title: NC_3

status: Public on Mar 31 2020

type: SRA

city: Fujisawa

first: Masato

last: Yugami

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

department: Research

country: Japan

institute: Takeda Pharmaceutical Company

library_source: transcriptomic

data_processing:
processed with ArrayStudio (OmicSoft Corporation)
Genome_build: hg19
Supplementary_files_format_and_content: .txt including GeneID, GeneName GeneDescription, EntrezID, FPKM, Foldchange and p-value

molecule: total RNA

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in DMEM medium.

extract_protocol:
3 days after transfection, the cells were treated with 50 ng/mL PMA and 500 nM A23187 for 4 hrs, and then subjected to mRNA-library generation
TruSeq Stranded mRNA Library Prep Kit for NeoPrep

treatment_protocol: Negative control or HNRNPU silencer select siRNA (Ambion) were transfected with Lipofectamine RNAi MAX for 3 days.

tag: cell line

value: HeLa

tag: transfection

value: control siRNA


title: NC_1


title: NC_2


title: HNRNPU-KD_3

value: siRNA against HNRNPU


title: HNRNPU-KD_2


title: HNRNPU-KD_1


title: 3-S39

city: Brno

first: Petra

last: Bencurova

address: Kamenice 5

department: Brain and Mind Research

country: Czech Republic

institute: Masaryk University, CEITEC

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S39
raw reads: reads.xlsx/chronic/rawCount_3-S39

data_processing:
All samples were adapter trimmed. The raw miRNA expression levels were quantified by seqBuster (1.2.4a6) (maximum of 1 mismatch) (Pantano et al., 2010) with miRBase annotation (v22) (Kozomara and Griffiths-Jones, 2014).
Samples 1-S5; 1-S7; 1-S21;1-S27; 1S-31; 1-S34 were excluded from analysis due to low number of miRNA reads - below 300 000 reads per library
Differential expression was evaluated by R package DESeq2 (1.16.1) .
Genome_build: miRBase v22
Supplementary_files_format_and_content: tab-delimited text file containing miRNAs mapped in each sample and its read count

organism: Rattus norvegicus

source_name: Hippocampal tissue

extract_protocol:
Total RNA was isolated from from frozen hippocampal tissue using  TRI Reagent® (Biotech)  according to the manufacturer`s protocol. Libraries for sequencing were prepared from 1.1 µg of total RNA using a NEXTflex Small RNA-Seq Kit v3 (Bioo Scientific) according to the manufacturer`s protocol.
small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Hippocampal tissue

tag: subject

value: control

tag: onset age

value: P12 (Infantcy)

tag: epilepsy stage

value: Chronic - 3 months after SE


title: 3-S40

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S40
raw reads: reads.xlsx/chronic/rawCount_3-S40


title: 3-S38

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S38
raw reads: reads.xlsx/chronic/rawCount_3-S38


title: 3-S36

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S36
raw reads: reads.xlsx/chronic/rawCount_3-S36


title: 3-S37

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S37
raw reads: reads.xlsx/chronic/rawCount_3-S37


title: 3-S35

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S35
raw reads: reads.xlsx/chronic/rawCount_3-S35


title: 3-S33

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S33
raw reads: reads.xlsx/chronic/rawCount_3-S33


title: 3-S34

description:
miRNA
not processed - below 300 000 miRNA reads
-
-


title: 3-S32

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S32
raw reads: reads.xlsx/chronic/rawCount_3-S32


title: 3-S31

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S31
raw reads: reads.xlsx/chronic/rawCount_3-S31


title: 3-S26

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S26
raw reads: reads.xlsx/chronic/rawCount_3-S26

value: pilocarpine induced SE


title: 3-S30

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S30
raw reads: reads.xlsx/chronic/rawCount_3-S30


title: 3-S28

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S28
raw reads: reads.xlsx/chronic/rawCount_3-S28


title: 3-S29

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S29
raw reads: reads.xlsx/chronic/rawCount_3-S29


title: 3-S27

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S27
raw reads: reads.xlsx/chronic/rawCount_3-S27


title: 3-S25

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S25
raw reads: reads.xlsx/chronic/rawCount_3-S25


