title: 1012-00007.Psoriasis.LS.Week1.Ustekinumab45mg


title: 2012-00019.Psoriasis.LS.Week1.Ustekinumab45mg

status: Public on Feb 01 2019

type: RNA

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

country: USA

institute: The Rockefeller University

description: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lesional tissue of psoriasis patient

label_protocol: GeneChip Affymetrix protocol

extract_protocol: QIAGEN Rneasy Kit

tag: subjectid

tag: condition

value: Psoriasis

tag: tissue

value: Lesional

tag: timepoint

value: Week 1

tag: treatment

value: Ustekinumab 45 mg

tag: pasi75 response at week 12

value: R

tag: pasi

tag: technique

value: Vivo

tag: amplification cycles


title: 1006-00005.Psoriasis.LS.Week1.Ustekinumab45mg


title: 1025-00004.Psoriasis.LS.Week1.Ustekinumab45mg

value: NR


title: 1022-00003.Psoriasis.LS.Week1.Ustekinumab45mg


title: 1022-00020.Psoriasis.LS.Week1.Ustekinumab45mg


title: 2016-00001.Psoriasis.LS.Week1.Ustekinumab45mg


title: 1019-00001.Psoriasis.LS.Week1.Ustekinumab90mg

value: Ustekinumab 90 mg


title: 1016-00016.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1012-00008.Psoriasis.LS.Week1.Ustekinumab90mg


title: 2016-00009.Psoriasis.LS.Week1.Ustekinumab90mg


title: 2012-00031.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1022-00025.Psoriasis.LS.Week1.Ustekinumab90mg


title: 2016-00025.Psoriasis.LS.Week1.Ustekinumab90mg


title: 2016-00013.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1022-00026.Psoriasis.LS.Week1.Ustekinumab90mg


title: 2016-00007.Psoriasis.LS.Week1.Ustekinumab90mg


title: 2012-00023.Psoriasis.LS.Week1.Ustekinumab90mg


title: 2016-00037.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1019-00010.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1022-00014.Psoriasis.LS.Week1.Ustekinumab90mg


title: 2012-00008.Psoriasis.LS.Week1.Ustekinumab90mg


title: 2016-00020.Psoriasis.LS.Baseline.Etanercept

value: Baseline

value: Etanercept


title: 1019-00004.Psoriasis.LS.Baseline.Etanercept


title: 1022-00001.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1022-00002.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1019-00008.Psoriasis.LS.Week1.Ustekinumab90mg


title: 2012-00042.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1016-00014.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1025-00009.Psoriasis.LS.Week1.Ustekinumab90mg


title: 2016-00035.Psoriasis.LS.Baseline.Etanercept


title: 1025-00002.Psoriasis.LS.Baseline.Etanercept


title: 1022-00019.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1019-00003.Psoriasis.LS.Baseline.Etanercept


title: 1012-00003.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1025-00005.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1025-00008.Psoriasis.LS.Baseline.Etanercept


title: 1025-00006.Psoriasis.LS.Baseline.Etanercept


title: 2015-00002.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1016-00003.Psoriasis.LS.Baseline.Etanercept


title: 1012-00005.Psoriasis.LS.Baseline.Etanercept


title: 1022-00004.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1006-00002.Psoriasis.LS.Baseline.Etanercept


title: 1006-00004.Psoriasis.LS.Baseline.Etanercept


title: 2012-00036.Psoriasis.LS.Baseline.Etanercept


title: 2015-00005.Psoriasis.LS.Baseline.Etanercept


title: 2016-00026.Psoriasis.LS.Baseline.Etanercept


title: 1022-00017.Psoriasis.LS.Baseline.Etanercept


title: 1022-00012.Psoriasis.LS.Baseline.Etanercept


title: 1016-00013.Psoriasis.LS.Baseline.Etanercept


title: 1019-00014.Psoriasis.LS.Baseline.Etanercept


title: 2016-00031.Psoriasis.LS.Baseline.Etanercept


title: 1016-00017.Psoriasis.LS.Baseline.Etanercept


title: 1022-00006.Psoriasis.LS.Baseline.Etanercept


title: 2016-00006.Psoriasis.LS.Baseline.Etanercept


title: 2015-00012.Psoriasis.LS.Baseline.Etanercept


title: 2012-00038.Psoriasis.LS.Baseline.Etanercept


title: 1012-00007.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 1012-00004.Psoriasis.LS.Baseline.Etanercept


title: 1016-00008.Psoriasis.LS.Baseline.Etanercept


title: 1025-00004.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 2016-00018.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 1022-00027.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 1022-00009.Psoriasis.LS.Baseline.Etanercept


title: 2012-00019.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 2016-00001.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 2016-00019.Psoriasis.LS.Baseline.Etanercept


title: 1022-00003.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 1012-00002.Psoriasis.LS.Baseline.Etanercept


title: 2015-00001.Psoriasis.LS.Baseline.Etanercept


title: 1019-00016.Psoriasis.LS.Baseline.Etanercept


title: 1022-00005.Psoriasis.LS.Baseline.Etanercept


title: 1019-00015.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 1016-00011.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 2016-00008.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 1016-00010.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 1016-00019.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 1022-00020.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 2012-00008.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1019-00001.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1022-00024.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 1005-00009.Psoriasis.LS.Baseline.Etanercept


title: 1012-00003.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1022-00001.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 2012-00031.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1025-00005.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1019-00010.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 2016-00037.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1019-00013.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 1022-00016.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 2015-00007.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1022-00021.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1025-00009.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1019-00009.Psoriasis.LS.Baseline.Etanercept


title: 1019-00008.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1022-00021.Psoriasis.LS.Week1.Ustekinumab90mg


title: 1022-00002.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1006-00005.Psoriasis.LS.Baseline.Ustekinumab45mg


title: 2012-00023.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 2016-00013.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 2016-00007.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1016-00014.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1016-00016.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1022-00004.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1022-00026.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1016-00001.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1012-00001.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 2012-00042.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1022-00014.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1022-00025.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 2012-00034.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1022-00018.Psoriasis.NL.Baseline.Etanercept

source_name: Non-lesional tissue of psoriasis patient

value: Non-lesional


title: 1016-00017.Psoriasis.NL.Baseline.Etanercept


title: 1019-00016.Psoriasis.NL.Baseline.Etanercept


title: 1025-00006.Psoriasis.NL.Baseline.Etanercept


title: 1016-00008.Psoriasis.NL.Baseline.Etanercept


title: 1012-00008.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 2016-00009.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1019-00003.Psoriasis.NL.Baseline.Etanercept


title: 2016-00026.Psoriasis.NL.Baseline.Etanercept


title: 2015-00002.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 2015-00005.Psoriasis.NL.Baseline.Etanercept


title: 2016-00019.Psoriasis.NL.Baseline.Etanercept


title: 1016-00003.Psoriasis.NL.Baseline.Etanercept


title: 1019-00007.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 2016-00025.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1006-00004.Psoriasis.NL.Baseline.Etanercept


title: 1022-00005.Psoriasis.NL.Baseline.Etanercept


title: 1025-00002.Psoriasis.NL.Baseline.Etanercept


title: 1025-00008.Psoriasis.NL.Baseline.Etanercept


title: 1022-00009.Psoriasis.NL.Baseline.Etanercept


title: 2015-00014.Psoriasis.LS.Baseline.Ustekinumab90mg


title: 1019-00009.Psoriasis.NL.Baseline.Etanercept


title: 1016-00013.Psoriasis.NL.Baseline.Etanercept


title: 1022-00012.Psoriasis.NL.Baseline.Etanercept


title: 2016-00006.Psoriasis.NL.Baseline.Etanercept


title: 2016-00020.Psoriasis.NL.Baseline.Etanercept


title: 2012-00036.Psoriasis.NL.Baseline.Etanercept


title: 1022-00017.Psoriasis.NL.Baseline.Etanercept


title: 1012-00005.Psoriasis.NL.Baseline.Etanercept


title: 1005-00009.Psoriasis.NL.Baseline.Etanercept


title: 2015-00001.Psoriasis.NL.Baseline.Etanercept


title: 1022-00024.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 2015-00012.Psoriasis.NL.Baseline.Etanercept


title: 2016-00027.Psoriasis.NL.Baseline.Etanercept


title: 1012-00002.Psoriasis.NL.Baseline.Etanercept


title: 1012-00004.Psoriasis.NL.Baseline.Etanercept


title: 1006-00002.Psoriasis.NL.Baseline.Etanercept


title: 1022-00027.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 1019-00015.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 1022-00016.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 1022-00006.Psoriasis.NL.Baseline.Etanercept


title: 2016-00001.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 1019-00013.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 2012-00038.Psoriasis.NL.Baseline.Etanercept


title: 1019-00005.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 2016-00018.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 1022-00020.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 1012-00007.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 1022-00008.Psoriasis.NL.Baseline.Etanercept


title: 1016-00019.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 1016-00011.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 1006-00005.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 2012-00019.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 1022-00003.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 1022-00002.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1022-00026.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1022-00025.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1025-00005.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 2012-00034.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1019-00008.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1012-00003.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 2012-00008.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1022-00014.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 2016-00008.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 1012-00001.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 2015-00007.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1019-00007.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 2015-00002.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1022-00019.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1012-00006.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 2016-00025.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1022-00021.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1016-00016.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 2016-00037.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 2016-00009.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1012-00008.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1016-00010.Psoriasis.NL.Baseline.Ustekinumab45mg


title: 2015-00014.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 2016-00013.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 2012-00042.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1019-00010.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1022-00004.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1016-00001.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1019-00001.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1025-00009.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1022-00001.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 2012-00031.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 2012-00023.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 1016-00014.Psoriasis.NL.Baseline.Ustekinumab90mg


title: 2016-00037 LS Week 0

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

institute: Janssen R&D

description: LS Week 0

hyb_protocol: Following fragmentation, 11 microg of cDNA were hybridized for 16 hr at 45oC on GeneChip HG U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data was normalized by GCRMA.

