title: long read RNA-seq from renal cortex interstitium (ENCLB557DBE)

description:
https://www.encodeproject.org/experiments/ENCSR961RJV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR961RJV
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB557DBE

source_name: Homo sapiens male embryo (105 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: John Stamatoyannopoulos, UW

value: ENCBS992YNH at ENCODE; https://www.encodeproject.org/ENCBS992YNH/


title: long read RNA-seq from renal pelvis (ENCLB209UII)

status: Public on Jul 24 2026

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR382JPG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR382JPG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB209UII

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens male embryo (120 days) renal pelvis tissue

value: renal pelvis

value: tissue

tag: biosample encode accession

tag: encode accession

tag: Sex

value: male

tag: dev stage

value: embryonic

tag: age

value: 120 day

tag: lab

tag: source

value: Ian Glass

tag: link

value: ENCBS711ZXF at ENCODE; https://www.encodeproject.org/ENCBS711ZXF/


title: long read RNA-seq from heart (ENCLB388KSG)

description:
https://www.encodeproject.org/experiments/ENCSR930RNO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR930RNO
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB388KSG

source_name: Homo sapiens female embryo (117 days) heart tissue

value: heart

value: female

value: 117 day

value: ENCBS722NUF at ENCODE; https://www.encodeproject.org/ENCBS722NUF/


title: long read RNA-seq from large intestine (ENCLB376BFO)

description:
https://www.encodeproject.org/experiments/ENCSR354MMF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR354MMF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB376BFO

source_name: Homo sapiens female embryo (110 days) large intestine tissue

value: large intestine

value: 110 day

value: ENCBS684FZG at ENCODE; https://www.encodeproject.org/ENCBS684FZG/


title: long read RNA-seq from right lung (ENCLB177EWE)

description:
https://www.encodeproject.org/experiments/ENCSR373VQC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR373VQC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB177EWE

source_name: Homo sapiens male embryo (115 days) right lung tissue

value: right lung

value: 115 day

value: ENCBS319IJK at ENCODE; https://www.encodeproject.org/ENCBS319IJK/


title: long read RNA-seq from heart (ENCLB722AMI)

description:
https://www.encodeproject.org/experiments/ENCSR351AFA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR351AFA
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB722AMI

source_name: Homo sapiens male embryo (120 days) heart tissue

value: John Stamatoyannopoulos, UW

value: ENCBS978SNN at ENCODE; https://www.encodeproject.org/ENCBS978SNN/


title: long read RNA-seq from adrenal gland (ENCLB295UUT)

description:
https://www.encodeproject.org/experiments/ENCSR348TSX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR348TSX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB295UUT

source_name: Homo sapiens female embryo (85 days) adrenal gland tissue

value: adrenal gland

value: tissue

value: 85 day

value: ENCBS182HLE at ENCODE; https://www.encodeproject.org/ENCBS182HLE/


title: long read RNA-seq from adrenal gland (ENCLB516BLD)

description:
https://www.encodeproject.org/experiments/ENCSR891GFR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR891GFR
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB516BLD

source_name: Homo sapiens male embryo (108 days) adrenal gland tissue

value: male

value: embryonic

value: 108 day

value: Ian Glass

value: ENCBS647ZQM at ENCODE; https://www.encodeproject.org/ENCBS647ZQM/


title: long read RNA-seq from kidney (ENCLB100OLL)

description:
https://www.encodeproject.org/experiments/ENCSR337PJI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR337PJI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB100OLL

source_name: Homo sapiens male embryo (113 days) kidney tissue

value: kidney

value: 113 day

value: ENCBS030JKL at ENCODE; https://www.encodeproject.org/ENCBS030JKL/


title: long read RNA-seq from kidney (ENCLB356AWT)

description:
https://www.encodeproject.org/experiments/ENCSR332ZOH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR332ZOH
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB356AWT

source_name: Homo sapiens female embryo (108 days) kidney tissue

value: female

value: ENCBS565APE at ENCODE; https://www.encodeproject.org/ENCBS565APE/


title: long read RNA-seq from brain (ENCLB225GWA)

description:
https://www.encodeproject.org/experiments/ENCSR327TOR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR327TOR
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB225GWA

source_name: Homo sapiens female embryo (117 days) brain tissue

value: brain

tag: note

value: Brain tissue from a healthy 117 day old female human fetus. Tissue provided by Ian Glass of University of Washington, Congenital Defects Lab.

value: 117 day

tag: url

value: ENCBS871FYX at ENCODE; https://www.encodeproject.org/ENCBS871FYX/


title: long read RNA-seq from right lung (ENCLB752FKU)

description:
https://www.encodeproject.org/experiments/ENCSR328GKH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR328GKH
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB752FKU

source_name: Homo sapiens female embryo (107 days) right lung tissue

value: right lung

value: tissue

value: 107 day

value: John Stamatoyannopoulos, UW

value: ENCBS424FCT at ENCODE; https://www.encodeproject.org/ENCBS424FCT/


title: long read RNA-seq from thymus (ENCLB724JST)

description:
https://www.encodeproject.org/experiments/ENCSR888AJG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR888AJG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB724JST

source_name: Homo sapiens female embryo (85 days) thymus tissue

value: thymus

value: embryonic

value: 85 day

value: ENCBS892FBG at ENCODE; https://www.encodeproject.org/ENCBS892FBG/


title: long read RNA-seq from renal cortex interstitium (ENCLB751JKR)

description:
https://www.encodeproject.org/experiments/ENCSR321AWD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR321AWD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB751JKR

source_name: Homo sapiens male embryo (108 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: male

value: 108 day

value: Ian Glass

value: ENCBS737MAA at ENCODE; https://www.encodeproject.org/ENCBS737MAA/


title: long read RNA-seq from stomach (ENCLB776YZG)

description:
https://www.encodeproject.org/experiments/ENCSR319ZJH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR319ZJH
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB776YZG

source_name: Homo sapiens female embryo (107 days) stomach tissue

value: stomach

value: female

value: ENCBS887ZTZ at ENCODE; https://www.encodeproject.org/ENCBS887ZTZ/


title: long read RNA-seq from adrenal gland (ENCLB456OFC)

description:
https://www.encodeproject.org/experiments/ENCSR309URD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR309URD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB456OFC

source_name: Homo sapiens female embryo (108 days) adrenal gland tissue

value: adrenal gland

value: ENCBS965EUG at ENCODE; https://www.encodeproject.org/ENCBS965EUG/


title: long read RNA-seq from left kidney (ENCLB026HQD)

description:
https://www.encodeproject.org/experiments/ENCSR324XFA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR324XFA
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB026HQD

source_name: Homo sapiens male embryo (87 days) left kidney tissue

value: left kidney

value: tissue

value: 87 day

value: ENCBS058XIV at ENCODE; https://www.encodeproject.org/ENCBS058XIV/


title: long read RNA-seq from muscle of back (ENCLB012VOT)

description:
https://www.encodeproject.org/experiments/ENCSR325LUL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR325LUL
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB012VOT

source_name: Homo sapiens female embryo (113 days) muscle of back tissue

value: muscle of back

value: embryonic

value: 113 day

value: John Stamatoyannopoulos, UW

value: ENCBS122SKS at ENCODE; https://www.encodeproject.org/ENCBS122SKS/


title: long read RNA-seq from brain (ENCLB265ZCT)

description:
https://www.encodeproject.org/experiments/ENCSR307SHM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR307SHM
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB265ZCT

source_name: Homo sapiens female embryo (85 days) brain tissue

value: brain

value: Brain tissue from a healthy day 85 female fetus from Ian Glass of University of Washington, Congenital Defects Lab.