title: 3-S24

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S24
raw reads: reads.xlsx/chronic/rawCount_3-S24


title: 3-S19

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S19
raw reads: reads.xlsx/chronic/rawCount_3-S19

value: P60 (Adult)


title: 3-S18

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S18
raw reads: reads.xlsx/chronic/rawCount_3-S18


title: 3-S20

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S20
raw reads: reads.xlsx/chronic/rawCount_3-S20


title: 3-S21

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S21
raw reads: reads.xlsx/chronic/rawCount_3-S21


title: 3-S22

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S22
raw reads: reads.xlsx/chronic/rawCount_3-S22


title: 3-S17

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S17
raw reads: reads.xlsx/chronic/rawCount_3-S17


title: 3-S23

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S23
raw reads: reads.xlsx/chronic/rawCount_3-S23


title: 3-S16

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S16
raw reads: reads.xlsx/chronic/rawCount_3-S16


title: 3-S15

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S15
raw reads: reads.xlsx/chronic/rawCount_3-S15


title: 3-S14

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S14
raw reads: reads.xlsx/chronic/rawCount_3-S14


title: 3-S12

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S12
raw reads: reads.xlsx/chronic/rawCount_3-S12


title: 3-S13

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S13
raw reads: reads.xlsx/chronic/rawCount_3-S13


title: 3-S10

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S10
raw reads: reads.xlsx/chronic/rawCount_3-S10


title: 3-S11

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S11
raw reads: reads.xlsx/chronic/rawCount_3-S11


title: 3-S9

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S9
raw reads: reads.xlsx/chronic/rawCount_3-S9


title: 3-S8

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S8
raw reads: reads.xlsx/chronic/rawCount_3-S8


title: 3-S7

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S7
raw reads: reads.xlsx/chronic/rawCount_3-S7


title: 3-S3

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S3
raw reads: reads.xlsx/chronic/rawCount_3-S3


title: 3-S5

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S5
raw reads: reads.xlsx/chronic/rawCount_3-S5


title: 3-S6

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S6
raw reads: reads.xlsx/chronic/rawCount_3-S6


title: 3-S2

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S2
raw reads: reads.xlsx/chronic/rawCount_3-S2


title: 3-S4

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S4
raw reads: reads.xlsx/chronic/rawCount_3-S4


title: 3-S1

description:
miRNA
processed
normalised reads: reads.xlsx/chronic/normCount_3-S1
raw reads: reads.xlsx/chronic/rawCount_3-S1


title: 2-S40

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S40
raw reads: reads.xlsx/latent/rawCount_2-S40

value: Latent - 1 week after SE


title: 2-S38

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S38
raw reads: reads.xlsx/latent/rawCount_2-S38


title: 2-S37

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S37
raw reads: reads.xlsx/latent/rawCount_2-S37


title: 2-S36

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S36
raw reads: reads.xlsx/latent/rawCount_2-S36


title: 2-S34

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S34
raw reads: reads.xlsx/latent/rawCount_2-S34


title: 2-S35

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S35
raw reads: reads.xlsx/latent/rawCount_2-S35


title: 2-S39

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S39
raw reads: reads.xlsx/latent/rawCount_2-S39


title: 2-S29

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S29
raw reads: reads.xlsx/latent/rawCount_2-S29


title: 2-S31

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S31
raw reads: reads.xlsx/latent/rawCount_2-S31


title: 2-S28

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S28
raw reads: reads.xlsx/latent/rawCount_2-S28


title: 2-S30

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S30
raw reads: reads.xlsx/latent/rawCount_2-S30


title: 2-S27

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S27
raw reads: reads.xlsx/latent/rawCount_2-S27


title: 2-S24

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S24
raw reads: reads.xlsx/latent/rawCount_2-S24


title: 2-S26

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S26
raw reads: reads.xlsx/latent/rawCount_2-S26


title: 2-S33

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S33
raw reads: reads.xlsx/latent/rawCount_2-S33


title: 2-S32

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S32
raw reads: reads.xlsx/latent/rawCount_2-S32


title: 2-S25

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S25
raw reads: reads.xlsx/latent/rawCount_2-S25


