title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G8_AD010_indexed


title: V208_Minus01

status: Public on Sep 07 2020

type: RNA

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit (Affymetrix)

scan_protocol: GeneChip Human Transcriptome Array 2.0 (Affymetrix)

data_processing: Scan data were processed in the R environment using oligo and affy packages, with raw data summarised at transcript level with pd.hta.2.0

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

label_protocol: GeneChip WT Plus Reagent Kit (Affymetrix)

extract_protocol: Tempus Spin RNA Isolation Kit (Applied Biosystems) with DNase-treatment

tag: tissue

value: whole blood

tag: day

value: day -1

tag: individual

tag: gender

value: M

tag: age

tag: country

value: Pakistan


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G9_AD007_indexed

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: PAL

tag: Sex

value: male

tag: strain


title: V106_Plus04

value: day 4

value: F

value: UK


title: V106_Plus06

value: day 6


title: V106_Plus02

value: day 2


title: V106_PlusDOD

value: diagnosis


title: V104_PlusDOD

value: Malaysia


title: V106_Minus01


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G8_AD006_indexed


title: V206_Plus10

value: Kenya


title: V106_Plus08

value: day 8


title: V104_Plus06


title: V104_Plus08


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G8_AD008_indexed


title: V104_Minus01


title: V206_Plus06


title: V104_Plus02


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G8_AD007_indexed


title: V206_Plus02


title: V104_Plus04


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G8_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G8_AD004_indexed


title: V027_PlusDOD


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G8_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G7_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G7_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G7_AD008_indexed


title: V027_Plus08


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G7_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G7_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G6_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G6_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G7_AD002_indexed


title: V027_Plus04


title: V027_Plus06


title: V027_Minus01


title: V027_Plus02


title: V026_Plus08


title: V026_PlusDOD


title: V026_Plus04


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G6_AD007_indexed


title: V026_Minus01


title: V026_Plus02


title: V024_PlusDOD


title: V024_Plus10

value: day 10


title: V024_Plus08


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G5_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G5_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G6_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G6_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G5_AD002_indexed


title: V026_Plus06


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G5_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G4_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G4_AD010_indexed


title: V024_Plus04


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G4_AD007_indexed


title: V022_Plus10


title: V024_Plus06


title: V206_Plus04


title: V022_Plus06


title: V022_Plus02


title: V022_Plus08


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G7_AD006_indexed


title: V022_Minus01


title: V024_Minus01


title: V020_Plus08


title: V024_Plus02


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G5_AD001_indexed


title: V020_Plus06


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G3_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G3_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G3_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G4_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G3_AD007_indexed


title: V022_Plus04


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G3_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G2_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G1_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G1_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H11_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G12_AD006_indexed


title: V020_PlusDOD


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G12_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G12_AD001_indexed


title: V019_Plus06


title: V018_Plus08

value: Switzerland


title: V020_Plus04

value: whole blood


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G11_AD010_indexed


title: V020_Plus02


title: V019_PlusDOD


title: V020_Minus01

value: day -1


title: V018_Plus06


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G1_AD004_indexed


title: V019_Plus02

value: M


title: V019_Minus01


title: V019_Plus04


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G1_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G11_AD008_indexed


title: V019_Plus08


title: V018_Plus04


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G11_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G11_AD007_indexed


title: V018_PlusDOD


title: V018_Minus01


title: V017_Plus10

value: Albania


title: V018_Plus02


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G11_AD004_indexed

value: PAL


title: S7YTE9_L7

city: Poznań

first: Arkadiusz

last: Kajdasz

state: wielkopolskie

address: ul. Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

library_source: transcriptomic

data_processing:
RNA-Seq raw paired-end reads were trimmed with cutadapt
Reads were aligned to Ensembl Sscrofa11.1 procine genome with STAR (v2.7)
BAM files were merged with samtools (v1.10)
Counts were obtained using featureCounts v1.6.3
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Table with gene expression raw reads in csv format.

organism: Sus scrofa

source_name: trophectoderm (TE)

growth_protocol: In vitro maturation of porcine  cumulus-oocyte complexes (COCs) was performed in 500 µl of IVM medium (NCSU-23; North Carolina State University Medium-23) in four-well plates (Nunc, NY, USA). Each 500 µl IVM medium consisted of 70 COCs that were matured in HeraCell 150 incubator (Thermo Scientific, MA, USA) under conditions: 5% CO2 in atmosphere, 38.5°C and maximum humidity. The first 24h of porcine IVM included medium supplemented with hormones: 10U PMSG (pregnant mare serum gonadotropin, Chorulon, MSD Animal Health, NL) and 10U hCG (Folligon, MSD Animal Health, NL). The next step included the transfer of COCs to fresh, equilibrated medium without hormones for 20 hours maturation.

extract_protocol:
SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Takara) was used to generate high-quality cDNA from samples
Nextera XT DNA and Nextera XT Index Kit v2 (Illumina)

treatment_protocol: Denuded oocytes were activated using 5 μM ionomycin in TALP-medium (5 minutes) and incubated in 2 mM 6-DMAP for 4 hours in final embryo culture medium supplemented with BSA (for the prevention of the second polar body extrusion). NCSU23 and SOF were used as embryo culture media up to blastocyst stage. At the 5th day of bovine embryo development half of the medium was changed with fresh and equilibrated SOF. The blastocyst rate was calculated in relation to activated oocytes.

tag: replicate

value: sample S7YTE9 repeat2

value: trophectoderm (TE)


title: V017_Plus08


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G10_AD004_indexed

value: male


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F9_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G10_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G10_AD002_indexed


title: S7YTE9_L8

value: sample S7YTE9 repeat3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G10_AD012_indexed


title: S7YTE8_L5

value: sample S7YTE8 repeat1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G10_AD010_indexed


title: V017_PlusDOD


title: V017_Plus06

value: day 6


title: V017_Plus04

value: day 4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F9_AD007_indexed


title: V017_Plus02

value: day 2


title: V016_Plus08

value: UK


title: S7YTE9_L5

value: sample S7YTE9 repeat1


title: S7YTE10_L8

value: sample S7YTE10 repeat3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G11_AD001_indexed


title: S7YTE8_L6

value: sample S7YTE8 repeat2


title: S7YTE10_L2

value: sample S7YTE10 repeat1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F8_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G10_AD006_indexed


title: S7YTE10_L7

value: sample S7YTE10 repeat2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F9_AD006_indexed


title: V016_Plus10

value: whole blood

value: diagnosis

value: M


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F9_AD004_indexed

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F8_AD004_indexed


title: V016_Plus02


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F8_AD002_indexed


title: S7YICM9_L7

source_name: inner cell mass (ICM)

value: sample S7YICM9 repeat2

value: inner cell mass (ICM)


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F9_AD002_indexed

value: male


title: V016_Plus06


title: S7YICM9_L5

value: sample S7YICM9 repeat1


title: V016_Minus01

value: day -1


title: V016_Plus04

value: day 4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F8_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F9_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F8_AD012_indexed


title: S7YICM8_L6

value: sample S7YICM8 repeat2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F8_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F7_AD002_indexed


title: S7YICM8_L5

value: sample S7YICM8 repeat1


title: S7YICM9_L8

value: sample S7YICM9 repeat3


title: V013_Plus10

value: day 10

value: Belgium


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F6_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F8_AD007_indexed


title: V017_Minus01

value: Albania


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F7_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F7_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F6_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F6_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F6_AD008_indexed


title: S7YICM10_L8

value: sample S7YICM10 repeat3


title: V013_PlusDOD

value: whole blood


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G4_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G4_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F7_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F5_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F6_AD006_indexed


title: S7YW15_L5

source_name: blastocyst

value: sample S7YW15 repeat1

value: whole blastocyst


title: V013_Plus04

value: M


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F4_AD007_indexed

value: PAL


title: S7YW12_L8

value: sample S7YW12 repeat4


title: V013_Plus02

value: day 2


title: S7YICM10_L2

value: sample S7YICM10 repeat1

value: inner cell mass (ICM)


title: V013_Plus06

value: day 6


title: V012_PlusDOD

value: diagnosis

value: UK


title: V012_Plus06


title: V013_Plus08

value: day 8


title: V012_Plus04

value: day 4


title: S7YICM10_L7

value: sample S7YICM10 repeat2


title: V013_Minus01

value: day -1

value: Belgium


title: S7YW12_L7

value: sample S7YW12 repeat3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F4_AD001_indexed

value: male


title: S7YW12_L3

value: sample S7YW12 repeat1

value: whole blastocyst


title: S7YW15_L7

value: sample S7YW15 repeat2


title: V012_Plus02

value: whole blood

value: M


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F4_AD008_indexed

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F5_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F2_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F4_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F2_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F4_AD002_indexed


title: BC4_Plus10

value: day 10

value: uninfected control D

value: ND


title: S7Y3W_L7

value: sample S7Y3W repeat2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F2_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F5_AD002_indexed


title: S7Y3W_L5

value: sample S7Y3W repeat1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F3_AD012_indexed


title: S7YW12_L4

value: sample S7YW12 repeat2


title: S7Y2W_L7

value: sample S7Y2W repeat2


title: V012_Minus01

value: day -1

value: UK


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F3_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F2_AD006_indexed


title: S7Y3W_L8

value: sample S7Y3W repeat3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F1_AD002_indexed

value: male


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F1_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F3_AD008_indexed


title: BC4_Plus04

value: day 4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F2_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F3_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F2_AD002_indexed


title: S7Y2W_L8

value: sample S7Y2W repeat3

value: whole blastocyst


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F12_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F1_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F1_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F5_AD012_indexed


title: BC4_Minus01

value: whole blood


title: BC3_Plus12

value: day 12

value: uninfected control C


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F1_AD007_indexed

value: PAL


title: BC4_Plus12

value: uninfected control D


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F12_AD007_indexed


title: BC4_Plus02

value: day 2

value: ND


title: S7Y2W_L1

value: sample S7Y2W repeat1


title: Ptet-sigB vs Ptet-slucopt hyb4 induced no thiamphenicol, rep 4

city: Braunschweig

first: Rebekka

last: Biedendieck

address: Rebenring 56

department: Institute of Microbiology

country: Germany

institute: Technische Universtität Braunschweig

description: D.S.4 vs D.L.4

hyb_protocol: 300 ng of Cy3-labeled RNA and 300 ng of Cy5-labeled RNA were mixed and fragmented, and hybridized to the microarray at 65 °C for 17 hours using the Agilent Hybridization Chamber according to the manufacturer’s instructions.

