitive, --no-unal ,--no-mixed and --no-discordant options. Reads with low mapping quality (MAPQ < 5) were discarded using Samtools. PCR duplicates were removed using MarkDuplicates command in Picard (v3.3.0, Broad Institute). BigWig files were created using bamCoverage command in deepTools (v3.5.5) with --normaliseUsing CPM, --binSize 25, --smoothLength 100, --extendReads and --centerReads options. Log2(ChIP/input) was caluculated using bigwigCompare command in deepTools.
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: TT2 mESCs are kindly gifted from Dr. Tachibana in Osaka university. mESCs were cultured on dishes coated with 0.1% gelatin in DMEM (Nacalai, 08458-16) supplemented with 10% Knockout Serum Replacement (Gibco, 10828028), 1% FBS (HyClone, SH30070.03), 1× sodium pyruvate (Wako, 190-14881), 1× non-essential amino acids (Wako, 139-15651), 0.1 mM 2-mercaptoethanol (Wako, 133-14571), penicillin-streptomycin (Gibco, 15140122), and LIF (produced in-house) at 37˚C with 5% CO2. mESCs were passaged every 2-3 days using 0.05% trypsin-EDTA (Nacalai, 32777-44).  For retinoic acid differentiation, cells were cultured in ES medium without LIF and supplemented with 5 µM retinoic acid. After 72 hours of induction, the cells were used for subsequent analysis.

extract_protocol:
ChIP was performed as described previously (Nozawa et al., NCB, 2010) with a few modifications. Approximately 1×10^7 cells were prepared in 10 cm culture dishes and crosslinked with 5% formaldehyde (Thermo Fisher Scientific, 28908) for 5 min, whereas RCOR2-FLAG and HDAC1 ChIP samples were crosslinked with 1% formaldehyde for 10 min. Crosslinking was quenched with 200 mM glycine for 5 min and then cells were lysed with the lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 0.5% NP-40 or 0.5% IGEPAL CA-630, 0.1mM PMSF, 2 µg/ml leupeptin) for 7 min. Cells were collected in 1.5 ml tubes and centrifuged at 800g for 3 min. The supernatant was then discarded, and pellets were resuspended with the SDS lysis buffer (50 mM Tris-HCl, 10 mM EDTA, 1% SDS, 0.1mM PMSF, 2 µg/ml leupeptin). Lysates were diluted with ChIP dilution buffer (50 mM Tris-HCl, 167 mM NaCl, 1.1% Triton X-100, 0.11% SDS, 0.1mM PMSF, 2 µg/ml leupeptin) and sonicated for 24 cycles (15 s ON/30 s OFF per cycle) using Bioruptor (Cosmo Bio, UCD-250). The sonicated chromatin was centrifuged at 16,000g for 15 min and the supernatant was collected. The chromatin was then snap-frozen in liquid nitrogen and stored at -80˚C until further use. 50 µl of Dynabeads M-280 Sheep anti-Mouse IgG (Thermo Fisher Scientific, 11202D) for mouse IgG or Dynabeads Protein A (Thermo Fisher Scientific, 10002D) for rabbit IgG were incubated with 1 µg of purified IgG or 10 µl of hybridoma culture supernatant at 4°C for 2 hours. Chromatin from 3–5×106 cells was incubated with the pre-incubated beads at 4˚C for 2 hours, followed by washing once with RIPA-150 buffer (50 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 0.1 mM PMSF, 2 µg/ml leupeptin), once with RIPA-500 buffer (50 mM Tris-HCl, 500 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 0.1 mM PMSF, 2 µg/ml leupeptin), and twice with TE buffer (10 mM Tris-HCl, 1 mM EDTA, 0.1 mM PMSF, 2 µg/ml leupeptin). Reverse-crosslinking and elution were performed with ChIP direct elution buffer (10 mM Tris-HCl, 300 mM NaCl, 5 mM EDTA, 0.5% SDS, 0.1 mM PMSF, 2 µg/ml leupeptin) at 65°C overnight. The eluted chromatin was treated with 0.5 µg/ml RNase at 37°C for 30 minutes, followed by the addition of 50 µg/ml Proteinase K at 55°C for 1 hour. ChIPed or input DNA was purified using a QIAquick PCR Purification Kit (Qiagen, 28104).
ChIP libraries were prepared with up to 20 ng of DNA using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L). Library quality control was performed using a Qubit 4 Fluorometer (Thermo Fisher Scientific, Q33238) and an Agilent 2100 Bioanalyzer (Agilent Technologies), followed by sequencing on an Illumina NovaSeq X Plus platform with a paired-end 150 bp system (Macrogen Japan Inc.).