title: 2-S22

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S22
raw reads: reads.xlsx/latent/rawCount_2-S22


title: 2-S23

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S23
raw reads: reads.xlsx/latent/rawCount_2-S23


title: 2-S21

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S21
raw reads: reads.xlsx/latent/rawCount_2-S21


title: 2-S17

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S17
raw reads: reads.xlsx/latent/rawCount_2-S17


title: 2-S20

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S20
raw reads: reads.xlsx/latent/rawCount_2-S20


title: 2-S18

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S18
raw reads: reads.xlsx/latent/rawCount_2-S18


title: 2-S16

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S16
raw reads: reads.xlsx/latent/rawCount_2-S16


title: 2-S19

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S19
raw reads: reads.xlsx/latent/rawCount_2-S19


title: 2-S14

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S14
raw reads: reads.xlsx/latent/rawCount_2-S14


title: 2-S15

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S15
raw reads: reads.xlsx/latent/rawCount_2-S15


title: 2-S11

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S11
raw reads: reads.xlsx/latent/rawCount_2-S11


title: 2-S13

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S13
raw reads: reads.xlsx/latent/rawCount_2-S13


title: 2-S9

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S9
raw reads: reads.xlsx/latent/rawCount_2-S9


title: 2-S12

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S12
raw reads: reads.xlsx/latent/rawCount_2-S12


title: 2-S10

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S10
raw reads: reads.xlsx/latent/rawCount_2-S10


title: 2-S8

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S8
raw reads: reads.xlsx/latent/rawCount_2-S8


title: 2-S7

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S7
raw reads: reads.xlsx/latent/rawCount_2-S7


title: 2-S4

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S4
raw reads: reads.xlsx/latent/rawCount_2-S4


title: 2-S2

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S2
raw reads: reads.xlsx/latent/rawCount_2-S2


title: 2-S6

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S6
raw reads: reads.xlsx/latent/rawCount_2-S6


title: 2-S1

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S1
raw reads: reads.xlsx/latent/rawCount_2-S1


title: 1-S39

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S39
raw reads: reads.xlsx/acute/rawCount_1-S39

value: Acute - 24 hours after SE


title: 1-S40

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S40
raw reads: reads.xlsx/acute/rawCount_1-S40


title: 1-S28

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S28
raw reads: reads.xlsx/acute/rawCount_1-S28


title: 1-S27

description:
miRNA
not processed - below 300 000 miRNA reads
-
-


title: 1-S33

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S33
raw reads: reads.xlsx/acute/rawCount_1-S33


title: 1-S37

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S37
raw reads: reads.xlsx/acute/rawCount_1-S37


title: 1-S38

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S38
raw reads: reads.xlsx/acute/rawCount_1-S38


title: 1-S31


title: 1-S34

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S34
raw reads: reads.xlsx/acute/rawCount_1-S34


title: 2-S3

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S3
raw reads: reads.xlsx/latent/rawCount_2-S3


title: 1-S36

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S36
raw reads: reads.xlsx/acute/rawCount_1-S36


title: 1-S32

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S32
raw reads: reads.xlsx/acute/rawCount_1-S32


title: 1-S29

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S29
raw reads: reads.xlsx/acute/rawCount_1-S29


title: 1-S35

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S35
raw reads: reads.xlsx/acute/rawCount_1-S35


title: 2-S5

description:
miRNA
processed
normalised reads: reads.xlsx/latent/normCount_2-S5
raw reads: reads.xlsx/latent/rawCount_2-S5


title: 1-S26

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S26
raw reads: reads.xlsx/acute/rawCount_1-S26


title: 1-S11

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S11
raw reads: reads.xlsx/acute/rawCount_1-S11


title: 1-S8

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S8
raw reads: reads.xlsx/acute/rawCount_1-S8


title: 1-S10

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S10
raw reads: reads.xlsx/acute/rawCount_1-S10


title: 1-S2

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S2
raw reads: reads.xlsx/acute/rawCount_1-S2


title: 1-S21


title: 1-S14

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S14
raw reads: reads.xlsx/acute/rawCount_1-S14


title: 1-S1

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S1
raw reads: reads.xlsx/acute/rawCount_1-S1