scan_protocol: The microarrays were scanned with the help of the Agilent C Scanner (Agilent Technologies, USA) using the software Agilent Scan Controll 8.4.1

data_processing: For feature extraction the software Feature Extraction 10.7.3.1 (Agilent Technologies, USA) was used, data processing was carried out using the Bioconducter – Linear Models for Microarray analysis (LIMMA) package of the R language (http://www.r-project.org).

organism: Clostridioides difficile 630

source_name: C. difficile 630∆erm∆sigB + Ptet-sigB, induced at OD=0.3 with 100 ng/mL ATc, without thiampenicol

label_protocol: RNA samples were labelled with Cy3 (Ptet-sigB) and Cy5 (Ptet-slucopt) using the ULS fluorescent labelling kit (Kreatech, Germany).

growth_protocol: The C. difficile 630∆erm strain (DSM28645) (Hussain, HA, 2005) obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ, Braunschweig, Germany) was used for Clostron mutagenesis to remove sigma factor B. These strains were conjugated with pRPF185-based vectors containing Ptet-sigB and Ptet-slucopt (control). Exponentially growing starter cultures were diluted to an OD=0.05 and these strains were grown anaerobically at 37oC until an OD of approximately 0.3. Strains were grown with- or without 20 µg/mL thiamphenicol and were either induced (100 ng/µl ATc) or not induced for one hour after which cell pellets were collected.

extract_protocol: Bacterial RNA was extracted using the Qiagen RNeasy Kit Mini (Qiagen, Hilden, Germany) according to manufacturer’s instructions with minor modifications. Briefly, pellets from a 45 mL culture were resolved in 200 µl TE buffer and 15 mg/ml lysozyme, incubated for 30 min at room temperature and vigorously mixed every 2 min for 10 sec for enzymatically disruption of cells. Approximately 700 µL of RLT buffer and one spatula of glass beads were added and mixed vigorously for 3 min for mechanical disruption of cells. Samples were centrifuged (3 min, 10.000 rpm) and supernatant was mixed with 470 µL of 100% ethanol. Afterwards, RNA purification was carried out using the Qiagen RNeasy Kit protocol. DNA contaminating the RNA samples was removed using RNase-free DNase I twice (Qiagen, Hilden, Germany). The RNA was further assessed by analysis on the Bionanalyzer 2100 (Agilent, Santa Clara, CA) and RNA 6000 Nano Reagents (Agilent, Santa Clara, CA). The average RNA quality (RIN) was around 9.5 and therefore above the cutoff value of 7.

treatment_protocol: Cell pellets were harvested one hour post induction (or one hour after induction would have been initiated for the uninduced samples) by centrifugating 6000 rpm for 20 minutes at 4oC.

tag: genotype/vairation

tag: induced (+/-) and thiamphenicol (+/-)

value: Induced +, thiamphenicol -

source_name: C. difficile 630∆erm∆sigB + Ptet-slucopt, induced at OD=0.3 with 100 ng/mL ATc, without thiampenicol

tag: genotype/variation

value: {delta}erm{delta}sigB containing Ptet-slucopt (control)


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F1_AD006_indexed


title: BC3_Plus10

value: day 10


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F12_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F12_AD012_indexed


title: BC3_Plus08

value: day 8


title: BC4_Plus08


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F12_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F12_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F12_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F11_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F11_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F11_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F11_AD007_indexed


title: Ptet-sigB vs Ptet-slucopt hyb4 induced no thiamphenicol, rep 2

description: B.S.4 vs B.L.4


title: BC4_Plus06

value: day 6


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F11_AD006_indexed

value: male


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F10_AD012_indexed


title: BC3_Plus06


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F6_AD007_indexed


title: Ptet-sigB vs Ptet-slucopt hyb4 induced no thiamphenicol, rep 3

description: C.S.4 vs C.L.4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F10_AD010_indexed


title: Ptet-sigB vs Ptet-slucopt hyb3 uninduced no thiamphenicol, rep 4

description: D.S.3 vs D.L.3

source_name: C. difficile 630∆erm∆sigB + Ptet-sigB, uninduced at OD=0.3, without thiampenicol

value: Uninduced -, thiampehnicol -

source_name: C. difficile 630∆erm∆sigB + Ptet-slucopt, uninduced at OD=0.3, without thiampenicol


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F10_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F10_AD007_indexed


title: BC3_Minus01

value: day -1


title: BC3_Plus04

value: day 4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_F10_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E9_AD008_indexed


title: Ptet-sigB vs Ptet-slucopt hyb3 uninduced no thiamphenicol, rep 3

description: C.S.3 vs C.L.3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E9_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E9_AD006_indexed


title: BC2_Plus10

value: whole blood

value: uninfected control B


title: Ptet-sigB vs Ptet-slucopt hyb3 uninduced no thiamphenicol, rep 2

description: B.S.3 vs B.L.3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E9_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E8_AD012_indexed


title: Ptet-sigB vs Ptet-slucopt hyb2 induced with thiamphenicol, rep 4

description: D.S.2 vs D.L.2

source_name: C. difficile 630∆erm∆sigB + Ptet-sigB, induced at OD=0.3 with 100 ng/mL ATc, with 20 µg/mL thiampenicol

value: Induced +, thiamphenicol +

source_name: C. difficile 630∆erm∆sigB + Ptet-slucopt, induced at OD=0.3 with 100 ng/mL ATc, with 20 µg/mL thiampenicol


title: BC3_Plus02

value: uninfected control C


title: BC2_Plus06


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E8_AD010_indexed

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E8_AD008_indexed


title: Ptet-sigB vs Ptet-slucopt hyb2 induced with thiamphenicol, rep 3

description: C.S.2 vs C.L.2


title: Ptet-sigB vs Ptet-slucopt hyb2 induced with thiamphenicol, rep 2

description: B.S.2 vs B.L.2


title: BC2_Plus02

value: day 2


title: BC2_Plus04

value: ND


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E9_AD010_indexed


title: Ptet-sigB vs Ptet-slucopt hyb3 uninduced no thiamphenicol, rep 1

description: A.S.3 vs A.L.3


title: Ptet-sigB vs Ptet-slucopt hyb2 induced with thiamphenicol, rep 1

description: A.S.2 vs A.L.2


title: BC2_Plus08


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E8_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E8_AD007_indexed


title: BC2_Plus12

value: day 12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E8_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E8_AD006_indexed


title: Kdm5c+/+ (WT) Ing. SV 3

city: Los Angeles

first: Karen

last: Reue

address: 695 Charles E. Young Drive South

institute: University of California, Los Angeles

data_processing:
RNA-seq alignment was performed with STAR v2.7.2a to the mouse genome GRCm38.97.
The read-count per gene was quantified with STAR and Ensembl Mus_musculus.GRCm38.97 GTF file.
Differential gene analysis was performed with EdgeR (v3.26.8) with trimmed mean of M values (TMM) normalization. Significance was denoted as adjusted p value<0.05 and fold change>1.25.
Genome_build: GRCm38.97
Supplementary_files_format_and_content: RNA-seq_Kdm5c het mice_SV-MAT_CPM.csv, this processed data file contains counts per million (CPM) for all 12 samples for all mapped genes.

source_name: inguinal adipose tissue: stromal vascular fraction

extract_protocol:
Inguinal adipose tissue from two mice was pooled and minced in digestion buffer (100 mM HEPES, 120 mM NaCl, 50 mM KCl, 5 mM glucose, 1 mM CaCl2, 1.5% BSA) containing 20 mg/ml collagenase I (Sigma-Aldrich, St. Louis, MO). After 1h digestion at 37ºC , the sample was filtered through a 70 µm mesh and debris was pelleted at 50 x g. The supernatant and top fat layer were spun at 200 x g to separate the stromal vascular (pellet) and mature adipocyte (top layer) fractions. RNA was isolated from the cellular fractions with Qiagen RNeasy mini kit based on manufacturer's instructions.
Strand-specific RNA-seq libraries were constructed with the Universal plus mRNA-Seq Kit (NuGEN Technologies).

value: inguinal adipose tissue

tag: cell type

value: stromal vascular

tag: genotype

value: Kdm5c+/+ (WT)

value: female


title: Ptet-sigB vs Ptet-slucopt hyb1 uninduced with thiamphenicol, rep 3

description: C.S.1 vs C.L.1

source_name: C. difficile 630∆erm∆sigB + Ptet-sigB, uninduced at OD=0.3, with 20 µg/mL thiampenicol

value: Uninduced -, thiamphenicol +

source_name: C. difficile 630∆erm∆sigB + Ptet-slucopt, uninduced at OD=0.3, with 20 µg/mL thiampenicol

value: {delta}erm{delta}sigB containing Ptet-slucopt (control)