value: mouse embryoic stem cell

value: Rlf/Zfp292 KO


title: whole_blood_temperate_30C_d18_M [MA0050_5_16]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201314552


title: whole_blood_temperate_30C_d3_M [MA0050_5_33]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201316135


title: whole_blood_tropical_ambient_d0_M [MA0050_5_20]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331129


title: ChIP_WT-SL_H3K4me2

description: Library name: ChIP_WT-SL_H3K4me2

value: WT


title: whole_blood_temperate_30C_d18_M [MA0050_5_22]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313949


title: ChIP_DKO-RCOR2-FLAG-SL1FA_FLAG

description: Library name: ChIP_DKO-RCOR2-FLAG-SL1FA_FLAG

value: Rlf/Zfp292 KO RCOR2-FLAG


title: ChIP_RCOR2-FLAG-SL1FA_FLAG

description: Library name: ChIP_RCOR2-FLAG-SL1FA_FLAG


title: ChIP_DKO-RCOR2-FLAG-SL1FA_input

description: Library name: ChIP_DKO-RCOR2-FLAG-SL1FA_input


title: whole_blood_temperate_30C_d18_F [MA0050_5_19]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201314543


title: ChIP_RCOR2-FLAG-SL1FA_input

description: Library name: ChIP_RCOR2-FLAG-SL1FA_input


title: ChIP_DKO-SL_H3K4me2

description: Library name: ChIP_DKO-SL_H3K4me2


title: whole_blood_temperate_30C_d18_M [MA0050_5_15]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313208


title: whole_blood_temperate_30C_d18_M [MA0050_5_21]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310914


title: whole_blood_temperate_24C_d0_F [MA0050_5_17]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313953


title: ChIP_DKO-SL1FA_input

description: Library name: ChIP_DKO-SL1FA_input


title: NC3, Cut&Tag

description: Library name: NC_rep3


title: Deep-Sequenced, Cerebellum, Integrated-ACE-Seq

city: Philadelphia

first: Rahul

middle: M.

last: Kohli

state: Pennsylvania

address: 3610 Hamilton Walk, 502B Johnson Pavilion

department: Department of Medicine

institute: University of Pennsylvania

description: Library name: DeepCerebellumIntegratedACE

data_processing:
For ACE/EM-Seq samples, raw reads were trimmed for base quality and adaptor sequences using Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and reads below a length of 20 bases were discarded.
For ACE/EM-Seq samples, the trimmed reads were then aligned to the reference genomes using Bismark (v0.22.3) with the following parameters -D 15 -R 2 -L 20 -N 0 –score_min L,0,-0.2.
For ACE/EM-Seq samples, to account for A3A failure due to double-stranded DNA, reads with three or more consecutive non-converted cytosines in the CpH context were removed using the filter_non_conversion script included in the Bismark package.
For Integrated-Seq samples, the Epimatcher code used for processing Integrated-Seq data is described and available at https://github.com/zhou-lab/epimatcher/tree/main
Assembly: mm10
Supplementary files format and content: Bismark.cov is a tab-delimited file containing the chromosome, start position, end position, methylation percentage, count methylated, count unmethylated
Supplementary files format and content: Mods.bed is a tab-delimited file containing the chromosome, start position, end position, count methylated, count hydroxymethylated, count unmethylated