source_name: skin biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

treatment_protocol: For each patient, one 4-mm skin punch biopsy was collected from lesion located on the trunk or extremities with approximately 0.5 mm or more of induration and approximately 5 mm from the edge of the plaque, and another from macroscopically normal non-lesion on a similar body area to the biopsy plaque (i.e. arm, arm or leg, leg).  Biopsies were kept frozen –80oC until RNA preparation.

value: skin

tag: patient diagnosis

value: psoriasis

tag: skin type

value: LS (psoriasis lesion)

tag: time

value: Week 0

tag: subject id

value: No


title: 2016-00037 LS Week 12

description: LS Week 12

value: Week 12


title: 2016-00031 LS Week 0

description: LS Week 0


title: 2016-00025 NL Week 0

description: NL Week 0

value: NL (non-lesion)


title: 2016-00020 LS Week 12

description: LS Week 12


title: 2016-00025 LS Week 12

description: LS Week 12


title: 2016-00031 LS Week 12

description: LS Week 12


title: 2016-00035 LS Week 0

description: LS Week 0

value: Yes


title: 2016-00037 NL Week 0

description: NL Week 0


title: 2016-00035 LS Week 12

description: LS Week 12


title: 2016-00027 NL Week 0

description: NL Week 0


title: 2016-00035 NL Week 0

description: NL Week 0


title: 2016-00026 NL Week 0

description: NL Week 0


title: 2016-00026 LS Week 0

description: LS Week 0


title: 2016-00027 LS Week 12

description: LS Week 12


title: 2016-00025 LS Week 0

description: LS Week 0


title: 2016-00020 NL Week 0

description: NL Week 0


title: 2016-00019 LS Week 0

description: LS Week 0


title: 2016-00035.Psoriasis.NL.Baseline.Etanercept

value: Psoriasis


title: 2016-00013 LS Week 12

description: LS Week 12


title: 2016-00020 LS Week 0

description: LS Week 0


title: 2016-00019 NL Week 0

description: NL Week 0


title: 2015-00014 LS Week 12

description: LS Week 12


title: 2016-00009 LS Week 12

description: LS Week 12


title: 2015-00014 LS Week 0

description: LS Week 0


title: 2015-00012 LS Week 0

description: LS Week 0


title: 2016-00013 NL Week 0

description: NL Week 0


title: 2016-00013 LS Week 0

description: LS Week 0


title: 2015-00007 NL Week 0

description: NL Week 0


title: 2016-00006 LS Week 12

description: LS Week 12


title: 2016-00006 LS Week 0

description: LS Week 0


title: 2016-00007 LS Week 12

description: LS Week 12


title: 2016-00006 NL Week 0

description: NL Week 0


title: 2015-00005 LS Week 12

description: LS Week 12


title: 2015-00002 NL Week 0

description: NL Week 0


title: 2012-00042 LS Week 12

description: LS Week 12


title: 2012-00042 LS Week 0

description: LS Week 0


title: 2015-00012 LS Week 12

description: LS Week 12


title: 2015-00001 LS Week 12

description: LS Week 12


title: 2015-00001 NL Week 0

description: NL Week 0


title: 2015-00005 NL Week 0

description: NL Week 0


title: 2015-00012 NL Week 0

description: NL Week 0


title: 2016-00007 LS Week 0

description: LS Week 0


title: 2015-00005 LS Week 0

description: LS Week 0


title: 2015-00002 LS Week 0

description: LS Week 0


title: 2015-00007 LS Week 0

description: LS Week 0


title: 2015-00014 NL Week 0

description: NL Week 0


title: 2016-00009 LS Week 0

description: LS Week 0


title: 2015-00007 LS Week 12

description: LS Week 12


title: 2016-00009 NL Week 0

description: NL Week 0


title: 2015-00001 LS Week 0

description: LS Week 0


title: 1025-00008 LS Week 0

description: LS Week 0


title: 2012-00008 LS Week 0

description: LS Week 0


title: 1025-00008 LS Week 12

description: LS Week 12


title: 1025-00009 NL Week 0

description: NL Week 0


title: 1025-00008 NL Week 0

description: NL Week 0


title: 2012-00036 LS Week 12

description: LS Week 12


title: 2012-00008 LS Week 12

description: LS Week 12


title: 2012-00042 NL Week 0

description: NL Week 0


title: 2012-00038 NL Week 0

description: NL Week 0


title: 2012-00036 NL Week 0

description: NL Week 0


title: 2012-00031 NL Week 0

description: NL Week 0


title: 2012-00031 LS Week 0

description: LS Week 0


title: 2012-00023 LS Week 0

description: LS Week 0


title: 2012-00036 LS Week 0

description: LS Week 0


title: 2012-00023 NL Week 0

description: NL Week 0


title: 1025-00006 LS Week 0

description: LS Week 0


title: 2012-00023 LS Week 12

description: LS Week 12


title: 2012-00038 LS Week 12

description: LS Week 12


title: 2012-00038 LS Week 0

description: LS Week 0


title: 2012-00034 LS Week 0

description: LS Week 0


title: 2012-00031 LS Week 12

description: LS Week 12


title: 2012-00008 NL Week 0

description: NL Week 0


title: 1025-00006 NL Week 0

description: NL Week 0


title: 1025-00005 LS Week 0

description: LS Week 0


title: 1025-00002 LS Week 12

description: LS Week 12


title: 1025-00005 NL Week 0

description: NL Week 0


title: 1025-00009 LS Week 0

description: LS Week 0


title: 1025-00006 LS Week 12

description: LS Week 12


title: 2012-00034 NL Week 0

description: NL Week 0


title: 1022-00018 NL Week 0

description: NL Week 0


title: 1025-00002 NL Week 0

description: NL Week 0


title: 1025-00002 LS Week 0

description: LS Week 0


title: 1022-00026 LS Week 0

description: LS Week 0


title: 1022-00025 LS Week 12

description: LS Week 12


title: 1022-00021 LS Week 0

description: LS Week 0


title: 1022-00019 NL Week 0

description: NL Week 0


title: 1022-00021 LS Week 12

description: LS Week 12


title: 1022-00025 NL Week 0

description: NL Week 0


title: 1022-00021 NL Week 0

description: NL Week 0


title: 1022-00012 LS Week 0

description: LS Week 0


title: 1022-00017 LS Week 12

description: LS Week 12


title: 1022-00025 LS Week 0

description: LS Week 0


title: 1022-00017 NL Week 0

description: NL Week 0


title: 1022-00012 LS Week 12

description: LS Week 12


title: 1022-00026 NL Week 0

description: NL Week 0


title: 1022-00014 LS Week 12

description: LS Week 12


title: 1022-00017 LS Week 0

description: LS Week 0


title: 1022-00012 NL Week 0

description: NL Week 0


title: 1022-00008 NL Week 0

description: NL Week 0


title: 1022-00009 NL Week 0

description: NL Week 0


title: 1022-00019 LS Week 12

description: LS Week 12


title: 1022-00014 LS Week 0

description: LS Week 0


title: 1022-00009 LS Week 0

description: LS Week 0


title: 1022-00014 NL Week 0

description: NL Week 0


title: 1022-00006 LS Week 12

description: LS Week 12


title: 1022-00008 LS Week 0

description: LS Week 0


title: 1022-00006 NL Week 0

description: NL Week 0


title: 1022-00009 LS Week 12

description: LS Week 12


title: 1022-00006 LS Week 0

description: LS Week 0


title: 1022-00005 LS Week 12

description: LS Week 12


title: 1022-00005 NL Week 0

description: NL Week 0


title: 1022-00002 LS Week 12

description: LS Week 12


title: 1022-00002 LS Week 0

description: LS Week 0


title: 1022-00004 LS Week 12

description: LS Week 12


title: 1022-00004 NL Week 0

description: NL Week 0


title: 1022-00004 LS Week 0

description: LS Week 0


title: 1019-00010 LS Week 0

description: LS Week 0


title: 1019-00014 LS Week 12

description: LS Week 12


title: 1022-00001 LS Week 0

description: LS Week 0


title: 1022-00002 NL Week 0

description: NL Week 0


title: 1019-00008 LS Week 0

description: LS Week 0


title: 1019-00010 NL Week 0

description: NL Week 0


title: 1022-00005 LS Week 0

description: LS Week 0


title: 1022-00001 NL Week 0

description: NL Week 0


title: 1019-00016 LS Week 12

description: LS Week 12


title: 1019-00014 LS Week 0

description: LS Week 0


title: 1019-00009 NL Week 0

description: NL Week 0


title: 1019-00014 NL Week 0

description: NL Week 0


title: 1019-00008 NL Week 0

description: NL Week 0


title: 1019-00007 LS Week 12

description: LS Week 12


title: 1019-00007 LS Week 0

description: LS Week 0


title: 1022-00001 LS Week 12

description: LS Week 12


title: 1019-00016 LS Week 0

description: LS Week 0


title: 1019-00009 LS Week 0

description: LS Week 0


title: 1019-00016 NL Week 0

description: NL Week 0


title: 1019-00008 LS Week 12

description: LS Week 12


title: 1019-00010 LS Week 12

description: LS Week 12


title: 1019-00004 LS Week 12

description: LS Week 12


title: 1019-00003 LS Week 0

description: LS Week 0


title: 1019-00001 LS Week 0

description: LS Week 0


title: 1019-00004 LS Week 0

description: LS Week 0


title: 1016-00014 LS Week 12

description: LS Week 12


title: 1019-00001 NL Week 0

description: NL Week 0


title: 1016-00013 LS Week 0

description: LS Week 0


title: 1016-00017 NL Week 0

description: NL Week 0


title: 1016-00013 NL Week 0

description: NL Week 0


title: 1016-00017 LS Week 0

description: LS Week 0


title: 1019-00007 NL Week 0

description: NL Week 0


title: 1016-00014 LS Week 0

description: LS Week 0


title: 1016-00016 LS Week 0

description: LS Week 0


title: 1016-00017 LS Week 12

description: LS Week 12


title: 1019-00003 LS Week 12

description: LS Week 12


title: 1016-00008 NL Week 0

description: NL Week 0


title: 1016-00008 LS Week 0

description: LS Week 0


title: 1019-00003 NL Week 0

description: NL Week 0


title: 1019-00001 LS Week 12

description: LS Week 12


title: 1016-00016 NL Week 0

description: NL Week 0


title: 1016-00008 LS Week 12

description: LS Week 12


title: 1016-00016 LS Week 12

description: LS Week 12


title: 1016-00001 NL Week 0

description: NL Week 0


title: 1012-00008 LS Week 12

description: LS Week 12


title: 1016-00003 LS Week 0

description: LS Week 0


title: 1016-00003 NL Week 0

description: NL Week 0


title: 1016-00014 NL Week 0

description: NL Week 0


title: 1016-00003 LS Week 12

description: LS Week 12