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E7_AD006_indexed

value: male


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E7_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E5_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E7_AD010_indexed


title: BC2_Minus01

value: day -1


title: Kdm5c+/+ (WT) Ing. SV 2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E7_AD007_indexed


title: BC1_Plus12

value: uninfected control A


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E7_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E7_AD008_indexed


title: BC1_Plus10

value: whole blood

value: day 10


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E6_AD012_indexed


title: BC1_Plus06

value: day 6


title: Kdm5c+/+ (WT) Ing. SV 1


title: Ptet-sigB vs Ptet-slucopt hyb1 uninduced with thiamphenicol, rep 1

description: A.S.1 vs A.L.1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E6_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E6_AD010_indexed


title: Ptet-sigB vs Ptet-slucopt hyb1 uninduced with thiamphenicol, rep 2

description: B.S.1 vs B.L.1


title: BC1_Plus04

value: day 4


title: BC1_Plus02


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E6_AD006_indexed

value: PAL


title: Kdm5c+/– Ing. SV 2


title: Kdm5c+/– Ing. SV 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E6_AD001_indexed


title: BC1_Plus08

value: day 8


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E5_AD010_indexed


title: Kdm5c+/– Ing. SV 3


title: 60-DNH03152018-siRNA5-GRN [60_quant]

first: Andreas

last: Zembrzycki

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Transcript level quantification was generated using Salmon (v0.8.2), and an index was built using cDNA sequences from the human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-92/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna. all.fa.gz).
Gene abundance estimates were created with Tximport (v1.8.0) using a tx2gene file containing Ensembl transcript IDs and their associated HGNC symbols. Samples were assigned to one of fifteen possible groups based on treatment type and day in vitro (DIV) (Untreated_DIV7, GRN_siRNA_DIV7, Control_siRNA_DIV7, etc.), and a DESeqDataSet was constructed using a design formula of ~ group in DESeq2
Genes with count means of less than 5 were removed prior to principal component analysis and pairwise comparisons. Differential expression was determined using the DESeq2 default of a Benjamini-Hochberg adjusted p-value cutoff of 0.10.
Genome_build: GRCh38 (ftp://ftp.ensembl.org/pub/release-92/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna. all.fa.gz
Supplementary_files_format_and_content: Matrix of normalized counts for each gene from DESeq2.

molecule: polyA RNA

source_name: iCell® GlutaNeurons_GRN_21 days in vitro

growth_protocol: iCell® GlutaNeurons (GNs) (FUJIFILM Cellular Dynamics Inc., FCDI) are human cells differentiated from a master bank of stably induced pluripotent stem (iPS) cells from normal donors (stemcell.com). The iPS cell lines were generated from human peripheral blood through ectopic expression of reprogramming factors (i.e. Oct4, Sox2, Nanog, Lin28, Klf4, L-Myc, SV40LT) by episomal transfection. The iPS cell clones were then engineered using nuclease-mediated methodologies to exhibit neomycin resistance under the control of a neuronal-specific promotor. GNs were cultured according to the manufacturer’s protocol. Clear, flat-bottom 96-well plates (Corning) were coated with 0.01% poly-L-ornithine (PLO, Sigma-Aldrich) for a minimum of 1 h at room temperature. After three washes with PBS (ThermoFisher Scientific), the wells were coated with 0.028 mg/mL Growth Factor Reduced Matrigel (Corning) for at least 1 h in a 37°C incubator. Cells were thawed for 2 min in a 37°C water bath, then slowly equilibrated by the dropwise addition of room-temperature complete medium [BrainPhys Neuronal Medium (STEMCELL Technologies) containing iCell® supplements (CDI), N-2 Supplement (ThermoFisher Scientific), laminin (1 µg/mL, Sigma-Aldrich), and penicillin-streptomycin (ThermoFisher Scientific)]. The cells were then plated and allowed to recover overnight at 37°C.

extract_protocol:
Plates containing GNs were washed with PBS and then frozen at -80˚C until they were thawed for RNA purification using the RNEasy UCP Micro Kit (Qiagen #73934). Four independent experiments were performed (two using lot 100839 and two using lot 101442), and there were 5-6 technical replicate wells per condition per experiment. The lysates from technical replicate wells were combined prior to RNA purification in order to yield sufficient quantities of RNA for RNA-Seq.
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module, and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

treatment_protocol: The Accell Human GRN siRNA SMARTpool (E-009285-00-0050) and Accell Non-targeting Pool (D-001910-10-50) were purchased from Dharmacon. The target sequences of the GRN SMARTpool are GUGCUGUGUUAUGGUCGAU, GAGAUGUCCCCUGUGAUAA, UUGUCCAGCUCGGUCAUGU, and GUGCGUUUCAAUAAAGUUU. The target sequences of the Non-targeting Pool are UGGUUUACAUGUCGACUAA, UGGUUUACAUGUUUUCUGA, UGGUUUACAUGUUUUCCUA, and UGGUUUACAUGUUGUGUGA. The siRNA was reconstituted to 100 µM with 1X Dharmacon siRNA Buffer (B-002000-UB-100) and added directly to the GN media immediately before use. All experiments using siRNA were done with 70,000 GNs per well in 96-well plates. The first 50% media change on day in vitro (DIV) 3 was done with 2X concentrated siRNA in order to achieve the desired concentration of siRNA in each well. All subsequent 50% media changes were done with freshly added 1X siRNA to maintain the desired siRNA concentration during the course of the culture.

tag: cell line

value: iCell GlutaNeurons

value: commercially-available IPSC-derived human neuron cell line

tag: sirna (nt = non-targeting, grn = progranulin)

value: GRN

tag: div (days in vitro)

tag: experiment id

tag: lot number


title: 59-DNH03152018-siRNA5-NTC [59_quant]

source_name: iCell® GlutaNeurons_NT_21 days in vitro

value: NT


title: 58-DNH03152018-siRNA5-Untreated [58_quant]

source_name: iCell® GlutaNeurons_Untreated_21 days in vitro

value: Untreated


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E5_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E7_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E4_AD006_indexed


title: Ptet-sigB vs Ptet-slucopt hyb4 induced no thiamphenicol, rep 1

description: A.S.4 vs A.L.4

value: Induced +, thiamphenicol -


title: Kdm5c+/+ (WT) Ing. MAT 3

source_name: inguinal adipose tissue: mature adipocyte fraction

tag: tissue

value: inguinal adipose tissue

value: mature adipocyte

value: Kdm5c+/+ (WT)

value: female


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E5_AD008_indexed

source_name: C57BL/6J Male P56 Mouse Brain

value: male

tag: age


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E5_AD006_indexed


title: Kdm5c+/+ (WT) Ing. MAT 2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E4_AD010_indexed


title: 55-DNH03152018-siRNA4-Untreated [55_quant]

source_name: iCell® GlutaNeurons_Untreated_17 days in vitro


title: 57-DNH03152018-siRNA4-GRN [57_quant]

source_name: iCell® GlutaNeurons_GRN_17 days in vitro


title: 54-DNH03152018-siRNA3-GRN [54_quant]

source_name: iCell® GlutaNeurons_GRN_14 days in vitro


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E3_AD012_indexed


title: BC1_Minus01

source_name: whole blood

value: whole blood

tag: day

value: day -1

tag: individual

value: uninfected control A

tag: gender

value: ND

tag: country


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E4_AD008_indexed

tag: brain region

value: PAL

tag: Sex

tag: strain


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E3_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E3_AD010_indexed


title: 56-DNH03152018-siRNA4-NTC [56_quant]

source_name: iCell® GlutaNeurons_NT_17 days in vitro


title: Kdm5c+/– Ing. MAT 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E5_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E4_AD007_indexed


title: Kdm5c+/– Ing. MAT 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E4_AD002_indexed


title: 51-DNH03132018-siRNA5-GRN [51_quant]


title: 53-DNH03152018-siRNA3-NTC [53_quant]

source_name: iCell® GlutaNeurons_NT_14 days in vitro


title: 52-DNH03152018-siRNA3-Untreated [52_quant]

source_name: iCell® GlutaNeurons_Untreated_14 days in vitro


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E2_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E4_AD001_indexed


title: Kdm5c+/– Ing. MAT 2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E3_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E2_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E2_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E2_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E2_AD010_indexed


title: eCG48h2

city: Sainte-Anne-de-Bellevue

first: Raj

last: Duggavathi

state: Quebec

address: 21111 Rue Lakeshore

department: Animal Science

country: Canada

institute: McGill University

data_processing:
Sequenced reads were assessed for quality using FastQC v 0.11.5.
Picard was used to split the paired end BAM files into 2 fastq files.
A splice aware aligner, STAR, was used for read alignment and to produce a counts matrix.
Read counts were uploaded to Network Analyst for differential expression analysis.
Differential transcript analysis was carried out using Kallisto sleuth.
Genome_build: mm10
Supplementary_files_format_and_content: eCG48h_vs_eCG0h_Counts.txt: Text file containing read counts.

source_name: Granulosa cells

extract_protocol:
Granulosa cells were isolated from the ovaries using follicular puncture. Total RNA was extracted using the Direct-Zol RNA MiniPrep Isolation Kit (Cedarlane).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were either left untreated (eCG0h) or treated with eCG (FSH) for 48 hours (eCG48h).