value: 85 day

value: ENCBS471MPZ at ENCODE; https://www.encodeproject.org/ENCBS471MPZ/


title: long read RNA-seq from right lung (ENCLB901MIX)

description:
https://www.encodeproject.org/experiments/ENCSR307QHG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR307QHG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB901MIX

source_name: Homo sapiens male embryo (96 days) right lung tissue

value: right lung

value: male

value: 96 day

value: Ian Glass

value: ENCBS406DRC at ENCODE; https://www.encodeproject.org/ENCBS406DRC/


title: long read RNA-seq from left lung (ENCLB977SYF)

description:
https://www.encodeproject.org/experiments/ENCSR296JRY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR296JRY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB977SYF

source_name: Homo sapiens male embryo (87 days) left lung tissue

value: left lung

value: tissue

value: ENCBS891ELQ at ENCODE; https://www.encodeproject.org/ENCBS891ELQ/


title: long read RNA-seq from left kidney (ENCLB298LIZ)

description:
https://www.encodeproject.org/experiments/ENCSR300AUI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR300AUI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB298LIZ

source_name: Homo sapiens male embryo (115 days) left kidney tissue

value: left kidney

value: 115 day

value: ENCBS424AKW at ENCODE; https://www.encodeproject.org/ENCBS424AKW/


title: long read RNA-seq from adrenal gland (ENCLB050ZGY)

description:
https://www.encodeproject.org/experiments/ENCSR294LJB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR294LJB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB050ZGY

source_name: Homo sapiens female embryo (113 days) adrenal gland tissue

value: adrenal gland

value: female

value: embryonic

value: 113 day

value: John Stamatoyannopoulos, UW

value: ENCBS306FKK at ENCODE; https://www.encodeproject.org/ENCBS306FKK/


title: long read RNA-seq from renal cortex interstitium (ENCLB792CKI)

description:
https://www.encodeproject.org/experiments/ENCSR302UOZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR302UOZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB792CKI

source_name: Homo sapiens male embryo (113 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: ENCBS870OPP at ENCODE; https://www.encodeproject.org/ENCBS870OPP/


title: long read RNA-seq from right lung (ENCLB192RQA)

description:
https://www.encodeproject.org/experiments/ENCSR287XKO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR287XKO
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB192RQA

source_name: Homo sapiens female embryo (117 days) right lung tissue

value: right lung

value: 117 day

value: ENCBS565ILB at ENCODE; https://www.encodeproject.org/ENCBS565ILB/


title: long read RNA-seq from spinal cord (ENCLB605FTF)

description:
https://www.encodeproject.org/experiments/ENCSR285JMB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR285JMB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB605FTF

source_name: Homo sapiens female embryo (89 days) spinal cord tissue

value: spinal cord

value: 89 day

value: Ian Glass

value: ENCBS030YZV at ENCODE; https://www.encodeproject.org/ENCBS030YZV/


title: long read RNA-seq from kidney (ENCLB755FOY)

description:
https://www.encodeproject.org/experiments/ENCSR281RTT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR281RTT
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB755FOY

source_name: Homo sapiens female embryo (85 days) kidney tissue

value: kidney

value: tissue

value: 85 day

value: ENCBS572XBW at ENCODE; https://www.encodeproject.org/ENCBS572XBW/


title: long read RNA-seq from left kidney (ENCLB946KES)

description:
https://www.encodeproject.org/experiments/ENCSR281BDV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR281BDV
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB946KES

source_name: Homo sapiens female embryo (107 days) left kidney tissue

value: left kidney

value: female

value: embryonic

value: 107 day

value: ENCBS900HNI at ENCODE; https://www.encodeproject.org/ENCBS900HNI/


title: long read RNA-seq from large intestine (ENCLB664VPH)

description:
https://www.encodeproject.org/experiments/ENCSR273NIW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR273NIW
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB664VPH

source_name: Homo sapiens male embryo (115 days) large intestine tissue

value: large intestine

value: male

value: 115 day

value: John Stamatoyannopoulos, UW

value: ENCBS061ZSI at ENCODE; https://www.encodeproject.org/ENCBS061ZSI/


title: long read RNA-seq from renal pelvis (ENCLB573KPW)

description:
https://www.encodeproject.org/experiments/ENCSR267ZNP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR267ZNP
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB573KPW

source_name: Homo sapiens male embryo (108 days) renal pelvis tissue

value: renal pelvis

value: 108 day

value: ENCBS444UQZ at ENCODE; https://www.encodeproject.org/ENCBS444UQZ/


title: long read RNA-seq from right kidney (ENCLB048WOF)

description:
https://www.encodeproject.org/experiments/ENCSR260VXZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR260VXZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB048WOF

source_name: Homo sapiens female embryo (87 days) right kidney tissue

value: right kidney

value: 87 day

value: Ian Glass

value: ENCBS981NIH at ENCODE; https://www.encodeproject.org/ENCBS981NIH/


title: long read RNA-seq from left kidney (ENCLB034ETM)

description:
https://www.encodeproject.org/experiments/ENCSR270XWF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR270XWF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB034ETM

source_name: Homo sapiens female embryo (110 days) left kidney tissue

value: left kidney

value: tissue

value: 110 day

value: ENCBS765ZMU at ENCODE; https://www.encodeproject.org/ENCBS765ZMU/


title: long read RNA-seq from renal cortex interstitium (ENCLB324FBL)

description:
https://www.encodeproject.org/experiments/ENCSR845JAP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR845JAP
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB324FBL

source_name: Homo sapiens male embryo (105 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: embryonic

value: 105 day

value: ENCBS091IRZ at ENCODE; https://www.encodeproject.org/ENCBS091IRZ/


title: long read RNA-seq from muscle of arm (ENCLB515EPG)

description:
https://www.encodeproject.org/experiments/ENCSR257NKC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR257NKC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB515EPG

source_name: Homo sapiens female embryo (85 days) muscle of arm tissue

value: muscle of arm

value: female

value: 85 day

value: John Stamatoyannopoulos, UW

value: ENCBS930FNA at ENCODE; https://www.encodeproject.org/ENCBS930FNA/


title: long read RNA-seq from renal cortex interstitium (ENCLB068HQK)

description:
https://www.encodeproject.org/experiments/ENCSR261AYY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR261AYY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB068HQK

value: male

value: ENCBS029BOW at ENCODE; https://www.encodeproject.org/ENCBS029BOW/


title: long read RNA-seq from lung (ENCLB341ANE)

description:
https://www.encodeproject.org/experiments/ENCSR246OTF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR246OTF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB341ANE

source_name: Homo sapiens male embryo (108 days) lung tissue

value: lung

value: 108 day

value: Ian Glass

value: ENCBS740DTJ at ENCODE; https://www.encodeproject.org/ENCBS740DTJ/


title: long read RNA-seq from left kidney (ENCLB189IRZ)

description:
https://www.encodeproject.org/experiments/ENCSR247GVU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR247GVU
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB189IRZ

source_name: Homo sapiens male embryo (96 days) left kidney tissue

value: left kidney

value: tissue

value: 96 day

value: ENCBS818DFZ at ENCODE; https://www.encodeproject.org/ENCBS818DFZ/


title: long read RNA-seq from left lung (ENCLB888MVI)

description:
https://www.encodeproject.org/experiments/ENCSR245XMK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR245XMK
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB888MVI

source_name: Homo sapiens female embryo (117 days) left lung tissue

value: left lung

value: embryonic

value: 117 day

value: ENCBS245YZC at ENCODE; https://www.encodeproject.org/ENCBS245YZC/


title: long read RNA-seq from muscle of leg (ENCLB931ZEF)

description:
https://www.encodeproject.org/experiments/ENCSR243FLD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR243FLD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB931ZEF

source_name: Homo sapiens male embryo (105 days) muscle of leg tissue

value: muscle of leg

value: 105 day

value: ENCBS286HRG at ENCODE; https://www.encodeproject.org/ENCBS286HRG/


title: long read RNA-seq from spinal cord (ENCLB215MJU)

description:
https://www.encodeproject.org/experiments/ENCSR246BOF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR246BOF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB215MJU

source_name: Homo sapiens male embryo (96 days) spinal cord tissue

value: spinal cord

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS400MSR at ENCODE; https://www.encodeproject.org/ENCBS400MSR/


title: long read RNA-seq from renal pelvis (ENCLB318ITR)

description:
https://www.encodeproject.org/experiments/ENCSR229ICS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR229ICS
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB318ITR

source_name: Homo sapiens male embryo (120 days) renal pelvis tissue

value: renal pelvis

value: 120 day

value: Ian Glass

value: ENCBS604TSI at ENCODE; https://www.encodeproject.org/ENCBS604TSI/


title: long read RNA-seq from left lung (ENCLB493QKY)

description:
https://www.encodeproject.org/experiments/ENCSR228HRA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR228HRA
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB493QKY

source_name: Homo sapiens male embryo (105 days) left lung tissue

value: tissue

value: ENCBS813EHD at ENCODE; https://www.encodeproject.org/ENCBS813EHD/


title: long read RNA-seq from kidney (ENCLB050UIS)

description:
https://www.encodeproject.org/experiments/ENCSR227LUE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR227LUE
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB050UIS

source_name: Homo sapiens male embryo (108 days) kidney tissue

value: kidney

value: 108 day

value: ENCBS839PTA at ENCODE; https://www.encodeproject.org/ENCBS839PTA/


title: long read RNA-seq from small intestine (ENCLB593FAA)

description:
https://www.encodeproject.org/experiments/ENCSR222RWQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR222RWQ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB593FAA

source_name: Homo sapiens female embryo (108 days) small intestine tissue

value: small intestine

value: female

value: embryonic

value: ENCBS973XLE at ENCODE; https://www.encodeproject.org/ENCBS973XLE/


title: long read RNA-seq from large intestine (ENCLB738IWU)