title: 1016-00001 LS Week 0

description: LS Week 0


title: 1016-00001 LS Week 12

description: LS Week 12


title: 1012-00005 LS Week 12

description: LS Week 12


title: 1012-00004 LS Week 0

description: LS Week 0


title: 1012-00005 NL Week 0

description: NL Week 0


title: 1012-00002 LS Week 0

description: LS Week 0


title: 1012-00008 LS Week 0

description: LS Week 0


title: 1012-00004 LS Week 12

description: LS Week 12


title: 1012-00001 NL Week 0

description: NL Week 0


title: 1012-00003 NL Week 0

description: NL Week 0


title: 1012-00005 LS Week 0

description: LS Week 0


title: 1012-00001 LS Week 0

description: LS Week 0


title: 1012-00003 LS Week 0

description: LS Week 0


title: 1006-00004 LS Week 12

description: LS Week 12


title: 1012-00001 LS Week 12

description: LS Week 12


title: 1012-00004 NL Week 0

description: NL Week 0


title: 1012-00008 NL Week 0

description: NL Week 0


title: 1006-00002 LS Week 0

description: LS Week 0


title: 1006-00002 LS Week 12

description: LS Week 12


title: 1012-00003 LS Week 12

description: LS Week 12


title: 1006-00002 NL Week 0

description: NL Week 0


title: 1006-00004 LS Week 0

description: LS Week 0


title: 1006-00004 NL Week 0

description: NL Week 0


title: 1012-00002 LS Week 12

description: LS Week 12


title: 1005-00009 LS Week 0

description: LS Week 0


title: 1005-00009 NL Week 0

description: NL Week 0


title: ETV6-RUNX1_R06

city: Taipei

first: Hsi-Che

last: Liu

address: No. 92, Sec. 2, Chung-San North Rd.

country: Taiwan

institute: Mackay Memorial Hospital

description: Gene expression data from bone marrow

hyb_protocol: Standard Affymetrix according to manufacturer's instructions.

data_processing: Probeset intensities were extracted from CEL-files using GeneChip Operating Software (GCOS) (Affymetrix). Probe intensities were normalized. Differentially expressed genes between mixed lineage leukemia translocation (tMLL) and MLL-partial tandem duplication (MLL-PTD) subgroups were calculated using the Student t-test.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The integrity of the RNA was assessed using the RNA 6000 Nano assay kit on a Bioanalyzer (Agilent Technologies).

tag: subject status

value: acute lymphoblastic leukemia patients

tag: genotype/variation

value: ETV6-RUNX1 translocation

tag: disease status

value: Remission

value: bone marrow


title: ETV6-RUNX1_R05

description: Gene expression data from bone marrow

scan_protocol: Standard Affymetrix according to manufacturer's instructions.


title: ETV6-RUNX1_R04

description: Gene expression data from bone marrow

label_protocol: Standard Affymetrix according to manufacturer's instructions.


title: ETV6-RUNX1_R03

description: Gene expression data from bone marrow


title: ETV6-RUNX1_R08

description: Gene expression data from bone marrow


title: ETV6-RUNX1_R09

description: Gene expression data from bone marrow


title: ETV6-RUNX1_R02

description: Gene expression data from bone marrow


title: ETV6-RUNX1_R07

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D27

description: Gene expression data from bone marrow

value: Diagnosis


title: ETV6-RUNX1_R01

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D25

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D23

description: Gene expression data from bone marrow


title: 1012-00002 NL Week 0

description: NL Week 0


title: ETV6-RUNX1_D19

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D24

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D22

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D20

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D10

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D14

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D18

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D21

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D26

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D16

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D15

description: Gene expression data from bone marrow


title: Col-0 LL_LDHH Control PM

type: SRA

city: Raleigh

first: Dmitry

middle: Olegovich

last: Grinevich

state: NC

address: 120 Broughton Drive, Rm 128

department: Biochemistry

institute: North Carolina State University

library_source: transcriptomic

data_processing:
Sequenced reads were aligned to TAIR10 Arabidopsis reference genome using Tophat2 (v2.1.0)
Counts were obtained using htseq-count(v0.6.0);  non-default parameters included reverse strand alignment and intersection not empty.
Genome_build: TAIR 10 Arabidopsis reference
Supplementary_files_format_and_content: tab-delimited text file of gene names and associated counts

organism: Arabidopsis thaliana

source_name: Whole plant tissue

growth_protocol: Arabidopsis thaliana (ecotype Col-0) seedlings were grown in 12-hour light/dark cycles (LDHH) at 23ºC on ½ Murashige-Skoog (0.6% w/v agar) plates.

extract_protocol:
Aerial tissue was harvested and frozen in liquid nitrogen prior to RNA extraction. Purified total RNA was extracted from 4 replicates of mock treated and heat shocked plants using Qiagen RNeasy Plant Minikits, following manufacturer protocols. Samples were diluted in order to acquire two micrograms of RNA in preparation for mRNA isolation. mRNA was separated using the NEBNext Poly(A) Magnetic mRNA isolation kit (New England Biolabs). Before library preparation, mRNA samples were heated to 95°C for 15 minutes to achieve 150-200 base pair fragment sizes.
NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) was then used to generate libraries for sequencing. cDNA was synthesized with random hexamers.  After performing end repair and adaptor ligation steps, Agencourt AMPure XP beads (Beckman Coulter) were used following recommended ratios in order to isolate 150-200 bp fragments and remove adaptors. After, end repair and adaptor ligation size selection was performed with AMPure beads to isolate 150-200bp fragments and removed adaptors. PCR library enrichment for fifteen cycles was performed. The libraries were run on Agilent Bioanalyzer high sensitivity DNA chip after a 1:4 (or 1:10 if the concentration is too high) dilution. NEBNext Library Quant Kit for Illumina was used to measure library quantity and quality. Finally, the libraries were diluted to 10 nmol/ul concentrations before sequencing.

treatment_protocol: Two-week old seedlings were either mock treated or heat shocked. Heat stressed plants were exposed to 30ºC for one hour at 30 minutes after dawn (ZT 0.5) or 30 minutes after dusk (ZT 12.5). After 1 hour, aerial tissue was harvested and frozen in liquid nitrogen prior to RNA extraction.

tag: organ

value: Whole plant tissue

tag: genotype


title: ETV6-RUNX1_D13

description: Gene expression data from bone marrow


title: Col-0 LL_LDHH Control AM


title: Col-0 LL_LDHH Heat AM


title: ETV6-RUNX1_D12

description: Gene expression data from bone marrow


title: Col-0 Heat PM Rep 4


title: ETV6-RUNX1_D11

description: Gene expression data from bone marrow


title: Col-0 Heat PM Rep 1


title: Col-0 Heat PM Rep 3


title: Col-0 Heat PM Rep 2


title: ETV6-RUNX1_D09

description: Gene expression data from bone marrow


title: Col-0 Heat AM Rep 4


title: ETV6-RUNX1_D07

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D05

description: Gene expression data from bone marrow


title: Col-0 Control PM Rep 4


title: ETV6-RUNX1_D04

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D06

description: Gene expression data from bone marrow


title: ETV6-RUNX1_D08

description: Gene expression data from bone marrow


title: Col-0 Heat AM Rep 1


title: ETV6-RUNX1_D02

description: Gene expression data from bone marrow


title: Col-0 Control PM Rep 1


title: Col-0 Control PM Rep 2


title: Col-0 Control PM Rep 3


title: Col-0 LL_LDHH Heat PM


title: Col-0 Heat AM Rep 3


title: Col-0 Heat AM Rep 2


title: Col-0 Control AM Rep 2


title: Col-0 Control AM Rep 1


title: Col-0 Control AM Rep 3


title: Col-0 Control AM Rep 4


title: JM2

city: Melbourne

first: Jane

last: Oliaro

state: Victoria

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Basecalls were performed using bcl2fastq v2.20.
Reads were trimmed to remove low-quality bases and poly(A) sequences using cutadapt v1.5 with parameters -a AAAAAAAAAA -q 10 -m 20 -u 12
Trimmed reads were aligned to hg19 or mm10 reference genomes using hisat2 v2.0.4 with parameters --qc-filter --rna-strandness F
Read counts per gene were quantified using htseq-count v0.6.1 with parameters -m intersection-nonempty -s yes -t exon -i gene_name
Genome_build: hg19/mm10
Supplementary_files_format_and_content: tab-delimited text files containing read counts per gene generated by htseq-count for each sample

source_name: Untreated Sample

growth_protocol: The cell line MC38 (engineered to express truncated human HER2), were cultured in DMEM medium and the cell line AU565 was cultured in RPMI medium

extract_protocol:
Cells were lysed and total RNA isolated as per manufacturer’s instructions (Nucleospin® RNA extraction kit, Macherey-Nagel, Bethlehem, PA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MC38 HER2/ AU565 cells were either left untreated or incubated with CAR T cells (in triplicate/ duplicate) at a 2:1 effector-target ratio for 6 hrs followed by 3’ RNA-Seq of viable cells.

tag: cell line

tag: cell type

value: Breast cancer cell line

tag: background strain


title: JM4

source_name: Human CAR T cell treated sample


title: JM1


title: ETV6-RUNX1_D03

description: Gene expression data from bone marrow

tag: tissue


title: shTS#1_rep1

city: PHILADELPHIA

first: Irfan

last: Asangani

address: 421 Curie Bld.