value: post natal day 21

value: Granulosa cells

tag: treatment

value: eCG (FSH) for 48h


title: eCG48h3

tag: cell type


title: eCG0h3

value: Untreated (0h)


title: eCG48h1


title: 50-DNH03132018-siRNA5-NTC [50_quant]

value: iCell GlutaNeurons

value: commercially-available IPSC-derived human neuron cell line

value: NT


title: eCG0h1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E1_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E1_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E2_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E2_AD002_indexed


title: 49-DNH03132018-siRNA5-Untreated [49_quant]

value: Untreated


title: Uninfected aGM-CSF treated - lung #20

city: London

first: Anne

last: OGarra

address: 1 Midland Road

institute: Francis Crick Insititue

description:
processed data header: TEI448A40
GEO_lung_DESEQ2_normalised_values.txt.gz

data_processing:
Raw counts were processed using the bioconductor package DESeq2 v1.12.4 in R v3.3.1, and normalized using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalized log2 gene expression values.
Genome_build: Ensembl GRCm38 (release 86)
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.

source_name: Lung

extract_protocol:
Blood was collected in Tempus reagent (Life Technologies) at 1:2 ratio. Total RNA was extracted using the Tempus™ Spin RNA isolation kit (Thermo Fisher Scientific). Globin RNA was depleted from total RNA (1.5–2 µg) using the GLOBINclear™-Mouse/Rat Globin mRNA removal kit (Thermo Fisher Scientific). Lungs were collected in TRI-Reagent (Sigma-Aldrich). Total RNA was extracted using the RiboPure™ Kit (Ambion).
KAPA mRNA polyA HyperPrep

treatment_protocol: C57Bl/6 female mice were infected with Mycobacterium tuberculosis strain HN878 and treated with anti-GM-CSF monoconal antibody (aGM-CSF) or isotype control (iso) the day prior to infection and then twice a week during the course of the experiment. Uninfected mice were also treated and used as uninfected controls. Three weeks post-infection, whole blood and lungs from each individual mouse were harvested and processed for RNA-sequencing.

value: Lung

tag: infection

value: Control

tag: stimulation

value: aGMCSF


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E2_AD001_indexed

value: male


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E1_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E12_AD012_indexed


title: 48-DNH03152018-siRNA2-GRN [48_quant]

source_name: iCell® GlutaNeurons_GRN_10 days in vitro

tag: cell line

tag: sirna (nt = non-targeting, grn = progranulin)

value: GRN


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E1_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E1_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E12_AD010_indexed


title: Uninfected aGM-CSF treated - lung #18

description:
processed data header: TEI448A38
GEO_lung_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E12_AD007_indexed


title: 47-DNH03152018-siRNA2-NTC [47_quant]

source_name: iCell® GlutaNeurons_NT_10 days in vitro

tag: div (days in vitro)

tag: experiment id


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E12_AD006_indexed


title: 46-DNH03152018-siRNA2-Untreated [46_quant]

source_name: iCell® GlutaNeurons_Untreated_10 days in vitro

tag: lot number


title: 45-DNH03152018-siRNA1-GRN [45_quant]

source_name: iCell® GlutaNeurons_GRN_7 days in vitro


title: eCG0h2

tag: age


title: Uninfected aGM-CSF treated - lung #19

description:
processed data header: TEI448A39
GEO_lung_DESEQ2_normalised_values.txt.gz

tag: tissue


title: 44-DNH03152018-siRNA1-NTC [44_quant]

source_name: iCell® GlutaNeurons_NT_7 days in vitro


title: Uninfected aGM-CSF treated - lung #17

description:
processed data header: TEI448A37
GEO_lung_DESEQ2_normalised_values.txt.gz


title: 42-DNH03132018-siRNA4-GRN [42_quant]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E11_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E11_AD007_indexed


title: 43-DNH03152018-siRNA1-Untreated [43_quant]

source_name: iCell® GlutaNeurons_Untreated_7 days in vitro


title: Uninfected aGM-CSF treated - lung #16

description:
processed data header: TEI448A36
GEO_lung_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E11_AD002_indexed


title: 41-DNH03132018-siRNA4-NTC [41_quant]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E11_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E10_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E10_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E11_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E10_AD004_indexed


title: Uninfected control - lung #13

description:
processed data header: TEI448A33
GEO_lung_DESEQ2_normalised_values.txt.gz

value: Iso


title: 39-DNH03092018-siRNA5-GRN [39_quant]

source_name: iCell® GlutaNeurons_GRN_21 days in vitro


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E11_AD010_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 38-DNH03092018-siRNA5-NTC [38_quant]

source_name: iCell® GlutaNeurons_NT_21 days in vitro


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D9_AD010_indexed


title: Uninfected control - lung #12

description:
processed data header: TEI448A32
GEO_lung_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_E11_AD008_indexed


title: Uninfected control - lung #11

description:
processed data header: TEI448A31
GEO_lung_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D9_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D9_AD006_indexed


title: 37-DNH03092018-siRNA5-Untreated [37_quant]

source_name: iCell® GlutaNeurons_Untreated_21 days in vitro


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D8_AD012_indexed


title: HN878-infected aGM-CSF treated - lung #10

description:
processed data header: TEI448A30
GEO_lung_DESEQ2_normalised_values.txt.gz

value: Infect


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D8_AD010_indexed


title: Uninfected control - lung #14

description:
processed data header: TEI448A34
GEO_lung_DESEQ2_normalised_values.txt.gz


title: 40-DNH03132018-siRNA4-Untreated [40_quant]

source_name: iCell® GlutaNeurons_Untreated_17 days in vitro


title: 36-DNH03132018-siRNA3-GRN [36_quant]

source_name: iCell® GlutaNeurons_GRN_14 days in vitro


title: HN878-infected aGM-CSF treated - lung #9

description:
processed data header: TEI448A29
GEO_lung_DESEQ2_normalised_values.txt.gz


title: Uninfected control - lung #15

description:
processed data header: TEI448A35
GEO_lung_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D8_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D8_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D7_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D8_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D7_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D7_AD008_indexed


title: 35-DNH03132018-siRNA3-NTC [35_quant]


title: 34-DNH03132018-siRNA3-Untreated [34_quant]


title: 33-DNH03132018-siRNA2-GRN [33_quant]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D9_AD004_indexed


title: Ptet-sigB vs Ptet-slucopt hyb1 uninduced with thiamphenicol, rep 4

description: D.S.1 vs D.L.1

source_name: C. difficile 630∆erm∆sigB + Ptet-sigB, uninduced at OD=0.3, with 20 µg/mL thiampenicol

tag: genotype/vairation

tag: induced (+/-) and thiamphenicol (+/-)

value: Uninduced -, thiamphenicol +

source_name: C. difficile 630∆erm∆sigB + Ptet-slucopt, uninduced at OD=0.3, with 20 µg/mL thiampenicol

tag: genotype/variation

value: {delta}erm{delta}sigB containing Ptet-slucopt (control)


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D7_AD006_indexed

tag: brain region

value: PAL


title: 32-DNH03132018-siRNA2-NTC [32_quant]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D7_AD002_indexed

tag: Sex


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D7_AD004_indexed

tag: strain


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D6_AD012_indexed


title: 31-DNH03132018-siRNA2-Untreated [31_quant]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D6_AD008_indexed


title: HN878-infected aGM-CSF treated - lung #7

description:
processed data header: TEI448A27
GEO_lung_DESEQ2_normalised_values.txt.gz


title: HN878-infected control - lung #5

description:
processed data header: TEI448A25
GEO_lung_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D6_AD010_indexed


title: 30-DNH03132018-siRNA1-GRN [30_quant]


title: HN878-infected control - lung #4

description:
processed data header: TEI448A24
GEO_lung_DESEQ2_normalised_values.txt.gz


title: HN878-infected control - lung #2

description:
processed data header: TEI448A22
GEO_lung_DESEQ2_normalised_values.txt.gz


title: 29-DNH03132018-siRNA1-NTC [29_quant]


title: HN878-infected aGM-CSF treated - lung #8

description:
processed data header: TEI448A28
GEO_lung_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D6_AD004_indexed


title: HN878-infected control - lung #1

description:
processed data header: TEI448A21
GEO_lung_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D6_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D6_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D5_AD012_indexed


title: HN878-infected aGM-CSF treated - lung #6

description:
processed data header: TEI448A26
GEO_lung_DESEQ2_normalised_values.txt.gz


title: 28-DNH03132018-siRNA1-Untreated [28_quant]


title: 27-DNH03092018-siRNA4-GRN [27_quant]

source_name: iCell® GlutaNeurons_GRN_17 days in vitro


title: Uninfected aGM-CSF treated - blood #20

description:
processed data header: TEI448A20
GEO_blood_DESEQ2_normalised_values.txt.gz

source_name: Blood

value: Blood


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D5_AD010_indexed


title: Uninfected aGM-CSF treated - blood #19

description:
processed data header: TEI448A19
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D4_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D5_AD006_indexed


title: 26-DNH03092018-siRNA4-NTC [26_quant]

source_name: iCell® GlutaNeurons_NT_17 days in vitro


title: Uninfected aGM-CSF treated - blood #18

description:
processed data header: TEI448A18
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D4_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D4_AD006_indexed


title: 25-DNH03092018-siRNA4-Untreated [25_quant]


title: Uninfected aGM-CSF treated - blood #17

description:
processed data header: TEI448A17
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D4_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D4_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D4_AD001_indexed