description:
https://www.encodeproject.org/experiments/ENCSR219RPB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR219RPB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB738IWU

source_name: Homo sapiens female embryo (103 days) large intestine tissue

value: large intestine

value: 103 day

value: ENCBS115BRD at ENCODE; https://www.encodeproject.org/ENCBS115BRD/


title: long read RNA-seq from muscle of back (ENCLB250GNO)

description:
https://www.encodeproject.org/experiments/ENCSR213OVS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR213OVS
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB250GNO

source_name: Homo sapiens female embryo (98 days) muscle of back tissue

value: muscle of back

value: 98 day

value: John Stamatoyannopoulos, UW

value: ENCBS181REZ at ENCODE; https://www.encodeproject.org/ENCBS181REZ/


title: long read RNA-seq from renal cortex interstitium (ENCLB181XXJ)

description:
https://www.encodeproject.org/experiments/ENCSR219CXA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR219CXA
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB181XXJ

source_name: Homo sapiens male embryo (120 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: male

value: 120 day

value: Ian Glass

value: ENCBS173RWD at ENCODE; https://www.encodeproject.org/ENCBS173RWD/


title: long read RNA-seq from muscle of trunk (ENCLB111PBC)

description:
https://www.encodeproject.org/experiments/ENCSR210ICG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR210ICG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB111PBC

source_name: Homo sapiens female embryo (113 days) muscle of trunk tissue

value: muscle of trunk

value: tissue

value: 113 day

value: ENCBS549IUS at ENCODE; https://www.encodeproject.org/ENCBS549IUS/


title: long read RNA-seq from small intestine (ENCLB685THC)

description:
https://www.encodeproject.org/experiments/ENCSR212XZB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR212XZB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB685THC

source_name: Homo sapiens male embryo (91 days) small intestine tissue

value: small intestine

value: embryonic

value: 91 day

value: ENCBS840RAU at ENCODE; https://www.encodeproject.org/ENCBS840RAU/


title: long read RNA-seq from spleen (ENCLB849ACG)

description:
https://www.encodeproject.org/experiments/ENCSR193BFC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR193BFC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB849ACG

source_name: Homo sapiens embryo (112 days) spleen tissue

value: spleen

value: not collected

value: 112 day

value: ENCBS788PGW at ENCODE; https://www.encodeproject.org/ENCBS788PGW/


title: long read RNA-seq from muscle of back (ENCLB378ZXE)

description:
https://www.encodeproject.org/experiments/ENCSR194VUL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR194VUL
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB378ZXE

source_name: Homo sapiens male embryo (104 days) muscle of back tissue

value: muscle of back

value: 104 day

value: John Stamatoyannopoulos, UW

value: ENCBS152WAR at ENCODE; https://www.encodeproject.org/ENCBS152WAR/


title: long read RNA-seq from left lung (ENCLB079PXY)

description:
https://www.encodeproject.org/experiments/ENCSR186JQU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR186JQU
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB079PXY

source_name: Homo sapiens male embryo (91 days) left lung tissue

value: left lung

value: male

value: Ian Glass

value: ENCBS370ANL at ENCODE; https://www.encodeproject.org/ENCBS370ANL/


title: long read RNA-seq from stomach (ENCLB412JWT)

description:
https://www.encodeproject.org/experiments/ENCSR179EYZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR179EYZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB412JWT

source_name: Homo sapiens female embryo stomach tissue

value: stomach

value: tissue

value: female

value: ENCBS525FUP at ENCODE; https://www.encodeproject.org/ENCBS525FUP/


title: long read RNA-seq from muscle of leg (ENCLB425JBW)

description:
https://www.encodeproject.org/experiments/ENCSR174AAK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR174AAK
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB425JBW

source_name: Homo sapiens female embryo (113 days) muscle of leg tissue

value: muscle of leg

value: embryonic

value: 113 day

value: ENCBS879TMF at ENCODE; https://www.encodeproject.org/ENCBS879TMF/


title: long read RNA-seq from renal cortex interstitium (ENCLB638SXL)

description:
https://www.encodeproject.org/experiments/ENCSR176MGF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR176MGF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB638SXL

source_name: Homo sapiens male embryo (97 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: 97 day

value: ENCBS464XTU at ENCODE; https://www.encodeproject.org/ENCBS464XTU/


title: long read RNA-seq from heart (ENCLB306AEY)

description:
https://www.encodeproject.org/experiments/ENCSR165CWR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR165CWR
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB306AEY

source_name: Homo sapiens embryo (96 days) heart tissue

value: heart

value: Primary heart tissue from a healthy 96 day old human fetus. Tissue provided by Ian Glass of University of Washington, Congenital Defects Lab.

value: not collected

value: 96 day

value: John Stamatoyannopoulos, UW

value: ENCBS114OIZ at ENCODE; https://www.encodeproject.org/ENCBS114OIZ/


title: long read RNA-seq from muscle of arm (ENCLB606UGD)

description:
https://www.encodeproject.org/experiments/ENCSR170QUW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR170QUW
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB606UGD

source_name: Homo sapiens female embryo (105 days) muscle of arm tissue

value: muscle of arm

value: 105 day

value: Ian Glass

value: ENCBS634XIB at ENCODE; https://www.encodeproject.org/ENCBS634XIB/


title: long read RNA-seq from placenta (ENCLB148KFK)

description:
https://www.encodeproject.org/experiments/ENCSR158RZR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR158RZR
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB148KFK

source_name: Homo sapiens female embryo (113 days) placenta tissue

value: placenta

value: tissue

value: female

value: ENCBS260UXC at ENCODE; https://www.encodeproject.org/ENCBS260UXC/


title: long read RNA-seq from left lung (ENCLB426GEG)

description:
https://www.encodeproject.org/experiments/ENCSR141JSO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR141JSO
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB426GEG

source_name: Homo sapiens female embryo (108 days) left lung tissue

value: left lung

value: embryonic

value: 108 day

value: ENCBS459KIK at ENCODE; https://www.encodeproject.org/ENCBS459KIK/


title: long read RNA-seq from small intestine (ENCLB900ZGN)

description:
https://www.encodeproject.org/experiments/ENCSR166KWG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR166KWG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB900ZGN

source_name: Homo sapiens female embryo (105 days) small intestine tissue

value: small intestine

value: ENCBS810YIH at ENCODE; https://www.encodeproject.org/ENCBS810YIH/


title: long read RNA-seq from lung (ENCLB649SXC)

description:
https://www.encodeproject.org/experiments/ENCSR137VJX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR137VJX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB649SXC

source_name: Homo sapiens embryo (112 days) lung tissue

value: lung

value: not collected

value: 112 day

value: ENCBS039NNX at ENCODE; https://www.encodeproject.org/ENCBS039NNX/


title: long read RNA-seq from muscle of leg (ENCLB850DIN)

description:
https://www.encodeproject.org/experiments/ENCSR125GHJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR125GHJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB850DIN

source_name: Homo sapiens embryo (101 days) muscle of leg tissue

value: muscle of leg

value: 101 day

value: John Stamatoyannopoulos, UW

value: ENCBS313CVW at ENCODE; https://www.encodeproject.org/ENCBS313CVW/


title: long read RNA-seq from renal pelvis (ENCLB476GEH)

description:
https://www.encodeproject.org/experiments/ENCSR746DTB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR746DTB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB476GEH

source_name: Homo sapiens female embryo (96 days) renal pelvis tissue

value: renal pelvis

value: tissue

value: 96 day

value: Ian Glass

value: ENCBS349HOT at ENCODE; https://www.encodeproject.org/ENCBS349HOT/


title: long read RNA-seq from muscle of leg (ENCLB704HBL)

description:
https://www.encodeproject.org/experiments/ENCSR136VYG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR136VYG
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB704HBL

source_name: Homo sapiens male embryo (96 days) muscle of leg tissue

value: male

value: embryonic

value: ENCBS126LYC at ENCODE; https://www.encodeproject.org/ENCBS126LYC/


title: long read RNA-seq from stomach (ENCLB719GHU)

description:
https://www.encodeproject.org/experiments/ENCSR122FHJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR122FHJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB719GHU

source_name: Homo sapiens embryo (101 days) stomach tissue

value: stomach

value: ENCBS874TAK at ENCODE; https://www.encodeproject.org/ENCBS874TAK/


title: long read RNA-seq from large intestine (ENCLB173MXN)

description:
https://www.encodeproject.org/experiments/ENCSR098FNB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR098FNB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB173MXN