source_name: Cerebellum

extract_protocol:
Genomic DNA from different tissue types (cerebellum, heart, kidney, blood) were extracted from C57BL/6J mice (Jackson Labs). Extraction was carried out using a phenol/chloroform/isoamyl alcohol protocol. 500 µL of the lysed mouse tissues were transferred to pre-centrifuged (at 20,000g for 1 min) 5PRIME Phase Lock Gel tube (Quanta bio, 10847- 802). In a fume hood, 500 µL of phenol/chloroform/isoamyl alcohol (Sigma-Aldrich, 77617) was added to the phase Lock Gel tube. The aqueous phase was then transferred to a new 1.5 mL tube. 500 µl of 100% isopropanol (MilliporeSigma), 1.7 µl of GlycoBlue (Invitrogen), and 33 µl of 7.5 M ammonium acetate solution (Sigma-Aldrich) were added. The mixture was vortexed and incubated at -20°C for 30 min overnight. The samples were subsequently centrifuged at 16,000g for 30 min at 4°C. Following centrifugation, the samples were washed twice with 1 mL of 70% ethanol (MilliporeSigma). After the final wash and removal of 70% ethanol, the samples were air-dried for 10 min and then resuspended in 46 to 200 µL of Tris buffer pH 8.0 at 55°C for 10 min. If the DNA was not fully dissolved, it was further incubated at 4°C for one to two days. DNA concentration was measured using a Qubit 4.0 Fluorometer (Invitrogen) with the dsDNA HS Assay Kit (Invitrogen).
For shallow-sequenced mouse tissues, 30 ng of purified mouse gDNA was mixed with 5% of unmethylated λ gDNA spike-in and 5% 5mCpG methylated plasmid spike-in, in a total volume of 50 µL in low TE buffer. This input DNA was then sheared to 350 bp using a Covaris instrument. Each sample was then split three ways to serve as technical replicates, with each treated as a sample starting from a 10 ng input. Libraries were prepared using the ACE-Seq, EM-Seq, Integrated ACE-Seq, or Integrated EM-Seq protocols detailed in the corresponding manuscript. Final libraries were quantified with a Qubit HS kit (Invitrogen), assessed for quality using an Agilent TapeStation D1000, and sequenced on an Illumina MiSeq. For deeply sequenced samples, the same protocol was used except with 50 ng of input used, without splitting.

value: Cerebellum


title: 24 month, replicate 2

city: Chicago

first: Aubrey

last: Converse

state: IL

address: 303 E superior

institute: Northwestern University Feinberg School of Medicine

description:
Library name: S22m_2_S99
Column name in ALL_deseq_unnormalized_counts_annotated.csv

data_processing:
The read quality, in FASTQ format, was evaluated using FastQC
Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt
Trimmed reads were aligned to the Mus musculus genome (mm10) using STAR
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for mm10 obtained from Ensembl
Assembly: mm10
Supplementary files format and content: Csv file contains unnormalized counts for each sample

source_name: Ovary

extract_protocol:
RNA was isolated with Trizol followed by RNeasy MinElute Cleanup Kit (Qiagen). An on-column DNase digestion step was included. Cell content was used as direct input for cDNA generation and 500ug of cDNA was used as input for library generation.
RNA libraries were prepared with an Illumina Stranded mRNA-Seq Library Prep kit following the manufacturer's protocol.

value: Ovary


title: whole_blood_temperate_24C_d0_F [MA0050_5_4]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201316133


title: ChIP_WT-SL1FA_HDAC1

description: Library name: ChIP_WT-SL1FA_HDAC1


title: Deep-Sequenced, Cerebellum, ACE-Seq

description: Library name: DeepCerebellumACE


title: ChIP_WT-SL1FA_input

description: Library name: ChIP_WT-SL1FA_input


title: whole_blood_temperate_30C_d18_M [MA0050_5_14]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310271


title: whole_blood_temperate_30C_d3_M [MA0050_5_6]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410524


title: whole_blood_temperate_24C_d0_F [MA0050_5_13]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310230


title: 18 month, replicate 2

description:
Library name: S18m_2_S95
Column name in ALL_deseq_unnormalized_counts_annotated.csv