title: Uninfected aGM-CSF treated - blood #16

description:
processed data header: TEI448A16
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D3_AD012_indexed


title: 24-DNH03092018-siRNA3-GRN [24_quant]


title: Uninfected control - blood #15

description:
processed data header: TEI448A15
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D4_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D3_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D5_AD007_indexed


title: Uninfected control - blood #14

description:
processed data header: TEI448A14
GEO_blood_DESEQ2_normalised_values.txt.gz


title: Uninfected control - blood #13

description:
processed data header: TEI448A13
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D3_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D3_AD006_indexed


title: 23-DNH03092018-siRNA3-NTC [23_quant]

source_name: iCell® GlutaNeurons_NT_14 days in vitro


title: 22-DNH03092018-siRNA3-Untreated [22_quant]

source_name: iCell® GlutaNeurons_Untreated_14 days in vitro


title: Uninfected control - blood #12

description:
processed data header: TEI448A12
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 21-DNH03092018-siRNA2-GRN [21_quant]

source_name: iCell® GlutaNeurons_GRN_10 days in vitro


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D3_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D2_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D2_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D2_AD012_indexed


title: 19-DNH03092018-siRNA2-Untreated [19_quant]

source_name: iCell® GlutaNeurons_Untreated_10 days in vitro


title: 20-DNH03092018-siRNA2-NTC [20_quant]

source_name: iCell® GlutaNeurons_NT_10 days in vitro


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D2_AD006_indexed


title: 18-DNH03092018-siRNA1-GRN [18_quant]

source_name: iCell® GlutaNeurons_GRN_7 days in vitro


title: HN878-infected aGM-CSF treated - blood #10

description:
processed data header: TEI448A10
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D2_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D2_AD002_indexed


title: 16-DNH03092018-siRNA1-Untreated [16_quant]

source_name: iCell® GlutaNeurons_Untreated_7 days in vitro


title: HN878-infected aGM-CSF treated - blood #9

description:
processed data header: TEI448A9
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D1_AD012_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: HN878-infected aGM-CSF treated - blood #8

description:
processed data header: TEI448A8
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D1_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D3_AD007_indexed


title: Kdm5c+/+ (WT) Ing. MAT 1

source_name: inguinal adipose tissue: mature adipocyte fraction

value: inguinal adipose tissue

value: mature adipocyte

tag: genotype

value: Kdm5c+/+ (WT)

value: female


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D1_AD006_indexed


title: 15-DNH03072018-siRNA5-GRN [15_quant]

source_name: iCell® GlutaNeurons_GRN_21 days in vitro

value: iCell GlutaNeurons

tag: cell type

value: commercially-available IPSC-derived human neuron cell line


title: Uninfected control - blood #11

description:
processed data header: TEI448A11
GEO_blood_DESEQ2_normalised_values.txt.gz

tag: infection


title: HN878-infected aGM-CSF treated - blood #7

description:
processed data header: TEI448A7
GEO_blood_DESEQ2_normalised_values.txt.gz

tag: stimulation


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D12_AD012_indexed


title: 14-DNH03072018-siRNA5-NTC [14_quant]

source_name: iCell® GlutaNeurons_NT_21 days in vitro

tag: cell line

value: NT


title: HN878-infected aGM-CSF treated - blood #6

description:
processed data header: TEI448A6
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D12_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D11_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D12_AD004_indexed


title: 13-DNH03072018-siRNA5-Untreated [13_quant]

source_name: iCell® GlutaNeurons_Untreated_21 days in vitro

tag: sirna (nt = non-targeting, grn = progranulin)

value: Untreated


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D11_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D1_AD004_indexed


title: HN878-infected control - blood #5

description:
processed data header: TEI448A5
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 17-DNH03092018-siRNA1-NTC [17_quant]

source_name: iCell® GlutaNeurons_NT_7 days in vitro

tag: div (days in vitro)


title: 12-DNH03072018-siRNA4-GRN [12_quant]

tag: experiment id


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D11_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D12_AD006_indexed


title: HN878-infected control - blood #2

description:
processed data header: TEI448A2
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 10-DNH03072018-siRNA4-Untreated [10_quant]

source_name: iCell® GlutaNeurons_Untreated_17 days in vitro

tag: lot number


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D11_AD004_indexed

tag: age


title: HN878-infected control - blood #4

description:
processed data header: TEI448A4
GEO_blood_DESEQ2_normalised_values.txt.gz

tag: tissue


title: HN878-infected control - blood #1

description:
processed data header: TEI448A1
GEO_blood_DESEQ2_normalised_values.txt.gz


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D11_AD001_indexed


title: 09-DNH03072018-siRNA3-GRN [09_quant]

source_name: iCell® GlutaNeurons_GRN_14 days in vitro


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D1_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D10_AD004_indexed


title: 08-DNH03072018-siRNA3-NTC [08_quant]


title: SEP3_rep4

city: Grenoble

first: Jérémy

last: LUCAS

address: 17 avenue des Martyrs

country: France

institute: CNRS

data_processing:
library strategy: sequential DNA affinity purification sequencing [DAP-seq]
Image data generated by Miseq is transferred into raw reads through base calling software (BCL2FASTQ v2.17)
Alignement to genome is done by Bowtie2 with parameters:
poor quality and multimapped reads are filtered out using samtools
peak-calling is done by MACS2 with parameters
Peaks called where Control read coverage is too high are removed from analysis
Genome_build: TAIR10
Supplementary_files_format_and_content: NarrowPeaks representing peaks positions and p-values
Supplementary_files_format_and_content: Bedgraphs are whole genome profile of reads

organism: Arabidopsis thaliana

growth_protocol: 2-weeks old seedlings of Arabidopsis thaliana

extract_protocol:
Recombiant proteins were produced by TnT in vitro transcription translation system from Promega
Genomic DNA was extracted by chloroform isoamyl alcohol dna extraction protocol
Libraries were contructed using Truseq Illumina kits
Illumina TruSeq adaptors with single end index

value: 2-weeks old seedlings

tag: primary protein epitope tags

tag: molecule subtype

value: PCR amplified genomic DNA


title: SEP3_rep3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D11_AD008_indexed

value: male


title: 11-DNH03072018-siRNA4-NTC [11_quant]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C9_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C9_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D10_AD010_indexed


title: 07-DNH03072018-siRNA3-Untreated [07_quant]


title: SEP3_rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C8_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C8_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C9_AD007_indexed


title: SEP3_rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C8_AD008_indexed


title: SEP3∆tet-AG_rep2

tag: secondary protein epitope tags


title: 05-DNH03072018-siRNA2-NTC [05_quant]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C7_AD012_indexed

tag: brain region


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C9_AD008_indexed

tag: Sex


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C7_AD008_indexed

tag: strain


title: SEP3AG_rep3


title: 04-DNH03072018-siRNA2-Untreated [04_quant]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D10_AD012_indexed


title: 03-DNH03072018-siRNA1-GRN [03_quant]

value: GRN


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C7_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_D10_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C7_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C7_AD004_indexed


title: 02-DNH03072018-siRNA1-NTC [02_quant]


title: 06-DNH03072018-siRNA2-GRN [06_quant]


title: SEP3AG_rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C7_AD001_indexed


title: 01-DNH03072018-siRNA1-Untreated [01_quant]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C6_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C6_AD010_indexed


title: SEP3AG_rep1


title: Vehicle-only control (DMSO) iAEC2s

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

description: BU3 NGST KRASG12D alveolospheres DMSO Control

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to GRCh38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Genome_build: GRCh38
Supplementary_files_format_and_content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: BU3 NGST KRAS G12D iPSC line

growth_protocol: This protocol is based on previously described approaches detailed in Jacob et al. 2017, 2019.

extract_protocol:
single cells were captured for library prepration and sequencing using the 10X Chromium platform, according to the manufacturer's instructions
10X chromium chemistry version 3

treatment_protocol: Add 1ug/ml of Dox v DMSO in culture media every 48hrs

value: induced AEC2s (iAEC2s)

tag: developmental stage

value: NKX2-1+ distal lung epithelium; Day 127, P7

tag: culture media

value: CK+DCI+ DMSO

tag: isolation method

value: cultured


title: SEP3∆tet-AG_rep1


title: Dox exposed iAEC2s

description: BU3 NGST KRASG12D alveolospheres +Dox

value: CK+DCI+ 1ug/ml Dox [C=CHIR99021; K=KGF;  DCI=dexamethasone, cAMP, IBMX]


title: Input DNA

source_name: Input DNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C6_AD004_indexed

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C5_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C5_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C5_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C4_AD012_indexed


title: d15_RUES2

city: Rozzano

first: Simone

last: Serio

state: Milano

address: Via Alessandro Manzoni, 56

department: Cardiovascular Medicine

country: Italy

institute: Humanitas Research Hospital

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using HISAT2 (PMID: 31375807).
BAM files with aligned paired-end reads were splitted into two strand-specific BAM files using SAMtools (PMID: 19505943). The properly paired reads originating from each strand were selected using SAM Flags 99 and 147 for one strand, 83 and 163 for the other strand. Forward and reverse strand was assigned in according of dUTP method used for sequencing. The transcript assembly was performed, on each strand specific BAM file, using StringTie (PMID: 25690850) with parameters -s 2 -g 100 for lncRNA identification. The potential transcripts identified were unified using StringTie –merge with parameters -T 0 -F 0. Transcripts with FPKM <0.1 were subsequently excluded using FPKM_count.py module from RSeQC software (PMID: 22743226).
Slncky (PMID: 26838501) was used to predict the orthologous transcripts in human samples.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigWig were generated using bamCoverage (PMID: 24799436).

