title: ATAC-seq from right lobe of liver (ENCLB368ROS)

description:
https://www.encodeproject.org/experiments/ENCSR516CPW/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human right lobe of liver
experiment encode accession: ENCSR516CPW
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB368ROS
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (47 years) right lobe of liver tissue, preserved by cryopreservation

value: right lobe of liver

value: tissue

value: Child biosample for Chang/Greenleaf lab

value: DM:no; HTN:yes; CAD:no

value: adult

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS690HLT at ENCODE; https://www.encodeproject.org/ENCBS690HLT/

value: Derived from ENCODE donor ENCDO912EIY; https://www.encodeproject.org/ENCDO912EIY/


title: ATAC-seq from right lobe of liver (ENCLB863COR)

status: Public on Mar 30 2021

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/ENCSR516CPW/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human right lobe of liver
experiment encode accession: ENCSR516CPW
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB863COR
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

tag: description

tag: biosample encode accession

tag: Sex

value: female

tag: health state

tag: dev stage

tag: age

tag: lab

tag: source

tag: link


title: ATAC-seq from heart right ventricle (ENCLB394FCF)

description:
https://www.encodeproject.org/experiments/ENCSR133CMC/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR133CMC
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB394FCF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (69 years) heart right ventricle tissue

value: heart right ventricle

value: male

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: 69 year

value: Shin Lin

value: ENCBS791FQA at ENCODE; https://www.encodeproject.org/ENCBS791FQA/

value: Derived from ENCODE donor ENCDO477WED; https://www.encodeproject.org/ENCDO477WED/


title: ATAC-seq from sciatic nerve (ENCLB092UDZ)

description:
https://www.encodeproject.org/experiments/ENCSR120MOY/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human sciatic nerve
experiment encode accession: ENCSR120MOY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB092UDZ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (26 years) sciatic nerve tissue, preserved by flash-freezing

value: sciatic nerve

value: tissue

value: DM:no; HTN:no; CAD:no

value: 26 year

value: ENCBS861FXG at ENCODE; https://www.encodeproject.org/ENCBS861FXG/

value: Derived from ENCODE donor ENCDO221IPH; https://www.encodeproject.org/ENCDO221IPH/


title: ATAC-seq from adrenal gland (ENCLB984HGB)

description:
https://www.encodeproject.org/experiments/ENCSR864ADD/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human adrenal gland
experiment encode accession: ENCSR864ADD
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB984HGB
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (41 years) adrenal gland tissue, preserved by cryopreservation

value: adrenal gland

value: adult

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS305CXN at ENCODE; https://www.encodeproject.org/ENCBS305CXN/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: Control ChIP-seq from HepG2 (ENCLB269QQU)

description:
https://www.encodeproject.org/experiments/ENCSR621FPD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR621FPD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-14
lab: Richard Myers, HAIB
library encode accession: ENCLB269QQU
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line

tag: line

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS746CQF at ENCODE; https://www.encodeproject.org/ENCBS746CQF/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: ATAC-seq from adrenal gland (ENCLB380AEA)

description:
https://www.encodeproject.org/experiments/ENCSR864ADD/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human adrenal gland
experiment encode accession: ENCSR864ADD
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB380AEA
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: tissue

value: female

value: DM:no; HTN:no; CAD:no


title: Control ChIP-seq from HepG2 (ENCLB652ECI)

description:
https://www.encodeproject.org/experiments/ENCSR313HFF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR313HFF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-26
lab: Richard Myers, HAIB
library encode accession: ENCLB652ECI
fragmentation methods: sonication (generic)

value: ENCBS369XNG at ENCODE; https://www.encodeproject.org/ENCBS369XNG/


title: Control ChIP-seq from HepG2 (ENCLB474TPC)

description:
https://www.encodeproject.org/experiments/ENCSR856RWG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR856RWG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-26
lab: Richard Myers, HAIB
library encode accession: ENCLB474TPC
fragmentation methods: sonication (generic)

value: ENCBS068VMM at ENCODE; https://www.encodeproject.org/ENCBS068VMM/


title: ATAC-seq from Right ventricle myocardium inferior (ENCLB816ZDW)

description:
https://www.encodeproject.org/experiments/ENCSR855BMI/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human right ventricle myocardium inferior
experiment encode accession: ENCSR855BMI
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB816ZDW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (60 years) Right ventricle myocardium inferior tissue, preserved by cryopreservation

value: Right ventricle myocardium inferior

value: Inferior wall of right ventricle.

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS083KRS at ENCODE; https://www.encodeproject.org/ENCBS083KRS/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: ATAC-seq from left cardiac atrium (ENCLB070MYF)

description:
https://www.encodeproject.org/experiments/ENCSR310UDW/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human left cardiac atrium
experiment encode accession: ENCSR310UDW
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB070MYF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (40 years) left cardiac atrium tissue, preserved by cryopreservation

value: left cardiac atrium

value: male

value: DM:no; HTN:yes; CAD:no

value: 40 year

value: ENCBS412TKM at ENCODE; https://www.encodeproject.org/ENCBS412TKM/

value: Derived from ENCODE donor ENCDO392CRK; https://www.encodeproject.org/ENCDO392CRK/


title: Control ChIP-seq from HepG2 (ENCLB265MAW)

description:
https://www.encodeproject.org/experiments/ENCSR550ZLZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR550ZLZ
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2017-02-17
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB265MAW
size range: 200-400

value: cell line

value: Control ChIP-seq on HepG2 cells

value: hepatocellular carcinoma

value: child

value: 15 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: ENCBS889CYZ at ENCODE; https://www.encodeproject.org/ENCBS889CYZ/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: ATAC-seq from mucosa of descending colon (ENCLB875UFQ)

description:
https://www.encodeproject.org/experiments/ENCSR496PPU/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human mucosa of descending colon
experiment encode accession: ENCSR496PPU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB875UFQ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (61 years) mucosa of descending colon tissue, preserved by cryopreservation

value: mucosa of descending colon

value: tissue

value: female

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: adult

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS917FSI at ENCODE; https://www.encodeproject.org/ENCBS917FSI/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: ATAC-seq from heart left ventricle (ENCLB664QYP)

description:
https://www.encodeproject.org/experiments/ENCSR310RJN/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR310RJN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB664QYP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (43 years) heart left ventricle tissue

value: heart left ventricle

value: male

value: nonischemic (EF 23%, LVEDD 6.1; RV moderate dilation, normal function)

value: 43 year

value: Shin Lin

value: ENCBS420JAE at ENCODE; https://www.encodeproject.org/ENCBS420JAE/

value: Derived from ENCODE donor ENCDO967KID; https://www.encodeproject.org/ENCDO967KID/


title: ATAC-seq from heart left ventricle (ENCLB043ELP)

description:
https://www.encodeproject.org/experiments/ENCSR310RJN/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR310RJN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB043ELP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000


title: PT9_3

city: New York

first: Sagar

last: Chhangawala

state: NY

address: 1300 York Ave.

department: PBSB

institute: Weill Cornell Medical College

data_processing:
Raw fastq files were first trimmed using trimmomatic (v0.35, Parameters: TruSeq3-PE adapters, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
The samples were then aligned to hg19 genome using bowtie2 (v2.2.6, Parameters: -X2000 –local –mm --no-mixed --no-discordant)
Duplicate read removal was performed using MarkDuplicates (v2.9.0)
In order to account for Tn5 shift, all positive strand reads were shifted by +4bps and all negative strand reads were shifted by -5bps
Peak calling was then performed on each of the libraries individually and after pooling replicates using MACS2 (v2.1.0, parameters: --nomodel --extsize 150 --shift -75 --slocal 5000 --llocal 20000 -B --SPMR --keep-dup all -p 0.01)
IDR (irreproducible discovery rate) was used to identify reproducible peaks from the duplicate libraries for each sample (IDR < 1 x 10−2). Reproducible peaks were merged to create an atlas of peaks found across all patients
Read counting for all peaks in the atlas was performed using GenomicRanges’s summarizeOverlaps function
normalized bigWigs were generated from BAM files using UCSC tools and normalization sizefactors from DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files containing normalized ATAC-seq signals
Supplementary_files_format_and_content: Tab delimited file containing atlas peaks coordinates and read counts

source_name: PDAC EpCAM+ primary tumor

extract_protocol:
Suspensions of 50,000 cells were first pelleted by centrifugation and then washed once with PBS followed by gentle (no rigorous vortex) resuspension in ATAC-seq lysis buffer (10mM Tris·Cl, pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1% (v/v) Igepal CA-630) in order to retrieve healthy nuclei from the cells. TN5 transposase was added to the buffer solution (Nextera DNA-library preparation kit, Illumina, Cat# FC-121-1030) and incubated at 370 C for 30 min. After the incubation, the transposed DNA fragments were extracted from the reaction solution using the Mini Elute PCR purification kit (Qiagen Cat# 28004) and then amplified by a 12-cycle PCR amplification step with specific primers
Nextera DNA-library preparation kit, Illumina, Cat# FC-121-1030

tag: tumor differentiation

value: moderately diff

tag: margin status

value: Positive

tag: tumor stage

value: T3 N0

tag: adjuvant therapy

value: Yes

tag: radiotherapy

value: No

tag: recurrence status


title: ATAC-seq from right lobe of liver (ENCLB651BJK)

description:
https://www.encodeproject.org/experiments/ENCSR952SPO/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human right lobe of liver
experiment encode accession: ENCSR952SPO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB651BJK
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female child (16 years) right lobe of liver tissue, preserved by cryopreservation

value: right lobe of liver

value: tissue

value: Child biosample for Chang/Greenleaf lab

value: female

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: ENCBS976GTM at ENCODE; https://www.encodeproject.org/ENCBS976GTM/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: PT9_2


title: PT71_2

value: unknown


title: ATAC-seq from sciatic nerve (ENCLB361DIU)

description:
https://www.encodeproject.org/experiments/ENCSR120MOY/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human sciatic nerve
experiment encode accession: ENCSR120MOY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB361DIU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: sciatic nerve

value: male

value: adult

value: 26 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS861FXG at ENCODE; https://www.encodeproject.org/ENCBS861FXG/

value: Derived from ENCODE donor ENCDO221IPH; https://www.encodeproject.org/ENCDO221IPH/


title: DNase-seq from kidney capillary endothelial cell (ENCLB493KAA)

description:
https://www.encodeproject.org/experiments/ENCSR988YKR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR988YKR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB493KAA

source_name: Homo sapiens female embryo (113 days) kidney capillary endothelial primary cell

value: kidney capillary endothelial cell

value: primary cell

value: embryonic

value: 113 day

value: John Stamatoyannopoulos, UW

value: BDRL

value: ENCBS294OHG at ENCODE; https://www.encodeproject.org/ENCBS294OHG/

value: Derived from ENCODE donor ENCDO987XTQ; https://www.encodeproject.org/ENCDO987XTQ/


title: ATAC-seq from mucosa of descending colon (ENCLB246GTQ)

description:
https://www.encodeproject.org/experiments/ENCSR496PPU/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human mucosa of descending colon
experiment encode accession: ENCSR496PPU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB246GTQ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: mucosa of descending colon