title: 1-S19

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S19
raw reads: reads.xlsx/acute/rawCount_1-S19


title: 1-S20

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S20
raw reads: reads.xlsx/acute/rawCount_1-S20


title: 1-S7

description:
miRNA
not processed - below 300 000 miRNA reads
-
-


title: 1-S25

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S25
raw reads: reads.xlsx/acute/rawCount_1-S25


title: 1-S15

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S15
raw reads: reads.xlsx/acute/rawCount_1-S15


title: 1-S12

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S12
raw reads: reads.xlsx/acute/rawCount_1-S12


title: 1-S16

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S16
raw reads: reads.xlsx/acute/rawCount_1-S16


title: 1-S24

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S24
raw reads: reads.xlsx/acute/rawCount_1-S24


title: 1-S4

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S4
raw reads: reads.xlsx/acute/rawCount_1-S4


title: 1-S18

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S18
raw reads: reads.xlsx/acute/rawCount_1-S18


title: 1-S9

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S9
raw reads: reads.xlsx/acute/rawCount_1-S9


title: 1-S6

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S6
raw reads: reads.xlsx/acute/rawCount_1-S6


title: 1-S13

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S13
raw reads: reads.xlsx/acute/rawCount_1-S13


title: 1-S22

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S22
raw reads: reads.xlsx/acute/rawCount_1-S22


title: 1-S3

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S3
raw reads: reads.xlsx/acute/rawCount_1-S3


title: 1-S5


title: 1-S17

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S17
raw reads: reads.xlsx/acute/rawCount_1-S17


title: 1-S23

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S23
raw reads: reads.xlsx/acute/rawCount_1-S23


title: S_203_DLX_T8

type: RNA

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

hyb_protocol: Standard Illumina protocol with the Whole-Genome Gene Expression Direct Hybridization Assay. Biotin labeled RNA is hybridized to streptavidin-Cy3

scan_protocol: Standard Illumina protocol

data_processing: All array probes and samples were subjected to quality control using Flexarray® package implemented in R (version 1.6.3). Data were normalized using background adjustment and log2 transformation, variance stabilization transformation (VST) correction, and quantile normalization.

label: biotin, Cy3

label_protocol: Standard Illumina protocol with the Whole-Genome Gene Expression Direct Hybridization Assay. RNA itself is labeled with biotin

extract_protocol: Whole blood samples were collected using PAXgene Blood RNA Tubes (PreAnalytix®). Total RNA was extracted using the Qiagen miRNeasy Micro Kit, with DNase treatment.

tag: visit

tag: treatment

value: DLX

tag: age

tag: gender

value: F

tag: response

value: whole blood


title: S_202_DLX_T8


title: S_203_DLX_T0


title: 1-S30

description:
miRNA
processed
normalised reads: reads.xlsx/acute/normCount_1-S30
raw reads: reads.xlsx/acute/rawCount_1-S30