source_name: Homo sapiens female embryo (108 days) large intestine tissue

value: large intestine

value: female

value: 108 day

value: ENCBS493XQP at ENCODE; https://www.encodeproject.org/ENCBS493XQP/


title: long read RNA-seq from renal cortex interstitium (ENCLB694NFH)

description:
https://www.encodeproject.org/experiments/ENCSR091MZX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR091MZX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB694NFH

source_name: Homo sapiens male embryo (105 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: 105 day

value: ENCBS967UQQ at ENCODE; https://www.encodeproject.org/ENCBS967UQQ/


title: long read RNA-seq from large intestine (ENCLB818BSX)

description:
https://www.encodeproject.org/experiments/ENCSR085CHJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR085CHJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB818BSX

source_name: Homo sapiens male embryo (108 days) large intestine tissue

value: John Stamatoyannopoulos, UW

value: ENCBS259AIG at ENCODE; https://www.encodeproject.org/ENCBS259AIG/


title: long read RNA-seq from small intestine (ENCLB463GEP)

description:
https://www.encodeproject.org/experiments/ENCSR081FFD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR081FFD
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB463GEP

source_name: Homo sapiens female embryo (120 days) small intestine tissue

value: small intestine

value: tissue

value: 120 day

value: ENCBS165TTF at ENCODE; https://www.encodeproject.org/ENCBS165TTF/


title: long read RNA-seq from muscle of trunk (ENCLB402XTK)

description:
https://www.encodeproject.org/experiments/ENCSR091GMV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR091GMV
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB402XTK

source_name: Homo sapiens female embryo (108 days) muscle of trunk tissue

value: muscle of trunk

value: embryonic

value: Ian Glass

value: ENCBS956QGK at ENCODE; https://www.encodeproject.org/ENCBS956QGK/


title: long read RNA-seq from stomach (ENCLB264GAW)

description:
https://www.encodeproject.org/experiments/ENCSR071XIZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR071XIZ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB264GAW

source_name: Homo sapiens female embryo (96 days) stomach tissue

value: stomach

value: 96 day

value: ENCBS939KSM at ENCODE; https://www.encodeproject.org/ENCBS939KSM/


title: long read RNA-seq from thymus (ENCLB248LIP)

description:
https://www.encodeproject.org/experiments/ENCSR063MJL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR063MJL
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB248LIP

source_name: Homo sapiens female embryo thymus tissue

value: thymus

value: female

value: ENCBS986ATM at ENCODE; https://www.encodeproject.org/ENCBS986ATM/


title: long read RNA-seq from stomach (ENCLB495AYG)

description:
https://www.encodeproject.org/experiments/ENCSR710UTX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR710UTX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB495AYG

source_name: Homo sapiens female embryo (121 days) stomach tissue

value: 121 day

value: ENCBS330EKK at ENCODE; https://www.encodeproject.org/ENCBS330EKK/


title: long read RNA-seq from renal cortex interstitium (ENCLB927OIK)

description:
https://www.encodeproject.org/experiments/ENCSR057UZA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR057UZA
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB927OIK

source_name: Homo sapiens female embryo (89 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: 89 day

value: John Stamatoyannopoulos, UW

value: ENCBS254OLB at ENCODE; https://www.encodeproject.org/ENCBS254OLB/


title: long read RNA-seq from small intestine (ENCLB666IZJ)

description:
https://www.encodeproject.org/experiments/ENCSR047HDL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR047HDL
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB666IZJ

source_name: Homo sapiens female embryo (98 days) small intestine tissue

value: small intestine

value: tissue

value: 98 day

value: ENCBS137VKQ at ENCODE; https://www.encodeproject.org/ENCBS137VKQ/


title: long read RNA-seq from right kidney (ENCLB065RCY)

description:
https://www.encodeproject.org/experiments/ENCSR054SPN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR054SPN
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB065RCY

source_name: Homo sapiens male embryo (108 days) right kidney tissue

value: right kidney

value: male

value: embryonic

value: 108 day

value: Ian Glass

value: ENCBS026NKC at ENCODE; https://www.encodeproject.org/ENCBS026NKC/


title: long read RNA-seq from large intestine (ENCLB201WHT)

description:
https://www.encodeproject.org/experiments/ENCSR042HCJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR042HCJ
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB201WHT

source_name: Homo sapiens female embryo (105 days) large intestine tissue

value: large intestine

value: female

value: 105 day

value: ENCBS080GHU at ENCODE; https://www.encodeproject.org/ENCBS080GHU/


title: long read RNA-seq from muscle of leg (ENCLB274QDC)

description:
https://www.encodeproject.org/experiments/ENCSR032UWN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR032UWN
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB274QDC

source_name: Homo sapiens male embryo (101 days) muscle of leg tissue

value: muscle of leg

value: 101 day

value: ENCBS545VWB at ENCODE; https://www.encodeproject.org/ENCBS545VWB/


title: long read RNA-seq from renal pelvis (ENCLB468RNY)

description:
https://www.encodeproject.org/experiments/ENCSR024CQN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR024CQN
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB468RNY

source_name: Homo sapiens male embryo (105 days) renal pelvis tissue

value: renal pelvis

value: John Stamatoyannopoulos, UW

value: ENCBS553TCH at ENCODE; https://www.encodeproject.org/ENCBS553TCH/


title: long read RNA-seq from muscle of leg (ENCLB227BHZ)

description:
https://www.encodeproject.org/experiments/ENCSR017XQY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR017XQY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB227BHZ

source_name: Homo sapiens male embryo (113 days) muscle of leg tissue

value: tissue

value: 113 day

value: ENCBS869SZX at ENCODE; https://www.encodeproject.org/ENCBS869SZX/


title: long read RNA-seq from heart (ENCLB523DQT)

description:
https://www.encodeproject.org/experiments/ENCSR008AXU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR008AXU
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB523DQT

source_name: Homo sapiens female embryo (91 days) heart tissue

value: heart

value: embryonic

value: 91 day

value: ENCBS945CEQ at ENCODE; https://www.encodeproject.org/ENCBS945CEQ/


title: long read RNA-seq from adrenal gland (ENCLB620ZZS)

description:
https://www.encodeproject.org/experiments/ENCSR014HNT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR014HNT
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB620ZZS

source_name: Homo sapiens male embryo (108 days) adrenal gland tissue

value: adrenal gland

value: male

value: 108 day

value: Ian Glass

value: ENCBS106YHB at ENCODE; https://www.encodeproject.org/ENCBS106YHB/


title: long read RNA-seq from renal pelvis (ENCLB205KFT)

description:
https://www.encodeproject.org/experiments/ENCSR005ESF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR005ESF
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB205KFT

value: 105 day

value: ENCBS199VBZ at ENCODE; https://www.encodeproject.org/ENCBS199VBZ/


title: Brain_8-2_GDCA_ATAC

first: Meenakshi

last: Chakraborty

address: 269 Campus Drive

institute: Stanford University

description: Library name: Brain_8-2_GDCA_ATAC

data_processing:
Read trimming (https://github.com/georgimarinov/GeorgiScripts/blob/master/PEFastqToTabDelimited.py)
Alignment to mm10 using bowtie v1.0.1
Removal of mitochondrial reads
Deduplication using MarkDuplicates from Picard Tools (v1.99)
Conversion to bigWig using https://github.com/georgimarinov/GeorgiScripts/blob/master/makewigglefromBAM-NH.py and wigToBigWig from UCSC Utils
Assembly: mm10
Supplementary files format and content: bigWig files using RPM as the normalization method

organism: Mus musculus

source_name: brain

extract_protocol:
Nuclei were isolated from frozen right brain hemispheres by detergent-based dounce homogenization, filtration, mild formaldehyde crosslinking, and OptiPrep density-gradient centrifugation.
Approximately 100,000 nuclei per reaction were Tn5-transposed, reverse-crosslinked, purified, PCR-amplified, purified again, and quality-controlled by Qubit and TapeStation. See our preprint for additional details (https://doi.org/10.1101/2025.10.03.680371).