value: tissue

value: female

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: 61 year

value: ENCBS917FSI at ENCODE; https://www.encodeproject.org/ENCBS917FSI/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: PT71_1

value: unknown

value: T3 N0

value: Yes

value: No


title: DNase-seq from RCC (ENCLB993FHL)

description:
https://www.encodeproject.org/experiments/ENCSR337IRF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR337IRF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB993FHL
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens RCC cell line

value: RCC

value: cell line

value: adult

value: 80 year

value: Unknown Source

value: ENCBS967MVM at ENCODE; https://www.encodeproject.org/ENCBS967MVM/

value: Derived from ENCODE donor ENCDO421EJG; https://www.encodeproject.org/ENCDO421EJG/


title: ATAC-seq from left cardiac atrium (ENCLB648ZBR)

description:
https://www.encodeproject.org/experiments/ENCSR310UDW/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human left cardiac atrium
experiment encode accession: ENCSR310UDW
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB648ZBR
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: left cardiac atrium

value: tissue

value: male

value: DM:no; HTN:yes; CAD:no

value: 40 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS412TKM at ENCODE; https://www.encodeproject.org/ENCBS412TKM/

value: Derived from ENCODE donor ENCDO392CRK; https://www.encodeproject.org/ENCDO392CRK/


title: Control ChIP-seq from skin epidermis (ENCLB341NAV)

description:
https://www.encodeproject.org/experiments/ENCSR578ORB/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq of skin epidermis male adult (84 years). Note that tissue excised from donor is adjacent epidermis from Mohs cancer removal procedure.
experiment encode accession: ENCSR578ORB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-09-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB341NAV
size range: 200-600

source_name: Homo sapiens male adult (84 years) skin epidermis tissue

value: skin epidermis

value: tissue collected during keratinocyte carcinoma removal surgery under supervision of Maryam Asgari. These cells contain no tumor.

value: keratinocyte carcinoma surgical removal

value: 84 year

value: Bradley Bernstein, Broad

value: Maryam M. Asgari, MD, MPH

value: ENCBS391IST at ENCODE; https://www.encodeproject.org/ENCBS391IST/

value: Derived from ENCODE donor ENCDO799UNP; https://www.encodeproject.org/ENCDO799UNP/


title: ATAC-seq from right cardiac atrium (ENCLB771GVY)

description:
https://www.encodeproject.org/experiments/ENCSR177JWR/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human right cardiac atrium
experiment encode accession: ENCSR177JWR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB771GVY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (59 years) right cardiac atrium tissue, preserved by cryopreservation

value: right cardiac atrium

value: female

value: DM:yes; HTN:yes; CAD:no

value: adult

value: 59 year

value: ENCBS739EVX at ENCODE; https://www.encodeproject.org/ENCBS739EVX/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: PT70_2

value: poorly diff

value: Positive

value: T3 N1

value: Yes

value: No

value: unknown


title: PT70_1


title: PT69_2

value: moderately diff

value: Free

value: T3 N0


title: PT69_1


title: DNase-seq from RCC (ENCLB852HRP)

description:
https://www.encodeproject.org/experiments/ENCSR337IRF/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR337IRF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB852HRP
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: RCC

value: cell line

value: male

value: 62 year

value: John Stamatoyannopoulos, UW

value: Unknown Source

value: ENCBS354GLT at ENCODE; https://www.encodeproject.org/ENCBS354GLT/

value: Derived from ENCODE donor ENCDO335XPZ; https://www.encodeproject.org/ENCDO335XPZ/


title: PT66_2

value: moderately to poorly diff


title: PT67_1

value: Positive


title: ATAC-seq from Right ventricle myocardium inferior (ENCLB122LSW)

description:
https://www.encodeproject.org/experiments/ENCSR855BMI/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human right ventricle myocardium inferior
experiment encode accession: ENCSR855BMI
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB122LSW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: Right ventricle myocardium inferior

value: tissue

value: Inferior wall of right ventricle.

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS083KRS at ENCODE; https://www.encodeproject.org/ENCBS083KRS/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: DNase-seq from kidney capillary endothelial cell (ENCLB773BKG)

description:
https://www.encodeproject.org/experiments/ENCSR988YKR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR988YKR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB773BKG

value: kidney capillary endothelial cell

value: primary cell

value: female

value: embryonic

value: 113 day

value: BDRL

value: ENCBS294OHG at ENCODE; https://www.encodeproject.org/ENCBS294OHG/

value: Derived from ENCODE donor ENCDO987XTQ; https://www.encodeproject.org/ENCDO987XTQ/


title: PT66_1

value: moderately to poorly diff

value: Free

value: T3 N1

value: unknown


title: Control ChIP-seq from K562 (ENCLB856QUB)

description:
https://www.encodeproject.org/experiments/ENCSR397ZZR/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq in K562
experiment encode accession: ENCSR397ZZR
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2017-02-02
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB856QUB
size range: 200-400

source_name: Homo sapiens K562 cell line

value: cell line

value: Control ChIP-seq in K562

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: ENCBS277GLZ at ENCODE; https://www.encodeproject.org/ENCBS277GLZ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: PT60_2

value: T3 N0

value: Yes

value: No


title: PT61_1

value: moderately diff


title: PT61_2


title: PT64_1

value: poorly diff

value: Positive


title: PT60_1

value: Free


title: PT64_2

value: T3 N1

value: unknown


title: PT57_1


title: PT55_2


title: PT56_1


title: PT55_1


title: PT59_2


title: PT56_2


title: PT57_2


title: PT53_2


title: PT67_2


title: PT53_1


title: PT52_1


title: PT52_2


title: PT5_3


title: PT5_1


title: Control ChIP-seq from HepG2 (ENCLB650MIJ)

description:
https://www.encodeproject.org/experiments/ENCSR550ZLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR550ZLZ
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2017-02-17
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB650MIJ
size range: 200-400

value: cell line

value: Control ChIP-seq on HepG2 cells

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS091JMF at ENCODE; https://www.encodeproject.org/ENCBS091JMF/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: PT49_1


title: PT46_1


title: PT59_1

value: T3 N0


title: PT45_1

value: Yes


title: PT43_2

value: No


title: PT43_1

value: moderately diff


title: PT4_3

value: moderately to poorly diff


title: PT41_2

value: Positive


title: PT42_1

value: Free


title: PT4_2

value: T3 N1


title: PT39_1

value: unknown


title: PT36_2


title: PT51_2


title: PT39_2


title: PT41_1


title: PT51_1


title: PT35_1

value: T2 N1


title: PT35_2


title: PT36_1


title: PT32_2


title: PT32_1


title: PT34_1


title: PT26_2

value: poorly diff


title: PT46_2


title: PT45_2


title: PT24_2


title: PT24_1


title: PT42_2


title: PT23_2


title: PT49_2


title: PT23_1


title: PT21_1


title: PT21_2


title: PT20_1


title: PT18_2


title: PT17_1


title: PT17_2


title: PT16_1


title: PT18_1


title: PT34_2


title: PT16_2


title: PT13_1


title: PT14_2


title: PT14_1


title: PT12_1


title: PT13_2


title: PT12_2


title: PT26_1


title: rna_MeOH_rep2

status: Public on Mar 29 2021

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: Bioscience Bldg. 2-1, Hirosawa

country: Japan

institute: RIKEN

library_source: transcriptomic

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
The processed datafile use the public ids  (UCSC) from the URL as below,
https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=718346243_SO4o0BwCnsGKo6NhsocAvichpTxI
Genome_build: hg19
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

molecule: total RNA

source_name: HeLa S3 cells

extract_protocol:
Truseq stranded mRNA library prep
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or TruSeq (illumina) (for mRNA-seq)

treatment_protocol: HeLa S3 cells with either 100ng/mL spliceostatin A (SSA) or methanol (MeOH) (solvent for SSA as negative control) for 6 hours.

tag: treatment

value: MeOH

tag: cell line

value: HeLa S3


title: rna_SSA

value: SSA


title: ribo_MeOH_rep1

data_processing:
Library strategy: Ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
The processed datafile use the public ids  (UCSC) from the URL as below,
https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=718346243_SO4o0BwCnsGKo6NhsocAvichpTxI
Genome_build: hg19
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

extract_protocol:
Rnase I footprinting, ribosome pelleting, RNA extraction
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or TruSeq (illumina) (for mRNA-seq)


title: rna_MeOH_rep1


title: ribo_SSA


title: Control6-1-RNA-MM

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
WT control for GacS (MM)
paired-end RNA-seq data of Pseudomonas sringae 1448A

data_processing:
ChIP-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using Bowtie2 (version 2.3.4.3). Only the uniquely mapped reads were kept for the subsequent analyses. Bam files were transformed into bigWig files by deeptools (version 3.1.3)
RNA-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
Genome_build: Pseudomonas sringae 1448A NC_005773.3
Supplementary_files_format_and_content: bigWig files were generated from ChIP-seq, containing dense data that can be displayed as a graph. txt files were generated from RNA-seq, containing raw read counts mapped to each gene.

organism: Pseudomonas savastanoi pv. phaseolicola 1448A

source_name: liquid culture in KB (King's B)  medium

growth_protocol: KB/MM

extract_protocol: NEBNext® UltraTM II RNA Library Prep Kit protocol (Illumina)

treatment_protocol: grow until mid-log phase OD600=0.6

tag: genotype

value: WT


title: ribo_MeOH_rep2


title: Control5-2-RNA-MM

description:
WT control for RpoN (MM)
paired-end RNA-seq data of Pseudomonas sringae 1448A


title: Control6-2-RNA-MM


title: PT20_2


title: Control4-1-RNA-MM

description:
WT control for PilR, PilS, OmpR, EnvZ, PsrA, AefR, Vfr, CvsS (MM)
paired-end RNA-seq data of Pseudomonas sringae 1448A


title: Control3-2-RNA-MM

description:
WT control for RhpR, TsiS (MM)
paired-end RNA-seq data of Pseudomonas sringae 1448A


title: Control3-1-RNA-MM


title: Control1-2-RNA-MM

description:
WT control for HrpL, HrpR, PhoP, MgrA, AlgU (MM)
paired-end RNA-seq data of Pseudomonas sringae 1448A


title: Control2-2-RNA-MM

description:
WT control for HrpS, GacA (MM)
paired-end RNA-seq data of Pseudomonas sringae 1448A


title: Control1-1-RNA-MM


title: Control4-2-RNA-MM


title: Control8-2-RNA-KB

description:
WT control for GacS (KB)
paired-end RNA-seq data of Pseudomonas sringae 1448A


title: Control8-1-RNA-KB


title: Control7-2-RNA-KB

description:
WT control for  RpoN (KB)
paired-end RNA-seq data of Pseudomonas sringae 1448A


title: Control5-2-RNA-KB

description:
WT control for PilR, PilS,OmpR (KB)
paired-end RNA-seq data of Pseudomonas sringae 1448A


title: Control4-2-RNA-KB

description:
WT control for MgrA (KB)
paired-end RNA-seq data of Pseudomonas sringae 1448A


title: Control6-2-RNA-KB

description:
WT control for TsiS, EnvZ, GacA, PsrA, AefR, Vfr, CvsS (KB)
paired-end RNA-seq data of Pseudomonas sringae 1448A