title: S_192_PLB_T0

value: PLB


title: S_193_DLX_T0


title: S_198_PLB_T0


title: S_200_DLX_T8

value: M


title: S_189_PLB_T0


title: S_197_PLB_T8


title: S_195_DLX_T8


title: S_192_PLB_T8


title: S_200_DLX_T0


title: S_191_DLX_T0


title: S_198_PLB_T8


title: S_191_DLX_T8


title: S_201_DLX_T0


title: S_190_PLB_T0


title: S_199_PLB_T0


title: S_194_DLX_T0


title: S_196_PLB_T8


title: S_201_DLX_T8


title: S_194_DLX_T8


title: S_197_PLB_T0


title: S_199_PLB_T8


title: S_189_PLB_T8


title: S_190_PLB_T8


title: S_188_DLX_T0


title: S_187_DLX_T8


title: S_188_DLX_T8


title: S_202_DLX_T0


title: S_193_DLX_T8


title: S_196_PLB_T0


title: S_195_DLX_T0


title: Sample19_24hr_CD_5

city: Toronto

first: Stephen

last: Matthews

state: Ontario

address: 1 King's College Circle

institute: University of Toronto

library_source: genomic

data_processing:
Adaptor sequences were trimmed using Trim Galore.
Additional filtering was performed to remove reads that did not contain an MspI site signature at the 5’ end using a script provided by NuGEN (https://github.com/nugentechnologies/NuMetRRBS/blob/master/  trimRRBSdiversityAdaptCustomers.py).
The reads were then aligned using Bismark (version 0.16.0) and sorted by Samtools (version 1.7).
We then used MethPipe (version 3.4.2) to identify significant differentially methylated CpG sites (DMCs) with at least 30X reads with FDR ≤ 0.05.
CompEpitool was used to annotate the differentially methylated CpG sites to the human genome (hg38).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files with at least 30X reads (formatted as "chr", "loc", "strand", "fdr", )

molecule: genomic DNA

source_name: whole cord blood on dried blood spot

extract_protocol:
DNA from whole blood was extracted using a QIAamp DNA Blood Mini Kit (Qiagen: Cat. #51104). For DNA extraction from dried blood spots, one half of a single blood spot  79 was cut into small pieces and incubated with lysis buffer (1218μL) and Proteinase K (33μL) using Gensolve reagents (GenTegra: GVR-113) in an Incubator/vortex shaker set at 1400rpm for 90min, at 56°C (ThermoMixer® C, Eppendorf). The lysate was processed using a QIAamp DNA Blood Mini Kit (Qiagen: Cat. #51104).
RRBS libraries were generated from 100ng of high-quality dsDNA using the RRBS Methyl_seq System 1-16 (Ovation: Part #0353) and EpiTect Fast DNA Bisulfite kit (Qiagen: Cat. #59824) following the manufacturer’s protocols.

tag: storage time

tag: subject id


title: Sample18_4hr_CD_7

description: card4h_card24h_counts_fdr.txt.gz, card4h_card7d_counts_fdr.txt.gz


title: Sample17_4hr_CD_6


title: Sample15_4hr_CD_3


title: Sample16_4hr_CD_5


title: S_185_DLX_T0


title: S_187_DLX_T0


title: S_178_DLX_T0


title: S_177_DLX_T8


title: S_183_PLB_T8


title: S_184_DLX_T8


title: Sample23_7d_CD_6


title: S_179_PLB_T8


title: S_180_DLX_T0


title: S_179_PLB_T0


title: Sample13_4hr_CD_1


title: Sample14_4hr_CD_2


title: S_178_DLX_T8


title: S_184_DLX_T0


title: Sample22_7d_CD_5


title: S_182_DLX_T0


title: Sample21_24hr_CD_7


title: Sample12_0hr_BL_3

source_name: whole cord blood


title: S_181_DLX_T8


title: Sample11_0hr_BL_2


title: Sample10_0hr_BL_1


title: S_181_DLX_T0


title: S_182_DLX_T8


title: S_185_DLX_T8


title: Sample9_24hr_BL_4


title: Sample6_4hr_BL_4


title: S_180_DLX_T8


title: S_176_PLB_T8


title: S_175_DLX_T8


title: S_177_DLX_T0


title: Sample5_4hr_BL_3


title: Sample4_4hr_BL_2


title: Sample3_0hr_BL_4

description: blood0h_blood4h_counts_fdr.txt.gz, blood0h_blood24h_counts_fdr.txt.gz


title: S_186_PLB_T0


title: Sample8_24hr_BL_3


title: Sample7_24hr_BL_2


title: Sample2_0hr_BL_3


title: S_183_PLB_T0


title: S_174_PLB_T8


title: S_175_DLX_T0


title: S_171_PLB_T8


title: S_172_PLB_T0


title: S_176_PLB_T0


title: S_186_PLB_T8


title: S_171_PLB_T0


title: S_173_PLB_T8


title: S_174_PLB_T0


title: S_173_PLB_T0


title: S_172_PLB_T8


title: Sample1_0hr_BL_2


title: S_170_PLB_T0


title: Sample24_7d_CD_7


title: NHA B16 ATXN1L KO 3

city: Vancouver

first: Derek

last: Wong

state: British Columbia

address: 675 W 10th Ave

department: Molecular Oncology

institute: University of British Columbia

data_processing:
STAR aligners
Cufflinks
Illumina Sequence Hub
Genome_build: hg19
Supplementary_files_format_and_content: text file, raw counts