title: whole_blood_temperate_30C_d3_M [MA0050_5_9]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310271


title: whole_blood_temperate_24C_d0_M [MA0050_5_11]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201411222


title: 2 month, replicate 4

description:
Library name: S8wk_4_S93
Column name in ALL_deseq_unnormalized_counts_annotated.csv


title: whole_blood_tropical_ambient_d0_F [MA0050_5_7]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330351


title: RNA_DKO-RA72h_rep3

description: Library name: RNA_DKO-RA72h_rep3

data_processing:
eads were trimmed using Trim Galore (v0.6.10) and aligned to the mm10 genome using STAR (v2.7.11b). Read counts per gene were counted using featureCounts command in Subread package (v2.0.6). Raw count data were normalized, and differential gene expression analysis was performed using DESeq2 (v1.44.0). Differentially expressed genes (DEGs) were defined by an adjusted p-value < 0.05 and |Log2(fold change)| > 1.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Total RNA was extracted using ISOGEN according to the manufacturer's instructions.
Libraries were prepared from three biological replicates per sample and sequenced with Illumina NovaSeq X plus using a paired-end 150 bp system at Novogene (Beijing, China).

value: 5 µM retinoic acid 72h


title: whole_blood_temperate_30C_d18_F [MA0050_5_12]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201312425


title: whole_blood_temperate_24C_d0_M [MA0050_5_5]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313919


title: whole_blood_temperate_30C_d3_F [MA0050_5_10]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201312469


title: 2 month, replicate 2

description:
Library name: S8wk_2_S91
Column name in ALL_deseq_unnormalized_counts_annotated.csv


title: whole_blood_temperate_24C_d0_M [MA0050_4_93]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315557


title: 2 month, replicate 1

description:
Library name: S8wk_1_S90
Column name in ALL_deseq_unnormalized_counts_annotated.csv


title: 24 month, replicate 3

description:
Library name: S22m_3_S100
Column name in ALL_deseq_unnormalized_counts_annotated.csv


title: 18 month, replicate 4

description:
Library name: S18m_4_S97
Column name in ALL_deseq_unnormalized_counts_annotated.csv


title: whole_blood_temperate_30C_d18_F [MA0050_5_3]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315280


title: 2 month, replicate 3

description:
Library name: S8wk_3_S92
Column name in ALL_deseq_unnormalized_counts_annotated.csv


title: whole_blood_temperate_30C_d18_F [MA0050_5_1]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201314542


title: whole_blood_tropical_ambient_d0_M [MA0050_5_2]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331515


title: RNA_WT-RA72h_rep1

description: Library name: RNA_WT-RA72h_rep1


title: whole_blood_temperate_30C_d18_M [MA0050_4_96]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315549


title: whole_blood_temperate_30C_d3_M [MA0050_4_90]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311654


title: 18 month, replicate 1

description:
Library name: S18m_1_S94
Column name in ALL_deseq_unnormalized_counts_annotated.csv


title: 24 month, replicate 1

description:
Library name: S22m_1_S98
Column name in ALL_deseq_unnormalized_counts_annotated.csv


title: 18 month, replicate 3

description:
Library name: S18m_3_S96
Column name in ALL_deseq_unnormalized_counts_annotated.csv


title: whole_blood_temperate_24C_d0_F [MA0050_4_95]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313151


title: RNA_DKO-RA72h_rep1

description: Library name: RNA_DKO-RA72h_rep1


title: whole_blood_temperate_30C_d18_M [MA0050_4_94]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201411301


title: RNA_DKO-RA72h_rep2

description: Library name: RNA_DKO-RA72h_rep2


title: whole_blood_temperate_30C_d18_F [MA0050_4_85]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315552


title: whole_blood_temperate_24C_d0_M [MA0050_4_92]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313205