title: Control6-1-RNA-KB


title: Control5-1-RNA-KB


title: Control4-1-RNA-KB


title: Control3-1-RNA-KB

description:
WT control for RhpR (KB)
paired-end RNA-seq data of Pseudomonas sringae 1448A


title: Control3-2-RNA-KB


title: Control2-2-RNA-KB

description:
WT control for HrpS (KB)
paired-end RNA-seq data of Pseudomonas sringae 1448A


title: Control1-2-RNA-KB

description:
WT control for HrpL, HrpR, PhoP, AlgU (KB)
paired-end RNA-seq data of Pseudomonas sringae 1448A


title: Control2-1-RNA-KB


title: Control1-1-RNA-KB


title: RpoN-2-RNA-MM

description: paired-end RNA-seq data of Pseudomonas sringae 1448A

source_name: liquid culture in minimal medium (MM)

value: over-expressed rpoN


title: Control2-1-RNA-MM


title: Control7-1-RNA-KB


title: RpoN-1-RNA-KB


title: RpoN-2-RNA-KB


title: CvsS-1-RNA-MM

value: cvsS mutant


title: CvsS-2-RNA-MM


title: AlgU-2-RNA-MM

value: algU mutant


title: CvsS-2-RNA-KB


title: CvsS-1-RNA-KB


title: AlgU-2-RNA-KB


title: RpoN-1-RNA-MM


title: AlgU-1-RNA-KB


title: Vfr-2-RNA-MM

value: vfr mutant


title: Vfr-1-RNA-MM


title: AlgU-1-RNA-MM


title: Vfr-2-RNA-KB


title: 80 - T8M-18: muscle of control (immature) trout 33 weeks after the initial sampling, sample 18

type: RNA

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Normalization and statistical analysis were performed using GeneSpring software (Agilent).

organism: Oncorhynchus mykiss

label_protocol: Labeling and hybridization steps were performed following the “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling)”Agilent protocol. Briefly, for each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

growth_protocol: Briefly, diploid female rainbow trout from the same autumnal strain cohort were reared in the INRAE's experimental facilities (PEIMA, Sizun, France). After ovulation and stripping, female that spawned at the same date were placed into a circular 2m diameter tank containing 2m3 of water. A total of nine experimental groups of post-spawning fish were constituted. Fish were fed with the same diet throughout the course of the trial.

extract_protocol: Total RNA extraction was performed using TRIzol (Invitrogen, Carlsbad, CA, USA) reagent following the manufacturer’s instructions. RNA integrity was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: During sampling, post-spawning fish (n = 20) from the same tank were sequentially slaughtered at 0, 1, 2, 4, 8, 13, 16, 24, and 33 weeks after ovulation. At slaughter, fish were anaesthetized with Tricaine Pharmaq (5g/100L) in a 500L tank, killed by a blow onto the head, and then led by gill arch section. An overdose of anesthetic (5g/50L) was used for euthanizing fish in another tank. After death, fish were measured for quality parameters and a slice of fast skeletal muscle was carefully dissected from the dorsal region of the musculature, frozen in liquid nitrogen and stored at -80°C until RNA extraction

tag: tissue

value: trout muscle

tag: time


title: 78 - T8M-15: muscle of control (immature) trout 33 weeks after the initial sampling, sample 15


title: Vfr-1-RNA-KB


title: 67 - 8M-4: Trout muscle 33 weeks post-spawning sample 4


title: 74 - T8M-4: muscle of control (immature) trout 33 weeks after the initial sampling, sample 4


title: 73 - T8M-1: muscle of control (immature) trout 33 weeks after the initial sampling, sample 1


title: 79 - T8M-17: muscle of control (immature) trout 33 weeks after the initial sampling, sample 17


title: 71 - 8M-14: Trout muscle 33 weeks post-spawning sample 14


title: AefR-2-RNA-MM

value: aefR mutant


title: 77 - T8M-14: muscle of control (immature) trout 33 weeks after the initial sampling, sample 14


title: 66 - 8M-2: Trout muscle 33 weeks post-spawning sample 2


title: 76 - T8M-9: muscle of control (immature) trout 33 weeks after the initial sampling, sample 9


title: Control5-1-RNA-MM


title: 69 - 8M-10: Trout muscle 33 weeks post-spawning sample 10


title: 75 - T8M-7: muscle of control (immature) trout 33 weeks after the initial sampling, sample 7


title: 72 - 8M-16: Trout muscle 33 weeks post-spawning sample 16


title: 70 - 8M-11: Trout muscle 33 weeks post-spawning sample 11


title: 68 - 8M-6: Trout muscle 33 weeks post-spawning sample 6


title: AefR-2-RNA-KB


title: AefR-1-RNA-MM


title: 63 - 6M-18: Trout muscle 24 weeks post-spawning sample 18


title: AefR-1-RNA-KB


title: 65 - 8M-1: Trout muscle 33 weeks post-spawning sample 1


title: 64 - 6M-19: Trout muscle 24 weeks post-spawning sample 19


title: PsrA-2-RNA-MM

value: psrA mutant


title: 62 - 6M-15: Trout muscle 24 weeks post-spawning sample 15


title: 60 - 6M-12: Trout muscle 24 weeks post-spawning sample 12


title: 58 - 6M-5: Trout muscle 24 weeks post-spawning sample 5


title: GacA-1-RNA-MM

value: gacA mutant


title: GacA-2-RNA-MM


title: GacA-2-RNA-KB


title: PsrA-1-RNA-MM


title: PsrA-1-RNA-KB


title: GacA-1-RNA-KB


title: GacS-2-RNA-MM

value: gacS mutant


title: GacS-2-RNA-KB


title: PsrA-2-RNA-KB


title: 61 - 6M-13: Trout muscle 24 weeks post-spawning sample 13


title: GacS-1-RNA-MM


title: 57 - 6M-2: Trout muscle 24 weeks post-spawning sample 2


title: GacS-1-RNA-KB


title: EnvZ-2-RNA-MM

value: envZ mutant


title: 55 - 4M-18: Trout muscle 16 weeks post-spawning sample 18


title: 52 - 4M-8: Trout muscle 16 weeks post-spawning sample 8


title: 54 - 4M-14: Trout muscle 16 weeks post-spawning sample 14


title: 56 - 4M-19: Trout muscle 16 weeks post-spawning sample 19


title: 53 - 4M-9: Trout muscle 16 weeks post-spawning sample 9


title: ATAC-seq from left ventricle myocardium superior (ENCLB758OFF)

description:
https://www.encodeproject.org/experiments/ENCSR133WJY/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human left ventricle myocardium superior
experiment encode accession: ENCSR133WJY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-09-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB758OFF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (60 years) left ventricle myocardium superior tissue, preserved by cryopreservation

value: left ventricle myocardium superior

value: tissue

tag: description

value: Superior wall of left ventricle.

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

tag: dev stage

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS512EYJ at ENCODE; https://www.encodeproject.org/ENCBS512EYJ/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: EnvZ-1-RNA-MM


title: 59 - 6M-10: Trout muscle 24 weeks post-spawning sample 10

value: trout muscle


title: EnvZ-2-RNA-KB


title: 48 - 3M-19: Trout muscle 13 weeks post-spawning sample 19


title: OmpR-1-RNA-MM

value: ompR mutant


title: EnvZ-1-RNA-KB


title: OmpR-2-RNA-MM


title: 51 - 4M-7: Trout muscle 16 weeks post-spawning sample 7


title: 49 - 4M-5: Trout muscle 16 weeks post-spawning sample 5


title: OmpR-2-RNA-KB


title: 46 - 3M-13: Trout muscle 13 weeks post-spawning sample 13


title: OmpR-1-RNA-KB


title: 47 - 3M-16: Trout muscle 13 weeks post-spawning sample 16


title: 45 - 3M-12: Trout muscle 13 weeks post-spawning sample 12


title: PilS-2-RNA-MM

value: pilS mutant


title: PilS-1-RNA-MM


title: PilS-2-RNA-KB


title: 43 - 3M-8: Trout muscle 13 weeks post-spawning sample 8


title: PilS-1-RNA-KB


title: PilR-2-RNA-MM

value: pilR mutant


title: PilR-1-RNA-MM


title: PilR-2-RNA-KB


title: 50 - 4M-6: Trout muscle 16 weeks post-spawning sample 6


title: TsiS-1-RNA-MM

value: tsiS mutant


title: 44 - 3M-9: Trout muscle 13 weeks post-spawning sample 9


title: TsiS-2-RNA-KB


title: PilR-1-RNA-KB


title: 42 - 3M-5: Trout muscle 13 weeks post-spawning sample 5


title: TsiS-2-RNA-MM


title: PhoP-2-RNA-MM

value: phoP mutant


title: TsiS-1-RNA-KB


title: 40 - 2M-18: Trout muscle 8 weeks post-spawning sample 18


title: 41 - 3M-1: Trout muscle 13 weeks post-spawning sample 1


title: PhoP-1-RNA-MM


title: 39 - 2M-16: Trout muscle 8 weeks post-spawning sample 16


title: 37 - 2M-12: Trout muscle 8 weeks post-spawning sample 12


title: 38 - 2M-13: Trout muscle 8 weeks post-spawning sample 13


title: 34 - 2M-7: Trout muscle 8 weeks post-spawning sample 7


title: PhoP-2-RNA-KB


title: 35 - 2M-8: Trout muscle 8 weeks post-spawning sample 8


title: 30 - 1M-14: Trout muscle 4 weeks post-spawning sample 14


title: 27 - 1M-6: Trout muscle 4 weeks post-spawning sample 6


title: 29 - 1M-10: Trout muscle 4 weeks post-spawning sample 10


title: 31 - 1M-18: Trout muscle 4 weeks post-spawning sample 18


title: PhoP-1-RNA-KB


title: 28 - 1M-7: Trout muscle 4 weeks post-spawning sample 7


title: 36 - 2M-10: Trout muscle 8 weeks post-spawning sample 10


title: 33 - 2M-2: Trout muscle 8 weeks post-spawning sample 2


title: 32 - 1M-20: Trout muscle 4 weeks post-spawning sample 20


title: RhpS-2-RNA-MM

value: rhpS mutant


title: RhpS-1-RNA-MM


title: RhpS-1-RNA-KB


title: HrpS-2-RNA-MM

value: hrpS mutant


title: RhpS-2-RNA-KB


title: HrpS-1-RNA-MM


title: HrpS-1-RNA-KB


title: HrpR-2-RNA-KB

value: hrpR mutant


title: HrpL-1-RNA-MM

value: hrpL mutant


title: HrpL-2-RNA-MM


title: HrpR-1-RNA-KB


title: HrpL-2-RNA-KB


title: HrpS-2-RNA-KB


title: HrpR-2-RNA-MM


title: HrpL-1-RNA-KB


title: 20 - 2S-14: Trout muscle 2 weeks post-spawning sample 14


title: 25 - 1M-3: Trout muscle 4 weeks post-spawning sample 1


title: HrpR-1-RNA-MM


title: 23 - 2S-17: Trout muscle 2 weeks post-spawning sample 17


title: Input6-2-ChIP

description:
Input for AlgU, PsrA
paired-end ChIP-seq data of Pseudomonas sringae 1448A

extract_protocol: NEXTflex™ ChIP-Seq Kit (Bioo Scientific)

value: WT

tag: chip antibody

value: Monoclonal Anti-HA-Agarose antibody produced in mouse, SigmaAldrich, A2095


title: 18 - 2S-6: Trout muscle 2 weeks post-spawning sample 6


title: 22 - 2S-16: Trout muscle 2 weeks post-spawning sample 16


title: 26 - 1M-5: Trout muscle 4 weeks post-spawning sample 5


title: Input6-1-ChIP


title: 24 - 2S-18: Trout muscle 2 weeks post-spawning sample 18


title: 21 - 2S-15: Trout muscle 2 weeks post-spawning sample 15


title: Input5-2-ChIP

description:
Input for PilR, OmpR, Vfr, CvsR, AefR, RpoN
paired-end ChIP-seq data of Pseudomonas sringae 1448A


title: 16 - TOv-16: muscle of control (immature) trout (C0) sample 16

value: TOv


title: 19 - 2S-7: Trout muscle 2 weeks post-spawning sample 7


title: 17 - 2S-1: Trout muscle 2 weeks post-spawning sample 1


title: 14 - TOv-12: muscle of control (immature) trout (C0) sample 12


title: Input4-2-ChIP

description:
Input for MgrA, TsiR
paired-end ChIP-seq data of Pseudomonas sringae 1448A


title: Input4-1-ChIP


title: 10 - TOv-4: muscle of control (immature) trout (C0) sample 4


title: 12 - TOv10: muscle of control (immature) trout (C0) sample 10


title: Input3-2-ChIP

description:
Input for PhoP, GacA
paired-end ChIP-seq data of Pseudomonas sringae 1448A


title: 15 - TOv-15: muscle of control (immature) trout (C0) sample 15


title: Input3-1-ChIP


title: 8 - Ov-18: trout muscle the day of spawning sample 18

value: Ov


title: Input1-2-ChIP

description:
Input for HrpL, HrpR, HrpS
paired-end ChIP-seq data of Pseudomonas sringae 1448A


title: RpoN-2-ChIP

description: paired-end ChIP-seq data of Pseudomonas sringae 1448A


title: RpoN-1-ChIP


title: Input1-1-ChIP


title: 13 - TOv-11: muscle of control (immature) trout (C0) sample 11


title: 6 - Ov-12: trout muscle the day of spawning sample 12


title: Input5-1-ChIP


title: 9 -TOv-3: muscle of control (immature) trout (C0) sample 3


title: 11 - TOv-9: muscle of control (immature) trout (C0) sample 9


title: AefR-1-ChIP


title: 4 - Ov-8: trout muscle the day of spawning sample 8


title: 2 - Ov-4: trout muscle the day of spawning sample 4


title: PsrA-2-ChIP


title: Input2-2-ChIP

description:
Input for RhpR
paired-end ChIP-seq data of Pseudomonas sringae 1448A


title: 3 - Ov-7: trout muscle the day of spawning sample 7


title: 5 - Ov-11: trout muscle the day of spawning sample 11


title: 1 - Ov-3: trout muscle the day of spawning sample 3


title: AlgU-2-ChIP


title: 7 - Ov-17: trout muscle the day of spawning sample 17


title: CvsR-1-ChIP


title: GacA-1-ChIP


title: OmpR-2-ChIP


title: GacA-2-ChIP


title: PsrA-1-ChIP


title: Vfr-1-ChIP


title: CvsR-2-ChIP


title: Vfr-2-ChIP


title: AefR-2-ChIP


title: Input2-1-ChIP


title: AlgU-1-ChIP


title: TsiR-1-ChIP


title: RhpR-2-ChIP

description: single-read ChIP-seq data of Pseudomonas sringae 1448A


title: PilR-1-ChIP


title: PilR-2-ChIP


title: TsiR-2-ChIP


title: HrpS-1-ChIP


title: HrpS-2-ChIP


title: RhpR-1-ChIP


title: HrpR-1-ChIP


title: HrpL-2-ChIP


title: HrpR-2-ChIP


title: HrpL-1-ChIP


title: MgrA-2-RNA-MM

data_processing:
ChIP-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using Bowtie2 (version 2.3.4.3). Only the uniquely mapped reads were kept for the subsequent analyses. Bam files were transformed into bigWig files by deeptools (version 3.1.3)
RNA-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
Genome_build: Pseudomonas sringae 1448A NC_005773.3
Supplementary_files_format_and_content: bigWig files were generated from ChIP-seq, containing dense data that can be displayed as a graph. txt files were generated from RNA-seq, containing differenttial expressed genes

extract_protocol:
NEXTflex™ ChIP-Seq Kit (Bioo Scientific) and NEBNext® UltraTM II RNA Library Prep Kit protocol (Illumina)
NEXTflex™ ChIP-Seq Kit (Bioo Scientific) and NEBNext® UltraTM II RNA Library Prep Kit protocol (Illumina)

value: mgrA mutant

tag: growth protocol

value: liquid culture in minimal medium (MM)


title: MgrA-2-RNA-KB

value: liquid culture in KB (King's B)  medium


title: MgrA-1-RNA-MM


title: MgrA-1-RNA-KB


title: PhoP-1-ChIP


title: PhoP-2-ChIP


title: MgrA-2-ChIP


title: bone marrow cells, CAR8

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

institute: Institut Pasteur

data_processing:
Cell Ranger (V3.0.1) mkfastq program for demultiplexing and basecalling
Cell Ranger (V3.1.0) count program for the generation of count table
Genome_build: mm10
Supplementary_files_format_and_content: Cell ranger output, including barcode file, features (genes) file and count matrix

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
Bone marrow cells from one tibia and one femur per mouse were harvested 3 days after initiation of therapy. Erythroblast cells were magnetically removed using anti-Ter-119 biotin-labeled monoclonal antibodies and streptavidin-labeled magnetic beads (Mojosort streptavidin nanobeads, BioLegend).
scRNA librairies were prepared for sequencing using standard 10x protocol (Single Cell 3' Reagent Kit v3)
single cell RNA-Seq

tag: strain

value: Bone Marrow

value: injected i.v. with CAR8


title: bone marrow cells, untreated

value: Untreated


title: bone marrow cells, CAR4

value: injected i.v. with CAR4


title: LT_CD112high_3

status: Public on Mar 25 2021

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

data_processing:
Reads were aligned with STAR v2.5.2b annotated with ensembl v90. Default parameters were used except for the following: --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5.
Read counts were generated using HTSeq v0.7.2 and general statistics were obtained from picard v2.6.0.
Genome_build: hg38
Supplementary_files_format_and_content: Read counts per gene per sample (tsv), and copiled, variance stabilized expression per gene in all samples

source_name: human cord blood hematopoietic stem cells

growth_protocol: Cells were cultured in 96-well round-bottom plates with  X-VIVO 10 media, 1 % BSA supplemented with 1x Pen/Strep, L-Glutamine and the the following cytokines: SCF (100 ng/ml), Flt3L (100 ng/ml), TPO (50 ng/ml) and IL7 (10 ng/ml)

extract_protocol:
PicoPure RNA Isolation Kit (Thermo Fisher). Samples that passed quality control according to integrity (RIN>7) and concentration as verified on a Bioanalyzer were further processed. cDNA conversion was performed using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara)
Nextera XT DNA Library Preparation Kit (Illumina)

treatment_protocol: CD112high and CD112low LT-HSC, total LT-HSC and ST-HSC were FACS-sorted from 3 independent CB pools and either directly resuspended and frozen (-80°C) in PicoPure RNA Isolation Kit Extraction Buffer or after transduction (after 16 h prestimulation) followed by a second sort (PI-BFP+) on day 6 post-transduction (average cell count: 104; range 0.25-3x10^4)

tag: cell type

value: hematopoietic stem cells

tag: donor pool

value: cord blood pool 3

tag: lentiviral vector

tag: culture and second sort (bfp+)

value: no


title: LT_CD112low_3


title: LT_CD112low_1

value: cord blood pool 1


title: input DNA

status: Public on Mar 26 2021

city: Nanjing

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

country: China

institute: Nanjing University

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2.
Peaks were called using MACS2 with defaults.
Bedgraph files were generated with MACS2 peak calling.
Genome_build: mm10
Supplementary_files_format_and_content: peak file: Foxc1_peaks.narrowPeak, Foxc2_peaks.narrowPeak; bdg file: Foxc1_treat_pileup.bdg, Foxc2_treat_pileup.bdg

source_name: kidney glomeruli

extract_protocol:
Adult mouse was perfused with magnetic beads. The kidney cortex was dissected and digested. Glomeruli with magnetic beads were collcted by MPC. Isolated glomeruli were fixed and sonicated. ChIP were carried out with specific antibody.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, libararies were generated with KAPA library amplificateion kit. Libraries were sequenced on Illumina Hiseq 2500.

tag: development stage

value: 8 weeks

value: kidney glomeruli


title: LT_CD112low_2

value: cord blood pool 2


title: LT_CD112high_2


title: Foxc1_ChIPSeq

tag: antibody

value: Foxc1 (D8A6, CST)


title: OmpR-1-ChIP

tag: genotype

value: WT

value: Monoclonal Anti-HA-Agarose antibody produced in mouse, SigmaAldrich, A2095


title: CD45 positive obese donor 3

status: Public on Mar 09 2021

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced by Illumina NovaSeq Sequencing System.
fastq files were generated using Cellranger mkfastq (version 3.1.0). The raw reads were mapped to human reference genome (refdata-cellranger-GRCh38-3.0.0) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: human adipose cell

extract_protocol:
Cells were sorted by CD45 and seprated into CD45 positive and negatives.
Library was generated by Chromium™ Single Cell 3’ Library Construction (10x Genomics).

tag: individual

value: donor 3

tag: phenotype

value: obese

value: CD45 positive adipose cell


title: CD45 positive obese donor 2

value: donor 2


title: MgrA-1-ChIP

value: liquid culture in KB (King's B)  medium


title: CD45 positive lean donor 2

value: lean


title: CD45 positive obese donor 1

value: donor 1


title: CD45 positive lean donor 3


title: HSPC_CML

city: Kanazawa

first: Tomohisa

last: Baba

address: Kakuma-machi

institute: Kanazawa University

description: Gene expression 24 hours after treatment

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. Fragmented cRNA hybridized to SurePrint G3 Mouse GE v2 8x60K Microarray (Agilent) using Gene Expression Hybridization Kit (Agilent) according to the manufacturer's instructions. After hybridization, microarrays were washed using Gene Expression Wash Pack (Agilent) according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol AgilentGE1_1200_Jun14 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: BM, HSPC, 24h, CML exosome

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: S-Clone SF-03 supplemented with 1% BSA, 100 ng/ml SCF, 10 ng/ml IL-6, and 10 ng/ml IL-3

extract_protocol: Total RNA was extracted using RNesy mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: HSPCs were treated with 150 µg/ml exosomes for 24 hours.

tag: tissue

value: Bone marrow

value: Hematopoietic stem/progenitor cells

tag: exosome source

value: CML mouse spleen


title: CD45 positive lean donor 1

data_processing:
Libraries were sequenced by Illumina NovaSeq Sequencing System.
fastq files were generated using Cellranger mkfastq (version 3.1.0). The raw reads were mapped to human reference genome (refdata-cellranger-GRCh38-3.0.0) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build:hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell


title: CD45 negative obese donor 3

value: CD45 negative adipose cell


title: CD45 negative obese donor 2


title: HSPC_Control

source_name: BM, HSPC, 24h, control exosome

value: normal mouse spleen


title: hsa-normal-2

status: Public on Mar 28 2021

city: shanghai

first: Yunjie

last: Wang

address: West Beijing Road 1400

institute: Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University

description: Gene expression data from hiPSCs derived from a healthy individual

hyb_protocol: 5.2 ug of biotin labeled sscDNA were hybridized for 16 hr at 45 °C on human transcriptome array (HTA 2.0) in GeneChip Hybridization Oven 645. Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G with the software Genechip Command Console (GCC).

data_processing: All data were reprocessed from raw images. Signal intensities, quality control, data normalization, and gene expression values for these samples were processed together with the RMA processing algorithm using the oligo package in R/Bioconductor. The alternative splicing events were analysed using EventPointer  package in R/Bioconductor and the TAC 4.0 software from thermofisher scientific.

label: biotin

source_name: ATCC® ACS-1011™

label_protocol: By using WT Amplification Kit Module 1 and WT Amplification Kit Module 2 in the GeneChip WT PLUS Kit (ThermoFisher Scientific, USA), 100 ng of total RNA as input was performed in vitro transcription (IVT) to synthesize cRNA, and then reverse transcription and purification to obtain single-stranded cDNA (sscDNA). The GeneChip WT end labeling kit was used to fragment and label sscDNA with biotin.

growth_protocol: HiPSCs were cultured using Gibco’s StemFlexTM medium (ThermoFisher Scientific, USA). The petri dishes were pre-treated with Matrigel, and the medium was changed daily. After culturing for 4 to 5 days, the iPSCs were digested, and the suspended cell clusters were collected and subcultured at a ratio of 1:6 at 37C, 5% CO2

extract_protocol: DS hiPSC and normal hiPSC were seeded in a 6-well plate, each cultured for three days, and then digested to harvest about 500000 cells. The experiment was repeated three times. The total RNA was extracted with TRIzol reagent (ThermoFisher Scientific, USA) and was first detected by the Agilent 2100 bioanalyzer with the Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany) according to the instruction of the manufacture. Total RNAs with an RNA integrity index (RIN) greater than 7.0 were used for subsequent experiments.

tag: disease

value: Normal


title: hsa-normal-3


title: Foxc2_ChIPSeq

value: 8 weeks

value: kidney glomeruli

value: Foxc2 (AF6989, R&D Systems)


title: CD45 negative obese donor 1


title: CD45 negative lean donor 3


title: CD45 negative lean donor 1


title: CD45 negative lean donor 2


title: GABAergic BNST -> PBN Projecting Neurons, TRAP Immunoprecipitate (gat_5_ip)

status: Public on Mar 02 2021

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

description:
gat_5_ip
GABAergic BNST -> PBN Projecting Neurons, TRAP Immunoprecipitate

data_processing:
Illumina adapter trimming with Trimmomatic 0.38
Mouse rRNA removal from reads using Bowtie 1.2.2
Alignment to mm10 using STAR aligner 2.6.0c
Gene-level counts using Htseq 0.9.1
Genome_build: GRCm38.p5 (Ensembl Build 90)
Supplementary_files_format_and_content: Htseq gene counts by sample

source_name: Bed nucleus stria terminalis

extract_protocol:
BAC-TRAP, as described in Mulvey 2018 in Cell Reports
rRNA depletion using Ribo-Zero --> polyA-primed cDNA synthesis using Clontech SMARTer kit

value: BNST

tag: cre driver

value: vGat-Cre

tag: sample type (trap immunoprecipitate or input lysate)

value: TRAP

tag: Sex

value: Male


title: EpiSC_2

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

description:
PGC_EPI_matrix.tsv
EpiSC_P14

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 ensembl v79) transcriptome using rsem (version 1.3.1)
The gene expression level was calculated by using  RSEM
The RNA-seq data processing was performed as described45. To analyze the regular gene expression, the reads were aligned to the reference transcriptome by RSEM46 and bowtie2 (—bowtie2— bowtie2-sensitivity-level very_sensitive —no-bam-output —estimate -rspd) using the index built by RSEM with the mouse genome, mm10, and Ensembl gene annotation track v79
Genome_build: mm10
Supplementary_files_format_and_content: PGC_EPI_matrix.tsv (RSEM results.txt), *.genes.results (counts, TPMs, FPKMs)

source_name: epiblast stem cell

growth_protocol: EpiSCs were cultured and maintained in N2B27 medium with Activin A (20ng/ml, PeproTech), bFGF (15ng/ml, PeproTech) and XAV939 (1uM, Selleck) on fetal bovine serum (FBS, NATOCOR)-coated dishes. For induction of BVSC double positive (BV+SC+) cells, the EpiSCs containing BVSC reporter were cultured in iCD1 medium which comprised of Vitamin C (50 μg/ml, Sigma), bFGF (10 ng/ml, PeproTech), LiCl (5 mM, Sigma), LIF (1000 U/ml, Millipore) and CHIR99021 (1 μM, synthesized in GIBH), with the addition of BMP4 (5-10 ng/ml,  R&D Systems), EPZ5676 (2.5 μM, Selleck ) and EPZ6438 (1 μM, TargetMol) for 3 days, and then in N2B27 medium with 2i (PD0325901, 1uM, synthesized in GIBH; CHIR99021, 3uM, synthesized in GIBH) and Vitamin C (50 μg/ml, Sigma) for another 3 days.  Fluorescence-activated cell sorting (FACS) was performed with a FACSAriaIII (BD) cell sorter for purifying BV+SC+ cells.

extract_protocol:
total RNA
Total RNAs were extracted as described above. The VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (VAHTS, #NR603) was used for RNA library preparation. In brief, 1 μg total RNAs were hybridized with the rRNA probe (H/M/R) and digested by RNase H to remove ribosomal RNAs. After DNase I digestion, the ribosomal-depleted RNAs were fragmented at 94°C for 8min. Then the first-strand and second-strand cDNAs were synthesized successively using the provided reagents. The cDNA was purified by VAHTS DNA Clean Beads (VAHTS, #NR411), followed by end repaired, dA-tailing, adapter ligation, and second strand cDNA digestion. After two-round of purification, the cDNAs was PCR-amplified and purified by VAHTS DNA Clean Beads. High- throughput sequencing was performed using Illumina HiSeq Xten (Illumina) platform with PE150 (pair-end sequencing, 150 bp reads).

value: epiblast stem cell


title: BNST, input (gat_3_pre)

description:
gat_3_pre
BNST (total lysate, no immunoprecipitation)

value: Input


title: BV+SC+_D6_1

description:
PGC_EPI_matrix.tsv
BV+SC+_D6_2iJi

source_name: PGCLC

value: Day6 BV+SC+ PGCLC cell


title: BV+SC+_D6_2

description:
PGC_EPI_matrix.tsv
BV+SC+_D6_GK15


title: hsa-DS-1

description: Gene expression data from hiPSCs derived from a DS patient

source_name: ATCC® ACS-1003™

value: Down syndrome


title: hsa-normal-1


title: EpiSC_1

description:
PGC_EPI_matrix.tsv
EpiSC_0613


title: BNST, input (glut_4_pre)

description:
glut_4_pre
BNST (total lysate, no immunoprecipitation)

value: vGlut-Cre


title: Glutamatergic BNST -> PBN Projecting Neurons, TRAP Immunoprecipitate (glut_4_ip)

description:
glut_4_ip
Glutamatergic BNST -> PBN Projecting Neurons, TRAP Immunoprecipitate


title: hsa-DS-2


title: hsa-DS-3


title: Glutamatergic BNST -> PBN Projecting Neurons, TRAP Immunoprecipitate (glut_1_ip)

description:
glut_1_ip
Glutamatergic BNST -> PBN Projecting Neurons, TRAP Immunoprecipitate


title: BNST, input (glut_1_pre)

description:
glut_1_pre
BNST (total lysate, no immunoprecipitation)


title: AOCS1_Adh_r1

status: Public on Feb 24 2021

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
RNA-Seq reads were mapped to the human genome (hg19, Genome Reference Consortium GRCh37)  using BWA mem (version 0.7.15-r1140) as part of the Oxford Genomics Centre pipeline.
Number of reads aligned to the exonic region of each gene were counted using htseq-count based on the Ensembl annotation.
Genes that achieved at least one read count per million reads (CPM) in at least 25% of the samples were kept. Conditional quantile normalisation (cqn) was performed counting for gene length and GC content and the log2 RPKM expression matrix was generated
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 RPKM values for each Sample

source_name: AOCS1 Adherent

growth_protocol: DMEM/F12 (Gibco, UK)

extract_protocol:
RNA was prepared from cell cultures using the RNeasy Mini Kit and the RNase free DNase set (Qiagen)
Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using RNA-Seq Ribozero kits (Illumina, Inc)

treatment_protocol: SB431542 and GANT61 (Sigma-Aldrich, UK)

tag: cell types

tag: culture type

value: 2D adherent - monoculture

tag: growth

value: 24h - adherent flask. DMEM/F12 + 10% FBS

tag: treatment

value: Untreated


title: EpiSC_3

description:
PGC_EPI_matrix.tsv
EpiSC_P16

tag: cell type


title: 9581 (RNA-seq)

status: Public on Feb 12 2021

city: San Francisco

first: Aaron

last: Diaz

department: Neurological Surgery

institute: University of California, San Francisco

data_processing:
Sequenced reads were aligned with HISAT2 to hg38
Gene expression was quantified using the ENSEMBL reference with featureCounts from subreads version 2.0.0.
Genome_build: hg38
Supplementary_files_format_and_content: feature count tables. Txt files.

source_name: Brain

extract_protocol:
FFPE blocks were reviewed by a pathologist to identify regions of high tumor purity. Total RNA was purified from freshly punched cores via a Qiagen RNeasy FFPE purification column. RNA and DNA were quantified via both Bioanalyzer and Qubit to ensure sample quality. All samples yielded over 100ng RNA with DV200>30% and negligible DNA contamination.
We used the Illumina TruSeq RNA Exome kit according to the manufacturer’s instructions.
Paired-end sequencing was done on the Illumina NovaSeq platform yielding over million read-pairs per sample. Sequenced reads were aligned with HISAT2 to grCh38. Gene expression was quantified using the ENSEMBL reference with featureCounts. Only correctly paired, uniquely mapped reads were retained.

tag: sample id

tag: sf#

tag: primary/recurrent

value: Primary

tag: patient id

tag: age

value: F

tag: idh mutation

value: WT

tag: disease state

value: Glioblastoma


title: BNST, input (gat_5_pre)

description:
gat_5_pre
BNST (total lysate, no immunoprecipitation)

tag: tissue


title: AOCS1_Sph_r1

source_name: AOCS1 Spheroids

value: spheroids - monoculture

value: 24h - low attachment flask. DMEM/F12 + 10% FBS


title: 6136 (RNA-seq)

value: Recurrent


title: 9037 (RNA-seq)

value: M


title: 4567 (RNA-seq)


title: 10497 (RNA-seq)


title: 4831 (RNA-seq)


title: BNST, input (glut_3_pre)

description:
glut_3_pre
BNST (total lysate, no immunoprecipitation)

value: BNST

value: Male


title: 8570 (RNA-seq)


title: 4987 (RNA-seq)


title: P101_1

status: Public on Feb 01 2021

city: Boston

first: Eriene-Heidi

last: Sidhom

state: MA

address: 4 Blackfan Circle HIM 536

institute: Harvard Medical School

description: bulk RNA

data_processing:
Reads were aligned to the mm10 mouse genome using STAR aligner
RSEM v1.3.0 was used to estimate gene expression.
FastQC used to evaluate the quality of raw reads.
Genome_build: mm10
Supplementary_files_format_and_content: .txt, RSEM estimated gene expression

source_name: Immortalized mouse podocytes

growth_protocol: Conditionally immortalized mouse podocytes (RRID:CVCL_AS86) were cultured under permissive conditions (33oC) in RPMI-1640 with 10% FBS, 100 U/ml penicillin and 100 mg/ml streptomycin and interferon- on type I collagen. Induction of differentiation is mediated by thermo-shift to 37oC without interferon-gamma.

extract_protocol:
Total RNA extraction was performed using RNeasy Mini Kit. RNA was eluted using Nuclease-Free water and total yield and purity of RNA were assessed using NanoDrop™ 2000 (Thermo Fisher).
RNA from cells quantified using the Quant-iTTM RiboGreen® RNA Assay Kit and normalized to 5 ng/μL. An automated variant of the Illumina TruSeqTM Stranded mRNA Sample Preparation Kit was used for library preparation from a 200 ng aliquot of RNA. This method preserves strand orientation of the RNA transcript and uses oligo dT beads to select mRNA from the total RNA sample. Following cDNA synthesis and enrichment, cDNA libraries were quantified with qPCR using KAPA Library Quantification Kit for Illumina Sequencing Platforms and then pooled equimolarly.

treatment_protocol: Podocytes were plated into 10-cm dishes (90K/plate) for differentiation, transduced with shRNA lentivirus on day 7 of differentiation and RNA was collected on day 14 of differentiation.

tag: shRNA

value: podocyte


title: P103_1

description: bulk RNA


title: GABAergic BNST -> PBN Projecting Neurons, TRAP Immunoprecipitate (gat_3_ip)

description:
gat_3_ip
GABAergic BNST -> PBN Projecting Neurons, TRAP Immunoprecipitate

tag: cre driver

value: vGat-Cre

value: TRAP


title: RIP1-1

status: Public on Jan 22 2021

city: beijing

first: cheng

last: jin

address: 49 Huayuan Bei Lu

institute: Peking University Third Hospital

data_processing:
mRNA:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
miRNA
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to rat genome.
count counting
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Rattus norvegicus

source_name: primary rat chondrocytes

growth_protocol: The cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM; Gibco) supplemented with 10% fetal bovine serum (FBS; HyClone) and antibiotics (penicillin G and streptomycin).

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
Hiseq Sequencing Protocol

treatment_protocol: The cells were infected with replication-defective adenovirus encoding the complete Rip1 open reading frame (Ad-Rip1) or adenoviral vector (Ad-Ctl) at a multiplicity of infection (MOI) of 100 for 24 hrs.

tag: strain background

value: Sprague Dawley

value: primary rat chondrocytes

tag: genotype/variation

value: Transfection of adenovirus expressing RIP1


title: RIP1-3


title: AOCS1_Sph_r2

tag: cell types

value: Untreated


title: CTL-3

value: Transfection of adenovirus expressing vector control


title: CTL-2


title: E14_singlecell_Osr2-KICre;Runx2fl/fl

status: Public on Jan 27 2021

city: LA

first: Xia

last: Han

address: 2250 Alcazar Street

institute: University of Southern California

data_processing:
Raw read counts were analyzed using the Seurat R 3.4.1 package
Cell clusters and variably expressed genes in each cluster were identified by using Log Normalize, Find Variable Genes, Scale Data and RunPCA functions.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output

source_name: E14.5 Osr2-KICre;Runx2fl/fl

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
Soft palate tissue (posterior third of the palatal region) was digested from E14.5 Osr2-KICre;Runx2fl/fl embryos by TrypLE express enzyme (Thermo Fisher Scientific) at 37°C with shaking at 600 rpm for 20 min.
Chrominum Single Cell 3' Gene Expression Library: Full-length cDNA was reverse transcribed from poly-adenylated mRNA using primers containing: an illumina TruSeq Read 1, 16 nt 10x Barcode, 12 nt unique molecular identifier (UMI) and 30 nt poly(dT) sequence. Silane magnetic beads are used to purify the first-strand cDNA from post GEM-RT reaction mixture. Barcoded, full-length cDNA is amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. P5, P7, a sample index and TruSeq Read 2 are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplication.

tag: strain

tag: Stage

value: soft palate

tag: genotype


title: AOCS1_Adh_r2

tag: culture type

value: 2D adherent - monoculture

tag: growth

value: 24h - adherent flask. DMEM/F12 + 10% FBS

tag: treatment


title: 13126-6_trap

status: Public on Jan 21 2021

data_processing:
Sequencing results were quality checked using FastQC version 0.11.7
Reads aligned to the mouse rRNA were removed by bowtie2 version 2.3.5
Illumina sequencing adaptors were removed and the remaining RNA-seq reads were then aligned to the Ensembl release 97 primary assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by htseq-count version 0.9.1
Genome_build: Mouse: Ensembl 97
Supplementary_files_format_and_content: Gene counts

source_name: Cortex

extract_protocol:
RNA was extracted into Trizol-LS according to manufacturer's protocols and then purified using the Zymo RNA Clean & Concentrator-5 kit according to manufacturer's protocols.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.

value: Cortex

value: Postnatal Day 21

tag: sample group

value: negative


title: CTL-1

tag: cell type


title: 13126-3_trap

tag: age

value: positive


title: 11839-8_trap


title: 13126-1_trap


title: 11839-6_trap


title: 11839-5_trap


title: 11839-3_trap


title: 11839-1_trap


title: 11839-4_input

value: input


title: 11839-4_trap


title: Qk3: QK-6 IP mRNA

description: PCR Duplicates removed

data_processing:
Trimming - Trimmomatic
Alignment - STAR
Read counts - Subread
peak calling - Piranha
Peak differential expression - edgeR
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts

source_name: Forebrain

extract_protocol:
mRNA was run from SDS-PAGE, transferred to a membrane then extracted from the membrane. RNA was cleaned on Zymo clean and concentrator-5 kit. Libraries were prepared using a custom, in house protocol according to methods in the accompanying publication.
Libraries were made by ligating a custom adaptor to the mRNA, and cDNA was made including the addition of a unique molecular identifier (UMI) to remove PCR duplicates

value: Postnatal day 21

tag: sample

value: QK-6 IP mRNA


title: 11839-8_input


title: Input5: Input mRNA

description: PCR Duplicates removed

value: Input mRNA


title: Input3: Input mRNA

description: PCR Duplicates removed


title: Input1: Input mRNA

description: PCR Duplicates removed


title: Qk5: QK-6 IP mRNA

description: PCR Duplicates removed


title: IgG5: IgG IP mRNA

description: PCR Duplicates removed

value: IgG IP mRNA


title: Input4: Input mRNA

description: PCR Duplicates removed


title: Qk4: QK-6 IP mRNA

description: PCR Duplicates removed


title: RIP1-2

value: Sprague Dawley


title: Glutamatergic BNST -> PBN Projecting Neurons, TRAP Immunoprecipitate (glut_3_ip)

description:
glut_3_ip
Glutamatergic BNST -> PBN Projecting Neurons, TRAP Immunoprecipitate

value: BNST

value: vGlut-Cre

tag: sample type (trap immunoprecipitate or input lysate)

value: TRAP

tag: Sex

value: Male


title: IgG4: IgG IP mRNA

description: PCR Duplicates removed


title: CELF6 5HT TRAP & Total RNA wt-3_2-input

status: Public on Jan 11 2021

description:
CELF6 5HT TRAP & Total RNA
sequencing run 2; wt-3_2-input file is a QC run on wt-3-input sample to confirm reproducibility across different sequencing runs and not used in analysis
C6JD60_input_KvW_allv2annotations.tab
C6JD60_input_KvW_tandemUTR.tab

data_processing:
Quality Trimming with TRIMMOMATIC, parameters: ILLUMINACLIP:2:55:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:30,CROP:30
rRNA read depletion using STAR to a custom genome of rRNA sequences and using only unmapped reads in subsequent steps, parameters: limitBAMsortRAM 15000000000, runThreadN 1, readFilesCommand zcat, outReadsUnmapped Fastx, outSAMunmapped Within, outSAMtype BAM SortedByCoordinate, outFilterMultimapNmax 100000
Read alignment to mm10 Mus musculus genome (Ensembl75) with STAR, parameters: limitBAMsortRAM 15000000000, runThreadN 1, readFilesCommand zcat, genomeLoad NoSharedMemory, outReadsUnmapped Fastx, sjdbScore 2, outSAMunmapped Within, outSAMtype BAM SortedByCoordinate
Count reads mapping to annotated genes using Subread FeatureCounts, GTF UCSC mm10 Annotated Genes, parameters: -t exon, -g gene_id
Analyze alternative splicing event probabilities using Mixtures of Isoforms (MISO), parameters: --run SE --read-len 30. Annotation sets: "Tandem UTR" (alternative polyadenylation), Alternative 3' Splice Site, Alternative 5' Splice Site, Retained Intron, Mutually Exclusive Exons, Skipped Exons. For more information see ( https://miso.readthedocs.io/en/fastmiso/# )
Summarize MISO settings: Only Keep Percent Spliced In (PSI) with confidence interval width <= 0.20 . Combine PSI values across MISO summary files from alternative annotation sets into a common table with annotation type (e.g. Skipped Exon) displayed
Genome_build: mm10/Ensembl75
Supplementary_files_format_and_content: tab separated values containing counts (for *.count files), or summaries of MISO PSI values for different alternative splicing events (*.tab files)

source_name: mouse brain

growth_protocol: Animals are maintained in a barrier facility with ad libidum food and water.

extract_protocol:
Brains were dissected at post-natal day 9 with cortices removed and region just posterior to thalamus was used in preparation. Total RNA ("inputs") was extracted using Trizol LS reagent followed by DNase treatment and Qiagen RNeasy cleanup. TRAP samples were processed according to the method in Doyle et al. Cell 2008 (10.1016/j.cell.2008.10.029) to purify serotonin cell RNA on translating ribosomes, using the Serotonin Cell specific TRAP allele described in Dougherty et al. J Neurosci 2013 (10.1523/JNEUROSCI.4762-12.2013) and purified by Trizol LS followed by DNase treatment and Qiagen RNeasy cleanup.
cDNA was amplified using Nugen Ovation 2 kit, followed by library preparation using NEBNext Ultra DNA Library Prep kit.

value: add strain info

tag: developmental stage

value: post-natal day 9

tag: fraction

value: total RNA

value: wild-type


title: CELF6 5HT TRAP & Total RNA wt-4-input

description:
CELF6 5HT TRAP & Total RNA
sequencing run 2; strong outlier in alignment and counting - not used in analysis
C6JD60_input_KvW_allv2annotations.tab
C6JD60_input_KvW_tandemUTR.tab


title: CELF6 5HT TRAP & Total RNA ko-5-trap

description:
CELF6 5HT TRAP & Total RNA
sequencing run 2
C6JD60_trap_KvW_allv2annotations.tab
C6JD60_trap_KvW_tandemUTR.tab

value: serotonin cell TRAP

value: celf6 knockout


title: CELF6 5HT TRAP & Total RNA wt-5-trap


title: CELF6 5HT TRAP & Total RNA ko-5-input

description:
CELF6 5HT TRAP & Total RNA
sequencing run 2
C6JD60_input_KvW_allv2annotations.tab
C6JD60_input_KvW_tandemUTR.tab


title: CELF6 5HT TRAP & Total RNA ko-4-input


title: CELF6 5HT TRAP & Total RNA ko-4-trap


title: CELF6 5HT TRAP & Total RNA wt-3_2-trap

description:
CELF6 5HT TRAP & Total RNA
sequencing run 2; wt-3_2-trap file is a QC run on wt-3-trap sample to confirm reproducibility across different sequencing runs and not used in analysis
C6JD60_trap_KvW_allv2annotations.tab
C6JD60_trap_KvW_tandemUTR.tab


title: CELF6 5HT TRAP & Total RNA wt-5-input


title: CELF6 5HT TRAP & Total RNA ko-3_2-trap

description:
CELF6 5HT TRAP & Total RNA
sequencing run 2; ko-3_2-trap file is a QC run on ko-3-trap sample to confirm reproducibility across different sequencing runs and not used in analysis
C6JD60_trap_KvW_allv2annotations.tab
C6JD60_trap_KvW_tandemUTR.tab


title: CELF6 5HT TRAP & Total RNA wt-4-trap


title: CELF6 5HT TRAP & Total RNA wt-3-input

description:
CELF6 5HT TRAP & Total RNA
sequencing run 1
C6JD60_input_KvW_allv2annotations.tab
C6JD60_input_KvW_tandemUTR.tab


title: CELF6 5HT TRAP & Total RNA wt-3-trap

description:
CELF6 5HT TRAP & Total RNA
sequencing run 1
C6JD60_trap_KvW_allv2annotations.tab
C6JD60_trap_KvW_tandemUTR.tab


title: CELF6 5HT TRAP & Total RNA ko-3-trap


title: CELF6 5HT TRAP & Total RNA wt-2-input


title: Input2: Input mRNA

description: PCR Duplicates removed


title: CELF6 5HT TRAP & Total RNA wt-2-trap


title: CELF6 5HT TRAP & Total RNA ko-2-input


title: CELF6 5HT TRAP & Total RNA ko-3-input


title: IgG3: IgG IP mRNA

description: PCR Duplicates removed


title: CELF6 5HT TRAP & Total RNA ko-2-trap


title: CELF6 5HT TRAP & Total RNA wt-1-trap


title: Dora_RNAseq_3

status: Public on Jan 05 2021

city: Cambridge

first: Elena

last: Kingston

state: Massachusetts

address: Nine Cambridge Center

institute: Whitehead Institute MIT

description:
RNAseq_siRNA_counts.csv
Dora_RNAseq3

data_processing:
Small-RNA sequencing reads were processed by trimming the 5′ and 3′ ends using fastx_trimmer (FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/) and cutadapt (Martin 2011), respectively, and then filtering for greater than 99.9% accuracy for all bases using fastq_quality_filter (FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/) with the parameters ‘-q 30 –p 100’.
To call miRNA reads, the first 19 nucleotides of filtered and trimmed reads were string-matched to a dictionary of miRNA sequences. The miRNA dictionary was curated by filtering miRbase_v21 miRNA annotations for all conserved or confidently annotated small RNA species (as annotated by TargetScanFly, release 7.2) as well as their passenger-strand partners. The few species that could not be called unambiguously using only the first 19 nucleotides were collapsed into a single dictionary entry (the sequence of which was chosen randomly to be that of one of the collapsed species), which was listed under a merged name (for example, dme-miR-276a-5p and dme-miR-276b-5p became dme-miR-276ab-5p).
To count reads mapping to siRNA-producing loci, a list of unique, non-overlapping regions in the genome that encompassed all previously published long hairpin loci, all transposons, and all regions of overlapping antisense-transcribed mRNAs (Chung et al. 2008; Czech et al. 2008; Ghildiyal et al. 2008; Kawamura et al. 2008; Okamura et al. 2008; Okamura et al. 2008; Watanabe et al. 2008) was manually curated (Supplemental Table S4). Any regions overlapping with an annotated miRNA transcript were removed from this list. Trimmed and filtered reads from small RNA libraries were then aligned to the genome (UCSC dm6.08 reference assembly) with STAR (V2.4, with the parameters “--alignIntronMax 1 --outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSJfilterReads All”). RPKM values for reads mapping to siRNA-generating loci were then enumerated using cufflinks (v2.2.1, with the parameters “--library-type fr-secondstrand --multi-read-correct --max-multiread-fraction 1.0 --no-length-correction --max-bundle-frags 1000000000") (Trapnell et al. 2010) and the curated list of siRNA-producing loci. For the Hen1 samples, siRNA counts were enumerated with the genes.read_group_tracking output file from CuffDiff (v2.2.1, with the parameters “--library-type fr-secondstrand --no-length-correction --multi-read-correct --total-hits-norm --max-bundle-frags 1000000000”).
To count reads mapping to individual siRNAs, a dictionary of highly abundant individual siRNAs was curated by enumerating from the periodate-treated wild-type libraries the top 21 sequences that mapped to an siRNA-generating locus. As with the miRNA analyses, reads corresponding to these individual siRNAs were identified by string-matching the first 19 nucleotides of the filtered and trimmed reads to this dictionary.
For RNAseq data, reads were aligned to the genome, mapped to siRNA-generating loci, and analyzed as described for the small-RNA-seq reads that mapped to siRNA-generating loci but with the command “fr-firststrand” to account for the opposite stranded-ness of the libraries.
Genome_build: dm6
Supplementary_files_format_and_content:  All processed .txt files contain non-normalized miRNA counts for the indicated samples
Supplementary_files_format_and_content:  All processed .csv files contain RPKM values for either small-RNA sequencing reads or RNA sequencing reads mapping to siRNA-producing loci for the indicated samples with the exception of the Hen1_siRNA_counts.csv file, which contains Cuffdiff estimated counts of reads mapping to siRNA-producing loci in WT and Hen1 cells

organism: Drosophila melanogaster

source_name: Drosophila S2 cells

growth_protocol: Drosophila S2 cells were grown at 26°C in Schneider’s Drosophila Medium (Life Technologies) supplemented with 10% heat-inactivated FBS (Life Technologies). Cells were passaged 1:5 every 3–5 days.

extract_protocol:
RNA was extracted with TRI Reagent (Life Technologies), according to the manufacturer’s protocol. Briefly, samples were homogenized in TRI reagent, and RNA was phase-separated by the addition of chloroform (J.T. Baker Analytical) at a ratio of 250 µL per 1 mL TRI Reagent. RNA was then precipitated with isopropanol, with GlycoBlue (Life Technologies) added as a co-precipitant when necessary, and pellets were washed twice with 70% ethanol prior to resuspension in water.
RNA-seq samples were prepared using the NEXTflex Rapid Directional mRNA-seq Kit (Bioo Scientific). Samples first were enriched for mRNAs using NEXTflex Poly(A) Beads (Bioo Scientific), and the enriched mRNAs were fragmented, synthesized into cDNA, ligated to adaptors, and PCR amplified according to the manufacturer’s protocol.

treatment_protocol: generation of cell lines: To generate knockout lines, cells were transfected with either one (for single-gene knockout) or two (for double knockout) cloned versions of pAc-sgRNA-Cas9 (Addgene #49330), constructed as per previously published protocols (Bassett 2014). Starting 3 d after transfection, cells were selected with 5 ug/mL puromycin (Life Technologies). After one week of selection, single cells were sorted into wells to generate clonal lines. After culture for 2–3 weeks, clonal lines were screen for lesions by PCR amplification of the targeted locus followed by TIDE analysis of the amplicon (Brinkman et al. 2014).

tag: cell line

value: dora

tag: ip target

value: untreated

tag: rna population

value: mRNA


title: Dora_RNAseq_1

description:
RNAseq_siRNA_counts.csv
Dora_RNAseq1


title: Dora_RNAseq_2

description:
RNAseq_siRNA_counts.csv
Dora_RNAseq2


title: WT_RNAseq_3

description:
RNAseq_siRNA_counts.csv
WT_RNAseq3


title: CELF6 5HT TRAP & Total RNA ko-3_2-input

description:
CELF6 5HT TRAP & Total RNA
sequencing run 2; ko-3_2-input file is a QC run on ko-3-input sample to confirm reproducibility across different sequencing runs and not used in analysis
C6JD60_input_KvW_allv2annotations.tab
C6JD60_input_KvW_tandemUTR.tab

tag: strain


title: CELF6 5HT TRAP & Total RNA wt-1-input


title: CELF6 5HT TRAP & Total RNA ko-1-input


title: WT_RNAseq_2

description:
RNAseq_siRNA_counts.csv
WT_RNAseq2


title: AGO1_Dora_2

description:
AGO1_miRNA_counts.txt
AGO1_siRNA_counts.csv
AGO1_Dora2

extract_protocol:
AGO1 was isolated using a FLAG-GST-tagged fragment of TNRC6B (Hauptmann et al. 2015). Pelleted cells were lysed in NET buffer (50 mM Tris, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 10% glycerol, supplemented with protease inhibitors (complete, mini, EDTA-free protease inhibitor tablets, Sigma Aldrich); 100 uL buffer per ~1.5 million cells) on ice at 4°C for 20 min. Lysate was then clarified by centrifugation at 15000g for 20 min. Anti-FLAG M2 Magnetic beads (Sigma Aldrich, 25 uL per 100 uL of lysate) were washed once with PBST (1xPBS supplemented with 0.02% Tween-20), and resuspended in 500 uL of PBST per each 25 uL beads. The TNRC6B fragment was then coupled to the washed beads by adding 12.5 ug of fragment per 25 uL of beads and rotating for 2 h at 4°C. Following coupling, beads were washed three times with PBS, and then the clarified lysate was added and the slurry was rotated at 4°C for 3 h. The beads were then washed four times with NET buffer and once with PBS before the RNA was eluted with Trizol.
Small-RNA libraries were generated as described in the step-by-step protocol available at http://bartellab.wi.mit.edu/protocols.html, with slight modifications. Briefly, between 5–10 g of total RNA was mixed with size-selection markers (18 and 32 nt 5′-radiolabeled RNAs), and for the total-sRNA libraries quantitative sequencing standards were added (0.05 fmol per 1 g total RNA). The samples were first size-selected, before undergoing subtractive hybridization to remove the 2S rRNA (Seitz et al. 2008). Degenerate adaptors (each containing 4 random-sequence nucleotides abutting the ligation junction) were then ligated to the 3′ and 5′ ends of the RNA in the presence of 10% Polyethylene Glycol (PEG 8000, NEB) and 0.5 L of Superasin (Thermo Fisher Scientific) with T4 RNA Ligase 2, truncated K227Q (NEB) and T4 RNA Ligase 1 (NEB), respectively. Reverse transcription was carried out with SuperScript III (NEB), and the cDNA was PCR-amplified using Kapa HiFi HotStart Ready Mix (VWR).