tag: tissue

value: brain

tag: treatment

value: GDCA


title: Brain_8-1_GDCA_ATAC

description: Library name: Brain_8-1_GDCA_ATAC


title: Brain_7-2_Saline_ATAC

description: Library name: Brain_7-2_Saline_ATAC

value: Saline


title: Brain_6-1_GDCA_ATAC

description: Library name: Brain_6-1_GDCA_ATAC


title: Brain_6-2_GDCA_ATAC

description: Library name: Brain_6-2_GDCA_ATAC


title: Brain_5-2_Saline_ATAC

description: Library name: Brain_5-2_Saline_ATAC


title: Brain_5-1_Saline_ATAC

description: Library name: Brain_5-1_Saline_ATAC


title: Brain_4-2_GDCA_ATAC

description: Library name: Brain_4-2_GDCA_ATAC


title: Brain_4-1_GDCA_ATAC

description: Library name: Brain_4-1_GDCA_ATAC


title: Brain_3-2_Saline_ATAC

description: Library name: Brain_3-2_Saline_ATAC


title: Brain_7-1_Saline_ATAC

description: Library name: Brain_7-1_Saline_ATAC


title: Brain_2-2_GDCA_ATAC

description: Library name: Brain_2-2_GDCA_ATAC


title: Brain_2-1_GDCA_ATAC

description: Library name: Brain_2-1_GDCA_ATAC


title: Brain_3-1_Saline_ATAC

description: Library name: Brain_3-1_Saline_ATAC


title: Brain_1-2_Saline_ATAC

description: Library name: Brain_1-2_Saline_ATAC


title: K>R 3 sample 2, ABA treatment, 4 hours

city: Atlanta

first: Roger

last: Deal

state: GA

address: 1510 Clifton Rd NE, Room 2006

department: Biology

institute: Emory University

description: Library name: KR3_ABA_2

library_source: transcriptomic

data_processing:
Read 1 was used for all downstream analysis, and read 2 was discarded because the second read generated using the QuantSeq FWD 3’ mRNA-Seq V2 Library Prep Kit (Lexogen) starts with the poly(A) tail, which lowers its quality
Reads were trimmed using TrimGalore (Krueger et al. 2021) to remove adapter content
Trimmed reads were then aligned to the Col-PEK reference genome (Hou et al. 2022) using STAR (Dobin et al. 2013)
Expression quantification of the aligned  BAM files in transcripts per million (TPM) was generated using RSEM (Li and Dewey 2011). RSEM gene-level results were imported into R using tximport (Soneson et al. 2015) for downstream analyses.
Assembly: Col-PEK
Supplementary files format and content: Tab delimited files showing the TPM and FPKM

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: 3 week old leaf

growth_protocol: Following stratification of seeds at 4 °C for 72 hours, all plants were grown either on soil or on ½ Murashige and Skoog (MS) (Murashige and Skoog 1962) plates in a 20 °C growth chamber, with a 16-hour light and 8-hour dark cycle, with a light intensity of 330 μmol/m2s.

extract_protocol:
RNA was isolated from ~100 mg of leaf tissue per replicate using the RNeasy plant mini kit (Qiagen). Isolated RNA was then treated with Turbo DNase (Ambion) and quantified by spectrophotometry
500 ng of RNA per sample was input into the QuantSeq FWD 3’ mRNA-Seq V2 Library Prep Kit with UDI (Lexogen) to prepare libraries for sequencing. Libraries were pooled and sent to Novogene for paired-end sequencing on an Illumina NovaSeq 6000 in PE150 mode.

treatment_protocol: Three week old leaves were treated with either 10 uM ABA or mock solution (water with DMSO) with .01% SilWet L-77,  applied to the leaf with a paintbrush.

value: 3 week old leaf

tag: genotype

value: Abscisic Acid


title: K>R 3 sample 1, ABA treatment, 4 hours

description: Library name: KR3_ABA_1


title: K>R 3 sample 3, ABA treatment, 4 hours

description: Library name: KR3_ABA_3


title: K>R 3 sample 3, mock treatment, 4 hours

description: Library name: KR3_Mock_3

value: Mock


title: K>R 3 sample 2, mock treatment, 4 hours

description: Library name: KR3_Mock_2


title: K>R 1-9 sample 2, ABA treatment, 4 hours

description: Library name: KR1_9_ABA_2


title: K>R 1-9 sample 3, mock treatment, 4 hours

description: Library name: KR1_9_Mock_3


title: long read RNA-seq from renal cortex interstitium (ENCLB348RRV)

description:
https://www.encodeproject.org/experiments/ENCSR137BTX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR137BTX
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB348RRV

source_name: Homo sapiens female embryo (96 days) renal cortex interstitium tissue

value: renal cortex interstitium

value: tissue

value: female

value: 96 day

value: John Stamatoyannopoulos, UW

value: ENCBS783KKU at ENCODE; https://www.encodeproject.org/ENCBS783KKU/


title: K>R 1-9 sample 3, ABA treatment, 4 hours

description: Library name: KR1_9_ABA_3


title: K>R 1-9 sample 2, mock treatment, 4 hours

description: Library name: KR1_9_Mock_2


title: K>R 1-9 sample 1, ABA treatment, 4 hours

description: Library name: KR1_9_ABA_1


title: Delta28 sample 3, ABA treatment, 4 hours

description: Library name: Delta28_ABA_3


title: Delta28 sample 2, ABA treatment, 4 hours

description: Library name: Delta28_ABA_2


title: Delta28 sample 1, ABA treatment, 4 hours

description: Library name: Delta28_ABA_1


title: Delta28 sample 2, mock treatment, 4 hours

description: Library name: Delta28_Mock_2


title: Delta28 sample 1, mock treatment, 4 hours

description: Library name: Delta28_Mock_1


title: WT sample 3, ABA treatment, 4 hours

description: Library name: WT_ABA_3

value: WT


title: WT sample 1, ABA treatment, 4 hours

description: Library name: WT_ABA_1


title: WT sample 2, ABA treatment, 4 hours

description: Library name: WT_ABA_2


title: WT sample 2, mock treatment, 4 hours

description: Library name: WT_Mock_2


title: CHX +alpha-amanitin 6h rep3

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: Library name: C_6h_3

data_processing:
In our sequencing strategy, the R1 reads of pooled libraries contain two parts of UMI split by the barcode. We rearrange UMI sequences to position them next to each other and remove additional low-quality nucleotides, including  the oligo(dT) fragment and those that follow it. For this, we utilise the awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 of pooled libraries were demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex and R1 with parameters -p UB -UMI 14 -n 1. The resulting reads were trimmed to eliminate potential contamination with the poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then, they were mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes.
Assembly: TAIR10
Supplementary files format and content: Arabidopsis genes count text files

molecule: total RNA

source_name: seed

growth_protocol: Plants were grown in a greenhouse under a long day-night cycle at 22°C. Seeds from 8 to 12 plants were combined to create a single biological replicate.

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211).
500 ng of seed RNA was used for reverse transcription (2.5 ul of 1000x-diluted ERCC spiked into each sample) with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.25 of each reaction was pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed for indicated times in the presence of 250 μM α-amanitin (Merck; prepared from a 1 mM stock solution in water) and 500 μM cycloheximide (Merck; from a 100 mg/ml stock solution in ethanol).

value: seed

value: 6h imbibed

tag: treatment inhibitor

value: CHX +alpha-amanitin

tag: batch


title: CHX +alpha-amanitin 6h rep4

description: Library name: C_6h_4


title: CHX +alpha-amanitin 6h rep1

description: Library name: C_6h_1


title: CHX +alpha-amanitin 3h rep4

description: Library name: C_3h_4

value: 3h imbibed


title: WT sample 3, mock treatment, 4 hours

description: Library name: WT_Mock_3


title: CHX +alpha-amanitin 3h rep3

description: Library name: C_3h_3


title: CHX +alpha-amanitin 3h rep1

description: Library name: C_3h_1


title: WT sample 1, mock treatment, 4 hours

description: Library name: WT_Mock_1


title: CHX +alpha-amanitin 3h rep2

description: Library name: C_3h_2


title: CHX + alpha-amanitin 1h rep4

description: Library name: C_1h_4

value: 1h imbibed


title: CHX + alpha-amanitin 1h rep3

description: Library name: C_1h_3


title: CHX + alpha-amanitin 1h rep2

description: Library name: C_1h_2


title: alpha-amanitin 6h rep4

description: Library name: M_6h_4

value: alpha-amanitin


title: CHX + alpha-amanitin 1h rep1

description: Library name: C_1h_1


title: alpha-amanitin 6h rep3

description: Library name: M_6h_3


title: alpha-amanitin 6h rep2

description: Library name: M_6h_2


title: alpha-amanitin 3h rep4

description: Library name: M_3h_4


title: alpha-amanitin 3h rep3

description: Library name: M_3h_3


title: alpha-amanitin 3h rep2

description: Library name: M_3h_2


title: alpha-amanitin 3h rep1

description: Library name: M_3h_1


title: alpha-amanitin 1h rep4

description: Library name: M_1h_4


title: alpha-amanitin 1h rep3

description: Library name: M_1h_3


title: alpha-amanitin 1h rep2

description: Library name: M_1h_2


title: alpha-amanitin 1h rep1

description: Library name: M_1h_1


title: dry rep3

description: Library name: dry_3

value: dry


title: dry rep2

description: Library name: dry_2


title: new 6h imbibition rep4

description: Library name: new_6h_4

data_processing:
In our sequencing strategy, the R1 reads of pooled libraries contain two parts of UMI split by the barcode. We rearrange UMI sequences to position them next to each other and remove additional low-quality nucleotides, including  the oligo(dT) fragment and those that follow it. For this, we utilise the awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 of pooled libraries were demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex and R1 with parameters -p UB -UMI 14 -n 1. The resulting reads were trimmed to eliminate potential contamination with the poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then, they were mapped using STAR (v 2.7.8a) to a custom genome containing both Arabidopsis chromosomes and spike-in sequences with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes.
Assembly: TAIR10
Supplementary files format and content: gene count text files