source_name: Embryonic stem cell

growth_protocol: Cardiomyocytes were obtained from iPSC through directed differentiation following a chemically-defined serum-free protocol based on sequential modulation of the Wnt pathway in RPMI-B27 medium. Specifically, 85-90% confluent iPSC were subjected to the treatment with CHIR99021 (12uM) for 24 hours and subsequently exposed to the Wnt inhibitor IWR-1 (5uM) for 3 days in RPMI-B27 medium. At d10 of induction, medium is supplemented with insulin. Contracting cardiomyocytes appear around d7 and harvested for the sequencing at d15.

extract_protocol:
RNA was isolated using Trizol reagent according to the manufacture’s protocol.
DNase I-treated RNA analysed on the LabChip GXT (PerkinElmer) shown an RNA integrity number (RIN) greater than 7. Indexed sequencing libraries were generated using TruSeq® Stranded Total RNA LT with Ribo-Zero™ Human/Mouse/Rat (Illumina) following manufacture’s instruction. Electrophoresis of the libraries on a LabChip GXT instrument showed average library size of 311bp. Paired-end multiplexed libraries were sequenced using NextSeq500 instrument. 140 million reads for each sample were obtained.
Paired end sequence reads (75-bp in length) were generated on an Illumina NextSeq 500 (Samples 1 to 2)

tag: cell type

value: human embryonic stem cell (ESC) line

tag: time point

value: Day 15 of differentiation


title: HOM HUVEC

city: Belfast

first: Guilherme

last: Costa

address: 97 Lisburn Road

institute: Queen's University of Belfast

data_processing:
The stranded paired-end RNA-seq reads were quality assessed using FastQC (v0.11.3) and FastQ Screen (v0.9.2).
The raw reads were processed with BBDuk (part of the BBMap suite; v36.32) to trim the adapter sequences and low-quality bases.
Processed reads from the human-derived samples were mapped against the reference assembly hg38 using STAR (v2.7.2b) with “–quantMode GeneCounts” option to obtain read count for each gene annotated in GENCODE v32, whereas reads from the zebrafish-derived samples were mapped against the reference assembly GRCz11 and gene annotation from Ensembl v99.
Genome_build: hg38 (HUVEC samples); GRCz11 (zebrafish samples)
Supplementary_files_format_and_content: bigWig files include RPKM values for each sample

source_name: HUVECs

growth_protocol: HUVECs were cultured in complete ECGM2 in gelatin-coated dishes. Zebrafish were maintained and bred according to standard conditions.

extract_protocol:
Zebrafish – zygote stage embryos were injected with sgRNA-Cas9 ribonucleoproteins and grown to adult stages. Germline transmission of targeted deletion was performed by PCR and 1 desired founder animal (F0) was identified. The F0 was outcrossed to Wt animals to generate F1 heterozygous animals. F1 animals were incrossed and the resulting offspring was grown 28 hours stage embryos. Heads were dissected for PCR-genotyping and the trunks of 2 WT and 2 HOM embryos were processed for RNA extraction.
RNA-seq library prepared with TruSeq Stranded mRNA (Illumina)

treatment_protocol: HUVECs – cells were transfected with sgRNA-Cas9 ribonucleoproteins and a GFP expressing plasmid. GFP+ cells were harvested 48 hours later and single cell FACS sorted in 96 well plates.  After amplification, cells were PCR genotyped and RNA was extracted from 1 non-edited exemplar clone (WT) and 1 exemplar clone with bi-allelic targeted deletion.

value: Umbilical vein vascular wall

tag: genotype

value: Homozygous RAB13 3' UTR mutant

tag: passage


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C5_AD004_indexed


title: WT HUVEC

value: Wild type


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C5_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C4_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C4_AD010_indexed


title: PBS control, sample EM8 [miRNA]

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

description:
conditioned_Day5_media vs PBS_control - tRNA results.txt
conditioned_Day5_media vs PBS_control - miRNA results.txt

data_processing:
Filter and adaptor trim using fastX_toolkit and cutadapt (small RNA) and trim_galore (total RNA)
Filtered smallRNA reads mapped to tRNAs from GtRNAdb and mature miRNA transcriptome from miRBase v22 using bowtie (small RNA)
Differential expression analysis in R using DESeq2 (small RNA)
Filtered total RNA reads mapped human genome GRCh37/hg19 (total RNA). We do not have processed data for the total RNA samples since very low numbers of reads mapped to annotated genes.
Quantification of genes from Gencode gene annotation v29 detected using featureCounts (total RNA)
Genome_build: GRCh37/hg19 and mirBase mature v22
Supplementary_files_format_and_content: txt files with DESeq2 output and normalized expression values for tRNA and miRNA

source_name: spent culture medium from human in vitro fertilized blastocysts

growth_protocol: Ovarian stimulation, oocyte retrieval and fertilization using IVF or ICIS were performed according to standard procedures. Embryos were cultured in SAGE 1 step medium in individual wells until day 5.  Control media from the same batch was placed alongside the embryo. The spent culture medium and corresponding control were collected individually on day 5 from all embryos that were selected for transfer or cryopreservation and stored in individually labelled vials at -80 C until analysis.

extract_protocol:
RNA was extracted using the Qiagen miRNeasy serum/plasma advanced kit
Total RNA sequencing libraries were prepared using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) and for small RNA sequencing the QIAseq RNA Library Prep kit (Qiagen) was used

tag: sample type

value: PBS control


title: PBS control, sample EM9 [RNA]


title: PBS control, sample EM9 [miRNA]


title: Media control, sample EM7 [RNA]

value: Media control


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C4_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C4_AD006_indexed


title: PBS control, sample EM8 [RNA]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C4_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C6_AD002_indexed


title: Media control, sample EM7 [miRNA]

description:
conditioned_Day5_media vs Media_control - tRNA results.txt
conditioned_Day5_media vs Media_control - miRNA results.txt


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C3_AD012_indexed


title: Media control, sample EM6 [RNA]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C3_AD008_indexed


title: Media control, sample EM5 [miRNA]


title: Media control, sample EM5 [RNA]


title: Media control, sample EM11 [RNA]


title: d15_hiPSC

source_name: hiPSC-derived cardiomyocyte

value: Induced pluripotent stem cell derived cardiomyocyte


title: Media control, sample EM6 [miRNA]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C3_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C3_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C3_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C3_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C2_AD010_indexed


title: conditioned Day5 media, sample EM3 [miRNA]

description:
conditioned_Day5_media vs PBS_control - tRNA results.txt
conditioned_Day5_media vs Media_control - tRNA results.txt
conditioned_Day5_media vs PBS_control - miRNA results.txt
conditioned_Day5_media vs Media_control - miRNA results.txt

value: spent culture medium conditioned Day5 media


title: conditioned Day5 media, sample EM4 [RNA]


title: conditioned Day5 media, sample EM4 [miRNA]


title: conditioned Day5 media, sample EM3 [RNA]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C2_AD007_indexed

value: male


title: conditioned Day5 media, sample EM2 [miRNA]


title: conditioned Day5 media, sample EM1 [miRNA]


title: conditioned Day5 media, sample EM2 [RNA]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C1_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C1_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C1_AD007_indexed


title: L540_RP2_100nM_6h

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using STAR v2.5 (PMID: 23104886)
Transcript abundance was obtained using the internally  developed RNA read counter of STAR v2.5 (PMID: 23104886)
Differentially expressed genes were identified using R and edgeR (PMID: 19910308)
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigWig were generated using bam2wig.py module in RSeQC v2.6.3 (PMID: 22743226)

source_name: L-540 cell line

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen), and treated with DNase according to the manufacture’s protocol.
Total RNA quality was evaluated using the Agilent Bioanalyzer and the RNA Nano kit: only samples with RIN score ≥ 8 were processed further. RNA-seq libraries were sequenced using the TruSeq mRNA stranded kit (Illumina) according manufacturer’s indications. Briefly, the polyA fraction was isolated starting form 300 ng of high quality total RNA. All libraries were quantified using Qubit (Thermo Fisher Scientific Logo) and Bioanalyzer 2100 (Agilent) instruments. According to index compatibility, the libraries were grouped into pools at a concentration of 8 pM to obtain ~15 million clusters for each sample, for single run.
Single end sequence reads (75-bp in length) were generated on an Illumina NextSeq 500  (Sample 1 to 24)

treatment_protocol: L-540 and KM-H2 Hodgkin lymphoma cell lines were treated with the novel PI3Kδ/γ inhibitor RP6530 (100nM and 10uM) for 6 hours and RP6530 (10uM) for 24 hours

tag: cell line

value: Hodgkin lymphoma cell line

tag: treatment group

value: RP6530 100nM Treated 6 hr

tag: sequencing library pool


title: conditioned Day5 media, sample EM1 [RNA]