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Illumina Nextseq500 reads were trimmed and clipped for quality control in …
Read quality was checked for each sample usign FastQC.
Alignment of reads were performed using STAR aligner with the default setting in Illumina Basespace (https:// basespace.illumina.com/home/indexIllumina)
Aligned reads were assembled using CUFFQUANT and normalized  using CUFFNORM
Differential expression analysis was performed using DESeq2 with DMSO samples for each cellline as the respective control
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values for each sample

growth_protocol: MDA-MB-231 (ATCC) cells were maintained in RPMI-1640 media (Sigma) supplemented with 10% FBS (Sigma), 1%Pen/Strep (Sigma) and 1%L-Glutamine (Sigma).  Cells were grown at 37°C in a 5% CO 2 incubator.

extract_protocol:
Total RNA was isolated using miRNeasy Kit (Invitrogen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-231 were transduced with lentivirus to generate shTS#1 (TS knock down) and pLKO (control). Cells were selected in 3µg/ml puromycin and culture was maintained in 1µg/ml Puromycin. No other treatment was done on the cells.

value: Breast Cancer

value: knock down of Thymidylate Synthase


title: PLKO_rep2

value: scrambled pLKO control


title: shTS#1_rep2


title: 5637-CM272-3

city: Madrid

first: Monica

last: Martinez-Fernandez

address: Avda Complutense 40

country: Spain

institute: CIEMAT

hyb_protocol: Following fragmentation, 5,5 ug of fragmented and labeled ss-DNA were hybridized for 16 hr at 45ºC at 60 rpm on Hybridization Oven 640 de Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G de Affymetrix

data_processing: Expression data were normalized, background-and batch corrected using the Guanine Cytosine Count Normalization (GCCN) and Signal Space Transformation (SST), and prior to summarizing using the Robust Multi-Array Average (RMA) algorithm implemented in the Affymetrix Expression Console software.

source_name: 5637 cell line treated with CM272 (IC50) replicate 3

label_protocol: cRNA is converted to biotinylated sense-strand DNA prepared according to the standard Affymetrix protocol from 12 ngs total RNA (GeneChip Whole Trasncript WT Expression Arrays, Affymetrix).

growth_protocol: The bladder cancer cell lines were maintained in Dulbecco's Modified Eagle Medium GlutaMAX™ (Gibco-BRL Life Technologies) with 10% fetal bovine serum (Hyclone) and 1% antibiotic-antimycotic (Gibco-BRL Life Technologies) at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Extraction of total RNA was performed using miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: CM272 was added at a concentration corresponding to its inhibitory concentration IC50

tag: treatment


title: ETV6-RUNX1_D01

description: Gene expression data from bone marrow


title: PLKO_rep1


title: Sample 24_Human neutrophils, donor 24

city: Parkville

first: Sara-Jane

last: Dawson

state: VIC

address: 305 Grattan street

institute: Peter MacCallum Cancer Center

description:
rnash2_hd24_dnase
rnash2_hd24_dnase/rnash2_hd24_dnase.rmd.bam

data_processing:
The short reads were aligned with STAR (https://www.ncbi.nlm.nih.gov/pubmed/23104886) version 2.5.0a to the human reference genome GRCh37.p13 with basic two pass method. The counts were then generated using the featureCounts program from the subread toolkit (https://www.ncbi.nlm.nih.gov/pubmed/24227677) version 1.5.1 .
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: counts

extract_protocol:
RNA isolation RNeasey Mini Kit (Quiagen) according to vendor protocol. Samples 1-8 were not treated with extra DNAse, Sample 9-24 were treated with DNAse.
Magnetic oligo-dT beads (NEB) were used for mRNA enrichment starting with 1 to 10 ng total RNA with RIN values above 9. The NEBNext Ultra II directional RNA Library prep Kit (NEB) was used to prepare RNA-Seq libraries according to the manufacturer’s protocol. Paired-end sequencing was performed with 2x 75 cycles on an Illumina NextSeq 500

treatment_protocol: Cell isolation with Miltenyi MacsXpress neutrophil negative selection kit and erythrocyte depeltion kit, all according to vendor protocol. After isolation washed twice in PBS before RNA isolation

tag: source

value: fresh venous EDTA blood

value: Neutrophil granulocyte

tag: treatment group

value: treated with DNAse


title: 5637 C1

source_name: 5637 cell line control 1


title: Sample 20_Human neutrophils, donor 20

description:
rnash2_hd20_dnase
rnash2_hd20_dnase/rnash2_hd20_dnase.rmd.bam


title: RT112-CM272-2

source_name: RT112 cell line treated with CM272 (IC50) replicate 2


title: 5637 C3

source_name: 5637 cell line control 3


title: Sample 18_Human neutrophils, donor 18

description:
rnash2_hd18_dnase
rnash2_hd18_dnase/rnash2_hd18_dnase.rmd.bam


title: Sample 19_Human neutrophils, donor 19

description:
rnash2_hd19_dnase
rnash2_hd19_dnase/rnash2_hd19_dnase.rmd.bam


title: RT112-CM272-3

source_name: RT112 cell line treated with CM272 (IC50) replicate 3


title: Sample 23_Human neutrophils, donor 23

description:
rnash2_hd23_dnase
rnash2_hd23_dnase/rnash2_hd23_dnase.rmd.bam


title: Sample 21_Human neutrophils, donor 21

description:
rnash2_hd21_dnase
rnash2_hd21_dnase/rnash2_hd21_dnase.rmd.bam


title: JM3


title: Sample 17_Human neutrophils, donor 17

description:
rnash2_hd17_dnase
rnash2_hd17_dnase/rnash2_hd17_dnase.rmd.bam


title: RT112 C1

source_name: RT112 cell line control 1


title: Sample 12_Human neutrophils, donor 12

description:
rnash2_hd12_dnase
rnash2_hd12_dnase/rnash2_hd12_dnase.rmd.bam


title: Sample 14_Human neutrophils, donor 14

description:
rnash2_hd14_dnase
rnash2_hd14_dnase/rnash2_hd14_dnase.rmd.bam


title: Sample 16_Human neutrophils, donor 16

description:
rnash2_hd16_dnase
rnash2_hd16_dnase/rnash2_hd16_dnase.rmd.bam


title: 5637-CM272-2

source_name: 5637 cell line treated with CM272 (IC50) replicate 2


title: Sample 11_Human neutrophils, donor 11

description:
rnash2_hd11_dnase
rnash2_hd11_dnase/rnash2_hd11_dnase.rmd.bam


title: RT112 C2

source_name: RT112 cell line control 2


title: RT112 C3

source_name: RT112 cell line control 3


title: RT112-CM272-1

source_name: RT112 cell line treated with CM272 (IC50) replicate 1


title: Sample 10_Human neutrophils, donor 10

description:
rnash2_hd10_dnase
rnash2_hd10_dnase/rnash2_hd10_dnase.rmd.bam


title: Sample 9_Human neutrophils, donor 9

description:
rnash2_hd9_dnase
rnash2_hd9_dnase/rnash2_hd9_dnase.rmd.bam


title: Sample 8_Human neutrophils, donor 8

description:
rnash2_hd8_nodnase
rnash2_hd8_nodnase/rnash2_hd8_nodnase.rmd.bam

source_name: unstimulated neutrophil granulocytes_no DNAse

value: not treated with extra DNAse


title: Sample 7_Human neutrophils, donor 7

description:
rnash2_hd7_nodnase
rnash2_hd7_nodnase/rnash2_hd7_nodnase.rmd.bam


title: Sample 6_Human neutrophils, donor 6

description:
rnash2_hd6_nodnase
rnash2_hd6_nodnase/rnash2_hd6_nodnase.rmd.bam


title: Sample 5_Human neutrophils, donor 5

description:
rnash2_hd5_nodnase
rnash2_hd5_nodnase/rnash2_hd5_nodnase.rmd.bam


title: Sample 3_Human neutrophils, donor 3

description:
rnash2_hd3_nodnase
rnash2_hd3_nodnase/rnash2_hd3_nodnase.rmd.bam


title: Sample 22_Human neutrophils, donor 22

description:
rnash2_hd22_dnase
rnash2_hd22_dnase/rnash2_hd22_dnase.rmd.bam


title: Rb_T826

city: Charlestown

first: Robert

last: Morris

state: Massachusetts

address: 149 13th Street

institute: Mass. General Hospital Cancer Center

data_processing:
reads were generated using the NextSeq 500 sequencing system
reads were trimming for adaptor sequences and low quality using trimmomatic (v0.3)
Reads were mapped to the GRCh38 genome using TopHat (v2.01) using the default parameters
Aligned reads for each sample were merged across the multiplexed lanes and raw counts were generated using HTSeq.
Normalized counts were generated using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited text file of normalized counts across all samples

source_name: RPE1 cells

growth_protocol: hTERT-RPE1 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 5% Fetal Bovine Serum (FBS) and antibiotics (100 units/ml Penicillin and 100 μg/ml Streptomycin; P/S).

extract_protocol:
Total RNA was extracted from RPE1 cells expressing RB wild-type, RBΔcdk or the 14 mP-RB mutant alleles, using the Direct-zol RNA MiniPrep Plus kit (Zymo Research, Cat. No. R2073).
Multiplexed RNA sequencing libraries were prepared using the TruSeq library prep kit (Illumina, Cat. No. RS-122-2301/2).

treatment_protocol: RB1knock down and replacement of the endogenous by exogenous RB protein in RPE1 cells transduced with pINDUCER11 and/or pINDUCER20 constructs were induced by addition of 0.5 μg/ml DOX (Sigma, Cat. No. D9891) for 48h.