source_name: Normal Human Astrocytes

extract_protocol:
Qiagen RNAeasy kit, Trizol preservation
NEBnext Ultra ii Stranded mRNA

value: Brain

tag: cell type

value: Normal Human Astrocytes

tag: genotype

value: ATXN1L Knockout

tag: immortalization


title: S_170_PLB_T8


title: NHA B16 ATXN1L KO 2


title: S_168_PLB_T8


title: S_168_PLB_T0


title: S_165_DLX_T8


title: S_167_DLX_T0


title: S_163_PLB_T8


title: Sample20_24hr_CD_6


title: S_166_PLB_T0


title: NHA B16 ATXN1L KO 1


title: NHA B82 ATXN1L KO 3


title: S_167_DLX_T8


title: S_165_DLX_T0


title: S_169_DLX_T8


title: S_166_PLB_T8


title: S_164_PLB_T0


title: S_162_DLX_T8


title: S_169_DLX_T0


title: S_162_DLX_T0


title: S_160_PLB_T8


title: S_164_PLB_T8


title: NHA B82 ATXN1L KO 2


title: S_163_PLB_T0


title: S_159_PLB_T8


title: NHA B82 ATXN1L KO 1


title: S_160_PLB_T0


title: NHA H9 CIC KO 3

value: CIC Knockout


title: S_159_PLB_T0


title: NHA H9 CIC KO 2


title: NHA A2 CIC KO 3


title: NHA H9 CIC KO 1


title: NHA A2 CIC KO 2


title: NHA A2 CIC KO 1


title: NHA WT 3

value: parental line

value: WT


title: NHA WT 1


title: S_158_PLB_T8


title: S_158_PLB_T0


title: S_157_DLX_T8


title: S_161_PLB_T0


title: 17014-0026: WT_3 Af_6h

city: Braga

first: Nuno

middle: S.

last: Osório

address: Campus de Gualtar

country: Portugal

institute: ICVS

data_processing:
Read counts and quality for each sample were evaluated with the CLC Genomics Workbench 9.5.3 “Create Sequencing QC report” tool.
The RNA-Seq analysis was performed with the CLC Genomics Workbench 9.5.3  “RNA-Seq analysis” tool.
To analyze statistically significant expression results, the CLC Genomics Workbench 9.5.3  tool “Empirical analysis of DGE” (EDGE) was used.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each sample

source_name: monocyte-derived macrophages

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen)
Library preparation was performed using the TruSeq® Stranded mRNA HT technology (Illumina)