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C1_AD008_indexed

tag: age


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C2_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C1_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C1_AD006_indexed


title: L540_RP1_100nM_6h


title: L540_C2_100nM_6h

value: vehicle-treated Control 6 hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C10_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C1_AD001_indexed


title: HUVECs, COMP 5

first: Alexandre

last: Gingras

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

data_processing:
Data was processed using the systempipeR workflow.
RNAseq reads were aligned to has GRCh38 genome assembly using Hisat2 version XXX with the following parameters: hisat2 -p 7 -k 1 --min-intronlen 30 --max-intronlen 3000
differential gene expression was calculated using edgeR.
Genome_build: GRCh38 release 96
Supplementary_files_format_and_content: BigWig files were generated in R using GenomicAlignments and rtracklayer packages

source_name: HUVEC

growth_protocol: HUVECs were cultured in M199 medium (Sigma) supplemented with 10% FBS, 4 U/ml heparin, 3 ng/ml β-EC grwth factor (sigma), 4 U/ml heparin, and 100 units/ml penicillin-streptomycin.

extract_protocol:
RNA was isolated with MagMAX™-96 Total RNA Isolation Kit (ThermoFisher)
mRNA was purified from total RNA using NEXTflex Poly(A) Beads (Bioo Scientific).  Following purification, libraried were prepared using NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific) according to the manufacturer's instructions.

treatment_protocol: Cells were treated with 75 µM HKi3 (2-hydroxy-1-naphthaldehyde) or vehicle control (DMSO) - (stock was at 10mM in DMSO)

value: HUVECs (Human Umbilical Vein Endothelial Cells)

tag: treatment

value: HEG-KRIT1 inhibitor (HKi3)


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C11_AD012_indexed


title: HUVECs, COMP 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C11_AD008_indexed


title: HUVECs, COMP 2


title: L540_C1_100nM_6h


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C11_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C11_AD010_indexed


title: KMH2_RP2_100nM_6h

source_name: KM-H2 cell line


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C11_AD002_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B8_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C2_AD006_indexed


title: HUVECs, COMP 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C10_AD008_indexed


title: KMH2_C2_100nM_6h


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C12_AD007_indexed


title: KMH2_RP1_100nM_6h


title: HUVECs, CTRL 4

value: control


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B9_AD010_indexed

value: PAL


title: HUVECs, COMP 4


title: L540_RP2_10uM_24h

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen), and treated with DNase according to the manufacture’s protocol.
Total RNA quality was evaluated using the Agilent Bioanalyzer and the RNA Nano kit: only samples with RIN score ≥ 8 were processed further. RNA-seq libraries were sequenced using the TruSeq mRNA stranded kit (Illumina) according manufacturer’s indications. Briefly, the polyA fraction was isolated starting form 300 ng of high quality total RNA. All libraries were quantified using Qubit (Thermo Fisher Scientific Logo) and Bioanalyzer 2100 (Agilent) instruments. According to index compatibility, the libraries were grouped into pools at a concentration of 8 pM to obtain ~15 million clusters for each sample, for single run.
Single end sequence reads (75-bp in length) were generated on an Illumina NextSeq 500 (Samples 1 to 16)

value: RP6530 10uM Treated 24 hr


title: HUVECs, CTRL 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B9_AD008_indexed


title: HUVECs, CTRL 2


title: L540_RP2_10uM_6h

value: RP6530 10uM Treated 6 hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B9_AD004_indexed


title: KMH2_C1_100nM_6h


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B8_AD012_indexed


title: HUVECs, CTRL 1


title: PS2

data_processing:
Unmapped paired-end sequences from an Illumina HiSeq4000 sequencer were tested by FastQC.
Sequence adapters were removed and reads were quality trimmed using Trimmomatic_0.36 (PMID: 24695404).
The reads were mapped against the reference human genome and counts per gene were calculated using annotation from GENCODE 30 (http://www.gencodegenes.org/) using STAR_2.5.3 (PMID: 23104886).
Differential expression was calculated with DESeq2_1.24.0 (PMID:25516281).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file include RPKM values for each sample

growth_protocol: HUVECs were cultured for two hours on Transwell upper chambers, in medium containing 1% serum.

extract_protocol:
Cell bodies and protrusions were harvested with cell scrapers and RNA isolated with RNAqueous™-Micro Total RNA Isolation Kit (ThermoFisher Scientific)
RNA-seq library prepared with TruSeq Stranded mRNA (Illumina)

treatment_protocol: 25ng/ml VEGF-A was added to the lower Transwell chamber to promote the migration of HUVECs through the membranes over the next hour.

tag: tissue source

value: Umbilical vein vascular wall

value: Human Umbilical Vein Endothelial Cells (HUVECs)

tag: cell fraction

value: Protrusions

tag: passages


title: L540_RP1_10uM_6h


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B8_AD008_indexed

tag: brain region

tag: Sex

tag: strain


title: PS1


title: L540_RP1_10uM_24h


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B7_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B7_AD010_indexed


title: L540_C2_10uM_24h

value: vehicle-treated Control 24 hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B7_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B9_AD012_indexed


title: CB1

source_name: HUVECs_cell body

value: Cell body


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B7_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B6_AD012_indexed


title: L540_C2_10uM_6h


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B7_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B6_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B9_AD007_indexed


title: L540_C1_10uM_24h


title: INO80-FRB Mot1-FRB Break-seq 100 mM HU rep2

city: Worcester

first: Salih

last: Topal

address: 373 Plantation Street

institute: UMass Medical School

data_processing:
Library strategy: Break-seq
FASTQ files from paired end libraries were collapsed by barcode and the Illumina adapter sequence was trimmed from the 3’ end.
Reads were aligned to the S. cerevisiae genome (SacCer3, SGD) using Bowtie2 with a maximum fragment length for valid paired-end alignments set to 500 bp.
Aligned reads were then filtered for quality and only uniquely mapped paired reads were used for future analyses
BAM files were uploaded to SeqMonk and normalized by scaling to 1 million reads.
MACS Peak Caller was used to identify new peaks inINO80-FRB, Mot1-FRB or INO80-FRB Mot1-FRB biological replicates using the mean WT file as the input (p-value 1x10e-5, 500 bp fragment size).
Genome_build: SacCer3
Supplementary_files_format_and_content: bed file of peaks called by MACS

organism: Saccharomyces cerevisiae

source_name: log phase S. cerevisiae

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.1 to mid-log phase with an OD of 1

extract_protocol:
Cells were harvested and resuspended in 1 mL of 50 mM EDTA. Cells (50 μL) were combined with 50 μL of 1% low melting temperature agarose (Lonza).
Following in gel labeling and sonication, libraries were prepared as in (Hoffman et al., 2015). Paired-end sequencing was performed on an Illumina NextSeq 500 with a read length of 75 bp.

treatment_protocol: Rapamycin was added for 3 hours prior to harvest.

value: INO80-FRB Mot1-FRB

tag: protocol

value: Break-seq


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B6_AD007_indexed

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: male


title: conditioned Day5 media, sample EM10 [RNA]

value: spent culture medium conditioned Day5 media


title: INO80-FRB Mot1-FRB Break-seq 100 mM HU rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_C10_AD012_indexed


title: L540_C1_10uM_6h

tag: cell type

value: Hodgkin lymphoma cell line


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B8_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B6_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B6_AD004_indexed


title: KMH2_RP2_10uM_24h


title: INO80-FRB Mot1-FRB Break-seq rep2


title: INO80-FRB Mot1-FRB Break-seq rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B5_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B5_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B5_AD010_indexed


title: KMH2_RP1_10uM_24h


title: CB2


title: Mot1-FRB Break-seq 100 mM HU rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B4_AD010_indexed


title: KMH2_RP1_10uM_6h


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B6_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B4_AD007_indexed


title: KMH2_C2_10uM_24h


title: Mot1-FRB Break-seq rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B4_AD001_indexed


title: Mot1-FRB Break-seq 100 mM HU rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B4_AD006_indexed


title: KMH2_RP2_10uM_6h


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B4_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B3_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B3_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B3_AD001_indexed


title: INO80-FRB Break-seq 100 mM HU rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B3_AD006_indexed


title: Mot1-FRB Break-seq rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B5_AD004_indexed


title: INO80-FRB Break-seq rep2


title: KMH2_C1_10uM_24h


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B2_AD010_indexed


title: BPATE3

data_processing:
RNA-Seq raw paired-end reads were trimmed with cutadapt
Reads were aligned to Ensembl ARS-UCD1.2 bovine genome with STAR (v2.7)
Counts were obtained using featureCounts v1.6.3
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Table with gene expression raw reads in csv format.

organism: Bos taurus

source_name: trophectoderm (TE)

growth_protocol: The cumulus-oocyte complexes were matured in 39°C, 5% CO2 at maximum humidity in TCM199 medium supplemented with 0.006g/ml fafBSA, 0.25mM Na-pyruvate, 1x conc. penicillin-streptomycin, 0.02U/ml LH, 0.002mg/ml FHS and 0.001mg/ml β-estradiol for 24h. After IVM, COCs were denuded and all oocytes with first polar body and no signs of degeneration were activated for parthenogenetic development.

extract_protocol:
SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Takara) was used to generate high-quality cDNA from samples
Nextera XT DNA and Nextera XT Index Kit v2 (Illumina)

tag: tissue

value: trophectoderm (TE)


title: BPATE2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B3_AD007_indexed

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B2_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B2_AD007_indexed


title: KMH2_C2_10uM_6h

value: vehicle-treated Control 6 hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B2_AD004_indexed


title: INO80-FRB Break-seq rep1

tag: genotype


title: BPATE1


title: BPAICM3

source_name: inner cell mass (ICM)

value: inner cell mass (ICM)