value: telomerase-expressing non-transformed human retina epithelial cells


title: Sample 2_Human neutrophils, donor 2

description:
rnash2_hd2_nodnase
rnash2_hd2_nodnase/rnash2_hd2_nodnase.rmd.bam


title: Sample 1_Human neutrophils, donor 1

description:
rnash2_hd1_nodnase
rnash2_hd1_nodnase/rnash2_hd1_nodnase.rmd.bam


title: Rb_S811


title: Rb_T821


title: 5637 C2

source_name: 5637 cell line control 2


title: Rb_S780


title: Rb_S795


title: Rb_S807


title: 5637-CM272-1

source_name: 5637 cell line treated with CM272 (IC50) replicate 1


title: Rb_S612


title: Rb_S249


title: Rb_T252


title: Rb_T373


title: Rb_S608


title: Rb_Delta_CDK


title: NN_23

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17
Alignment of reads was done using STAR (v2.4.0j)
For each gene all reads were counted that aligned to exonic regions using featureCounts (v1.4.3-p1) with Homo_sapiens.GRCh38.87.gtf annotation from Ensembl
Differentially expression analysis was done in R limma trend (v2.13.0), taking the donor as batch factor in the model. Genes with less than 1 CPM in 3 or more samples were removed from further analysis. Groups (cell type) were compared in contrasts and genes with an FDR-adjusted p-value < 0.05 were considered significant.
Genome_build: hg38
Supplementary_files_format_and_content: Raw read count per gene

source_name: CD8+ T cell IL-7RαloKLRG1lo

extract_protocol:
Qiagen Rneasy mini kit
NEBNext Ultra Directional RNA Library Prep Kit for Illumina

value: CD8+ T cell IL-7R{alpha}loKLRG1lo

tag: donor

value: F

value: Blood


title: NP_22

source_name: CD8+ T cell IL-7RαloKLRG1hi

value: CD8+ T cell IL-7R{alpha}loKLRG1hi


title: PN_20

source_name: CD8+ T cell IL-7RαhiKLRG1lo

value: CD8+ T cell IL-7R{alpha}hiKLRG1lo

value: E


title: Sample 4_Human neutrophils, donor 4

description:
rnash2_hd4_nodnase
rnash2_hd4_nodnase/rnash2_hd4_nodnase.rmd.bam


title: NN_19


title: NP_18


title: PP_17

source_name: CD8+ T cell IL-7RαhiKLRG1hi

value: CD8+ T cell IL-7R{alpha}hiKLRG1hi


title: PN_16

value: D


title: PP_13


title: NP_6

value: B


title: PN_12

value: C


title: PN_4

value: A


title: PP_5


title: NP_2


title: NN_3


title: PP_1


title: PN_24


title: Rb_S230


title: UT-03

organism: Mus musculus

source_name: Untreated Sample

value: MC38 HER2

value: Adenocarcinoma cell line


title: UT-02


title: Rb_Wildtype


title: CAR-02

source_name: Mouse CAR T cell treated sample


title: CAR-01


title: PN_8


title: CAR-03


title: PP_21


title: 08-C128_S4

city: Miami

first: Thomas

last: Malek

state: FL

address: 1600 NW 10th Ave

institute: University of Miami

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to mm10 whole genome using STAR v2.5.0b with default parameters
Raw read counts were quantified using featureCounts v1.5.0
Genome_build: mm10/GRCm38 with gencode vM13 reference
Supplementary_files_format_and_content: Comma-delimited (.csv) text file includes raw counts for each Sample

source_name: spleen

extract_protocol:
Spleen: FACS purification of CD25 KO Tregs from tamoxifen-inducible, Treg-targeted CD25 conditional KO mice and CD25 WT reporter controls. Splenic Tregs were harvested 10-14 days after tamoxifen induction, which was carried out when mice were 7-10 weeks old.
RNA was isolated from sorted Tregs using TRIzol Reagent (Thermo Fisher) and column purified using miRNeasy Micro Kit (Qiagen). RNA quality was assessed using an Agilent 2100 BioAnalyzer and was quantified using Qubit RNA assay.
RNA-Seq libraries were prepared from 25 ng of total RNA using KAPA’s RNA Hyperprep with RiboErase protocol and quantified using Qubit DNA and KAPA qPCR Library Quantification kit for Illumina (KapaBiosystems).

value: regulatory T cells

tag: strain

value: spleen

value: Il2ra (CD25) KO


title: 07-C127_S2


title: Rb_T356

value: telomerase-expressing non-transformed human retina epithelial cells


title: 04-B19_S1

value: WT


title: 05-C125_S5


title: 03-B18_S6


title: 09-Y4_S5

source_name: thymus

extract_protocol:
Thymus: FACS purification of Tregs from Foxp3/RFP mice (CD25 WT controls) and Treg-targeted CD25 conditional KO mice at 3-4 weeks of age. Conditional KO mice were previously "cured" of autoimmunity by neonatal IV injection of WT splenocytes.
RNA was isolated from sorted Tregs using TRIzol Reagent (Thermo Fisher) and column purified using miRNeasy Micro Kit (Qiagen). RNA quality was assessed using an Agilent 2100 BioAnalyzer and was quantified using Qubit RNA assay.
RNA-Seq libraries were prepared from 25 ng of total RNA using KAPA’s RNA Hyperprep with RiboErase protocol and quantified using Qubit DNA and KAPA qPCR Library Quantification kit for Illumina (KapaBiosystems).

value: thymus


title: 10-Y5_S4


title: 01-B16_S8


title: 06-C126_S3


title: 08-Y3_S6


title: 07-Y2_S7


title: 05-R5_S9


title: 02-R2_S2


title: 04-R4_S10


title: UT-01


title: 06-Y1_S8


title: 01-R1_S3


title: 02-B17_S7


title: qd328_pmk1_PA14_1

city: Cambridge

first: Dennis

last: Kim

state: MA

address: 31 Ames Street

institute: MIT

description:
qd328_pmk1_PA14_vs_N2_PA14_summit_peaks.narrowPeak
qd328_pmk1_PA14.tdf
D17-4497

library_source: genomic

data_processing:
Base-calling was performed using Illumina's HiSeq control software, v. 2.2.58.
Quality control: Reads were aligned against C. elegans (ws258/WBPS9) using bwa aln/ samse v. 0.7.12-r1039 with flags –t 16 –f and mapping rates, fraction of multiply-mapping reads and number of unique 20-mers at the 5’ end of the reads were calculated using dedicated perl scripts and bedtools v. 2.25.0.64. The resulting bam files were sorted and indexed using samtools v. 1.5.
For each replicate, tdf and wig files were generated using IGVtools v.  2.1.24 with parameters count -e 150 ce_ws258_WBPS9 on the bam files. In addition, replicates were pooled by condition for downstream analysis using samtools merge.
Peaks were called using MACS2  v. 2.1.1.20160309 in callpeak mode with flags  -g ce --keep-dup all --call-summits --extsize 150 -p 1e-3 --nomodel -B against the pooled  N2_PA14_control samples.
Genome_build: ws258/WBPS9
Supplementary_files_format_and_content: For each replicate, tdf and wig files are provided (generated with IGV tools), and for the pooled replicates, ENCODE narrowPeak and tdf files that were used for the analysis are included.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Animals were synchronized by bleach prep. Arrested L1s dropped onto agar plates seeded with OP50 and grown at 20 degrees C until the L4 larval stage.

extract_protocol:
After three washes in M9 buffer, animal pellets were resuspended in an equal volume of PBS + complete ULTRA protease inhibitor tablets (Roche) and flash frozen in liquid nitrogen and stored at -80°C until chromatin immunoprecipitation (ChIP). ChIP was preformed using Abcam antibody Ab290.
Libraries were prepared using the SPRIworks Fragment Library System (Beckman Coulter) and single-end sequenced on an Illumina HiSeq2000 sequencer with v3 chemistry in high-output mode.

treatment_protocol: L4 animals were washed to agar plates seeded with non-pathogenic (OP50) or pathogenic (PA14) bacteria for a period of 4 hours at 25 degrees C before animals were harvested for ChIP

value: whole animal

tag: bacterial exposure

tag: exposure length

value: 4 hours

tag: age

tag: antibody

value: Ab290 (ChIP-grade polyclonal antibody from Abcam)


title: qd328_pmk1_PA14_2

description:
qd328_pmk1_PA14_vs_N2_PA14_summit_peaks.narrowPeak
qd328_pmk1_PA14.tdf
D17-4498


title: qd328_pmk1_OP50_2

description:
qd328_pmk1_OP50_vs_N2_PA14_summit_peaks.narrowPeak
qd328_pmk1_OP50.tdf
D17-4495


title: qd328_pmk1_OP50_3

description:
qd328_pmk1_OP50_vs_N2_PA14_summit_peaks.narrowPeak
qd328_pmk1_OP50.tdf
D17-4496


title: qd328_pmk1_OP50_1

description:
qd328_pmk1_OP50_vs_N2_PA14_summit_peaks.narrowPeak
qd328_pmk1_OP50.tdf
D17-4494


title: qd328_pmk1_PA14_3

description:
qd328_pmk1_PA14_vs_N2_PA14_summit_peaks.narrowPeak
qd328_pmk1_PA14.tdf
D17-4499


title: qd328_PA14_2

description:
qd328_PA14_vs_N2_PA14_summit_peaks.narrowPeak
qd328_PA14.tdf
D17-4714


title: N2_PA14_3

description:
no GFP control
N2_PA14_control.tdf
D17-4488


title: qd328_OP50_3

description:
qd328_OP50_vs_N2_PA14_summit_peaks.narrowPeak
qd328_OP50.tdf
D17-4491


title: N2_PA14_2

description:
no GFP control
N2_PA14_control.tdf
D17-4487


title: qd328_OP50_2

description:
qd328_OP50_vs_N2_PA14_summit_peaks.narrowPeak
qd328_OP50.tdf
D17-4490


title: N2_PA14_1

description:
no GFP control
N2_PA14_control.tdf
D17-4486


title: ZebrafishAbdominalOrgans_PBSinjection_14d_rep1

city: Tampere

first: Markus

middle: Juhani Tapani

last: Ojanen

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

description: Gene expression at 14 days post injection in adult zebrafish

hyb_protocol: 1.65 ug of Cy-3 labeled sample was hybridized onto Agilent’s 4x44K Zebrafish v3 array (Design ID 026437) at 65°C overnight using Agilent’s GE Hybridization Kit (Product number 5188-5242) and washed with Agilent’s Gene Expression Wash Pack (Product number 5188-5327) with 0.005% Triton X-102.

scan_protocol: Microarrays were scanned with an Agilent scanner G2565CA using a profile AgilentHD_GX_1Color producing TIFF images, each 158.2 MB, 7625 x 4320 resolution.