title: RNA_WT-RA72h_rep2

description: Library name: RNA_WT-RA72h_rep2


title: RNA_WT-RA72h_rep3

description: Library name: RNA_WT-RA72h_rep3


title: ChIP_DKO-SL_LSD1

description: Library name: ChIP_DKO-SL_LSD1

extract_protocol:
ChIP was performed as described previously (Nozawa et al., NCB, 2010) with a few modifications. Approximately 1×107 cells were prepared in 10 cm culture dishes and crosslinked with 5% formaldehyde (Thermo Fisher Scientific, 28908) for 5 min. Crosslinking was quenched with 200 mM glycine for 5 min and then cells were lysed with the lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 0.5% NP-40 or 0.5% IGEPAL CA-630, 0.1mM PMSF, 2 µg/ml leupeptin) for 7 min. Cells were collected in 1.5 ml tubes and centrifuged at 800g for 3 min. The supernatant was then discarded, and pellets were resuspended with the SDS lysis buffer (50 mM Tris-HCl, 10 mM EDTA, 1% SDS, 0.1mM PMSF, 2 µg/ml leupeptin). Lysates were diluted with ChIP dilution buffer (50 mM Tris-HCl, 167 mM NaCl, 1.1% Triton X-100, 0.11% SDS, 0.1mM PMSF, 2 µg/ml leupeptin) and sonicated for 24 cycles (15 s ON/30 s OFF per cycle) using Bioruptor (Cosmo Bio, UCD-250). The sonicated chromatin was centrifuged at 16,000g for 15 min and the supernatant was collected. The chromatin was then snap-frozen in liquid nitrogen and stored at -80˚C until further use. 50 µl of Dynabeads M-280 Sheep anti-Mouse IgG (Thermo Fisher Scientific, 11202D) for mouse IgG or Dynabeads Protein A (Thermo Fisher Scientific, 10002D) for rabbit IgG were incubated with 1 µg of purified IgG or 10 µl of hybridoma culture supernatant at 4°C for 2 hours. Chromatin from 3–5×106 cells was incubated with the pre-incubated beads at 4˚C for 2 hours, followed by washing once with RIPA-150 buffer (50 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 0.1 mM PMSF, 2 µg/ml leupeptin), once with RIPA-500 buffer (50 mM Tris-HCl, 500 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 0.1 mM PMSF, 2 µg/ml leupeptin), and twice with TE buffer (10 mM Tris-HCl, 1 mM EDTA, 0.1 mM PMSF, 2 µg/ml leupeptin). Reverse-crosslinking and elution were performed with ChIP direct elution buffer (10 mM Tris-HCl, 300 mM NaCl, 5 mM EDTA, 0.5% SDS, 0.1 mM PMSF, 2 µg/ml leupeptin) at 65°C overnight. The eluted chromatin was treated with 0.5 µg/ml RNase at 37°C for 30 minutes, followed by the addition of 50 µg/ml Proteinase K at 55°C for 1 hour. ChIPed or input DNA was purified using a QIAquick PCR Purification Kit (Qiagen, 28104).
ChIP libraries were prepared with up to 20 ng of DNA using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L). Library quality control was performed using a Qubit 4 Fluorometer (Thermo Fisher Scientific, Q33238) and an Agilent 2100 Bioanalyzer (Agilent Technologies), followed by sequencing on an Illumina NovaSeq X Plus platform with a paired-end 150 bp system (Macrogen Japan Inc.).


title: whole_blood_temperate_24C_d0_F [MA0050_4_88]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310029


title: RNA_DKO-SL_rep1

description: Library name: RNA_DKO-SL_rep1


title: whole_blood_temperate_24C_d0_M [MA0050_4_91]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201316038


title: RNA_DKO-SL_rep3

description: Library name: RNA_DKO-SL_rep3


title: whole_blood_temperate_30C_d3_F [MA0050_4_89]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313953


title: whole_blood_temperate_30C_d18_M [MA0050_4_86]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410523


title: whole_blood_temperate_30C_d18_M [MA0050_4_84]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310888


title: whole_blood_tropical_ambient_d0_M [MA0050_4_83]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331214


title: whole_blood_temperate_24C_d0_F [MA0050_4_80]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410592


title: RNA_DKO-SL_rep2

description: Library name: RNA_DKO-SL_rep2