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B1_AD010_indexed


title: INO80-FRB Break-seq 100 mM HU rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B1_AD008_indexed


title: KMH2_C1_10uM_6h


title: WT-FRB Break-seq 100 mM HU rep1

value: WT-FRB


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B1_AD007_indexed

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B2_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B1_AD006_indexed


title: BPAICM2


title: WT-FRB Break-seq rep1


title: WT-FRB Break-seq rep2


title: BPA2W

source_name: blastocyst

value: whole blastocyst


title: INO80-FRB Mot1-FRB NET-seq rep2

description: nascent RNA

data_processing:
Library strategy: NET-seq
The adapter sequence was (ATCTCGTATGCCGTCTTCTGCTTG) removed and the random hexamer sequence was removed from the 5’ end. The 3’ ends of the reads were then trimmed for quality using FASTQ Quality Timmer by sliding window (Blankenberg et al., 2010) with a window size of 10 and a step size of 5. The reads were trimmed until the aggregate score was ≥ 21.
Reads were first aligned using Bowtie2 to a combined FASTA file of S. cerevisiae and S. pombe rRNA, tRNA, and RDN sequences to remove contaminating reads.
Reads were then aligned to a combined version of the S. cerevisiae genome (SacCer3, SGD) and the S. pombe genome (ASM294v.2, PomBase) with TopHat2, allowing up to three mismatches.
reads were separated by their respective genomes with SAMtools, and only uniquely mapped reads were used for further analyses
libraries were normalized by scaling the uniquely mapped S. pombe reads to 100,000 reads. This scaling factor was then used to scale the uniquely mapped S. cerevisiae reads. the pombe-scaled WT S. cerevisiae read counts were then scaled to 1 M reads, and this additional scaling factor was included to scale the sample reads
Only the 5’ end of the sequencing read, which corresponds to the 3’ end of the nascent RNA was recorded and used for downstream analyses.
Genome_build: SacCer3, ASM294v.2
Supplementary_files_format_and_content: bigwig

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8.

extract_protocol:
Cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004).
RNA Pol II IP, RNA purification, and library construction was carried out as described previously (Churchman and Weissman, 2011; Mayer et al., 2015). 3’ end sequencing was performed on an Illumina NextSeq 500 with a read length of 75 bp.

treatment_protocol: Rapamycin was added for 1 hour prior to harvest (for anchor-away strains). S. pombe cells containing a flag-tagged Rpb3 were added in a 1:10 ratio at time of harvest for library spike-in

value: Native elongating transcript sequencing (NET-seq)


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B10_AD012_indexed


title: BPAICM1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B11_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B11_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B10_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B10_AD007_indexed


title: BPA1W


title: INO80-FRB Mot1-FRB NET-seq rep1

description: nascent RNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A9_AD008_indexed


title: Mot1-FRB NET-seq rep2

description: nascent RNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B1_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A9_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A9_AD012_indexed


title: WT-FRB Break-seq 100 mM HU rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A8_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_B12_AD007_indexed


title: rna_PVneg_gpe_Sham_rep1

city: Pittsburgh

first: Alyssa

middle: J

last: Lawler

state: PA

address: 4400 Fifth Ave

department: Computational Biology

institute: Carnegie Mellon University

data_processing:
RNA-Seq alignment:  Fastq files were mapped to the mm10 genome (downloaded from UCSC in November 2015) using Hisat2 with default parameters.
RNA-Seq filtering:  Duplicate UMIs were removed using NuDup (https://github.com/tecangenomics/nudup).
Generation of RNA-Seq count matrix:  A counts per gene per sample matrix was constructed using Subread featureCounts version 1.6.4 with GRCm38 gene annotations (Ensembl version 79).
ATAC-seq alignment:  Reads were mapped to the mm10 genome with Bowtie2 using the ENCODE ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines) with default parameters.
ATAC-seq filtering:  Duplicate reads, mitochondrial reads, and blacklist region reads were filtered out as a part of the ENCODE ATAC-seq pipeline.
ATAC-seq peak calling:  Peaks were called on each sample individually using MACS2 within the ENCODE ATAC-seq pipeline workflow and reproducible peaks were determined on biological replicates with an IDR threshold of 0.1.
Generation of ATAC-seq count matrix:  The IDR peaks across all biological replicates were merged to create the genomic ranges of interest. Read counts per sample in these regions were computed with Rsubread featureCounts version 1.28.1 on the filtered bam alignments.
More information on all data processing and conclusions can be found in the publication.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every sample
Supplementary_files_format_and_content: Genomic coordinates of merged ATAC-seq peak regions
Supplementary_files_format_and_content: Matrix table with raw read counts for every peak region and every sample
Supplementary_files_format_and_content: ATAC-seq peaks called in each sample
Supplementary_files_format_and_content: MACS2 pval signal tracks for each sample in bigwig format

extract_protocol:
PV neuron nuclei were tagged and isolated using cSNAIL, a virus-based adaptation of the INTACT method. Nuclei populations were then partitioned for total RNA extraction with the Qiagen RNeasy Micro Kit or ATAC-seq tagmentation with tn5 transposase.
RNA libraries were constructed using the Ovation SoLo RNA-seq System with Mouse AnyDeplete to remove ribosomal RNA. To retain immature nuclear transcripts, no polyA selection was performed. ATAC-seq libraries were constructed with standard amplification and size selection methods. See publication for more details.

treatment_protocol: Mice underwent dopamine depletion with bilateral, acute 6-OHDA lesion to the medial forebrain bundle or received a sham surgery injecting saline instead of the toxin.

value: gpe

value: PVneg

value: Sham

tag: dopamine remaining

value: M

value: 9 to 12 weeks


title: Mot1-FRB NET-seq rep1

description: Nascent RNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A8_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A8_AD008_indexed


title: rna_PVneg_gpe_DD_rep4

value: DD

value: F


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A8_AD006_indexed

value: male


title: INO80-FRB NET-seq rep2

description: Nascent RNA


title: rna_PVneg_gpe_DD_rep3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A6_AD010_indexed


title: rna_PVneg_gpe_DD_rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A7_AD008_indexed


title: INO80-FRB NET-seq rep1

description: Nascent RNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A6_AD008_indexed


title: WT_FRB NET-seq rep2

description: Nascent RNA


title: WT-FRB NET-seq rep1

description: Nascent RNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A5_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A6_AD007_indexed


title: rna_PVneg_gpe_Sham_rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A6_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A5_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A5_AD008_indexed


title: rna_PVpos_gpe_Sham_rep2

value: PVpos


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A5_AD007_indexed


title: rna_PVpos_gpe_Sham_rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A4_AD012_indexed


title: rna_PVpos_gpe_DD_rep4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A4_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A4_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A4_AD006_indexed


title: rna_PVpos_gpe_DD_rep3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A4_AD004_indexed


title: rna_PVneg_gpe_DD_rep1


title: rna_PVpos_gpe_DD_rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A4_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A3_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A3_AD008_indexed


title: rna_PVneg_striatum_Sham_rep2

value: striatum


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A3_AD007_indexed


title: rna_PVpos_gpe_DD_rep1


title: PMP8

city: Beijing

first: Mingyi

last: Qu

state: Beijing

address: 27 Taiping Road

country: China

institute: Institute of Health Service and Transfusion Medicine

description: miRNA expression in human PMPs

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human miRNA（8*60K，Design ID：046064） for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: healthy human PMP

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

value: cord clood

value: platelet-derived microparticle


title: PMP5

description: miRNA expression in human PMPs


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A2_AD012_indexed


title: tongue8-A64033

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were adapter- and quality-trimmed with Trimmomatic.
The sequencing reads were aligned to the human genome (build hg38/GRCh38) using the splice-aware STAR aligner.
The raw counts were normalized using the DESeq2 R package.
The featureCounts program was utilized to generate counts for each gene based on how many aligned reads overlap its exons.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

source_name: tongue

extract_protocol:
Total RNA was extracted from 30 mg of fresh frozen oral cancer tissue and clinically normal contralateral gingiva or tongue tissues from oral cancer patients using the Qiagen RNeasy kit (Catalog No: 74104) following the manufacturer’s protocol including the recommended DNase treatment.  Homogenized tissue lysates were prepared by using a small hand-held pestle followed by passing the lysate at least five times through a blunt 20-gauge needle fitted to an RNase-free syringe.  The RNA concentration and integrity were determined using an Agilent 2100 Bioanalyzer, equipped with an RNA 6000 Nano kit (part number 5067-1511), following the manufacturer’s instructions.
Ribodepleted strand specific RNA libraries were prepared from 24 total RNA samples.  Samples were pooled and 125 base paired end sequencing was performed on the Illumina 2500.

value: tongue

tag: patient id

tag: diagnosis

value: cancer tissue

tag: ptnm stage

tag: pain score


title: PMP4

description: miRNA expression in human PMPs


title: tongue7-A64032


title: rna_PVneg_striatum_Sham_rep1

tag: age


title: PMP2

description: miRNA expression in human PMPs


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A2_AD004_indexed

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A12_AD008_indexed


title: tongue6-A64031

value: Not available


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A12_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A2_AD010_indexed


title: rna_PVneg_striatum_DD_rep2

tag: treatment


title: rna_PVneg_striatum_DD_rep3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A1_AD008_indexed


title: rna_PVneg_striatum_DD_rep1


title: tongue9-A64034


title: tongue5-A64029


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A1_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A11_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A11_AD012_indexed


title: tongue4-A64028


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A11_AD008_indexed


title: PMP1

description: miRNA expression in human PMPs


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A12_AD012_indexed


title: rna_PVpos_striatum_Sham_rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_A10_AD010_indexed


title: rna_PVpos_striatum_Sham_rep2