value: monocyte-derived macrophages

tag: infection status

value: 6h post-infection

tag: agent

value: Aspergillus fumigatus A1163


title: 17014-0009: WT_3 Af_2h

value: 2h post-infection


title: 17014-0020: WT_1 Af_6h


title: 17014-0022: WT_2 Af_6h


title: S_156_DLX_T0


title: S_154_DLX_T8


title: S_157_DLX_T0


title: S_154_DLX_T0


title: 17014-0008: WT_2 Af_2h


title: S_156_DLX_T8


title: S_153_PLB_T0


title: S_153_PLB_T8


title: S_151_DLX_T8


title: S_152_DLX_T0


title: S_155_PLB_T8


title: NHA WT 2

tag: cell line


title: S_152_DLX_T8

tag: tissue


title: 17014-0003: WT_3 Ctrl

value: uninfected


title: 17014-0002: WT_2 Ctrl


title: S_155_PLB_T0


title: 17014-0001: WT_1 Ctrl


title: 17014-0007: WT_1 Af_2h


title: S_149_PLB_T8


title: S_150_PLB_T8


title: S_151_DLX_T0


title: S_150_PLB_T0


title: S_148_PLB_T8


title: S_147_PLB_T8


title: S_146_PLB_T0


title: S_148_PLB_T0


title: S_145_DLX_T8


title: S_147_PLB_T0


title: S_143_DLX_T0


title: S_143_DLX_T8


title: S_146_PLB_T8


title: S_149_PLB_T0


title: S_138_PLB_T0


title: S_142_PLB_T8


title: S_144_PLB_T8


title: S_138_PLB_T8


title: S_141_PLB_T0


title: S_144_PLB_T0


title: S_141_PLB_T8


title: S_139_DLX_T0


title: S_142_PLB_T0


title: S_137_PLB_T8


title: S_145_DLX_T0


title: S_140_PLB_T0


title: S_139_DLX_T8


title: S_137_PLB_T0


title: S_136_DLX_T8


title: S_140_PLB_T8


title: S_136_DLX_T0


title: S_135_PLB_T8


title: S_134_DLX_T0


title: S_135_PLB_T0


title: S_133_DLX_T8


title: S_134_DLX_T8


title: S_131_DLX_T8


title: S_130_DLX_T8


title: S_129_PLB_T0


title: S_128_PLB_T8


title: S_133_DLX_T0


title: S_130_DLX_T0


title: S_129_PLB_T8


title: S_128_PLB_T0


title: S_131_DLX_T0


title: S_127_DLX_T8


title: S_124_PLB_T8


title: S_125_DLX_T8


title: S_132_PLB_T8


title: S_127_DLX_T0


title: S_126_DLX_T8


title: S_125_DLX_T0


title: S_126_DLX_T0


title: S_161_PLB_T8


title: S_124_PLB_T0


title: S_123_DLX_T8


title: S_123_DLX_T0


title: S_132_PLB_T0


title: S_121_PLB_T8


title: S_122_PLB_T0


title: S_120_PLB_T8


title: S_117_DLX_T8


title: S_120_PLB_T0


title: S_119_PLB_T8


title: S_118_DLX_T8


title: S_119_PLB_T0


title: S_118_DLX_T0


title: S_115_PLB_T8


title: S_115_PLB_T0


title: S_114_PLB_T0


title: S_116_PLB_T8


title: S_117_DLX_T0


title: S_116_PLB_T0


title: S_114_PLB_T8


title: S_113_DLX_T8


title: S_112_DLX_T8


title: S_113_DLX_T0


title: S_112_DLX_T0


title: S_110_DLX_T8


title: S_111_DLX_T0


title: S_110_DLX_T0


title: S_109_PLB_T8


title: Chicken DRG E4 Brachial

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

description:
miRNA profile
39

data_processing:
Illlumina software used for base calling
Adaptor removel and barcode extraction was used Mirprof tool by defalt settings.  http://srna-workbench.cmp.uea.ac.uk/mirprof-tutorial/
Data are then loaded to The Small RNA workbench software for aligment, normalisation and comparsion analysis. ( Bioinformatics. 2012 Aug 1; 28(15): 2059–2061.)
Genome_build: mm9, galgal4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Gallus gallus

source_name: Chicken Brachial DRG at embryonic day 4

extract_protocol:
DRG has dissected and immediately disolved in Extraction buffer and proceed as Thermoscientific miRNA extraction kit (PureLink® miRNA Isolation Kit, K157001)
Using illumina standard protocols

treatment_protocol: Dissociated mouse DRG neurons were obtained after enzymatic digestion of whole DRG using collagenase/dispase (C/D, 1mg/ml; Roche) and DNAse (0.5 mg/ml; Sigma) in N2 medium (DMEM/F12 med- ium with N2 supplement) with B27 supplement (Gibco). Cells were plated at low density (300 cells/well) in 24-well plates on glass coverslips precoated with poly-L-lysine (0.01%; Sigma)/laminin (10mg/ml; R&D Systems) or matrigel when indicated (BD Bioscience). Cells were cultured in N2 medium, treatment of neurotrophins, proteins activators and neurontransmitters from sample  29-36  at 10 ng/ml for 14hrs.