data_processing: The scanned images were analyzed to extract numerical results with Agilent Feature Extraction Software version 10.7.3 using  protocol GE1_107_Sep09 and grid 026437_D_F_20131128. This produced 5 text files, 1 for each sample.

organism: Danio rerio

label_protocol: Cyanine-3 (Cy3) labeled cRNA was produced using the Agilent   Low Input Quick Amp Labeling Kit, One-Color (Product number 5190-2305) and Agilent RNA Spike-In Kit, Single-Color kit (Product number 5188-5282). cRNA was   quantified using the NanoDrop NDP1000 UV-VIS Spectrophotometer and controlled   using Agilent 2100 bioanalyzer RNA 6000 Nano kit (Product number 5067-1511).

growth_protocol: The zebrafish were maintained according to standard protocols.

extract_protocol: Total RNA was extracted from the adult zebrafish abdominal organs using TRI reagent (TR 118, Molecular Research Center, Ohio, USA) according to the manufacturer’s instructions. The samples were treated with DNase to remove genomic DNA.

treatment_protocol: Wild-type AB zebrafish were infected with 20 CFU (SD 6 CFU) of ATCC 927 strain Mycobacterium marinum or PBS (control samples) and the RNA was collected at 14 days post injection.

value: wild type AB

tag: gender

value: male

value: PBS (control)

tag: time point

value: 14 days post injection

value: abdominal organs


title: KO-INF6

city: Lille

first: Joel

last: Haas

address: 1 Rue du Professeur Calmette

country: France

institute: Institut Pasteur de Lille

hyb_protocol: Following fragmentation, 5,5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: Data were processed and normalized using RMA as calculated by the oligo package from the bioconductor suite in the R environment (R-project.org)

label: Biotin

source_name: liver

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix). Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

extract_protocol: Trizol extraction was performed according to manufacturer's instructions

value: Ppara -/-

tag: infection status

value: Infected

value: liver


title: ZebrafishAbdominalOrgans_PBSinjection_14d_rep2


title: 03-R3_S1

value: regulatory T cells

tag: genotype/variation


title: KO-INF5

tag: genotype


title: KO-INF3


title: KO-INF2


title: ZebrafishAbdominalOrgans_PBSinjection_14d_rep3


title: ZebrafishAbdominalOrgans_MycobacteriumMarinumInfection_14d_rep1

value: ATCC 927 strain M. marinum


title: qd328_PA14_1

description:
qd328_PA14_vs_N2_PA14_summit_peaks.narrowPeak
qd328_PA14.tdf
D17-4492


title: ZebrafishAbdominalOrgans_MycobacteriumMarinumInfection_14d_rep2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ISS mice (rep. B, sequencing batch 5)

city: Aurora

first: Laura

last: Saba

state: CO

address: 12850 E. Montview Blvd

department: Skaggs School of Pharmacy and Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

description:
size-selected RNA
mRNA_expression_data_full.csv
ISS_HIGH_B_Ctl3_6

data_processing:
samples were aligned/quantified using MiR-MaGiC
Fastx toolkit  was used to clip adapters and filter reads for quality (>95% Q20 bases)
miRDeep2 was used to identify putative novel miRNAs
RUVr was used for batch correction and correcting for unwanted variation
CPMM or NBMM was used for normalization (HeritSeq R package)
A Variance stabilizing transformation was applied
Genome_build: Transcript database consisting of all NM and NR mouse transcripts in RefSeq (Release 67)

source_name: brain, right hemisphere

extract_protocol:
Libraries were constructed using the Illumina TruSeq Small RNA Sample Prep kit (Illumina, San Diego, CA, USA).  Fragments between 20-35 bp were size selected
small RNA sequencing

treatment_protocol: Storage in RNA later

value: ISS/IbgTejJ

tag: sequencing batch

tag: experimental treatment

tag: extraction protocol

value: RNA was collected from whole brain (right hemisphere) using the RNeasy Plus Universal Midi, Mini, and minElute kits for RNA sequencing (Qiagen, Valencia, CA, USA).


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS36 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS36_A


title: KO6

value: Control

tag: tissue


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ILS mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
ILS_MED_B_Ctl1_5

value: ILS/IbgTejJ


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS41 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS41_LOW_C_Ctl4_4


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS23 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS23_B


title: qd328_OP50_1

description:
qd328_OP50_vs_N2_PA14_summit_peaks.narrowPeak
qd328_OP50.tdf
D17-4489

value: whole animal


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS93 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS93_HIGH_C2


title: KO-INF4


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS43 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS43_MED_A2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS3 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS3_HIGH_B2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS19 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS19_LOW_B2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS24 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS24_LOW_A2


title: KO4


title: KO-INF1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS92 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS92_MED_A2


title: KO5


title: KO3


title: KO2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS107 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS107_LOW_C2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS115 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS115_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS122 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS122_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS122 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS122_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS123 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS123_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS115 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS115_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS97 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS97_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS98 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS98_A


title: WT-INF6

value: Ppara +/+


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS97 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS97_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS97 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS97_B


title: WT-INF5


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS96 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS96_B


title: WT-INF4


title: KO1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS96 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS96_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS89 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS89_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS101 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS101_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS89 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS89_C


title: WT6


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS87 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS87_C


title: WT-INF1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS87 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS87_B


title: WT-INF2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS86 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS86_C


title: WT-INF3


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS84 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS84_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS78 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS78_A


title: WT2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS75 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS75_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS64 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS64_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS76 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS76_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS70 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS70_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS73 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS73_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS70 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS70_C


title: WT3


title: Bone marrow macrophage treated RvD2 4h rep 2

city: Debrecen

first: Nikolaos

last: Giannakis

address: Egyetem ter 1

department: Department of Biochemistry and Molecular  Biology

country: Hungary

institute: University of Debrecen

description:
BMDMs_untreated_vs_treated_RvD2_4h_RNA_seq_normalized_counts.txt
RvD2_4h_2(normalized)

data_processing:
Alignment was performed  with TopHat v2.0.7 using default parameters.
Data analysis was performed using Strand NGS software, Version 2.8, Build 230243. © Strand Life Sciences, Bangalore, India
Read counts were calculated based on manufacturer's default parameters.
Normalisation of the read counts was performed with the Deseq method. The normalized counts are logtransformed  and baselined.This method is based on the paper ‘Differential expression analysis for sequence count data’ by  Simon Anders and Wolfgang Huber.
Changes in genes in the pairwise comparisions with FC>1.5 and p-value<0.05 were considered to be statistically significant.
Genome_build: mm10
Supplementary_files_format_and_content: normalised counts based on abundance measurements

source_name: Bone marrow

extract_protocol:
Total RNA was isolated with TRIZOL reagent according to the manufacturer’s recommendation. 20ug glycogen (Ambion) was added as carrier for RNA ethanol precipitation
cDNA library for RNA-Seq was generated from 100ng-400ng total RNA using TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. Briefly poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, and then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.

treatment_protocol:
For the bone marrow derived macrophages and only: Bone marrow was flushed from the tibiae and femurs of 8-10 week old male C57BL/6J mice using a 25 gauge needle and DMEM media (ATCC) containing 10% FBS, 20 mM HEPES and 1% penicillin/streptomycin. Once isolated, the bone marrow was plated in this medium supplemented with 10 ng/ml M-CSF (macrophage colony-stimulating factor; Sigma). On day four of differentiation, the media was replenished with fresh media (containing M-CSF). After seven days, the cells were liberated using a cell scraper centrifuged and re-plated in media lacking M-CSF. After 24 hours, cells were exposed to 10 nM RvD2 (Cayman Chemical) for four hours then collected in Buffer RLT (Qiagen) with 10 µl/ml 2-mercaptoethanol.
For the bone marrow derived macrophages and only: Bone marrow was flushed from the tibiae and femurs of 8-10 week old male C57BL/6J mice using a 25 gauge needle and DMEM media (ATCC) containing 10% FBS, 20 mM HEPES and 1% penicillin/streptomycin. Once isolated, the bone marrow was plated in this medium supplemented with 10 ng/ml M-CSF (macrophage colony-stimulating factor; Sigma). On day four of differentiation, the media was replenished with fresh media (containing M-CSF). After seven days, the cells were liberated using a cell scraper centrifuged and re-plated in media lacking M-CSF. After 24 hours, cells were exposed to 10 nM RvD2 (Cayman Chemical) for four hours then collected in Buffer RLT (Qiagen) with 10 µl/ml 2-mercaptoethanol.

value: Bone marrow

tag: cell type

value: bone marrow derived macrophages RvD2 4h treated

value: adult 2-4 months old

tag: Sex


title: Bone marrow macrophage treated RvD2 4h rep 3

description:
BMDMs_untreated_vs_treated_RvD2_4h_RNA_seq_normalized_counts.txt
RvD2_4h_3(normalized)

value: male


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS75 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS75_A


title: WT4


title: Bone marrow macrophage control untreated rep 3

description:
BMDMs_untreated_vs_treated_RvD2_4h_RNA_seq_normalized_counts.txt
ctrl_3(normalized)

treatment_protocol:
Bone marrow was flushed from the tibiae and femurs of 8-10 week old male C57BL/6J mice using a 25 gauge needle and DMEM media (ATCC) containing 10% FBS, 20 mM HEPES and 1% penicillin/streptomycin. Once isolated, the bone marrow was plated in this medium supplemented with 10 ng/ml M-CSF (macrophage colony-stimulating factor; Sigma). On day four of differentiation, the media was replenished with fresh media (containing M-CSF). After seven days, the cells were liberated using a cell scraper centrifuged and re-plated in media lacking M-CSF.
For the bone marrow derived macrophages and only: Bone marrow was flushed from the tibiae and femurs of 8-10 week old male C57BL/6J mice using a 25 gauge needle and DMEM media (ATCC) containing 10% FBS, 20 mM HEPES and 1% penicillin/streptomycin. Once isolated, the bone marrow was plated in this medium supplemented with 10 ng/ml M-CSF (macrophage colony-stimulating factor; Sigma). On day four of differentiation, the media was replenished with fresh media (containing M-CSF). After seven days, the cells were liberated using a cell scraper centrifuged and re-plated in media lacking M-CSF. After 24 hours, cells were exposed to 10 nM RvD2 (Cayman Chemical) for four hours then collected in Buffer RLT (Qiagen) with 10 µl/ml 2-mercaptoethanol.

value: bone marrow derived macrophages

tag: agent

value: untreated control


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS64 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS64_A

tag: strain


title: Bone marrow macrophage control untreated rep 2

description:
BMDMs_untreated_vs_treated_RvD2_4h_RNA_seq_normalized_counts.txt
ctrl_2(normalized)


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS86 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS86_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS86 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS86_B


title: Bone marrow macrophage control untreated rep 1

description:
BMDMs_untreated_vs_treated_RvD2_4h_RNA_seq_normalized_counts.txt
ctrl_1(normalized)


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS52 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS52_A


title: WT5


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS50 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS50_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS78 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS78_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS48 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS48_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS76 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS76_B


title: Bone marrow macrophage treated RvD2 4h rep 1

description:
BMDMs_untreated_vs_treated_RvD2_4h_RNA_seq_normalized_counts.txt
RvD2_4h_1(normalized)


title: Rb_S788

value: telomerase-expressing non-transformed human retina epithelial cells


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS39 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS39_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS64 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS64_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS23 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS23_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS42 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS42_C


title: TA muscle neutrophil day 1 after CTX rep 3

description:
Muscle_macrophages_neutrophils_after_CTX_normalised_counts.txt
[Neutrophils, Day 1, CTX](normalized)

source_name: TA muscle

treatment_protocol:
Mice were anaesthetized with isoflurane (adjusted flow rate or concentration to 1.5%) and 50 µl of cardiotoxin (12x10-6 M in PBS) (Latoxan) was injected in the tibialis anterior (TA) muscle. Muscles were recovered for flow cytometry analysis at day 4 post-injury or for muscle histology and IHC-Fr at days 0, 1, 2, 4 and 8 post-injury. TA muscles from CTX-injured animals were isolated and fascia of the TA was removed. Muscles were dissociated in RPMI containing 0.2% collagenase B (Roche Diagnostics GmbH) at 37°C for 1 hour and filtered through a 100 µm and a 40 µm filter. CD45+ cells were isolated using magnetic sorting (Miltenyi Biotec). For FACS, macrophages were treated with Fcγ receptor blocking antibodies and with 10% normal rat serum: normal mouse serum 1:1 mix, then stained with a combination of PE-conjugated anti-Ly6C antibody (HK1.4, eBioscience), APC-conjugated F4/80 antibody (BM8, eBioscience) and FITC-conjugated Ly6G antibody (1A8, Biolegend). Ly6Chigh F4/80low macrophages, Ly6Clow F4/80high macrophages and Ly6Ghigh Ly6Cint F4/80- neutrophils were quantified.
For the bone marrow derived macrophages and only: Bone marrow was flushed from the tibiae and femurs of 8-10 week old male C57BL/6J mice using a 25 gauge needle and DMEM media (ATCC) containing 10% FBS, 20 mM HEPES and 1% penicillin/streptomycin. Once isolated, the bone marrow was plated in this medium supplemented with 10 ng/ml M-CSF (macrophage colony-stimulating factor; Sigma). On day four of differentiation, the media was replenished with fresh media (containing M-CSF). After seven days, the cells were liberated using a cell scraper centrifuged and re-plated in media lacking M-CSF. After 24 hours, cells were exposed to 10 nM RvD2 (Cayman Chemical) for four hours then collected in Buffer RLT (Qiagen) with 10 µl/ml 2-mercaptoethanol.

value: muscle

value: neutrophils

value: day 1

value: CTX


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS60 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS60_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS36 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS36_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS9 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS9_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS123 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS123_C


title: TA muscle neutrophil day 1 after CTX rep 1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS8 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS8_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS101 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS101_C


title: WT1

value: liver


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS101 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS101_B

value: RNA was collected from whole brain (right hemisphere) using the RNeasy Plus Universal Midi, Mini, and minElute kits for RNA sequencing (Qiagen, Valencia, CA, USA).


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS123 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS123_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS122 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS122_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS60 mice (rep. A, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS60_A


title: siRPS3-rep1

city: Beijing

first: Xiaodong

last: He

country: China

institute: Peking Union Medical College Hospital

description: Gene expression data from SMMC-7721 cells transfected with siRPS3

data_processing:
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis.
Bowtie2 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.1.1
Fragments Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Per Million Mapped Fragments) was then calculated to estimate the expression level of genes in each sample.
Genome_build: Homo_sapiens.GRCh38.89.chr
Supplementary_files_format_and_content: a tab-delimited matrix table for each sample include FPKM values for each Sample.

growth_protocol: SMMC-7721 cells were cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin and 100 mg/mL streptomycin.

extract_protocol:
Total RNA was extracted using the TRIZOL reagent according to the manufacturer's instructions.
Library construction was performed following the manufacturer’s instructions provided by Illumina (San Diego, CA, USA)

treatment_protocol: SMMC-7721 cells were transfected with RPS3 siRNA or negative control siRNA using Lipofectamine RNAiMAX reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions.

tag: cell line

value: Hepatocellular carcinoma (HCC)

tag: treatment

value: siRNA targeting RPS3 (siRPS3)


title: siNC-rep1

description: Gene expression data from SMMC-7721 cells transfected with siNC

value: negative control siRNA(siNC)


title: siRPS3-rep2


title: siNC-rep2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS16 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS16_C


title: IsletBeta2

city: San Francisco

first: Gopika

last: Nair

state: CA

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

institute: UCSF

data_processing:
Base-calling performed using Illumina Hiseq 4000 Control and Real-Time analysis software
Read qualities were assessed by FASTQC tool on Galaxy.
Reads were then mapped to the human genome (hg38) using TopHat version 2.1.0 [52] using the corresponding sample’s mean inner distance between mate pairs, library-type fr-firststrand for strand determination leaving other parameters default.
The tuxedo suite tools were used for further analysis: rRNA and tRNA reads were masked during transcript assembly using Cufflinks and differential expression analysis was performed using Cuffdiff.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Human Primary Islet-derived beta cells

extract_protocol:
Total RNA was isolated from GFP-high cells FACS sorted from d27 eBCs, NECs and d20 immature clusters; and β-cells sorted from adult human islets using RNeasy Micro kits (Qiagen). RNA isolated from sorted cells was further concentrated employing RNA Clean & Concentrator (Zymo research).
rRNA was depleted by RiboGone (Clontech), and 325-350bp sized strand-specific cDNA libraries were prepared using the SMARTer Stranded Total RNA Sample Prep Kit – Low Input Mammalian Kit (Clontech).

value: Pancreatic Beta cells

tag: in vitro/in vivo

value: In vivo

tag: differentiation day

value: Adult


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS23 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS23_C


title: TA muscle Ly6Chigh macrophage day 4 after CTX rep 2

description:
Muscle_macrophages_neutrophils_after_CTX_normalised_counts.txt
[Ly6C hi, Day 4, CTX](normalized)

value: Ly6Chigh macrophages

value: day 4

tag: age

value: adult 2-4 months old


title: TA muscle neutrophil day 1 after CTX rep 2

tag: time point

value: male


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS16 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS16_B


title: IsletBeta1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS9 mice (rep. B, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS9_B


title: TA muscle Ly6Chigh macrophage day 4 after CTX rep 1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ISS mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
ISS_HIGH_B_Ctl3_5

value: ISS/IbgTejJ


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS16 mice (rep. A, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS16_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS76 mice (rep. C, sequencing batch 5)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS76_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS80 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS80_MED_B_Ctl2_4


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) ILS mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
ILS_MED_B_Ctl1_4

value: ILS/IbgTejJ


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS41 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS41_LOW_C_Ctl4_2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS22 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS22_MED_B2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS32 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS32_HIGH_C2


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS14 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS14_MED_B2


title: u3rna

first: Kat

last: Moore

institute: Sanquin Research

description:
Total RNAseq
u3

data_processing:
For peak calling ribosome footprint samples,the entire (very long) pipeline and all scripts can be found at: htts://git.lumc.nl/i.f.a.c.fokkema/ribosome-profiling.
For production of ribosome footprint read counts found in ribofoot_raw_reads_by_feature_plus_total_rnaseq.csv.gz, reads were adapter trimmed and aligned genome using STAR. Counts by feature type were produced usign HTSeq count with the corresponding feature type of 5'UTR, CDS, or 3'UTR. RNAseq read counts produced directly by STAR were subsequently added.
Ribfootprinting STAR parameters were –outFilterMultimapNmax 20 --outFilterMismatchNmax 1 --outSAMmultNmax 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts Also includes a UCSC refseq gtf file accessed on 11-9-15 passed to STAR with –sjdbGTFfile.
For RNAseq, alignment to genome via STAR, with parameters: --outFilterMultimapNmax 20 --outFilterMismatchNmax 1 --outSAMmultNmax 1 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM. Also includes a UCSC refseq gtf file accessed on 11-9-15 passed to STAR with –sjdbGTFfile.
For RNAseq, differential expression with edgeR
Genome_build: mm10/GRCm38.5
Supplementary_files_format_and_content: Wiggle files were produced either using STAR or using the custom script available at https://git.lumc.nl/i.f.a.c.fokkema/ribosome-profiling.
Merged wiggles of ribosome footprinting replicates are presented to compensate for lower depth. Individual RNAseq wiggle files are available per replicate.
Harringtonine peak files are a combination of both tunicamycin and cyclohexamide, presented separately for forward and reverse strands.
Read count tables in ribofoot_raw_reads_by_feature_plus_total_rnaseq.csv.gz include ribofootprinting reads reported separately for the 5', CDS, and 3'UTR and total RNAseq reads (across the entire transcript).

source_name: Erythroblasts

growth_protocol: Murine erythroblasts, isolated from p53-/- mouse fetal livers, were cultured in Stempro supplemented with L-glutamine and Pen/Strep (Thermo Fisher), 0.5 U/ml erythropoietin (Epo, Jansen-Cilag), 1% stem cell factor (supernatant) and 1 nM dexamethasone (Sigma).

extract_protocol:
Rneasy plus kit
Nebnext small RNA library prep set (for ribofootprint molecules) or Truseq (for RNAseq molecules)

treatment_protocol: Where applicable: tunicamycin 2.5ug.ml for 1.5h, cyclohexamide 100ug/ml for 5 min prior to harvest or 2ug/ml harringtonine prior to harvest.

value: FVB/n x C57BL/6

value: fetal liver

value: Erythroblasts

tag: translation stalled by

tag: stress induced by

value: untreated


title: u2rna

description:
Total RNAseq
u2

tag: genotype


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS99 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS99_LOW_C2

tag: sequencing batch

value: RNA was collected from whole brain (right hemisphere) using the RNeasy Plus Universal Midi, Mini, and minElute kits for RNA sequencing (Qiagen, Valencia, CA, USA).


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS115 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS115_B

tag: experimental treatment


title: u1rna

description:
Total RNAseq
u1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS99 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS99_LOW_B2

tag: extraction protocol


title: t3rna

description:
Total RNAseq
t3

tag: tissue

value: tunicamycin


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS102 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS102_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS102 mice (rep. A, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS102_A


title: t2rna

description:
Total RNAseq
t2

tag: cell type


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS98 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS98_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS102 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS102_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS98 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS98_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS100 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS100_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS96 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS96_C


title: t1rna

description:
Total RNAseq
t1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS90 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS9_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS89 mice (rep. A, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS89_A


title: G9a mutant 12 hours OS 2

city: Nijmegen

first: Human

last: Riahi Asl

state: Gelderland

address: Geert Grooteplein Zuid 10

department: Human Genetics

institute: Radboud UMC

description: G9a (DD1) heads after 12 hours oxidative stress exposure (paraquat)

data_processing:
Sequenced reads were aligned with Burrows-Wheeler algorithm (BWA) (Li & Durbin, 2010) to the Drosophila reference genome (BDGP.5, http://www.fruitfly.org/).
Per gene read counts were generated with HTSeq count (Anders et al, 2015) with following paramenters: intersection non-empty, non-stranded, quality filter = 15.
DESeq (Anders & Huber, 2010) was used to obtain library size-normalized read counts and to calculate differential expression of genes in 4 pairwise comparisons: 0 h versus 6 h and 0 h versus 12 h after OS in both G9a mutants and controls (fold change ≥1.5, adjusted p-value≤ 0.05, Benjamini-Hochberg).
Genome_build: Drosophila_melanogaster.BDGP5.70.gtf
Supplementary_files_format_and_content: Tab delimited file table of normalized count data. Tab delimited DESeq output files of  4 pairwise comparisons: wildtype 0 hours versus wildtype 6 hours (wt0VSwt6) and 12 hours (wt0VSwt12) after paraquat exposure. G9aDD1 mutant 0 hours versus G9aDD1 mutant 6 hours (mt0VSmt6) and 12 hours (mt0VSmt12) after paraquat exposure.

organism: Drosophila melanogaster

source_name: male fly head

growth_protocol: Flies were reared on standard medium (cornmeal/sugar/yeast) at 25 °C and 70 % humidity with a 12-h light/dark cycle. Flies were collected after eclosion and allowed to recover from CO2 exposure for 5 days prior to paraquat exposure.

extract_protocol:
200 fly heads per sample were used for total RNA extraction using QIAGEN lipid mini tissue kit.
mRNA libraries where prepared from 100 ng total RNA using Truseq RNA library prep v2 (Illumina). Samples where indexed and 4 samples where multiplexed on one sequencing lane. Samples 1, 2, 4 and 5 contain True-seq barcode 4, samples 19, 20, 22, 23 contain True-seq barcode 5 and samples 25, 26, 28, 29 contain True-seq barcode 6.

treatment_protocol: Flies (5-9 days) were transferred to paraquat containing food (50 mM) and incubated at 25 °C and 70 % humidity. At each time point, samples for RNA-seq were collected by flash freezing flies in liquid nitrogen followed by vortexing and filtering through a series of sieves to isolate heads from other body parts.

value: G9a homozygous mutant (DD1)

value: 50 mM Paraquat

tag: duration

value: 12 hours post treatment

value: 5-9 days

value: head


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS26 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS26_HIGH_C2


title: t3har

description:
Ribosome footprint
c4
merged_t_har_F.wig5.wig.gz
merged_t_har_R.wig5.wig.gz
harringtonin_peaks_F.txt
harringtonin_peaks_R.txt

data_processing:
Library strategy: Ribosome profiling
For peak calling ribosome footprint samples,the entire (very long) pipeline and all scripts can be found at: htts://git.lumc.nl/i.f.a.c.fokkema/ribosome-profiling.
For production of ribosome footprint read counts found in ribofoot_raw_reads_by_feature_plus_total_rnaseq.csv.gz, reads were adapter trimmed and aligned genome using STAR. Counts by feature type were produced usign HTSeq count with the corresponding feature type of 5'UTR, CDS, or 3'UTR. RNAseq read counts produced directly by STAR were subsequently added.
Ribfootprinting STAR parameters were –outFilterMultimapNmax 20 --outFilterMismatchNmax 1 --outSAMmultNmax 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts Also includes a UCSC refseq gtf file accessed on 11-9-15 passed to STAR with –sjdbGTFfile.
For RNAseq, alignment to genome via STAR, with parameters: --outFilterMultimapNmax 20 --outFilterMismatchNmax 1 --outSAMmultNmax 1 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM. Also includes a UCSC refseq gtf file accessed on 11-9-15 passed to STAR with –sjdbGTFfile.
For RNAseq, differential expression with edgeR
Genome_build: mm10/GRCm38.5
Supplementary_files_format_and_content: Wiggle files were produced either using STAR or using the custom script available at https://git.lumc.nl/i.f.a.c.fokkema/ribosome-profiling.
Merged wiggles of ribosome footprinting replicates are presented to compensate for lower depth. Individual RNAseq wiggle files are available per replicate.
Harringtonine peak files are a combination of both tunicamycin and cyclohexamide, presented separately for forward and reverse strands.
Read count tables in ribofoot_raw_reads_by_feature_plus_total_rnaseq.csv.gz include ribofootprinting reads reported separately for the 5', CDS, and 3'UTR and total RNAseq reads (across the entire transcript).

value: harringtonine


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS84 mice (rep. A, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS84_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS87 mice (rep. A, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS87_A


title: G9a mutant 12 hours OS 1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS84 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS84_B


title: t1har

description:
Ribosome footprint
a4
merged_t_har_F.wig5.wig.gz
merged_t_har_R.wig5.wig.gz
harringtonin_peaks_F.txt
harringtonin_peaks_R.txt


title: t2har

description:
Ribosome footprint
b4
merged_t_har_F.wig5.wig.gz
merged_t_har_R.wig5.wig.gz
harringtonin_peaks_F.txt
harringtonin_peaks_R.txt


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS78 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS78_C


title: G9a mutant 0 hours OS 2

description: G9a (DD1) heads after 0 hours oxidative stress exposure (paraquat)

value: no treatment

value: 0 hours post treament


title: G9a mutant 6 hours OS 1

description: G9a (DD1) heads after 6 hours oxidative stress exposure (paraquat)

value: 6 hours post treament


title: t3chx

description:
Ribosome footprint
c3
merged_t_chx_F.wig5.wig.gz
merged_t_chx_R.wig5.wig.gz

value: cyclohexamide


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS73 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS73_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS70 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS70_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS60 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS60_B


title: t1chx

description:
Ribosome footprint
a3
merged_t_chx_F.wig5.wig.gz
merged_t_chx_R.wig5.wig.gz


title: t2chx

description:
Ribosome footprint
b3
merged_t_chx_F.wig5.wig.gz
merged_t_chx_R.wig5.wig.gz


title: G9a mutant 0 hours OS 1


title: G9a mutant 6 hours OS 2


title: wt control 12 hours OS 2

description: G9a wild type heads after 12 hours oxidative stress exposure (paraquat)

value: wildtype control


title: u3har

description:
Ribosome footprint
c2
merged_u_har.F.wig5.wig.gz
merged_u_har.R.wig5.wig.gz
harringtonin_peaks_F.txt
harringtonin_peaks_R.txt

value: FVB/n x C57BL/6


title: wt control 12 hours OS 1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS52 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS52_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS52 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS52_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS48 mice (rep. A, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS48_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS42 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS42_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS48 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS48_C


title: u2har

description:
Ribosome footprint
b2
merged_u_har.F.wig5.wig.gz
merged_u_har.R.wig5.wig.gz
harringtonin_peaks_F.txt
harringtonin_peaks_R.txt

value: fetal liver


title: wt control 6 hours OS 2

description: G9a wild type heads after 6 hours oxidative stress exposure (paraquat)


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS42 mice (rep. A, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS42_A


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS75 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS75_C


title: wt control 6 hours OS 1


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS36 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS36_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS39 mice (rep. C, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS39_C


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS39 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS39_B


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS73 mice (rep. B, sequencing batch 4)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS73_B


title: u1har

description:
Ribosome footprint
a2
merged_u_har.F.wig5.wig.gz
merged_u_har.R.wig5.wig.gz
harringtonin_peaks_F.txt
harringtonin_peaks_R.txt

value: Erythroblasts


title: u3chx

description:
Ribosome footprint
c1
merged_u_chx_F.wig5.wig.gz
merged_u_chx_R.wig5.wig.gz

value: untreated


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS100 mice (rep. B, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS100_B

value: RNA was collected from whole brain (right hemisphere) using the RNeasy Plus Universal Midi, Mini, and minElute kits for RNA sequencing (Qiagen, Valencia, CA, USA).


title: u2chx

description:
Ribosome footprint
b1
merged_u_chx_F.wig5.wig.gz
merged_u_chx_R.wig5.wig.gz


title: Size selected RNA from whole brains (right hemisphere) from untreated (NVE) LXS100 mice (rep. A, sequencing batch 3)

description:
size-selected RNA
mRNA_expression_data_full.csv
LXS100_A


title: wt control 0 hours OS 1

description: G9a wild type heads after 0 hours oxidative stress exposure (paraquat)