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211). For 4-SU labelled RNAs enrichment, biotinylation was performed for 16 μg of freshly isolated RNA in a 200 μl reaction mixture (10 mM Tris pH 7.5; 1 mM EDTA; 0.2 mg/ml EZ-Link Biotin-HPDP (ThermoFisher)) for 1.5 h at 22°C. 1 µl of tenfold diluted ERCC RNA Spike-In Mix (ThermoFisher) and in vitro transcribed 4-SU labelled transcripts were added to the RNA before the biotinylation reactions, and a portion of the RNA after the addition of spike-ins (500 ng) was retained as an input. Unbound Biotin-HPDP was removed by chloroform/isoamyl alcohol (24:1) extraction. Subsequently, a 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added, and RNA was precipitated by centrifugation at 20,000g for 20 minutes. The pellet was washed with 1 ml of 80% ethanol, and after drying, it was resuspended in 25 μl of RNase-free water. Biotinylated RNA was purified using 50 μl of streptavidin C1 Dynabeads (ThermoFisher). The beads were washed in binding buffer (0.2 M NaCl; 0.1 M sodium phosphate pH 6.8; 25 mM MgCl2; 0.4% Tween), blocked in the binding buffer with 1 μg/μl glycogen for 10 minutes, and washed again in binding buffer. RNA samples were denatured at 65°C for 5 minutes, followed by 5 minutes on ice. Then, 25 μl of 2x binding buffer and 50 μl of washed streptavidin beads were added, mixed, and incubated at 22°C with gentle shaking for 20 minutes. The beads were washed three times with 0.5 ml of washing buffer (100 mM Tris-HCl pH 7.5; 10 mM EDTA; 1 M NaCl; 0.1% Tween20) at 65°C, followed by three washes at room temperature. Biotinylated RNA was eluted from the beads by two incubations with 50 μl of 200 mM DTT. RNA from the combined eluates was purified using RNA Clean & Concentrator-5 columns (Zymo), following the protocol for long RNA purification with DNase treatment. The entire volume of the sample was used for reverse transcription.
Input and enriched RNA samples were used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.25 of each input and whole enriched RNA RT reaction were pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed for 1h, 3h and 6h in the presence of 2 mM 4-thiouridine (Merck; from a 50 mM stock solution in 6% methanol).

tag: treatment enrichment

value: enriched


title: dry rep4

description: Library name: dry_4


title: new 6h imbibition rep3

description: Library name: new_6h_3


title: dry rep1

description: Library name: dry_1


title: new 6h imbibition rep1

description: Library name: new_6h_1


title: new 3h imbibition rep4

description: Library name: new_3h_4


title: new 6h imbibition rep2

description: Library name: new_6h_2


title: new 3h imbibition rep3

description: Library name: new_3h_3


title: new 3h imbibition rep2

description: Library name: new_3h_2


title: long read RNA-seq from small intestine (ENCLB659EYG)

description:
https://www.encodeproject.org/experiments/ENCSR000OEW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR000OEW
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB659EYG

source_name: Homo sapiens female embryo (110 days) small intestine tissue

value: small intestine

value: embryonic

value: 110 day

value: Ian Glass

value: ENCBS587DFP at ENCODE; https://www.encodeproject.org/ENCBS587DFP/


title: new 3h imbibition rep1

description: Library name: new_3h_1


title: new 1h imbibition rep4

description: Library name: new_1h_4


title: new 1h imbibition rep2

description: Library name: new_1h_2


title: new 1h imbibition rep3

description: Library name: new_1h_3


title: new 1h imbibition rep1

description: Library name: new_1h_1


title: input 6h imbibition rep3

description: Library name: inp_6h_3

value: input


title: input 6h imbibition rep1

description: Library name: inp_6h_1


title: input 3h imbibition rep2

description: Library name: inp_3h_2


title: input 1h imbibition rep4

description: Library name: inp_1h_4


title: new mock imbibition rep3

description: Library name: new_mock_3

data_processing:
In our sequencing strategy, the R1 reads of pooled libraries contain two parts of UMI split by the barcode. We rearrange UMI sequences to position them next to each other and remove additional low-quality nucleotides, including  the oligo(dT) fragment and those that follow it. For this, we utilise the awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 of pooled libraries were demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex and R1 with parameters -p UB -UMI 14 -n 1. The resulting reads were trimmed to eliminate potential contamination with the poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then, they were mapped using STAR (v 2.7.8a) to a custom genome containing both Arabidopsis chromosomes and ERCC spike-in sequences with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes.
Assembly: TAIR10
Supplementary files format and content: gene count text files

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211). For 4-SU labelled RNAs enrichment, biotinylation was performed for 22.5 μg of freshly isolated RNA in a 200 μl reaction mixture (10 mM Tris pH 7.5; 1 mM EDTA; 0.2 mg/ml EZ-Link Biotin-HPDP (ThermoFisher)) for 1.5 h at 22°C. 1 µl of tenfold diluted ERCC RNA Spike-In Mix (ThermoFisher) was added to the RNA before the biotinylation reactions, and a portion of the RNA after the addition of ERCC (500 ng) was retained as an input. Unbound Biotin-HPDP was removed by chloroform/isoamyl alcohol (24:1) extraction. Subsequently, a 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added, and RNA was precipitated by centrifugation at 20,000g for 20 minutes. The pellet was washed with 1 ml of 80% ethanol, and after drying, it was resuspended in 25 μl of RNase-free water. Biotinylated RNA was purified using 50 μl of streptavidin C1 Dynabeads (ThermoFisher). The beads were washed in binding buffer (0.2 M NaCl; 0.1 M sodium phosphate pH 6.8; 25 mM MgCl2; 0.4% Tween), blocked in the binding buffer with 1 μg/μl glycogen for 10 minutes, and washed again in binding buffer. RNA samples were denatured at 65°C for 5 minutes, followed by 5 minutes on ice. Then, 25 μl of 2x binding buffer and 50 μl of washed streptavidin beads were added, mixed, and incubated at 22°C with gentle shaking for 20 minutes. The beads were washed three times with 0.5 ml of washing buffer (100 mM Tris-HCl pH 7.5; 10 mM EDTA; 1 M NaCl; 0.1% Tween20) at 65°C, followed by three washes at room temperature. Biotinylated RNA was eluted from the beads by two incubations with 50 μl of 200 mM DTT. RNA from the combined eluates was purified using RNA Clean & Concentrator-5 columns (Zymo), following the protocol for long RNA purification with DNase treatment. The entire volume of the sample was used for reverse transcription.
Input and enriched RNA samples were used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.25 of each input and whole enriched RNA RT reaction were pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed for 6h in the presence of 2 mM 4-thiouridine (Merck; from a 50 mM stock solution in 6% methanol) in the presence of 500 μM cycloheximide (Merck; from a 100 mg/ml stock solution in ethanol); 4 mM puromycin (BioShop) or mock.