tag: genotype/variation

value: wildtype

value: brachical

tag: developmental stage


title: S_107_PLB_T0

value: F


title: S_109_PLB_T0

value: whole blood


title: S_103_DLX_T8

value: DLX


title: S_108_DLX_T8


title: S_111_DLX_T8


title: Chicken DRG E9 Lumbar

description:
miRNA profile
11

source_name: Chicken Lumbar DRG at embryonic day 9


title: S_108_DLX_T0


title: S_104_DLX_T8


title: S_107_PLB_T8

value: PLB


title: S_105_PLB_T8


title: S_105_PLB_T0


title: S_104_DLX_T0


title: S_103_DLX_T0


title: Chicken DRG E9 Brachial

description:
miRNA profile
10

source_name: Chicken Brachial DRG at embryonic day 9


title: S_121_PLB_T0


title: S_102_PLB_T0

value: M


title: S_102_PLB_T8


title: S_106_DLX_T8


title: S_100_DLX_T8


title: Chicken DRG E7 Lumbar

description:
miRNA profile
9

source_name: Chicken Lumbar DRG at embryonic day 7

value: lumbar


title: S_101_PLB_T0


title: S_99_PLB_T8


title: S_106_DLX_T0


title: S_101_PLB_T8


title: Chicken DRG E6 Lumbar

description:
miRNA profile
6

source_name: Chicken Lumbar DRG at embryonic day 6


title: Chicken DRG E7 Brachial

description:
miRNA profile
7

source_name: Chicken Brachial DRG at embryonic day 7


title: Chicken DRG E6 Thoracic

description:
miRNA profile
5

source_name: Chicken Thoracic DRG at embryonic day 6

value: thoracic


title: Chicken DRG E6 Brachial

description:
miRNA profile
4

source_name: Chicken Brachial DRG at embryonic day 6


title: Chicken DRG E5 Lumbar

description:
miRNA profile
3

source_name: Chicken Lumbar DRG at embryonic day 5


title: Chicken DRG E5 Thoracic

description:
miRNA profile
1

source_name: Chicken Thoracic DRG at embryonic day 5


title: wt_ribo_rep5

city: Worcester

first: Sneha

last: Shah

state: Massachusetts

address: 373 Biotech II, Suite 204, Plantation Street

department: Molecular Medicine

country: USA

institute: UMASS CHAN MEDICAL SCHOOL

data_processing:
Library strategy: Ribosome profiling
Ribosome protected footprints, 5nt UMI sequences
Individual samples were separated from the raw fastq files based on the barcode sequences. Adaptor sequences (TGGAATTCTCGGGTGCCAAGGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG) were removed with cutadapt (1.7.1). Trimmed fastq files were uploaded to the Dolphin platform (https://www.umassmed.edu/biocore/introducing-dolphin/) at the UMMS Bioinformatics Core for the mapping steps. Trimmed reads were quality filtered with Trimmomatic (0.32) and mapped to the mouse rRNA and then tRNA references with Bowtie2 (2.1.0). Unmapped reads were next mapped to the mm10 mouse genome with Tophat2 (2.0.9). Reads mapped to >1 loci of the genome were classified as “multimapped” reads and discarded. PCR duplicates were marked based on the UMI sequences with custom scripts and only uniquely mapped reads without duplicates were retained with Samtools (0.0.19) for the downstream analyses. RPF length distribution, P-site offsets, and frame preference were calculated with plastid (0.4.8). Counts at each nucleotide position were extracted using P-sites of RPFs and 5’end of mRNA reads with +11 offset, normalized to the library size, averaged across replicates, and plotted along mRNA positions with custom scripts.
Cleaned bam files were converted to fastq files with bedtools. For both ribosome profiling and RNA-seq, gene expression was quantified with RSEM (1.2.11) using the cleaned fastq files and Refseq (V69) mouse CDS without the first and last 30nt to avoid the translation initiation and termination peaks. Genes were filtered with minimum 10 reads across all replicates and then the read counts were batch-corrected with the Combat function in sva (3.24.4) using a full model matrix. Batch-corrected counts were normalized with trimmed mean of M values (TMM) method and used to identify differential expressed genes (DEGs) with anota2seq (1.0.0). Instead of the default setting, the priority of TE groups were set to be higher than that of mRNA only groups. A permutation test was performed to estimate the false discovery rate (FDR) with nominal p-value < 0.01, which was 0.097.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and count values for each Sample for both ribosome profiling and input RNA-seq as well as the output from the anota2seq program used for calculating TE

organism: Mus musculus

source_name: hippocampal-cortical brain slices

growth_protocol: Fmr1 KO mice were obtained from Dr. Stephen T. