title: AD 03-02

description: repeated in GSE95587: NA


title: AD 04-58

status: Public on Apr 17 2019

type: SRA

city: South San Francisco

first: Brad

middle: A

last: Friedman

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc.

description: repeated in GSE95587: NA

library_source: transcriptomic

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

molecule: total RNA

organism: Homo sapiens

source_name: RNA from fusiform gyrus

extract_protocol: RNA was extracted from frozen tissue sections.

tag: tissue

value: fusiform gyrus

tag: case id

tag: diagnosis

value: Alzheimer's disease

tag: age

tag: Sex

value: F

value: VI


title: AD 05-51

description: repeated in GSE95587: NA

value: M

value: V


title: CON 10-73

description: repeated in GSE95587: NA

value: control

value: IV


title: AD 02-19

description: repeated in GSE95587: NA


title: AD 08-18

description: repeated in GSE95587: NA


title: CON 99-23

description: repeated in GSE95587: NA


title: AD 00-50

description: repeated in GSE95587: NA


title: AD 99-35

description: repeated in GSE95587: NA


title: AD 07-57

description: repeated in GSE95587: GSM2516895


title: AD 13-04

description: repeated in GSE95587: NA


title: AD 10-05

description: repeated in GSE95587: NA


title: AD 07-27

description: repeated in GSE95587: NA


title: AD 11-77

description: repeated in GSE95587: NA


title: CON 01-31

description: repeated in GSE95587: NA

value: III


title: AD 11-78

description: repeated in GSE95587: NA


title: CON 11-28

description: repeated in GSE95587: GSM2516873


title: CON 98-32

description: repeated in GSE95587: NA


title: AD 09-39

description: repeated in GSE95587: GSM2516920


title: CON 11-05

description: repeated in GSE95587: GSM2516911


title: CON 08-77

description: repeated in GSE95587: NA


title: AD 11-40

description: repeated in GSE95587: NA


title: AD 08-51

description: repeated in GSE95587: NA


title: AD 05-43

description: repeated in GSE95587: NA


title: AD 12-24

description: repeated in GSE95587: NA


title: CON 03-58

description: repeated in GSE95587: NA


title: CON 12-44

description: repeated in GSE95587: GSM2516848


title: CON 05-28

description: repeated in GSE95587: NA


title: AD 10-04

description: repeated in GSE95587: NA


title: CON 09-34

description: repeated in GSE95587: GSM2516913


title: AD 05-05

description: repeated in GSE95587: NA


title: AD 13-26

description: repeated in GSE95587: NA


title: AD 11-21

description: repeated in GSE95587: GSM2516921


title: AD 04-33

description: repeated in GSE95587: NA


title: AD 99-21

description: repeated in GSE95587: NA


title: AD 09-02

description: repeated in GSE95587: NA


title: AD 03-32

description: repeated in GSE95587: NA


title: AD 11-97

description: repeated in GSE95587: NA


title: CON 07-26

description: repeated in GSE95587: NA


title: AD 07-39

description: repeated in GSE95587: NA


title: AD 00-12

description: repeated in GSE95587: GSM2516839


title: CON 03-10

description: repeated in GSE95587: NA


title: AD 06-60

description: repeated in GSE95587: GSM2516858


title: AD 11-13

description: repeated in GSE95587: NA


title: AD 03-57

description: repeated in GSE95587: GSM2516879


title: AD 05-57

description: repeated in GSE95587: GSM2516806


title: AD 04-16

description: repeated in GSE95587: NA


title: AD 00-17

description: repeated in GSE95587: NA


title: CON 02-24

description: repeated in GSE95587: GSM2516868


title: AD 10-87

description: repeated in GSE95587: GSM2516832


title: AD 10-44

description: repeated in GSE95587: NA


title: AD 13-01

description: repeated in GSE95587: NA


title: AD 06-46

description: repeated in GSE95587: NA


title: AD 13-07

description: repeated in GSE95587: NA


title: AD 09-42

description: repeated in GSE95587: GSM2516881


title: AD 10-55

description: repeated in GSE95587: GSM2516891


title: AD 12-69

description: repeated in GSE95587: NA


title: AD 11-19

description: repeated in GSE95587: GSM2516896


title: AD 01-49

description: repeated in GSE95587: NA


title: CON 01-46

description: repeated in GSE95587: NA


title: CON 11-43

description: repeated in GSE95587: NA


title: AD 07-45

description: repeated in GSE95587: NA


title: AD 10-67

description: repeated in GSE95587: GSM2516815


title: AD 11-35

description: repeated in GSE95587: NA


title: CON 06-15

description: repeated in GSE95587: NA


title: CON 02-04

description: repeated in GSE95587: GSM2516849


title: AD 02-05

description: repeated in GSE95587: NA


title: AD 09-03

description: repeated in GSE95587: NA


title: AD 08-82

description: repeated in GSE95587: NA

value: II


title: AD 09-18

description: repeated in GSE95587: GSM2516810


title: CON 05-16

description: repeated in GSE95587: GSM2516809


title: AD 10-45

description: repeated in GSE95587: NA


title: AD 10-47

description: repeated in GSE95587: NA


title: AD 11-23

description: repeated in GSE95587: NA


title: AD 12-37

description: repeated in GSE95587: NA


title: AD 04-02

description: repeated in GSE95587: NA


title: CON 04-38

description: repeated in GSE95587: GSM2516838


title: AD 12-57

description: repeated in GSE95587: NA


title: CON 03-28

description: repeated in GSE95587: GSM2516831

value: I


title: AD 13-41

description: repeated in GSE95587: NA


title: AD 06-04

description: repeated in GSE95587: NA


title: AD 05-15

description: repeated in GSE95587: NA


title: AD 09-14

description: repeated in GSE95587: GSM2516870


title: AD 11-27

description: repeated in GSE95587: GSM2516880


title: AD 12-58

description: repeated in GSE95587: NA


title: CON 08-40

description: repeated in GSE95587: GSM2516900


title: AD 03-34

description: repeated in GSE95587: GSM2516841


title: AD 11-92

description: repeated in GSE95587: NA


title: AD 08-34

description: repeated in GSE95587: NA


title: AD 11-01

description: repeated in GSE95587: GSM2516889


title: AD 11-20

description: repeated in GSE95587: GSM2516824


title: AD 10-11

description: repeated in GSE95587: NA


title: AD 11-11

description: repeated in GSE95587: GSM2516916


title: AD 05-23

description: repeated in GSE95587: GSM2516908


title: AD 04-45

description: repeated in GSE95587: NA


title: 04-33 AD neuron

source_name: RNA from sorted cells

extract_protocol: Frozen tissue was dissociated on ice as described in manuscript and ethanol-fixed single-positive cells were sorted for each of four cell type markers, Astrocyte (Gfap+), Endothelial (Cd31+), Myeloid (CD11b+) and Neuron (NeuN+). RNA was extracted and amplified using Nugen Ovation V2. Libraries were then sequenced and analyzed as described in manuscript.

value: Male

tag: cell type

value: neuron

value: AD

tag: apoe

tag: pmi


title: 08-41 AD endothelial

value: Female

value: endothelial


title: 03-21 AD astrocyte

value: astrocyte


title: CON 10-26

description: repeated in GSE95587: NA

value: fusiform gyrus


title: 04-33 AD astrocyte


title: 10-79 AD endothelial


title: 08-90 Control neuron

value: Control


title: 09-50 Control neuron


title: 03-21 AD endothelial


title: CON 04-30

description: repeated in GSE95587: GSM2516871

value: F


title: 04-33 AD myeloid

value: myeloid


title: 08-90 Control endothelial


title: 10-20 Control astrocyte


title: 03-21 AD myeloid

value: VI


title: 08-41 AD neuron


title: 10-20 Control neuron


title: AD 11-73

description: repeated in GSE95587: NA

value: Alzheimer's disease

value: M


title: 10-79 AD neuron

value: V


title: 10-20 Control myeloid


title: 07-28 Control endothelial


title: 09-35 Control myeloid


title: 10-22 Control endothelial


title: 09-35 Control endothelial


title: 10-63 Control myeloid


title: 02-27 Control myeloid


title: 07-28 Control myeloid


title: 08-90 Control astrocyte

value: III


title: 11-49 AD astrocyte


title: 11-49 AD neuron


title: 04-44 AD endothelial


title: 09-50 Control endothelial


title: 10-80 AD neuron


title: 11-98 Control myeloid


title: 03-21 AD neuron


title: 03-59 AD neuron


title: 10-80 AD myeloid


title: 03-15 Control endothelial

value: II


title: 02-27 Control neuron

value: I


title: 10-22 Control myeloid


title: 13-47 AD neuron


title: 11-105 AD endothelial


title: 11-38 AD neuron


title: 14-29 AD neuron


title: 03-63 Control myeloid


title: 13-40 Control neuron


title: 00-54 AD myeloid

value: Male


title: 11-98 Control neuron

value: neuron


title: 13-47 AD astrocyte

value: AD


title: 13-54 AD neuron

value: Female


title: 10-63 Control astrocyte


title: 03-15 Control neuron


title: 02-27 Control astrocyte


title: 10-70 Control neuron


title: 02-01 Control myeloid

value: IV


title: 07-20 AD neuron


title: 14-29 AD endothelial

value: endothelial


title: 06-26 AD endothelial


title: 04-44 AD neuron


title: 11-98 Control astrocyte

value: astrocyte


title: 04-54 AD myeloid


title: 14-29 AD myeloid


title: 11-105 AD myeloid


title: 00-54 AD neuron


title: 04-54 AD astrocyte


title: 07-15 AD neuron


title: 08-55 Control endothelial

value: Control


title: 03-59 AD endothelial


title: 03-59 AD myeloid


title: 10-80 AD astrocyte


title: 03-63 Control neuron


title: 02-27 Control endothelial


title: 00-54 AD astrocyte


title: 13-66 AD neuron


title: 03-63 Control endothelial


title: 02-01 Control neuron


title: 03-15 Control astrocyte


title: 07-28 Control neuron


title: 04-54 AD endothelial


title: 09-35 Control neuron


title: 11-105 AD neuron


title: 04-54 AD neuron


title: 05-58 AD neuron


title: 10-70 Control astrocyte


title: 08-55 Control neuron


title: 13-74 AD neuron


title: 13-49 Control endothelial


title: 10-80 AD endothelial


title: 11-98 Control endothelial


title: 13-49 Control neuron


title: 05-58 AD myeloid


title: 02-01 Control astrocyte


title: 13-40 Control myeloid


title: 10-63 Control endothelial


title: 06-26 AD neuron


title: 06-26 AD myeloid


title: 10-63 Control neuron


title: 10-70 Control myeloid


title: 10-22 Control neuron


title: Biliary Tract Cancer (BT114last)

type: RNA

city: Fukui

first: Yu

last: Akazawa

address: 23-3 Eiheiji-cho

department: Faculty of Medical Sciences

country: Japan

institute: University of Fukui

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: disease state

value: BTC

tag: individual

tag: time

value: last

value: serum


title: Biliary Tract Cancer (BT106last)


title: Biliary Tract Cancer (BT114post)

value: post


title: Biliary Tract Cancer (BT114pre)

value: pre


title: Biliary Tract Cancer (BT106pre)


title: Biliary Tract Cancer (BT089last)


title: Biliary Tract Cancer (BT106post)


title: A2_2_Bisulfite_Padlock_Seq

city: Grand Rapids

first: Peipei

last: Li

state: MI

address: 333 Bostwick Ave N.E.

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

description: Brain bank Sample code: A276/05

library_source: genomic

data_processing:
The libraries were sequenced on the HiSeq 2500 platform (Illumina) using custom sequencing primers.
The FASTQ reads were quality trimmed using Trimmomatic for trailing base with phred score < 30 and all reads with post-trimming length < 50 bp.
The trimmed reads were then aligned using Bismark version 0.14 and Bowtie 2 version 2.2.2 .
The aligned reads were further filtered to only include reads that have start and end positions that match the padlock probe annealing arm sequence with no more than 1 mismatch.
The filtered reads were subsequently PCR de-duplicated using unique molecular identifiers.
The filtered read pairs were then converted to methylation calls using the Bismark methylation extractor tool.
Genome_build: hg19
Supplementary_files_format_and_content: Each txt file contain the following information in order: chromosome #, genomic coordinate, strand, unmethylation count, methylation count, CHH/CHG/CG context of cytosine, exact sequence of the previous context

molecule: genomic DNA

source_name: Brain prefrontal cortex neurons(NeuN+)

growth_protocol: Human prefrontal cortex neurons. Biological sample: unique sample; Sample replicate: neuronal nuclei isolation from the same tissue, two per selected sample; Technical replicate: library prepared for same gDNA samples, three per selected sample; Sequencing replicate: same library run on sequencing machine, two per selected sample.

extract_protocol:
Neuronal nuclei from prefrontal cotex were isoated by an antibody (NeuN) and flow cytometry approach; DNA were extracted by standard phenol chloroform extraction; Bisulfite padlock probes were designed to humans brain enhancers and promoters (NIH Roadmap Chromm)
We scanned brain-relevant enhancers and promoters genome-wide using the bisulfite padlock probe approach. Padlock probes (n=59,008) were designed using the PP Designer software and synthesized using a programmable microfluidic microarray platform (CustomArray, Inc.). Isolated genomic DNA for each sample was bisulfite-converted and purified using the EZ DNA Methylation-Lightning Kit (Zymo Research). The bisulfite-converted DNA (140 ng) was hybridized to the padlock probes (1.5 ng). Targeted regions were extended using PfuTurbo Cx (Agilent Technologies) and circularization was completed using Ampligase (Epicentre). Non-circularized DNA was digested using an exonuclease cocktail and the remaining circularized DNA was amplified using a common linker sequence in the padlock probe. Libraries were PCR amplified, pooled in equimolar amounts, purified by QIAquick Gel Extraction kit (Qiagen) and quantified by qPCR (Kapa Biosystems) on a ViiA 7 Real-time PCR system (Applied Biosystems).

value: M

tag: braak stage

tag: brain bank

value: King's College

tag: replicate

value: Sequencing replicate


title: A1_2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 10//30

value: Manchester


title: P2C5_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 094/04

value: Biological sample


title: P2C6_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A283/12

value: F

value: Sample replicate


title: A3_2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A216/09


title: P2C7_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A048/09


title: Biliary Tract Cancer (BT089post)

value: Female


title: Biliary Tract Cancer (BT089pre)


title: P2C4_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A048/09


title: Biliary Tract Cancer (BT073pre)

value: Male


title: Biliary Tract Cancer (BT073last)


title: Biliary Tract Cancer (BT071pre)


title: Biliary Tract Cancer (BT049last)


title: Biliary Tract Cancer (BT071post)


title: Biliary Tract Cancer (BT073post)


title: 02-01 Control endothelial

value: endothelial

value: IV


title: Biliary Tract Cancer (BT071last)


title: Biliary Tract Cancer (BT025post)


title: P2B11_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 09//37

value: Technical replicate


title: P2C3_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 201/13


title: Biliary Tract Cancer (BT049pre)

value: BTC


title: P2B12_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 09//37


title: P2C2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A069/13


title: P2C1_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A082/14


title: Biliary Tract Cancer (BT025pre)


title: Biliary Tract Cancer (BT049post)


title: Biliary Tract Cancer (BT023last)

value: last


title: F10_2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A321/06


title: Biliary Tract Cancer (BT023post)

value: serum


title: Biliary Tract Cancer (BT025last)


title: P2B10_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A342/14


title: P2B7_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A212/06


title: Biliary Tract Cancer (BT016last)


title: P2B8_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A212/06


title: P2B6_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A303/09


title: P2B5_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A303/09


title: P2B4_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A383/12


title: P2B3_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A383/12


title: P2B2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 10//04


title: Biliary Tract Cancer (BT016post)

value: post


title: Biliary Tract Cancer (BT023pre)

value: pre


title: P2A8_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A265/08

value: M


title: P2A12_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A255/07

value: King's College


title: P2A9_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A160/12


title: P2A7_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 073/05


title: Biliary Tract Cancer (BT121post)


title: P2A11_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A255/07


title: P2B9_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A342/14


title: Biliary Tract Cancer (BT121pre)


title: Biliary Tract Cancer (BT111rec)

value: rec


title: P2A6_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 107/13


title: Biliary Tract Cancer (BT133pre)


title: Biliary Tract Cancer (BT111post)


title: Biliary Tract Cancer (BT110rec)


title: Biliary Tract Cancer (BT111pre)


title: Biliary Tract Cancer (BT133rec)


title: Biliary Tract Cancer (BT133post)


title: Biliary Tract Cancer (BT121rec)


title: Biliary Tract Cancer (BT016pre)


title: P2A5_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 051/14


title: P2B1_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 10//04

value: Manchester


title: P2A4_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 382/12

value: Biological sample


title: Biliary Tract Cancer (BT110post)


title: Biliary Tract Cancer (BT110pre)


title: P2A2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 002/13


title: Biliary Tract Cancer (BT107rec)


title: P2A1_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 319/11


title: H11_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 087/09


title: H12_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 292/06


title: H10_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 2014041

value: Newcastle


title: Biliary Tract Cancer (BT107pre)


title: H9_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 147/10

value: F


title: Biliary Tract Cancer (BT104rec)


title: H7_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 175/12


title: H6_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A187/06


title: Biliary Tract Cancer (BT104post)


title: H8_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 149/08


title: Biliary Tract Cancer (BT104pre)


title: H5_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A405/12


title: H4_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A174/14


title: P2A3_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 081/14 or 051/14

value: Sample replicate


title: Biliary Tract Cancer (BT068rec)

value: Male


title: H3_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 115/15


title: H2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A287/11


title: Biliary Tract Cancer (BT107post)


title: Biliary Tract Cancer (BT062post)

value: Female


title: H1_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A097/15


title: Biliary Tract Cancer (BT068post)


title: Biliary Tract Cancer (BT062rec)


title: Biliary Tract Cancer (BT068pre)


title: G11_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A253/12


title: G12_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A140/07


title: Biliary Tract Cancer (BT061pre)


title: Biliary Tract Cancer (BT061rec)


title: G10_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A122/04


title: Biliary Tract Cancer (BT062pre)


title: G9_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A166/12


title: Biliary Tract Cancer (BT057rec)


title: Biliary Tract Cancer (BT057post)


title: G6_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A274/07


title: Biliary Tract Cancer (BT027rec)


title: Biliary Tract Cancer (BT057pre)


title: Biliary Tract Cancer (BT027post)


title: Biliary Tract Cancer (BT061post)


title: G4_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A378/14


title: G5_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 20130894


title: G3_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A402/14


title: G2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A054/10


title: Biliary Tract Cancer (BT015post)


title: Biliary Tract Cancer (BT015pre)


title: Biliary Tract Cancer (BT015rec)


title: G1_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A246/05


title: Biliary Tract Cancer (BT005rec)


title: G8_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A133/12


title: Biliary Tract Cancer (BT005pre)


title: Biliary Tract Cancer (BT005post)


title: G7_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A282/14


title: F9_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A240/12


title: F8_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A283/12


title: F7_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A174/03


title: F5_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A307/07


title: F6_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A248/11


title: Biliary Tract Cancer (BT027pre)


title: F4_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A189/07


title: F12_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A265/08


title: F11_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A388/12


title: F3_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A331/07


title: F10_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A321/06


title: F1_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A176/15


title: E12_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 20131187


title: E11_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A305/12


title: ExVivoColon_DNBS+L. rhamnosus_rep5

city: Jouy en Josas

first: Rebeca

last: Martin Rosique

state: Yvelines

address: Domaine de Vilvert bat 440 R-2

department: MICALIS

country: France

institute: INRA

description:
Gene expression after 23 days of treatment by DNBS+L. rhamnosus
Sample name: 6.4

hyb_protocol: Samples were hybridized to SurePrint G3 mouse 8x60K v2  (G4858A-074809) arrays and  scanned by G2565CA Scanner System (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the  Agilent DNA Microarray Scanner (G2505C) using one color scan setting for  1x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye  channel is set to Green and Green PMT is set to 100%).

data_processing: Image analyses and raw signal intensities were  quantified by Feature Extraction Software v10.7.3.1 (Agilent Technologies)  according to the GE1_107_Sep09 protocol.

organism: Mus musculus

source_name: ExVivoColon_DNBS+L. rhamnosus

label_protocol: Labelling of total RNA (100ng) was performed with the  One-Color Low Input Quick Amp Labelling kit (Agilent Technologies).

extract_protocol: Total RNA was prepared from total tissue of colon   by using the column-based RNeasy® Micro Kit (Qiagen). RNA was quantified  using a NanoDrop-1000 spectrophotometer and RNA quality was monitored with  the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples with RNA integrity number (RIN) ranging from 8.5-10 were selected  for further analysis.

value: Colon

tag: gender

tag: strain

tag: treatment

value: DNBS+L. rhamnosus


title: ExVivoColon_DNBS+mix_rep4

description:
Gene expression after 23 days of treatment by DNBS+mix
Sample name: 12.4

tag: tissue

value: DNBS+mix


title: E9_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A220/07


title: F2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A206/07


title: ExVivoColon_DNBS+mutant pili_rep1

description:
Gene expression after 23 days of treatment by DNBS+mutant pili
Sample name: 7.1

source_name: ExVivoColon_DNBS+mutant pili

value: DNBS+mutant pili


title: ExVivoColon_DNBS+mutant 7292_rep2

description:
Gene expression after 23 days of treatment by DNBS+mutant 7292
Sample name: 14.2

source_name: ExVivoColon_DNBS+mutant 7292

value: DNBS+mutant 7292


title: ExVivoColon_VC+PBS_rep4

description:
Gene expression after 23 days of treatment by VC+PBS
Sample name: 2.3

value: VC+PBS


title: E10_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A330/07


title: ExVivoColon_DNBS+mutant 7358_rep2

description:
Gene expression after 23 days of treatment by DNBS+mutant 7358
Sample name: 15.4

source_name: ExVivoColon_DNBS+mutant 7358

value: DNBS+mutant 7358


title: ExVivoColon_DNBS+PBS_rep5

description:
Gene expression after 23 days of treatment by DNBS+PBS
Sample name: 4.4

value: DNBS+PBS


title: ExVivoColon_DNBS+mix_rep3

description:
Gene expression after 23 days of treatment by DNBS+mix
Sample name: 12.3


title: ExVivoColon_DNBS+mutant 7358_rep4

description:
Gene expression after 23 days of treatment by DNBS+mutant 7358
Sample name: 16.4


title: E7_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 136/10

value: King's College


title: ExVivoColon_DNBS+PBS_rep1

description:
Gene expression after 23 days of treatment by DNBS+PBS
Sample name: 3.4


title: ExVivoColon_DNBS+mutant 7292_rep1

description:
Gene expression after 23 days of treatment by DNBS+mutant 7292
Sample name: 13.3


title: ExVivoColon_DNBS+L. paracasei_rep1

description:
Gene expression after 23 days of treatment by DNBS+L. paracasei
Sample name: 17.1

source_name: ExVivoColon_DNBS+L. paracasei

value: DNBS+L. paracasei


title: ExVivoColon_VC+PBS_rep3

description:
Gene expression after 23 days of treatment by VC+PBS
Sample name: 2.2


title: E4_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A438/13

value: M


title: E5_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A057/12

value: Biological sample


title: E8_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A305/09


title: E3_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A213/12


title: E1_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A343/11


title: ExVivoColon_DNBS+mutant pili_rep4

description:
Gene expression after 23 days of treatment by DNBS+mutant pili
Sample name: 8.3


title: E6_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A205/07


title: ExVivoColon_DNBS+mix_rep2

description:
Gene expression after 23 days of treatment by DNBS+mix
Sample name: 12.1


title: E2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A282/11


title: D12_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A144/10


title: ExVivoColon_DNBS+PBS_rep4

description:
Gene expression after 23 days of treatment by DNBS+PBS
Sample name: 4.3


title: ExVivoColon_DNBS+L. paracasei_rep2

description:
Gene expression after 23 days of treatment by DNBS+L. paracasei
Sample name: 17.4


title: D10_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A162/15


title: D11_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A355/14


title: D6_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A152/06


title: D8_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A046/13


title: ExVivoColon_DNBS+L. rhamnosus_rep4

description:
Gene expression after 23 days of treatment by DNBS+L. rhamnosus
Sample name: 6.1


title: D7_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A237/14


title: ExVivoColon_DNBS+mutant 7292_rep4

description:
Gene expression after 23 days of treatment by DNBS+mutant 7292
Sample name: 14.4


title: D9_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 78/13


title: ExVivoColon_DNBS+L. paracasei_rep3

description:
Gene expression after 23 days of treatment by DNBS+L. paracasei
Sample name: 18.1


title: ExVivoColon_DNBS+L. rhamnosus_rep3

description:
Gene expression after 23 days of treatment by DNBS+L. rhamnosus
Sample name: 5.4


title: ExVivoColon_DNBS+mutant 7358_rep3

description:
Gene expression after 23 days of treatment by DNBS+mutant 7358
Sample name: 16.3


title: ExVivoColon_VC+PBS_rep1

description:
Gene expression after 23 days of treatment by VC+PBS
Sample name: 1.2


title: ExVivoColon_VC+PBS_rep2

description:
Gene expression after 23 days of treatment by VC+PBS
Sample name: 1.3


title: D4_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A112/07


title: D3_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A297/14


title: D1_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A407/13


title: D2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A160/12


title: ExVivoColon_DNBS+mix_rep1

description:
Gene expression after 23 days of treatment by DNBS+mix
Sample name: 11.1


title: C11_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A221/13


title: C12_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A139/15


title: ExVivoColon_DNBS+L. paracasei_rep4

description:
Gene expression after 23 days of treatment by DNBS+L. paracasei
Sample name: 18.3


title: D5_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A090/07


title: ExVivoColon_DNBS+L. rhamnosus_rep1

description:
Gene expression after 23 days of treatment by DNBS+L. rhamnosus
Sample name: 5.1


title: C10_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A074/05


title: ExVivoColon_DNBS+mutant 7358_rep1

description:
Gene expression after 23 days of treatment by DNBS+mutant 7358
Sample name: 15.1


title: ExVivoColon_DNBS+mutant pili_rep3

description:
Gene expression after 23 days of treatment by DNBS+mutant pili
Sample name: 7.4


title: ExVivoColon_DNBS+mutant pili_rep2

description:
Gene expression after 23 days of treatment by DNBS+mutant pili
Sample name: 7.2


title: ExVivoColon_DNBS+mutant 7292_rep3

description:
Gene expression after 23 days of treatment by DNBS+mutant 7292
Sample name: 14.3


title: C4_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A195/06


title: C7_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A310/09


title: C8_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A209/08


title: C9_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A067/09


title: C3_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A383/11


title: C6_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A073/14


title: RNA.HCV1.day10

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

data_processing:
RNA sequencing paired-end reads were aligned to the human hg19 UCSC reference using TopHat software (v2.0.14).
Gene expression levels (FPKM values) were estimated using Cuffquant and Cuffnorm of the Cufflinks package (v2.2.1).
Proteins and transcripts were mapped by constructing analysis groups.
The ComparativeMarkerSelection module in GenePattern was used to perform a differential expression analysis for mapped transcripts of day 7.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample and results of a differential expression analysis of mapped transcripts of day 7.

source_name: Hepatocellular carcinoma cell line

growth_protocol: For proliferation arrest and differentiation (Huh7.5.1dif cells), Huh7.5.1 cells were cultured in DMEM containing 1 % DMSO for 10 days prior to infection.

extract_protocol:
Cells were lysed in TCL buffer (Qiagen, Hilden, Germany) supplemented with 1 % 2-mercaptoethanol.
HCV RNA was co-amplified with cellular mRNA using a SMART-compatible primer (sequence: 5'-Biotin-AAG CAG TGG TAT CAA CGC AGA GTA CTC TGC GGA ACC GGT GAG TA-3')23. Cellular mRNA was isolated and analyzed according to the SmartSeq2 protocol.

tag: cell line

tag: timecourse day

value: day 10

tag: hcv infection

value: yes


title: RNA.HCV2.day10


title: RNA.HCV3.day10


title: C5_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A099/10

tag: Sex

tag: age


title: ExVivoColon_VC+PBS_rep5

description:
Gene expression after 23 days of treatment by VC+PBS
Sample name: 2.4


title: RNA.mock3.day10

value: no


title: C2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A397/14


title: C1_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A114/12


title: RNA.mock1.day10


title: RNA.mock2.day10


title: B12_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A364/11

value: F


title: B11_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A135/15


title: RNA.HCV3.day9

value: day 9


title: K562 cells_Imatinib treatment_I4

city: Beijing

first: Xuefei

last: Wang

state: Beijing

address: NO.1 West Beichen Road, Chaoyang District, Beijing 100101, China

country: China

institute: nstitute of Microbiology, Chinese Academy of Sciences (CAS)

description: Gene expression after Imatinib treatment in K562 cells

hyb_protocol: The labeled cRNAs were hybridized onto the microarray based on the manufacturer’s standard protocols.

scan_protocol: The arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies)

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring were employed to finish the basic analysis with the raw data.

source_name: K562 cells, Imatinib treatment

label_protocol: Total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP

extract_protocol: Total RNAs were isolated from three independent groups of K562 cells treated with Imatinib or DMSO respectively, using TRIzol reagent (Invitrogen, Carlsbad, CA)

treatment_protocol: K562 cells were treated with Imatinib (10uM) or DMSO respectively for 12h.

value: Imatinib


title: ExVivoColon_DNBS+PBS_rep2

description:
Gene expression after 23 days of treatment by DNBS+PBS
Sample name: 4.1

value: Colon

value: Male


title: B10_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A112/11


title: K562 cells_Imatinib treatment_I2


title: ExVivoColon_DNBS+L. rhamnosus_rep2

description:
Gene expression after 23 days of treatment by DNBS+L. rhamnosus
Sample name: 5.3

value: DNBS+L. rhamnosus


title: K562 cells_DMSO treatment_D4

description: Gene expression after DMSO treatment in K562 cells

source_name: K562 cells, DMSO treatment

value: DMSO


title: K562 cells_Imatinib treatment_I1


title: B9_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A097/13


title: RNA.mock2.day9


title: B5_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A160/06


title: RNA.HCV2.day8

value: day 8


title: RNA.HCV1.day8


title: RNA.HCV3.day8


title: RNA.mock1.day9


title: RNA.mock2.day8


title: B7_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A130/12


title: RNA.mock3.day9


title: B6_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A223/12


title: B3_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 20141916

value: Newcastle


title: B1_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A342/14

value: Technical replicate


title: RNA.mock3.day8


title: B2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 09//37

value: Manchester


title: RNA.mock1.day8


title: K562 cells_DMSO treatment_D1


title: RNA.HCV2.day9


title: B4_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A049/10

value: King's College


title: A12_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A212/06

value: M


title: ExVivoColon_DNBS+PBS_rep3

description:
Gene expression after 23 days of treatment by DNBS+PBS
Sample name: 4.2

value: DNBS+PBS


title: K562 cells_DMSO treatment_D2


title: RNA.HCV3.day7

value: day 7


title: B8_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A345/12

value: Biological sample


title: A10_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 10//27


title: RNA.HCV1.day7

value: yes


title: RNA.HCV2.day7


title: A9_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A270/06


title: RNA.mock3.day7

value: no


title: RNA.HCV3.day6

value: day 6


title: RNA.mock1.day7


title: RNA.HCV1.day9

value: day 9


title: A6_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A255/07


title: A4_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 12//11


title: A7_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 10//04

value: F


title: RNA.mock2.day7


title: RNA.mock3.day6


title: A1_Bisulfite_Padlock_Seq

description: Brain bank Sample code: 10//30


title: RNA.mock2.day6


title: A2_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A276/05


title: RNA.HCV3.day5

value: day 5


title: RNA.HCV2.day5


title: RNA.HCV1.day6


title: A11_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A303/09


title: A3_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A216/09


title: QkcKO_1

city: Niigata

first: Masato

last: Yano

address: 757, Ichibancho, Asahimachidori, Chuo-ku, Niigata-shi,

department: Division of Neurobiology and Anatomy

institute: Niigata University

data_processing:
alignment with OLego
to have BAM and Bed file
transcript level and alternative splicing events with Quantas
Genome_build: mm10
Supplementary_files_format_and_content: .txt gene_id gene_symbol, Tag_Number, RPKM, start and end position, strand and isoform tag_number
alt3 (alternative 3' splice sites), alt5 (alternative 5' splice sites, cass (cassette exon), iret (retained intron), mutx (mutually exclusive exons), taca (tandem cassette exons)

source_name: QkcKO_mouse E14.5 embryonic cortex

growth_protocol: Qk knock-out mice, Qkflox/flox mice were crossed with Nestin-Cre transgenic mice as previously (PMID:29021239)

extract_protocol:
Total RNA was obtained from independent two replicates of embryonic day14.5 mouse cortices from control and Qk conditional knockoouts. The RNA was extracted using QIAzol followed by the generation of mRNA libraries using Illumina TruSeq protocols for poly-A selection, fragmentation, and adaptor ligation according to the manufacturer’s instructions (illumine, TruSeq RNA Sample Prep Kit v2)
TruSeq RNA Sample Prep Kit v2

tag: genotype/variation

value: Qk knock-out

tag: developmental stage

value: embryonic cortex


title: RNA.mock1.day6


title: RNA.HCV1.day5


title: WT_2

source_name: WT_mouse E14.5 embryonic cortex

value: wild type


title: mES 4C-seq (Dek)

city: Illkirch

first: Tom

last: Sexton

address: 1 rue Laurent Fries

institute: IGBMC (Institute of Genetics and Molecular and Cellular Biology)

description: Genomic DNA after 4C-seq protocol and PCR amplification with bait-specific primers. Read length starts at 50, but is reduced to 26 when removing bait sequence during demultiplexing

data_processing:
Library strategy: 4C-seq
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq
Individual 4C-seq experiments were demultiplexed according to bait primer sequence using sabre, with two mismatches permitted (-m 2)
Reads were aligned using Bowtie (v1.0.0) with the settings -a -m 1 --best --strata
Mapped reads were filtered and mapped to DpnII restriction fragments, essentially as described in van de Werken, H.J. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods 910: 969-972.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain 4C-seq read counts for each DpnII fragment on the same chromosome as the bait (chr, start, end, read_count)

source_name: J1 embryonic stem cells

growth_protocol: J1 mouse ES cells were grown on gamma-irradiated mouse embryonic fibroblast cells under standard conditions (4.5 g/L glucose-DMEN, 15% FCS, 0.1 mM non-essential amino acids, 0.1 mM beta-mercaptoethanol, 1 mM glutamine, 500 U/mL LIF, gentamicin), then passaged onto feeder-free 0.2% gelatin-coated plates for at least two passages to remove feeder cells.

extract_protocol:
Cells were detached with trypsin, washed by centrifugation in PBS, and then fixed with 2% formaldehyde in mES culture medium for 10 min at 23°C. The fixation was quenched with cold glycine at a final concentration of 125 mM, then cells were washed with PBS and permeabilized on ice for 1 h with 10 mM Tris-HCl, pH 8, 100 mM NaCl, 0.1% NP-40 and protease inhibitors. Nuclei were resuspended in DpnII restriction buffer at 10 million nuclei/mL concentration, and 5 million nuclei aliquots were further permeabilized by treatment for 1 h with 0.4% SDS at 37°C, then a further 1h with 2.6% Triton-X100 at 37°C. Nuclei were digested overnight with 1000 U DpnII at 37°C, then washed twice by centrifuging and resuspending in T4 DNA ligase buffer. In situ ligation was performed in 400 μL T4 DNA ligase buffer with 20,000 U T4 DNA ligase overnight at 16°C. DNA was purified by reverse cross-linking with an overnight incubation at 65°C with proteinase K, followed by RNase A digestion, phenol/chloroform extraction and isopropanol precipitation. The DNA was digested with 5 U/μg Csp6I at 37°C overnight (for Dek) or 5 U/μg TaiI at 65°C for 2 h (for Hoxc5), then re-purified by phenol/chloroform extraction and isopropanol precipitation. The DNA was then circularized by ligation with 200 U/μg T4 DNA ligase under dilute conditions (5 ng/μL DNA), and purified by phenol/chloroform extraction and isopropanol precipitation. 50 ng aliquots of this DNA were used as template for PCR with bait-specific primers containing Illumina adapter termini (primer sequences and optimal PCR conditions available on request)
PCR reactions were pooled, primers removed by washing with 1.8x AMPure XP beads, then quantified on a Bioanalyzer (Agilent) before sequencing with a HiSeq 4000 (Illumina).

value: mES J1

tag: restriction enzymes

value: DpnII - Csp6I


title: A8_Bisulfite_Padlock_Seq

description: Brain bank Sample code: A383/12

tag: pmi

value: Technical replicate


title: RNA.mock2.day5


title: RNA.mock3.day5


title: mES 4C-seq (Hoxc5)

description: Genomic DNA after 4C-seq protocol and PCR amplification with bait-specific primers. Read length starts at 50, but is reduced to 36 when removing bait sequence during demultiplexing

value: DpnII - TaiI


title: WT_1


title: RNA.HCV2.day6


title: RNA.mock1.day5


title: RNA.HCV3.day4

value: day 4


title: Transgenic LMNA D300N 4

city: Houaton

first: Ali

middle: J

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

data_processing:
Reads were mapped to mm10 using Tophat2
Cufflinks was used to determine transcript FPKM  values
A FPKM cutoff was used to remove any transcript without  a FPKM value of at least  1 in one sample
Limma was used to identify differentially expressed genes.
Supplementary_files_format_and_content: FPKM values for each gene per sample and differential gene expression details (p-value, FDR) in a tab delimited format

source_name: Heart

growth_protocol: not applicable

extract_protocol:
A miRNeasy Mini Kit  (Qiagen, Cat:217004) was used to isolate the RNA following the manufacturer's guidelines
A Illumina TruSeq kit was used in library preparation following the manufacturer's guidelines.
Strand specific, ribosomal RNA depleted,  RNA-Seq

treatment_protocol: not applicable

tag: genotype


title: Transgenic LMNA D300N 2


title: RNA.HCV2.day4


title: Transgenic LMNA D300N 1


title: Control wildtype 4

value: wildtype


title: Control wildtype 3


title: QkcKO_2


title: RNA.mock3.day4


title: RNA.mock2.day4


title: Control wildtype 2


title: RNA.mock1.day4


title: RNA.HCV3.day3

value: day 3


title: RNA.HCV2.day3


title: RNA.HCV1.day3


title: KO_2_1_MeRIP-seq input

city: wuhan

first: yang

last: yang

address: 1 Shizishan Road

institute: Huazhong Agricultural Universit

data_processing:
Basecalls performed using CASAVA
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts using FastQC
RNA-Seq: Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12
RNA-Seq: HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
MeRIP-seq: Index of the reference genome was built using BWA v0.7.12 and clean reads were aligned to the reference genome using BWA mem v 0.7.12.
MeRIP-seq: For a specific RIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. the fragment size was estimated with MACS2 predicted method with default parameters.
MeRIP-seq: we used the MACS2 version 2.1.0  peak finding algorithm to indentify regions of IP enrichment over background
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: RPKM values for each Sample, MeRIP-seq: hyper_common m6A peak

growth_protocol: DMEM (Gibco, San Diego, CA, USA) containing 10% fetal bovine serum (FBS, Gibco) and 1% penicillin/streptomycin

extract_protocol:
RNA-Seq: RNA was harvested using Trizol reagent
MeRIP-seq: Fragmented RNA was incubated for 2 hr at 4C with 0.5 mg/ml anti-m6A polyclonal antibody in IP buffer (150mM NaCl, 0.1% Igepal CA-630, 10 mM Tris-HCl [pH 7.4]) supplemented with RNasin Plus RNase inhibitor
RNA-Seq: Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
MeRIP-seq: First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-) . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system . Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: 1 mM DEX, 0.5 mM isobutyl-methylxanthine, 10 mg/mL insulin and 100umol/L indometacin

value: growth and MDI

tag: time point

value: day 2


title: KO_2_2_MeRIP-seq input


title: KO_2_3_MeRIP-seq input


title: KO_2_3_MeRIP-seq

tag: rip antibody

value: anti-m6A polyclonal antibody (Abcam, ab151230, GR3180897-1)


title: RNA.mock2.day3

value: no


title: KO_2_1_MeRIP-seq


title: KO_2_2_MeRIP-seq


title: Transgenic LMNA D300N 3


title: RNA.HCV3.day2

value: yes


title: RNA.mock3.day3


title: KO_0_2_MeRIP-seq input

value: day 0


title: RNA.HCV2.day2


title: KO_0_3_MeRIP-seq input


title: RNA.HCV1.day2


title: RNA.mock3.day2


title: RNA.HCV1.day4


title: KO_0_3_MeRIP-seq


title: RNA.mock2.day2


title: RNA.mock1.day2


title: KO_0_2_MeRIP-seq


title: Control wildtype 1


title: WT_2_3_MeRIP-seq input


title: RNA.HCV3.day1

value: day 1


title: RNA.HCV2.day1


title: KO_0_1_MeRIP-seq


title: RNA.HCV1.day1


title: WT_2_1_MeRIP-seq input


title: WT_2_2_MeRIP-seq input


title: RNA.mock3.day1


title: WT_2_3_MeRIP-seq


title: RNA.mock2.day1


title: RNA.mock1.day3


title: WT_2_1_MeRIP-seq


title: WT_2_2_MeRIP-seq


title: RNA.mock2.day0


title: RNA.mock3.day0


title: WT_0_3_MeRIP-seq input


title: WT_0_2_MeRIP-seq input


title: RNA.mock1.day1


title: RNA.mock1.day0


title: WT_0_1_MeRIP-seq input


title: KO_0_1_MeRIP-seq input


title: C10_RNA_Seq

description: Brain bank Sample code: A074/05

data_processing:
Trimgalore (v0.11.5) was used to trim the 75 bp single ends reads prior to genome alignment (--quality 20 --length 50).
STAR31 (v2.3.5a) index was generated using Ensemble GRCh37 p13 primary assembly genome and the Gencode v19 primary assembly annotation (--sjdbOverhang 75).
Read alignment was performed using a STAR (--quantMode TranscriptomeSAM, --outFilterMismatchNoverLmax 0.1) and counted using RSEM.
Gene counts matrix was imported into R (v3.4.1) and low expressed genes (CPM < 1 in 70% of samples) were removed prior to trimmed mean of M-values normalization in EdgeR (v3.16.5).
Cell-type compositions for each sample was accessed using Cibersort (100 permutations) on normalized sample counts against cell-type specific markers, identifying the proportion of neurons in each sample.
The limma (v3.30.13) statistical package was used to transform the count matrix to log2-counts per million fit a robust linear model against a continuous Alzheimer’s Disease Braak stage model, adjusting for age, sex, post mortem interval and neuronal cell composition, with empirical bayes.
Differential expression P-values were adjusted for multiple testing correction using the benjamini-hochberg method in the stats package (v3.3.3).
Genome_build: hg19
Supplementary_files_format_and_content: Each .genes.results file contain the following information in order: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

source_name: Brain prefrontal cortex

growth_protocol: Frozen brain tissue was pulverized by CryoPREP (Covaris Inc.), and 20-30 mg of pulverized frozen tissue was lysed and homogenized in QIAzol (Qiagen) using the TissueLyser II (Qiagen).

extract_protocol:
Total RNA were immediately extracted using the RNeasy Universal Mini Kit (Qiagen) including DNase digestion. Resulting RNA quantity was assessed by Nanodrop 8000 (Thermo Scientific) and quality was assessed with the Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent Technologies, Inc.)
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific, Austin, TX, USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).

value: F

tag: braak stage

tag: brain bank

value: King's College

tag: replicate

value: Biological sample


title: WT_0_3_MeRIP-seq

value: wild type

tag: treatment


title: WT_0_2_MeRIP-seq


title: H4_RNA_Seq

description: Brain bank Sample code: A174/14

value: M


title: WT_0_1_MeRIP-seq


title: D5_RNA_Seq

description: Brain bank Sample code: A090/07


title: KO_2_2_RNA-seq


title: KO_2_1_RNA-seq


title: P2A2_RNA_Seq

description: Brain bank Sample code: 002/13


title: KO_2_3_RNA-seq


title: D10_RNA_Seq

description: Brain bank Sample code: A162/15


title: B4_RNA_Seq

description: Brain bank Sample code: A049/10


title: WT_2_3_RNA-seq


title: KO_0_1_RNA-seq


title: KO_0_2_RNA-seq


title: WT_2_1_RNA-seq


title: P2C2_RNA_Seq

description: Brain bank Sample code: A069/13


title: WT_2_2_RNA-seq


title: G8_RNA_Seq

description: Brain bank Sample code: A133/12


title: A10_RNA_Seq

description: Brain bank Sample code: 10//27

value: Manchester


title: E3_RNA_Seq

description: Brain bank Sample code: A213/12


title: E7_RNA_Seq

description: Brain bank Sample code: 136/10


title: WT_0_2_RNA-seq


title: WT_0_1_RNA-seq


title: WT_0_3_RNA-seq


title: E2_RNA_Seq

description: Brain bank Sample code: A282/11


title: D9_RNA_Seq

description: Brain bank Sample code: 78/13


title: B12_RNA_Seq

description: Brain bank Sample code: A364/11


title: E1_RNA_Seq

description: Brain bank Sample code: A343/11


title: H5_RNA_Seq

description: Brain bank Sample code: A405/12


title: KO_0_3_RNA-seq


title: B8_RNA_Seq

description: Brain bank Sample code: A345/12


title: A2_RNA_Seq

description: Brain bank Sample code: A276/05


title: B10_RNA_Seq

description: Brain bank Sample code: A112/11


title: G4_RNA_Seq

description: Brain bank Sample code: A378/14


title: F11_RNA_Seq

description: Brain bank Sample code: A388/12


title: E10_RNA_Seq

description: Brain bank Sample code: A330/07


title: P2C3_RNA_Seq

description: Brain bank Sample code: 201/13


title: P2A4_RNA_Seq

description: Brain bank Sample code: 382/12


title: Input-Fast-WT-PPARd-ChIP-seq II

city: Chicago

first: Grant

middle: D.

last: Barish

state: IL

address: 303 E Superior Street

department: Medicine

institute: Northwestern University

description: male wild type overnight fasted liver input for Samples 88-90

data_processing:
Alignment:  Sequenced reads were aligned to the mm10 reference mouse genome using Bowtie
Filtering: Aligned reads were filtered in HOMER to limit to count only one read per position per length of the read
Peak calling: Peaks were called in HOMER using "getDifferentialPeaksReplicates.pl" which uses DESeq2 to call peaks that pass 2-fold enrichment over input and FDR < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: Peak files (.txt)

source_name: liver

extract_protocol:
Crosslinked nuclei were sonicated and cleared. Protein-DNA complexes were isolated with antbody against BCL6, PPARa, PPARd, HDAC3, SMRT, NCoR or H3K27ac and then IgG paramagnetic beads. After decrosslinking, DNA was isolated with MinElute columns (Qiagen).
Kapa Hyper Prep Kit

tag: strain

tag: tissue

value: liver

value: Bcl6 fl/fl


title: PPARd-Fast-DKO-Rep2-ChIP-seq II

description: male whole-body Ppara knockout and heptocyte Bcl6 double knockout overnight fasted liver ChIP DNA w/PPARd

value: Ppara-/-;Bcl6 fl/fl Albumin-cre


title: PPARd-Fast-DKO-Rep1-ChIP-seq II


title: PPARd-Fast-PparaKO-Rep1-ChIP-seq II

description: male whole-body Ppara knockout overnight fasted liver ChIP DNA w/PPARd

value: Ppara-/-


title: PPARd-Fast-PparaKO-Rep2-ChIP-seq II


title: Input-Fast-DKO-PPARd-ChIP-seq II

description: male whole-body Ppara knockout and heptocyte Bcl6 double knockout overnight fasted liver input for Samples 96-98


title: PPARd-Fast-WT-Rep2-ChIP-seq II

description: male wild type overnight fasted liver ChIP DNA w/PPARd


title: PPARd-Fast-WT-Rep3-ChIP-seq II


title: Input-Fed-WT-SMRT-NCoR-HDAC3-ChIP-seq II

description: male wild type ad lib fed liver input for Samples 68-70, 74-76, 80-82


title: NCoR-Fed-LKO-Rep3-ChIP-seq II

description: male hepatocyte Bcl6 knockout ad lib fed liver ChIP DNA w/NCoR

value: Bcl6 fl/fl; Albumin-cre


title: Input-Fed-LKO-SMRT-NCoR-HDAC3-ChIP-seq II

description: male hepatocyte Bcl6 knockout ad lib fed liver input for Samples 71-73, 77-79, 83-85


title: PPARd-Fast-PparaKO-Rep3-ChIP-seq II


title: PPARd-Fast-WT-Rep1-ChIP-seq II


title: NCoR-Fed-LKO-Rep2-ChIP-seq II


title: NCoR-Fed-WT-Rep3-ChIP-seq II

description: male wild type ad lib fed liver ChIP DNA w/NCoR


title: Undifferentiated-Differentiated GSCs Sample 4

first: Hao

address: No.6 Tiantanxili

department: Department of Neurosurgery

institute: Beijing Tiantan Hospital, Capital Medical University

description:
UNDE-DE-GSCs-3
Biological replicate 4 of 4. undifferentiated glioblastoma stem cells vs. differentiated glioblastoma stem cells

hyb_protocol: To see manufacturer's website http://bioservices.capitalbio.com/fwpt/Agilentpt/15026.shtml

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.7.5).
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: glioblastoma stem cells-3

growth_protocol: GSCs were re-suspended and maintained in GSCs-propagating medium composed of DMEM/F-12 medium, 2 mM GlutaMAX (Invitrogen, USA), 20 ng/mL recombinant human epidermal growth factor (EGF) (R&D, USA), 20 ng/mL basic fibroblast growth factor (bFGF) (Invitrogen, USA), N2 supplement (Invitrogen, USA), and B27 supplement (Invitrogen, USA).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: GSCs differentiation: after 5 passages in GSCs-propagating medium, GSCs were re-suspended and cultured in DMEM/F12 medium containing 10% fetal bovine serum (FBS) (Gibco, Australia) and without N2 and B27 for 4 days

tag: gender

value: Male

value: Brain

tag: cell type

value: undifferentiated GSC

tag: grade

value: WHO Ⅳ

source_name: differentiated glioblastoma stem cells-3

value: differentiated GSC

tag: development stage


title: NCoR-Fed-LKO-Rep1-ChIP-seq II


title: NCoR-Fed-WT-Rep1-ChIP-seq II


title: Undifferentiated-Differentiated GSCs Sample 3

description:
UNDE-DE-GSCs-2
Biological replicate 3 of 4. undifferentiated glioblastoma stem cells vs. differentiated glioblastoma stem cells

scan_protocol: To see manufacturer's website http://bioservices.capitalbio.com/fwpt/Agilentpt/15026.shtml

source_name: glioblastoma stem cells-2

source_name: differentiated glioblastoma stem cells-2


title: SMRT-Fed-LKO-Rep3-ChIP-seq II

description: male hepatocyte Bcl6 knockout ad lib fed liver ChIP DNA w/SMRT


title: Undifferentiated-Differentiated GSCs Sample 2

description:
UNDE-DE-GSCs-1
Biological replicate 2 of 4. undifferentiated glioblastoma stem cells vs. differentiated glioblastoma stem cells

source_name: glioblastoma stem cells-1

label_protocol: To see manufacturer's website http://bioservices.capitalbio.com/fwpt/Agilentpt/15026.shtml

source_name: differentiated glioblastoma stem cells-1


title: F10_RNA_Seq

description: Brain bank Sample code: A321/06

tag: Sex

tag: age


title: Undifferentiated-Differentiated GSCs Sample 1

description:
UNDE-DE-GSCs-0
Biological replicate 1 of 4. undifferentiated glioblastoma stem cells vs. differentiated glioblastoma stem cells

source_name: glioblastoma stem cells-0

value: Female

source_name: differentiated glioblastoma stem cells-0


title: PPARd-Fast-DKO-Rep3-ChIP-seq II


title: Input-Fast-PparaKO-PPARd-ChIP-seq II

description: male whole-body Ppara knockout overnight fasted liver input for Samples 92-94


title: SMRT-Fed-WT-Rep3-ChIP-seq II

description: male wild type ad lib fed liver ChIP DNA w/SMRT


title: SMRT-Fed-WT-Rep2-ChIP-seq II


title: HDAC3-Fed-WT-Rep2-ChIP-seq II

description: male wild type ad lib fed liver ChIP DNA w/HDAC3


title: Input-Fed-LKO-H3K27ac-ChIP-seq II

description: male hepatocyte Bcl6 knockout ad lib fed liver input for Samples 64-66


title: HDAC3-Fed-WT-Rep3-ChIP-seq II


title: HDAC3-Fed-LKO-Rep2-ChIP-seq II

description: male hepatocyte Bcl6 knockout ad lib fed liver ChIP DNA w/HDAC3


title: H3K27ac-Fed-WT-Rep3-ChIP-seq II

description: male wild type ad lib fed liver ChIP DNA w/H3K27ac


title: HDAC3-Fed-LKO-Rep3-ChIP-seq II


title: H3K27ac-Fed-LKO-Rep3-ChIP-seq II

description: male hepatocyte Bcl6 knockout ad lib fed liver ChIP DNA w/H3K27ac


title: HDAC3-Fed-LKO-Rep1-ChIP-seq II


title: H3K27ac-Fed-LKO-Rep2-ChIP-seq II


title: Input-Fed-WT-H3K27ac-ChIP-seq II

description: male wild type ad lib fed liver input for Samples 60-62


title: HDAC3-Fed-WT-Rep1-ChIP-seq II


title: H3K27ac-Fed-LKO-Rep1-ChIP-seq II


title: SMRT-Fed-LKO-Rep1-ChIP-seq II


title: SMRT-Fed-LKO-Rep2-ChIP-seq II


title: H3K27ac-Fed-WT-Rep1-ChIP-seq II


title: H3K27ac-Fed-WT-Rep2-ChIP-seq II


title: NCoR-Fed-WT-Rep2-ChIP-seq II


title: SMRT-Fed-WT-Rep1-ChIP-seq II


title: Control untreated MCF7 cells

city: São Paulo

first: Erico

middle: T

last: Costa

address: R. Prof. Daher Cutait, 69

department: Instituto Sírio-Libanês de Ensino e Pesquisa

country: Brazil

institute: Hospital Sírio-Libanês

hyb_protocol: Prehybridization and hybridization were performed as described by Gomes and colleagues (Gomes et al., Anal Biochem 2003; 321: 244-251)

scan_protocol: Hybridized arrays were scanned on the ScanArrayTM Express (Packard BioScience Biochip Technologies, Billerica, Mass., USA). Data were extracted with the ScanArray Express software (Per- kin-Elmer Life Sciences, Boston, Mass., USA) using the histogram method. Spots G1 or R1 163,000 were excluded.

data_processing: After background subtraction, quantified signals were submitted to log transformation, and a nonlinear normalization (LOWESS) was applied within and across arraysas described by Yang and colleagues (Yang et al. Nucleic Acides Res 2002;30:e15).

label: Cy3, Cy5

source_name: Untreated MCF-7 cells

label_protocol: Labeled cDNA was generated in a reverse transcriptase reaction using 4ug of amplified RNA (aRNA), random hexamer primer, Cy3- or Cy5-labeled dCTP and SuperScript II, as described by Maschietto and colleagues (Maschietto et al., Oncology 2008; 75:81-91)

growth_protocol: Tumor cell lines (MCF-7, MDA-MB231 and MDA-MB435) and nontumor mammary epithleial cell line (HB4a) were maintained subconfluent at 37oC, under 5% CO2, in defined media. Cell lines are negative for micoplasma.

extract_protocol: Total RNA from cultured cells was isolated using CsCl gradient as described by Glisin and colleagues (Glisin V et al., Biochemistry 1974; 13:2633-2637).

treatment_protocol: Tumor cell lines (MCF-7, MDA-MB231 and MDA-MB435) growing under optimal conditions were treated with 1uM 5Aza-dC for 6 days (T1 samples).

tag: culture conditions

value: MCF-7 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), insulin (5 ug/ml) and L-glutamine (1%).

value: Breast

source_name: Untreated HB4a cells (reference for hybridizations)

value: HB4a cells were maintained at 37oC, under 5% CO2, in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), insulin (5 ug/ml), L-glutamine (1%) and hydrocortisone (5 ug/ml).


title: 5Aza-dC treated MDA-MB4351 cells

source_name: 5Aza-dC treated MDA-MB435 cells

value: MDA-MB435 cells were cultured in conventional conditions plus 1uM 5-Aza-dC for 6 days.

value: Melanoma


title: Control untreated MDA-MB231 cells

source_name: Untreated MDA-MB231 cells

value: MDA-MB231 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% L-glutamine.


title: 5Aza-dC treated MDA-MB231 cells

source_name: 5Aza-dC treated MDA-MB231 cells

value: MDA-MB231 cells were cultured in conventional conditions plus 1uM 5-Aza-dC for 6 days.


title: Control untreated MDA-MB435 cells

source_name: Untreated MDA-MB435 cells

value: MDA-MB435 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% L-glutamine.


title: 5Aza-dC treated MCF7 cells

source_name: 5Aza-dC treated MCF7

value: MCF-7 cells were cultured in conventional conditions plus 1uM 5-Aza-dC for 6 days.


title: Heart_MRflox_2month_rep3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from heart tissue, MRflox, 2month

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: heart tissue, MRflox, 2month

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Total RNA was harvested for microarray analysis using the RNeasy Mini Kit and RNase-Free DNase Kit (Qiagen) from whole hearts isolated from male cardioMRKO mice and their male littermate controls.

value: male

tag: genetic background

value: heart

tag: genotype/variation

value: MRflox


title: Heart_cardioMRKO_2month_rep1

description: Gene expression from heart tissue, cardioMRKO, 2month

source_name: heart tissue, cardioMRKO, 2month

value: cardioMRKO


title: Heart_cardioMRKO_2month_rep3


title: Heart_cardioMRKO_2month_rep2


title: Heart_cardioMRKO_1month_rep3

description: Gene expression from heart tissue, cardioMRKO, 1month

source_name: heart tissue, cardioMRKO, 1month


title: Heart_MRflox_1month_rep2

description: Gene expression from heart tissue, MRflox, 1month

source_name: heart tissue, MRflox, 1month


title: Heart_MRflox_2month_rep1


title: Heart_MRflox_1month_rep1


title: Heart_cardioMRKO_2month_rep4


title: Heart_cardioMRKO_1month_rep4


title: Heart_cardioGRKO_2month_rep2

description: Gene expression from heart tissue, cardioGRKO, 2month

source_name: heart tissue, cardioGRKO, 2month

extract_protocol: Total RNA was harvested for microarray analysis using the RNeasy Mini Kit and RNase-Free DNase Kit (Qiagen) from whole hearts isolated from male cardioGRKO mice and their male littermate controls.

value: cardioGRKO


title: Heart_MRflox_1month_rep3


title: Heart_cardioGRKO_2month_rep1


title: Heart_MRflox_2month_rep2


title: Heart_cardioMRKO_1month_rep1


title: Heart_cardioGRKO_2month_rep3


title: Heart_cardioGRKO_1month_rep2

description: Gene expression from heart tissue, cardioGRKO, 1month

source_name: heart tissue, cardioGRKO, 1month


title: Heart_cardioGRKO_1month_rep3


title: Heart_cardioMRKO_1month_rep2


title: Heart_MRflox_1month_rep4


title: Heart_GRflox_2month_rep2

description: Gene expression from heart tissue, GRflox, 2month

source_name: heart tissue, GRflox, 2month

value: GRflox


title: Heart_GRflox_2month_rep3


title: Heart_MRflox_2month_rep4


title: Heart_cardioGRKO_1month_rep1


title: Heart_GRflox_2month_rep1


title: Heart_GRflox_1month_rep1

description: Gene expression from heart tissue, GRflox, 1month

source_name: heart tissue, GRflox, 1month


title: Heart_cardioGRMRdKO_2month_rep3

description: Gene expression from heart tissue, cardioGRMRdKO, 2month

source_name: heart tissue, cardioGRMRdKO, 2month

extract_protocol: Total RNA was harvested for microarray analysis using the RNeasy Mini Kit and RNase-Free DNase Kit (Qiagen) from whole hearts isolated from male cardioGRMRdKO mice and their male littermate controls.

value: cardioGRMRdKO


title: HEK293T_ADAT2_CRISPR(4.2)

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description:
CRISPR ADAT2(4.2)
28618
WT transfected with a CRISPR/Cas9 plasmid and an RNA guide strand against human ADAT2 that generated a stable heterozygote cell line having only 50% ADAT2 expression  Replicate 4 Lane 2.
RNA-seq (size fractionation) - Fragments between 160bp and 220bp were selected.
processed data file: tRNA_gene_counts_hg38_summarizeOverlaps.xls

data_processing:
Solexa Illumina HiSeq 2000 small RNA-Seq data was aligned against the human reference genome hg38 with Bowtie2 version 2.2.2 using local alignment, allowing for 1 mismatch in the first 28 bases and using default options.
Soft clipped bases were removed from the aligned reads with the bamutils utility from the NGSutils software version 0.5.7.
In order to account for the repetitive nature of tRNA types across the genome, all reads (including those that could map to more than one position) were considered. However, reads aligning to two or more different tRNA types were identified with Bowtie2 and removed from the analyses in order to only use those reads aligning unequivocally to multiple copies of the same tRNA type. Finally, tRNA copies with a coverage depth below 10 reads at the anticodon position were also removed from the analysis.
Per replicate counts (pooled lanes) over hg38 tRNAs (Genomic tRNA database, http://gtrnadb.ucsc.edu , January 2016) were obtained with the summarizeOverlaps function from the GenomicAlignments package, using options mode=Union, ignore.strand=FALSE.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: tRNA_gene_counts_hg38_summarizeOverlaps.xls: Excel file contains per sample tRNA gene counts obtained with the SummarizeOverlaps function from the GenomicAlignments package.

source_name: Human Embryonic Kidney

extract_protocol:
Total RNA was extracted with TRIzol reagent, ethanol precipitated and resuspended in DEPC-treated water.
RNA libraries were performed with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB #E7300S) following the manufacturer’s protocol.

tag: cell line

value: Human embryonic kidney cell line

tag: transfection

tag: adat2 expression

tag: lane


title: HEK293T_ADAT2_CRISPR(4.1)

description:
CRISPR ADAT2(4.1)
28618
WT transfected with a CRISPR/Cas9 plasmid and an RNA guide strand against human ADAT2 that generated a stable heterozygote cell line having only 50% ADAT2 expression  Replicate 4 Lane 1.
RNA-seq (size fractionation) - Fragments between 160bp and 220bp were selected.
processed data file: tRNA_gene_counts_hg38_summarizeOverlaps.xls

tag: replicate


title: HEK293T_Control_CRISPR(4.1)

description:
CRISPR CTRL(4.1)
28617
WT transfected with a CRISPR/Cas9 plasmid lacking an RNA guide strand (non-target); resulting in a cell line with 100% expression of ADAT2 Replicate 4 Lane 1.
RNA-seq (size fractionation) - Fragments between 160bp and 220bp were selected.
processed data file: tRNA_gene_counts_hg38_summarizeOverlaps.xls


title: HEK293T_Control_CRISPR(4.2)

description:
CRISPR CTRL(4.2)
28617
WT transfected with a CRISPR/Cas9 plasmid lacking an RNA guide strand (non-target); resulting in a cell line with 100% expression of ADAT2 Replicate 4 Lane 2.
RNA-seq (size fractionation) - Fragments between 160bp and 220bp were selected.
processed data file: tRNA_gene_counts_hg38_summarizeOverlaps.xls


title: HEK293T_Control_CRISPR(3.2)

description:
CRISPR CTRL(3.2)
28615
WT transfected with a CRISPR/Cas9 plasmid lacking an RNA guide strand (non-target); resulting in a cell line with 100% expression of ADAT2 Replicate 3 Lane 2.
RNA-seq (size fractionation) - Fragments between 160bp and 220bp were selected.
processed data file: tRNA_gene_counts_hg38_summarizeOverlaps.xls


title: HEK293T_Control_CRISPR(3.1)

description:
CRISPR CTRL(3.1)
28615
WT transfected with a CRISPR/Cas9 plasmid lacking an RNA guide strand (non-target); resulting in a cell line with 100% expression of ADAT2 Replicate 3 Lane 1.
RNA-seq (size fractionation) - Fragments between 160bp and 220bp were selected.
processed data file: tRNA_gene_counts_hg38_summarizeOverlaps.xls


title: HEK293T_ADAT2_CRISPR(3.1)

description:
CRISPR ADAT2(3.1)
28616
WT transfected with a CRISPR/Cas9 plasmid and an RNA guide strand against human ADAT2 that generated a stable heterozygote cell line having only 50% ADAT2 expression  Replicate 3 Lane 1.
RNA-seq (size fractionation) - Fragments between 160bp and 220bp were selected.
processed data file: tRNA_gene_counts_hg38_summarizeOverlaps.xls


title: HEK293T_ADAT2_CRISPR(3.2)

description:
CRISPR ADAT2(3.2)
28616
WT transfected with a CRISPR/Cas9 plasmid and an RNA guide strand against human ADAT2 that generated a stable heterozygote cell line having only 50% ADAT2 expression  Replicate 3 Lane 2.
RNA-seq (size fractionation) - Fragments between 160bp and 220bp were selected.
processed data file: tRNA_gene_counts_hg38_summarizeOverlaps.xls


title: Heart_GRflox_1month_rep2


title: Heart_dflox_2month_rep2

description: Gene expression from heart tissue, dflox, 2month

source_name: heart tissue, dflox, 2month

value: dflox


title: Heart_cardioGRMRdKO_1month_rep2

description: Gene expression from heart tissue, cardioGRMRdKO, 1month

source_name: heart tissue, cardioGRMRdKO, 1month


title: Heart_dflox_2month_rep1


title: exp03_sigfp_clip_armi_comb

city: Cambridge

first: Marzia

last: Munafo

address: Robinson Way

department: Cancer Research UK - Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description: experiment 03 - Armi CLIP upon GFP knockdown

data_processing:
smallRNA seq and CLIPseq analysis
Raw fastq files generated by Illumina sequencing were analysed by a pipeline developed in-house. In short, for CLIP-seq the first 5 bases of each 50 bp read were removed using fastx trimmer (http://hannonlab.cshl.edu/fastx_toolkit/). After removal of rRNA mapped reads, high-quality reads were aligned to the Drosophila melanogaster genome release 6 (dm6; downloaded from Flybase) using STAR (Dobin et al. 2013). For transposon-wide analysis, genome multi-mapping reads were randomly assigned to one location using option '--outFilterMultimapNmax 1000 --outMultimapperOrder Random' and non-mapping reads were removed. Alignment files were then converted back to fastq format with samtools (Li et al. 2009) and re-aligned to the transposon consensus sequences allowing multi-mappers that were assigned to a random position. Generated bam alignment files were indexed using samtools index. For genome-wide analyses, multi-mapping reads were removed to ensure unique locations of reads. Normalization was achieved by calculating rpm (reads per million) using the deepTools2 bamCoverage function with 10 bp bin sizes (Ramirez et al. 2016). Reads mapping to genes were counted with htseq (Anders et al. 2015) and transposon derived reads were calculated using a custom script. Differential expression analysis was performed using custom built R scripts. Coordinates used for the piRNA clusters are chrX:21631891-22282863 (flam) and chrX:21520428-21556793 (20A).
For small RNA-seq, adapters were clipped from raw fastq files with fastx_clipper (adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) keeping only reads with at least 23 bp length. Then the first and last 4 bases were trimmed using seqtk (https://github.com/lh3/seqtk). After removal of cloning markers and 2S rRNA mapped reads, alignment was performed as described above and normalised to miRNA reads in the control library (set to rpm). Only high-quality small RNA reads with a length between 23 and 29 bp were used for further analysis of piRNA profiles.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files for all dm6 alignement files, normalized to rpm. For RNA- and smallRNA-seq, sequences were split in sense- and antisense-mapping reads before normalization.

organism: Drosophila melanogaster

source_name: ovarian somatic cells (OSC)

growth_protocol: cells were grown at 25°C

extract_protocol: SMARTer® Stranded RNA-seq Kit (Clontech)

treatment_protocol: OSCs were treated with siRNA and transfected with indicated plasmids

value: ovarian somatic cells (OSC)

tag: batch

tag: experiment

value: CLIPseq

value: GFP knockdown - transfected with Armi-3xFLAG-HALO


title: exp03_sigasz_clip_armi_comb

description: experiment 03 - Armi CLIP upon Gasz knockdown

tag: tissue

value: Gasz knockdown - transfected with Armi-3xFLAG-HALO


title: CG10880_het

description: small RNA seq library (19-28nt)

data_processing:
smallRNA seq analysis
Raw fastq files generated by Illumina sequencing were analysed by a pipeline developed in-house.
For small RNA-seq, adapters were clipped from raw fastq files with fastx_clipper (adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) keeping only reads with at least 23 bp length. Then the first and last 4 bases were trimmed using seqtk (https://github.com/lh3/seqtk). After removal of cloning markers and 2S rRNA mapped reads, alignment was performed as described above and normalised to miRNA reads in the control library (set to rpm). Only high-quality small RNA reads with a length between 23 and 29 bp were used for further analysis of piRNA profiles.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files for all dm6 alignement files, normalized to rpm. For smallRNA-seq, sequences were split in sense- and antisense-mapping reads before normalization.

source_name: ovary

growth_protocol: flies were grown at 25°C

extract_protocol:
ovaries were homogenized in Trizol and RNA extracted using Phenol/Chloroform
Adapted from: Jayaprakash, Anitha D. et al. “Identification and Remediation of Biases in the Activity of RNA Ligases in Small-RNA Deep Sequencing.” Nucleic Acids Research 39.21 (2011): e141. PMC. Web. 22 Oct. 2018.

value: ovary

tag: strain

value: smallRNA-seq

value: CG10880 KO het


title: gasz_homo

description: small RNA seq library (19-28nt)

value: gasz KO


title: exp02_sipiwi_clip_mock_comb

description: experiment 01 - mock IP upon Piwi knockdown

value: Piwi knockdown - transfected with ZsGreen 3xFLAG


title: gasz_het

description: small RNA seq library (19-28nt)

value: gasz het KO


title: exp02_sipiwi_clip_armi_comb

description: experiment 01 - Armi CLIP upon Piwi knockdown

value: Piwi knockdown - transfected with Armi-3xFLAG-HALO


title: Heart_GRflox_1month_rep3

tag: gender

value: male

value: heart


title: Heart_dflox_1month_rep3

description: Gene expression from heart tissue, dflox, 1month

source_name: heart tissue, dflox, 1month


title: Heart_cardioGRMRdKO_1month_rep1


title: Heart_cardioGRMRdKO_2month_rep2


title: Heart_dflox_1month_rep2


title: Heart_cardioGRMRdKO_2month_rep1


title: Heart_cardioGRMRdKO_1month_rep3


title: Heart_dflox_2month_rep3


title: Heart_dflox_1month_rep1


title: exp02_sigfp_clip_armi_comb

description: experiment 02 - Armi CLIP upon GFP knockdown


title: CG10880_homo

description: small RNA seq library (19-28nt)

value: CG10880 [delta2/oof1] KO


title: exp01_sigfp_clip_armi_comb

description: experiment 01 - Armi CLIP upon GFP knockdown


title: exp01_sizuc_clip_mock_comb

description: experiment 01 - mock IP upon Zuc knockdown

value: Zuc knockdown  - transfected with ZsGreen 3xFLAG


title: exp01_sizuc_clip_armi_comb

description: experiment 01 - Armi CLIP upon Zuc knockdown

value: Zuc knockdown - transfected with Armi-3xFLAG-HALO


title: exp02_sigfp_clip_mock_comb

description: experiment 02 - mock IP upon GFP knockdown

value: GFP knockdown - transfected with ZsGreen 3xFLAG


title: exp01_sigfp_clip_mock_comb

description: experiment 01 - mock IP upon GFP knockdown

value: ovarian somatic cells (OSC)


title: osc_srna_sizuc

description: small RNA seq library (19-28nt)

extract_protocol:
cells were homogenized in Trizol and RNA extracted using Phenol/Chloroform
Adapted from: Jayaprakash, Anitha D. et al. “Identification and Remediation of Biases in the Activity of RNA Ligases in Small-RNA Deep Sequencing.” Nucleic Acids Research 39.21 (2011): e141. PMC. Web. 22 Oct. 2018.

treatment_protocol: OSCs were treated with indicated siRNA

value: Zuc knockdown


title: osc_srna_siyb

description: small RNA seq library (19-28nt)

value: Yb knockdown


title: osc_srna_siarmi

description: small RNA seq library (19-28nt)

value: Armi knockdown


title: osc_srna_sigfp

description: small RNA seq library (19-28nt)

value: GFP knockdown


title: S. cerevisiae ARO4 library colony RNA-seq

city: San Francisco

first: Leqian

last: Liu

address: 1700 4th street

department: BTS

institute: UCSF

data_processing:
Base calls performed with bcl2fastq2.15.
Read 1 contains the barcode (bp 1-12) and UMI (bp 13-20).
Read 2 was aligned with Bowtie
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each colony; columns are colony, and rows are genes.
Genome_build: C. albicans SC5314; S. cerevisiae EF4
Supplementary_files_format_and_content: Digital expression matrices. Flat text files with tab delimiters.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: yeast colonies

growth_protocol: Yeast cells were single cell encapsulated in agarose hydrogel microdroplets followed by culture with standard yeast synthetic medium to form colonies

extract_protocol:
Colonies were lysed in droplet using a combination of enzyme and detergent. polyA RNA capature were performed based on Drop-seq protocol
Library construction were perfromed following Drop-seq protocol.

tag: growth stage

value: 18 hour culture


title: HC2_F&IM&2dpi_R4

city: Athens

first: Esther

last: van der Knaap

state: GA

address: 111 Riverbend Rd

department: Horticulture

institute: University of Georgia

data_processing:
Reads mapped to rRNA were filtered using bowtie2
The cleaned raw reads were then mapped to ITAG2.3 Released Tomato Genome through the Tophat2 high throughput short read aligner.
Genome_build: ITAG2.3 Released Tomato Genome
Supplementary_files_format_and_content: tab-delimited csv files include RPKM values for each gene per sample

organism: Solanum pimpinellifolium

source_name: floral and inflorescence meristems (F&IM) + 2dpi floral buds

growth_protocol: Plants were grown in two-gallon pots under natural light supplemented with artificial light (16/8 hr light/dark cycle) in the greenhouse in Wooster, OH, USA, 2013.

extract_protocol:
During the collection, all inflorescences were immediately immersed in ice-cold RNAlater (QIAGEN) solution at five times the volume of the sample in order to prevent RNA degradation. After sample collection, vacuum infiltration was applied until tissues sunk to the bottom of RNAlater solution. The tissues were then stored in RNAlater at -80℃.  For the dissection, meristems and buds of different developmental stages were isolated by forceps under a dissection microscope and immediately put into a 1.5 ml eppendorf tube in 1 ml of fresh RNAlater that was kept on ice. The samples were stored at -80 ℃ prior to the RNA extraction.RNA extraction was conducted using Trizol® (Invitrogen Inc. USA) following manufacture’s recommendation.
Strand directed RNA-seq libraries of approximately 250 bp fragments were prepared following the protocol of Zhong et al., 2011.

tag: genotype

value: Transgenic complementation lines of SlCLV3 in fas NILs

tag: background accession

tag: developmental stage

value: floral and inflorescence meristems (FandIM) + 2dpi floral buds


title: Rat_C6_Clozapine_5day_rep2

city: New Taipei City

first: Mao-Liang

last: Chen

address: No.289, Jianguo Rd., Xindian Dist.,

department: Department of Research

country: Taiwan

institute: Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation

description:
18548_Clo_2_4
miRNA
Clozapine treated C6 cells.

hyb_protocol: Assembled slide chamber in rotisserie in a hybridization oven set to 55°C for 20 hours. Set the hybridization rotator to rotate at 20 rpm.

scan_protocol: FE 10.7.3.1 using default parameters.

data_processing: FE 10.7.3.1 using default parameters.

organism: Rattus norvegicus

source_name: C6 Glioblastoma cells

label_protocol: Cyanine-3 (Cy3) labeled 100ng total RNA.

growth_protocol: C6 cells obtained from the Bioresource Collection and Research Center (BCRC) of the Food Industry Research and Development Institute (FRDI), Taiwan, were maintained in high-glucose DMEM (Gibco, Inc., NY, USA) supplemented with 26 mM NaHCO3, 2 mM L-glutamine, 100 units/ml penicillin, 100 ug/ml streptomycin, 10% horse serum and 2% FBS (Gibco, Inc.).

extract_protocol: Trizol Method.

treatment_protocol: Haloperidol, risperidone or clozapine was added to the medium daily for 5 days. The final concentrations of haloperidol (2 μg/ml), risperidone (4 μg/ml) and clozapine (25 μg/ml) were calculated based on therapeutic concentrations in the brain. The risperidone used in this study was purchased from Janssen Pharmaceutica (Beerse, Belgium), and clozapine and haloperidol were purchased from Sigma-Aldrich (MO, USA). Cells were harvested for miRNA extraction after 5-days-APD-treatment.

tag: cell type

value: Glioblastoma

tag: treatment

value: Clozapine

tag: time

value: 5 Days


title: HC2_4dpi_R4

source_name: 4dpi floral buds

value: 4dpi floral buds


title: HC2_6dpi_R4

source_name: 6dpi floral buds

value: 6dpi floral buds


title: Rat_C6_Haloperidol_5day_rep2

description:
18544_Hal_2_2
miRNA
Haloperidol treated C6 cells.

tag: cell line

value: Haloperidol


title: Rat_C6_Clozapine_5day_rep1

description:
18540_Clo_1_4
miRNA
Clozapine treated C6 cells.


title: Rat_C6_Risperidone_5day_rep2

description:
18546_Ris_2_3
miRNA
Riperidone treated C6 cells.

value: Risperidone


title: Rat_C6_Risperidone_5day_rep1

description:
18538_Ris_1_3
miRNA
Riperidone treated C6 cells.


title: Rat_C6_Haloperidol_5day_rep1

description:
18536_Hal_1_2
miRNA
Haloperidol treated C6 cells.


title: Rat_C6_Control_rep2

description:
18542_Ctrl_2_1
miRNA
Untreated C6 cells.

value: Untreated (Control)


title: Rat_C6_Control_rep1

description:
18534_Ctrl_1_1
miRNA
Untreated C6 cells.


title: HC2_6dpi_R3


title: HC2_4dpi_R3


title: HC2_F&IM&2dpi_R3


title: Psoriasis neutrophil01

city: Xi’an

first: Shuai

last: Shao

address: No. 127 of West Changle Road

department: Department of Dermatology

institute: Xijing Hospital, Fourth Military Medical University

hyb_protocol: The fragmented cRNA was hybridized to PrimeView Human Gene Expression Array containing about 36,000 transcripts. Hybridization was performed at 45 °Cwith rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640).

scan_protocol: The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin ) on an Affymetrix Fluidics Station 450 followed by scanning on a GeneChip Scanner 3000.

data_processing:
The scanned images were assessed and analyzed to generate raw data files saved as CEL files using Affymetrix GeneChip Operating software (GCOS 1.4). The quality of each CEL file was assessed using Affymetrix Expression Console Software according to the Affymetrix standard protocol.
All samples were normalized through the Robust Multi-array Average (RMA) using DNA-chip analyzer (dChip). The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998). Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).

label: biotin

source_name: human neutrophils from peripheral blood of psoriasis patients

label_protocol: 100ng of total RNA was used to synthesize double-stranded cDNA. The bio-tagged cRNA was produced by using the MessageAmp™ Premier RNA Amplification Kit and were fragmented to strands of 35–200 bases in length according to the protocols from Affymetrix.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The separation of peripheral neutrophils was performed using a magnetic-activated cell sorting method following the instructions, with anti-CD15 for human neutrophils.

tag: subject status

value: psoriasis patients

value: peripheral blood

value: neutrophils


title: HC2_6dpi_R2


title: Psoriasis neutrophil02


title: Healthy neutrophil03

source_name: human neutrophils from peripheral blood of healthy controls

value: healthy control


title: Healthy neutrophil01


title: Psoriasis neutrophil03


title: Healthy neutrophil02


title: Human ovarian granulosa cells at 15 day of culture, rep2

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: Poznań University of Medical Sciences

description:
15D.2
Gene expression data from human ovarian granulosa cells at 15 day of culture.

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to the Affymetrix® Human Genome U219 Array (48°C/20 h). Microarrays were then washed and stained according to the technical protocol using the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: The array strips were scanned employing Imaging Station of the GeneAtlas System.

data_processing: Obtained cel files were submitted to Bioconductor and R programing language. Each CEL file was merged with a description file. In order to correct background, normalize, and summarize results, we used the Robust Multiarray Averaging (RMA) algorithm.

source_name: Patients (18-40 years old) assigned to the procedure of in vitro fertilization (IVF)

label_protocol: Biotin labeling and fragmentation were performed by Affymetrix GeneChip® WT Terminal Labeling and Hybridization (Affymetrix).

growth_protocol: In this study we used GCs from 20 patients, aged 18-40 years, assigned to the procedure of in vitro fertilization (IVF). The exclusion criteria from the study have been: a potential risk of inadequate ovarian stimulation; patients with serum level of FSH above 15 mU / mL on the 2nd-3rd day of the cycle; polycystic ovary syndrome; endometriosis.

extract_protocol: For reverse transcription, 1 µg of each RNA sample was used. Reverse transcription was based on the protocols and reagents of SABiosciences (RT2 First Stand Kit - 330401), using a Veritimer 96 well Thermal Cycler. Real-time PCR was performed using the Light Cycler® 96 (Roche Diagnostic GmbH, Germany), RT2 SYBR® Green ROXTM qPCR Master Mix (Qiagen Sciences, Maryland, USA).

treatment_protocol: GCs was washed twice using Dulbecco’s Phosphate Buffered Saline (DPBS, Sigma-Aldrich, USA), and centrifugation at 200 x g for 10 min at RT. The culture medium consisted of Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma-Aldrich, USA), 2% fetal bovine serum FBS (FBS; Sigma-Aldrich Co., St. Louis, MO, USA), 4 mM L-glutamine (stock 200 mM, Invitrogen, USA), 10 mg/mL gentamicin (Invitrogen, USA), 10,000 units/mL penicillin, and 10,000 μg/mL streptomycin (Invitrogen, USA). GCs were cultivated at 37° C under aerobic conditions (5% CO2). GCs were cultivated for 30 days; total RNA was isolated after 1 day, 7 days, 15 days and 30 days.

value: Female

value: Ovarian granulosa cells

tag: time in culture

value: 15 days


title: HC2_4dpi_R2

value: Transgenic complementation lines of SlCLV3 in fas NILs


title: Human ovarian granulosa cells at 30 day of culture, rep1

description:
30D.1
Gene expression data from human ovarian granulosa cells at 30 day of culture.

value: 30 days


title: HC2_F&IM&2dpi_R2

value: floral and inflorescence meristems (FandIM) + 2dpi floral buds


title: Human ovarian granulosa cells at 7 day of culture, rep2

description:
7D.2
Gene expression data from human ovarian granulosa cells at 7 day of culture.

value: 7 days


title: Control 0100

type: genomic

city: Campinas

first: Benilton

middle: Sa

last: Carvalho

state: Sao Paulo

address: Tessália Vieira de Camargo, 126

department: Medical Genetics

institute: Universidade Estadual de Campinas

description: Hybridized to SNP6.0 Affymetrix

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The raw data (CEL files) were processed through SNPRMA and genotype calls obtained through CRLMM (both in the crlmm Bioconductor package)
primary data description: Alleles A and B intensities; Genotype calls (1=AA; 2=AB; 3=BB); Genotype confidence (integers: the larger, the better)

source_name: DNA Controle 0100

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from leukocytes of peripheral blood of 103 CM patients and 103 controls using the QIAamp DNA Blood Midi Kit (Qiagen®, Canada), following manufacturer’s instructions

tag: caso

tag: idade contínua

tag: idade mediana≤ 54

tag: sexo

tag: fototipo i+ii_outros

tag: cor pele

tag: cor olhos

tag: cor dos cabelos

tag: sardas

tag: nevos poucos_muitos

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma

tag: queimadura solar


title: Control 0098

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0098


title: Control 0101

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0101


title: Control 0103

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0103


title: Control 0102

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0102


title: Human ovarian granulosa cells at 24h of culture, rep2

description:
24H.2
Gene expression data from human ovarian granulosa cells at 24h of culture.

tag: gender

tag: cell type


title: Control 0099

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0099


title: Human ovarian granulosa cells at 15 day of culture, rep1

description:
15D.1
Gene expression data from human ovarian granulosa cells at 15 day of culture.


title: Control 0096

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0096


title: Human ovarian granulosa cells at 7 day of culture, rep1

description:
7D.1
Gene expression data from human ovarian granulosa cells at 7 day of culture.


title: Human ovarian granulosa cells at 24h of culture, rep1

description:
24H.1
Gene expression data from human ovarian granulosa cells at 24h of culture.


title: Human ovarian granulosa cells at 30 day of culture, rep2

description:
30D.2
Gene expression data from human ovarian granulosa cells at 30 day of culture.


title: HC2_4dpi_R1

tag: genotype

tag: background accession

tag: developmental stage


title: Control 0095

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0095

tag: caso

tag: idade contínua


title: Control 0097

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0097

tag: idade mediana≤ 54

tag: sexo


title: HC2_F&IM&2dpi_R1


title: Control 0092

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0092

tag: fototipo i+ii_outros

tag: cor pele


title: Control 0094

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0094

tag: cor olhos

tag: cor dos cabelos


title: Control 0093

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0093

tag: sardas

tag: nevos poucos_muitos


title: HC2_6dpi_R1


title: Control 0089

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0089

tag: tipo de exposicao cronica+intermitente_nenhuma

tag: tipo de exposicao solar c_i+nenhuma


title: Control 0090

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0090

tag: queimadura solar


title: Control 0087

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0087


title: RNAi_6dpi_R4

source_name: 6dpi floral buds

value: RNAi-SlCLV3 transgenic lines


title: Control 0088

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0088


title: Control 0091

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0091


title: RNAi_4dpi_R3

source_name: 4dpi floral buds

value: 4dpi floral buds


title: Control 0076

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0076


title: Control 0084

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0084


title: Control 0083

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0083


title: RNAi_F&IM&2dpi_R4

source_name: floral and inflorescence meristems (F&IM) + 2dpi floral buds


title: RNAi_6dpi_R2

value: 6dpi floral buds


title: RNAi_F&IM&2dpi_R2


title: RNAi_4dpi_R4


title: Control 0079

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0079


title: RNAi_4dpi_R2


title: Control 0075

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0075


title: Control 0082

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0082


title: Control 0086

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0086


title: Control 0081

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0081


title: RNAi_6dpi_R3


title: Control 0074

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0074


title: Control 0085

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0085


title: Control 0080

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0080


title: Control 0078

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0078


title: Control 0072

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0072


title: RNAi_6dpi_R1

source_name: 6dpi floral buds


title: Control 0073

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0073


title: RNAi_F&IM&2dpi_R3


title: Control 0077

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0077


title: Control 0071

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0071


title: Control 0068

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0068


title: Control 0069

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0069


title: RNAi_F&IM&2dpi_R1

source_name: floral and inflorescence meristems (F&IM) + 2dpi floral buds


title: RNAi_4dpi_R1

source_name: 4dpi floral buds


title: Control 0067

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0067


title: lc_fas_6dpi_R4

value: lc/fas double mutants


title: Control 0064

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0064


title: Control 0063

description: Hybridized to SNP6.0 Affymetrix

source_name: DNA Controle 0063