value: mock


title: new mock imbibition rep2

description: Library name: new_mock_2


title: input 1h imbibition rep1

description: Library name: inp_1h_1


title: new mock imbibition rep1

description: Library name: new_mock_1


title: new PUR imbibition rep3

description: Library name: new_PUR_3

value: PUR


title: new PUR imbibition rep2

description: Library name: new_PUR_2


title: new CHX imbibition rep3

description: Library name: new_CHX_3

value: CHX


title: new CHX imbibition rep1

description: Library name: new_CHX_1

value: seed


title: input mock imbibition rep2

description: Library name: inp_mock_2

value: 6h imbibed


title: input mock imbibition rep1

description: Library name: inp_mock_1


title: input 1h imbibition rep2

description: Library name: inp_1h_2


title: input PUR imbibition rep3

description: Library name: inp_PUR_3


title: input PUR imbibition rep1

description: Library name: inp_PUR_1


title: input PUR imbibition rep2

description: Library name: inp_PUR_2


title: input CHX imbibition rep3

description: Library name: inp_CHX_3


title: input CHX imbibition rep2

description: Library name: inp_CHX_2


title: input CHX imbibition rep1

description: Library name: inp_CHX_1


title: new 6h imbibition rep4

description: Library name: new_6h_4

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211). For 4-SU labelled RNAs enrichment, biotinylation was performed for 80 μg of freshly isolated RNA in a 200 μl reaction mixture (10 mM Tris pH 7.5; 1 mM EDTA; 0.2 mg/ml EZ-Link Biotin-HPDP (ThermoFisher)) for 1.5 h at 22°C. 1 µl of tenfold diluted ERCC RNA Spike-In Mix (ThermoFisher) was added to the RNA before the biotinylation reactions, and a portion of the RNA after the addition of spike-ins (500 ng) was retained as an input. Unbound Biotin-HPDP was removed by chloroform/isoamyl alcohol (24:1) extraction. Subsequently, a 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added, and RNA was precipitated by centrifugation at 20,000g for 20 minutes. The pellet was washed with 1 ml of 80% ethanol, and after drying, it was resuspended in 25 μl of RNase-free water. Biotinylated RNA was purified using 50 μl of streptavidin C1 Dynabeads (ThermoFisher). The beads were washed in binding buffer (0.2 M NaCl; 0.1 M sodium phosphate pH 6.8; 25 mM MgCl2; 0.4% Tween), blocked in the binding buffer with 1 μg/μl glycogen for 10 minutes, and washed again in binding buffer. RNA samples were denatured at 65°C for 5 minutes, followed by 5 minutes on ice. Then, 25 μl of 2x binding buffer and 50 μl of washed streptavidin beads were added, mixed, and incubated at 22°C with gentle shaking for 20 minutes. The beads were washed three times with 0.5 ml of washing buffer (100 mM Tris-HCl pH 7.5; 10 mM EDTA; 1 M NaCl; 0.1% Tween20) at 65°C, followed by three washes at room temperature. Biotinylated RNA was eluted from the beads by two incubations with 50 μl of 200 mM DTT. RNA from the combined eluates was purified using RNA Clean & Concentrator-5 columns (Zymo), following the protocol for long RNA purification with DNase treatment. The entire volume of the sample was used for reverse transcription.
Input and enriched RNA samples were used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.25 of each input and whole enriched RNA RT reaction were pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed for 2.5h and 5.5h.  Then the seeds were squeezed, yielding a mixture of seed coats, intact and fragmented embryos. Such mixture was incubated for 30 min in 1/2 MS  and 2 mM 4-thiouridine (Merck; from a 50 mM stock solution in 6% methanol).

value: 5.5h imbibed 30 min labelled


title: new 6h imbibition rep3

description: Library name: new_6h_3


title: new 6h imbibition rep2

description: Library name: new_6h_2


title: new 6h imbibition rep1

description: Library name: new_6h_1


title: new 3h imbibition rep4

description: Library name: new_3h_4

value: 2.5h imbibed 30 min labelled


title: new 3h imbibition rep3

description: Library name: new_3h_3


title: new 3h imbibition rep1

description: Library name: new_3h_1


title: input 6h imbibition rep4

description: Library name: inp_6h_4


title: input 6h imbibition rep2

description: Library name: inp_6h_2


title: input 6h imbibition rep3

description: Library name: inp_6h_3


title: input 6h imbibition rep1

description: Library name: inp_6h_1


title: input 3h imbibition rep4

description: Library name: inp_3h_4


title: input 3h imbibition rep3

description: Library name: inp_3h_3


title: input 3h imbibition rep2

description: Library name: inp_3h_2


title: input 3h imbibition rep1

description: Library name: inp_3h_1


title: enriched converted rep4

description: Library name: new_conv_4

data_processing:
In our sequencing strategy, the R1 reads of pooled libraries contain two parts of UMI split by the barcode. We rearrange UMI sequences to position them next to each other and remove additional low-quality nucleotides, including  the oligo(dT) fragment and those that follow it. For this, we utilise the awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 of pooled libraries were demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex and R1 with parameters -p UB -UMI 14 -n 1. The resulting reads were trimmed to eliminate potential contamination with the poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then, they were mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Files were annotated using BRBseqTools (v 1.6) AnnotateBAM and deduplicated using Picard MarkDuplicates. Finally, we used slamdunk all (v 0.4.3) with parameters --max-read-length 101 -5 1 -n 100 and bed files with coordinates of Arabidopsis genes.
Assembly: TAIR10
Supplementary files format and content: Tcount file with slamdunk satistics
Supplementary files format and content: counts

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211). For 4-SU labelled RNAs enrichment, biotinylation was performed for 80 μg of freshly isolated RNA in a 200 μl reaction mixture (10 mM Tris pH 7.5; 1 mM EDTA; 0.2 mg/ml EZ-Link Biotin-HPDP (ThermoFisher)) for 1.5 h at 22°C. 1 µl of tenfold diluted ERCC RNA Spike-In Mix (ThermoFisher) was added to the RNA before the biotinylation reactions, and a portion of the RNA after the addition of spike-ins (500 ng) was retained as an input. Unbound Biotin-HPDP was removed by chloroform/isoamyl alcohol (24:1) extraction. Subsequently, a 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added, and RNA was precipitated by centrifugation at 20,000g for 20 minutes. The pellet was washed with 1 ml of 80% ethanol, and after drying, it was resuspended in 25 μl of RNase-free water. Biotinylated RNA was purified using 50 μl of streptavidin C1 Dynabeads (ThermoFisher). The beads were washed in binding buffer (0.2 M NaCl; 0.1 M sodium phosphate pH 6.8; 25 mM MgCl2; 0.4% Tween), blocked in the binding buffer with 1 μg/μl glycogen for 10 minutes, and washed again in binding buffer. RNA samples were denatured at 65°C for 5 minutes, followed by 5 minutes on ice. Then, 25 μl of 2x binding buffer and 50 μl of washed streptavidin beads were added, mixed, and incubated at 22°C with gentle shaking for 20 minutes. The beads were washed three times with 0.5 ml of washing buffer (100 mM Tris-HCl pH 7.5; 10 mM EDTA; 1 M NaCl; 0.1% Tween20) at 65°C, followed by three washes at room temperature. Biotinylated RNA was eluted from the beads by two incubations with 50 μl of 200 mM DTT. RNA from the combined eluates was purified using RNA Clean & Concentrator-5 columns (Zymo). Labelled total and enriched RNA was combined with a reaction mixture (600 mM 2,2,2-trifluoroethylamine (TFEA); 1 mM EDTA; 100 mM sodium acetate pH 5.2). Following this, meta-chloroperoxybenzoic acid (mCPBA) was added to a concentration of 10 mM. The reaction was incubated at 45°C for 1 h, and subsequently, RNA was purified using an equal volume of RNAClean beads (Beckman) according to the manufacturer’s protocol. The RNA was eluted with 18 μl of water and mixed with 2 μl of 10x reducing mix (100 mM Tris-HCl pH 7.5; 100 mM DTT; 1 M NaCl; 10 mM EDTA). The reaction was incubated at 37°C for 30 minutes. RNA was again purified using an equal volume of RNAClean beads (Beckman) following the manufacturer's protocol, with an elution volume of 12 μl. This RNA was used for the 3’ RNA-seq library preparation.
RNA samples were used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. Whole RT reactions were pooled and cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed for 3h in the presence of 2 mM 4-thiouridine (Merck; from a 50 mM stock solution in 6% methanol).

value: 4-SU labelled and enriched

value: converted


title: enriched converted rep3

description: Library name: new_conv_3


title: enriched converted rep2

description: Library name: new_conv_2


title: enriched converted rep1

description: Library name: new_conv_1


title: total-non-converted rep4

description: Library name: inp_non_4

value: 4-SU labelled

value: non-converted


title: total-non-converted rep2

description: Library name: inp_non_2


title: total-non-converted rep1

description: Library name: inp_non_1


title: total converted rep4

description: Library name: inp_conv_4


title: total converted rep3

description: Library name: inp_conv_3


title: new 3h imbibition rep2

description: Library name: new_3h_2

value: enriched


title: Brain_1-1_Saline_ATAC

description: Library name: Brain_1-1_Saline_ATAC

value: brain

value: Saline


title: total converted rep2

description: Library name: inp_conv_2


title: total converted rep1

description: Library name: inp_conv_1


title: K>R 3 sample 1, mock treatment, 4 hours

description: Library name: KR3_Mock_1

value: 3 week old leaf

value: Mock


title: K>R 1-9 sample 1, mock treatment, 4 hours

description: Library name: KR1_9_Mock_1


title: Delta28 sample 3, mock treatment, 4 hours

description: Library name: Delta28_Mock_3


title: new mRNA matured 26C rep2

description: Library name: new_26C_2

data_processing:
In our sequencing strategy, the R1 reads of pooled libraries contain two parts of UMI split by the barcode. We rearrange UMI sequences to position them next to each other and remove additional low-quality nucleotides, including  the oligo(dT) fragment and those that follow it. For this, we utilise the awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 of pooled libraries were demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex and R1 with parameters -p UB -UMI 14 -n 1. The resulting reads were trimmed to eliminate potential contamination with the poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then, they were mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes.
Assembly: TAIR10
Supplementary files format and content: gene count text files

growth_protocol: Plants were grown until the bolting stage at 22°C under a long day photoperiod in a Percival growth chamber. Subsequently, some plants were transferred to other Percival chambers set for a long day photoperiod with temperatures of 15°C or 26°C. Seeds from 8 to 12 plants were combined to create a single biological replicate.