value: small RNAs


title: CELF6 5HT TRAP & Total RNA ko-1-trap


title: AGO1_Dora_3

description:
AGO1_miRNA_counts.txt
AGO1_siRNA_counts.csv
AGO1_Dora3


title: AGO2_Hen1_2

description:
AGO2_miRNA_counts.txt
AGO2_siRNA_counts.csv
AGO2_Hen1_2

extract_protocol:
For immunoprecipitation of FLAG-tagged AGO2, cells were lysed in TBS-N (10 mM Tris, pH 7.5, 150 mM NaCl, 0.5% NP-40, supplemented with protease inhibitors (complete, mini, EDTA-free protease inhibitor tablets, Sigma Aldrich); 500 uL buffer per ~10 million cells) on ice at 4°C for 20 min. Lysate was then clarified by centrifugation at 15000g for 20 min and added to Anti-FLAG M2 Magnetic beads (25 uL per 500 uL of lysate) that had been washed twice with PBST. After rotation at 4°C for 3 h, the beads were washed three times with 200 uL of PBST, and RNA was eluted with Trizol.
Small-RNA libraries were generated as described in the step-by-step protocol available at http://bartellab.wi.mit.edu/protocols.html, with slight modifications. Briefly, between 5–10 g of total RNA was mixed with size-selection markers (18 and 32 nt 5′-radiolabeled RNAs), and for the total-sRNA libraries quantitative sequencing standards were added (0.05 fmol per 1 g total RNA). The samples were first size-selected, before undergoing subtractive hybridization to remove the 2S rRNA (Seitz et al. 2008). Degenerate adaptors (each containing 4 random-sequence nucleotides abutting the ligation junction) were then ligated to the 3′ and 5′ ends of the RNA in the presence of 10% Polyethylene Glycol (PEG 8000, NEB) and 0.5 L of Superasin (Thermo Fisher Scientific) with T4 RNA Ligase 2, truncated K227Q (NEB) and T4 RNA Ligase 1 (NEB), respectively. Reverse transcription was carried out with SuperScript III (NEB), and the cDNA was PCR-amplified using Kapa HiFi HotStart Ready Mix (VWR).


title: Hen1Dora_2

description:
Hen1_miRNA_counts.txt
Hen1_siRNA_counts.csv
Hen1Dora_2

extract_protocol:
RNA was extracted with TRI Reagent (Life Technologies), according to the manufacturer’s protocol. Briefly, samples were homogenized in TRI reagent, and RNA was phase-separated by the addition of chloroform (J.T. Baker Analytical) at a ratio of 250 µL per 1 mL TRI Reagent. RNA was then precipitated with isopropanol, with GlycoBlue (Life Technologies) added as a co-precipitant when necessary, and pellets were washed twice with 70% ethanol prior to resuspension in water.
Small-RNA libraries were generated as described in the step-by-step protocol available at http://bartellab.wi.mit.edu/protocols.html, with slight modifications. Briefly, between 5–10 g of total RNA was mixed with size-selection markers (18 and 32 nt 5′-radiolabeled RNAs), and for the total-sRNA libraries quantitative sequencing standards were added (0.05 fmol per 1 g total RNA). The samples were first size-selected, before undergoing subtractive hybridization to remove the 2S rRNA (Seitz et al. 2008). Degenerate adaptors (each containing 4 random-sequence nucleotides abutting the ligation junction) were then ligated to the 3′ and 5′ ends of the RNA in the presence of 10% Polyethylene Glycol (PEG 8000, NEB) and 0.5 L of Superasin (Thermo Fisher Scientific) with T4 RNA Ligase 2, truncated K227Q (NEB) and T4 RNA Ligase 1 (NEB), respectively. Reverse transcription was carried out with SuperScript III (NEB), and the cDNA was PCR-amplified using Kapa HiFi HotStart Ready Mix (VWR).


title: AGO2_Hen1_3

description:
AGO2_miRNA_counts.txt
AGO2_siRNA_counts.csv
AGO2_Hen1_3


title: Hen1Dora_3

description:
Hen1_miRNA_counts.txt
Hen1_siRNA_counts.csv
Hen1Dora_3


title: Hen1_2

description:
Hen1_miRNA_counts.txt
Hen1_siRNA_counts.csv
Hen1_2


title: AGO1_Dora_1

description:
AGO1_miRNA_counts.txt
AGO1_siRNA_counts.csv
AGO1_Dora1


title: Hen1_1

description:
Hen1_miRNA_counts.txt
Hen1_siRNA_counts.csv
Hen1_1


title: Hen1_3

description:
Hen1_miRNA_counts.txt
Hen1_siRNA_counts.csv
Hen1_3


title: AGO1_WT_2

description:
AGO1_miRNA_counts.txt
AGO1_siRNA_counts.csv
AGO1_WT2


title: AGO2_Hen1Dora_3

description:
AGO2_miRNA_counts.txt
AGO2_siRNA_counts.csv
AGO2_Hen1Dora3


title: WT_RNAseq_1

description:
RNAseq_siRNA_counts.csv
WT_RNAseq1


title: AGO2_Hen1Dora_2

description:
AGO2_miRNA_counts.txt
AGO2_siRNA_counts.csv
AGO2_Hen1Dora2


title: Hen1Dora_1

description:
Hen1_miRNA_counts.txt
Hen1_siRNA_counts.csv
Hen1Dora_1


title: AGO1_WT_3

description:
AGO1_miRNA_counts.txt
AGO1_siRNA_counts.csv
AGO1_WT3


title: AGO2_Hen1_1

description:
AGO2_miRNA_counts.txt
AGO2_siRNA_counts.csv
AGO2_Hen1_1


title: AGO1_WT_1

description:
AGO1_miRNA_counts.txt
AGO1_siRNA_counts.csv
AGO1_WT1


title: AGO2_Hen1Dora_1

description:
AGO2_miRNA_counts.txt
AGO2_siRNA_counts.csv
AGO2_Hen1Dora1


title: tr_Dora_2

description:
tr_miRNA_counts.txt
tr_siRNA_counts.csv
tr_Dora2

treatment_protocol:
RNA was oxidized in a solution of 25 mM borax (VWR), 25 mM boric acid (Sigma), and 25 mM of sodium (meta)periodate (Sigma Aldrich) for 30 min at room temperature. Oxidation was quenched with glycerol (to a final concentration of 17%), and the reaction was ethanol precipitated. Pellets were resuspended in a solution of 60 mM borax, 60 mM boric acid and the oxidized base was beta-eliminated through the addition of NaOH to a final concentration of 50 mM NaOH and incubation at 45°C for 90 min. Samples were then ethanol precipitated.
generation of cell lines: To generate knockout lines, cells were transfected with either one (for single-gene knockout) or two (for double knockout) cloned versions of pAc-sgRNA-Cas9 (Addgene #49330), constructed as per previously published protocols (Bassett 2014). Starting 3 d after transfection, cells were selected with 5 ug/mL puromycin (Life Technologies). After one week of selection, single cells were sorted into wells to generate clonal lines. After culture for 2–3 weeks, clonal lines were screen for lesions by PCR amplification of the targeted locus followed by TIDE analysis of the amplicon (Brinkman et al. 2014).

value: sodium-periodate treated


title: tr_Dora_1

description:
tr_miRNA_counts.txt
tr_siRNA_counts.csv
tr_Dora1


title: tr_WT_3

description:
tr_miRNA_counts.txt
tr_siRNA_counts.csv
tr_WT3

value: sodium-peridate treated


title: tr_WT_1

description:
tr_miRNA_counts.txt
tr_siRNA_counts.csv
tr_WT1


title: tr_WT_2

description:
tr_miRNA_counts.txt
tr_siRNA_counts.csv
tr_WT2


title: total_Dora_3

description:
total_miRNA_counts.txt
total_siRNA_counts.csv
total_Dora3


title: total_Dora_2

description:
total_miRNA_counts.txt
total_siRNA_counts.csv
total_Dora2


title: total_Dora_1

description:
total_miRNA_counts.txt
total_siRNA_counts.csv
total_Dora1


title: total_WT_3

description:
total_miRNA_counts.txt
total_siRNA_counts.csv
total_WT3


title: total_WT_1

description:
total_miRNA_counts.txt
total_siRNA_counts.csv
total_WT1


title: tr_Dora_3

description:
tr_miRNA_counts.txt
tr_siRNA_counts.csv
tr_Dora3


title: total_WT_2

description:
total_miRNA_counts.txt
total_siRNA_counts.csv
total_WT2


title: Aged_STD_rep1 [AS1]

status: Public on Dec 31 2020

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description:
L27354_DG_1Y-S107
Methylated cytosines converted to uracil by treatment with sodium bisulfite

data_processing:
Trimming: Fastq reads were trimmed using Trim Galore 0.4.0 and the function Cutadapt 1.8.1. To remove cytosines that were filled in during ends preparation, an additional 2 bp were cut off from every sequence with detected adapter.
Alignment: Trimmed reads were mapped against mm10 using Bismark 0.16.1
Base-calling: MethylKit 1.5.2.
Genome_build: mm10
Supplementary_files_format_and_content: Methylation percentages of cytosines for individual samples. Txt file exported from Methylkit.

source_name: Aged_STD_dentate gyrus

growth_protocol: Mice housed in 12:12 light:dark cycle under SPF conditions and given ad libitum access to mouse chow and water.

extract_protocol:
Micro-dissection of the hippocampal dentate gyrus
Genomic DNA was isolated using the QIAamp DNA Micro Kit or the Allprep DNA/RNA Micro Kit (both QIAGEN) following the manufacturer’s manuals. RRBS libraries were prepared using the Premium RRBS Kit (Diagenode) and purified twice using Agencourt AMPure XP beads (Beckman Coulter; 1X bead volume). Quality and concentration of RRBS libraries were determined using the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical) and a fragment analyzer with capillary size of 33 cm (Advanced Analytical).

treatment_protocol: Mice were housed in either standard cages or in an enriched environment.

value: 14 months

value: Female

tag: housing

value: Standard housing

tag: tissue

value: Dentate gyrus


title: Young_ENR_rep1 [YE1]

description:
L27351_DG_4d-E1
Methylated cytosines converted to uracil by treatment with sodium bisulfite

source_name: Young_ENR_dentate gyrus

value: 1.5 months

value: Environmental enrichment


title: Young_ENR_rep4 [YE4]

description:
L37115_s4d_ENR4
Methylated cytosines converted to uracil by treatment with sodium bisulfite