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211). For 4-SU labelled RNAs enrichment, biotinylation was performed for 12 μg of freshly isolated RNA in a 200 μl reaction mixture (10 mM Tris pH 7.5; 1 mM EDTA; 0.2 mg/ml EZ-Link Biotin-HPDP (ThermoFisher)) for 1.5 h at 22°C. A portion of the RNA (400 ng) was retained as an input. Unbound Biotin-HPDP was removed by chloroform/isoamyl alcohol (24:1) extraction. Subsequently, a 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added, and RNA was precipitated by centrifugation at 20,000g for 20 minutes. The pellet was washed with 1 ml of 80% ethanol, and after drying, it was resuspended in 25 μl of RNase-free water. Biotinylated RNA was purified using 50 μl of streptavidin C1 Dynabeads (ThermoFisher). The beads were washed in binding buffer (0.2 M NaCl; 0.1 M sodium phosphate pH 6.8; 25 mM MgCl2; 0.4% Tween), blocked in the binding buffer with 1 μg/μl glycogen for 10 minutes, and washed again in binding buffer. RNA samples were denatured at 65°C for 5 minutes, followed by 5 minutes on ice. Then, 25 μl of 2x binding buffer and 50 μl of washed streptavidin beads were added, mixed, and incubated at 22°C with gentle shaking for 20 minutes. The beads were washed three times with 0.5 ml of washing buffer (100 mM Tris-HCl pH 7.5; 10 mM EDTA; 1 M NaCl; 0.1% Tween20) at 65°C, followed by three washes at room temperature. Biotinylated RNA was eluted from the beads by two incubations with 50 μl of 200 mM DTT. RNA from the combined eluates was purified using RNA Clean & Concentrator-5 columns (Zymo), following the protocol for long RNA purification with DNase treatment. The entire volume of the sample was used for reverse transcription.
Dry seed, input and enriched RNA samples were used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.25 of each input/dry and whole enriched RNA RT reaction were pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

tag: ecotype

value: 3h imbibed

value: maturation temp 26C


title: new mRNA matured 26C rep3

description: Library name: new_26C_3


title: new mRNA matured 22C rep3

description: Library name: new_22C_3

value: maturation temp 22C


title: new mRNA matured 26C rep1

description: Library name: new_26C_1


title: CHX +alpha-amanitin 6h rep2

description: Library name: C_6h_2

value: CHX +alpha-amanitin


title: new mRNA matured 22C rep1

description: Library name: new_22C_1

value: seed


title: new mRNA matured 15C rep3

description: Library name: new_15C_3

value: maturation temp 15C


title: new mRNA matured 15C rep1

description: Library name: new_15C_1


title: new mRNA matured 15C rep2

description: Library name: new_15C_2


title: imbibed matured 26C rep3

description: Library name: inp_26C_3

value: input


title: new mRNA matured 22C rep2

description: Library name: new_22C_2


title: imbibed matured 26C rep2

description: Library name: inp_26C_2


title: imbibed matured 26C rep1

description: Library name: inp_26C_1


title: alpha-amanitin 6h rep1

description: Library name: M_6h_1

value: 6h imbibed

value: alpha-amanitin


title: imbibed matured 22C rep3

description: Library name: inp_22C_3


title: imbibed matured 22C rep2

description: Library name: inp_22C_2


title: imbibed matured 22C rep1

description: Library name: inp_22C_1


title: imbibed matured 15C rep3

description: Library name: inp_15C_3


title: imbibed matured 15C rep1

description: Library name: inp_15C_1


title: imbibed matured 15C rep2

description: Library name: inp_15C_2


title: dry matured 26C rep3

description: Library name: dry_26C_3

value: dry


title: dry matured 26C rep2

description: Library name: dry_26C_2


title: dry matured 26C rep1

description: Library name: dry_26C_1


title: dry matured 22C rep2

description: Library name: dry_22C_2


title: dry matured 22C rep3

description: Library name: dry_22C_3


title: dry matured 15C rep3

description: Library name: dry_15C_3


title: dry matured 15C rep2

description: Library name: dry_15C_2


title: new 35C imbibition rep3

description: Library name: new_t35_3

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211). For 4-SU labelled RNAs enrichment, biotinylation was performed for 12.5 μg of freshly isolated RNA in a 200 μl reaction mixture (10 mM Tris pH 7.5; 1 mM EDTA; 0.2 mg/ml EZ-Link Biotin-HPDP (ThermoFisher)) for 1.5 h at 22°C. 1 µl of tenfold diluted ERCC RNA Spike-In Mix (ThermoFisher) was added to the RNA before the biotinylation reactions, and a portion of the RNA after the addition of ERCC (500 ng) was retained as an input. Unbound Biotin-HPDP was removed by chloroform/isoamyl alcohol (24:1) extraction. Subsequently, a 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added, and RNA was precipitated by centrifugation at 20,000g for 20 minutes. The pellet was washed with 1 ml of 80% ethanol, and after drying, it was resuspended in 25 μl of RNase-free water. Biotinylated RNA was purified using 50 μl of streptavidin C1 Dynabeads (ThermoFisher). The beads were washed in binding buffer (0.2 M NaCl; 0.1 M sodium phosphate pH 6.8; 25 mM MgCl2; 0.4% Tween), blocked in the binding buffer with 1 μg/μl glycogen for 10 minutes, and washed again in binding buffer. RNA samples were denatured at 65°C for 5 minutes, followed by 5 minutes on ice. Then, 25 μl of 2x binding buffer and 50 μl of washed streptavidin beads were added, mixed, and incubated at 22°C with gentle shaking for 20 minutes. The beads were washed three times with 0.5 ml of washing buffer (100 mM Tris-HCl pH 7.5; 10 mM EDTA; 1 M NaCl; 0.1% Tween20) at 65°C, followed by three washes at room temperature. Biotinylated RNA was eluted from the beads by two incubations with 50 μl of 200 mM DTT. RNA from the combined eluates was purified using RNA Clean & Concentrator-5 columns (Zymo), following the protocol for long RNA purification with DNase treatment. The entire volume of the sample was used for reverse transcription.
Input and enriched RNA samples were used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.25 of each input and whole enriched RNA RT reaction were pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed at 4C, 22C and 35C for 3h in the presence of 2 mM 4-thiouridine (Merck; from a 50 mM stock solution in 6% methanol).

value: 35C during imbibition


title: dry matured 15C rep1

description: Library name: dry_15C_1


title: total-non-converted rep3

description: Library name: inp_non_3

value: 4-SU labelled

value: non-converted


title: new 35C imbibition rep2

description: Library name: new_t35_2

value: enriched


title: new 35C imbibition rep1

description: Library name: new_t35_1


title: new 35C imbibition rep4

description: Library name: new_t35_4


title: new 22C imbibition rep4

description: Library name: new_t22_4

value: 22C during imbibition


title: new 22C imbibition rep3

description: Library name: new_t22_3


title: input 6h imbibition rep4

description: Library name: inp_6h_4


title: input 3h imbibition rep4

description: Library name: inp_3h_4


title: input 6h imbibition rep2

description: Library name: inp_6h_2


title: new 22C imbibition rep1

description: Library name: new_t22_1


title: new 22C imbibition rep2

description: Library name: new_t22_2


title: input 3h imbibition rep1

description: Library name: inp_3h_1


title: input 3h imbibition rep3

description: Library name: inp_3h_3


title: new 4C imbibition rep4

description: Library name: new_t04_4

value: 4C during imbibition


title: new 4C imbibition rep1

description: Library name: new_t04_1


title: new 4C imbibition rep3

description: Library name: new_t04_3


title: new 4C imbibition rep2

description: Library name: new_t04_2


title: dry matured 22C rep1

description: Library name: dry_22C_1


title: input 35C imbibition rep4

description: Library name: inp_t35_4


title: input 35C imbibition rep3

description: Library name: inp_t35_3


title: input 1h imbibition rep3

description: Library name: inp_1h_3

value: 1h imbibed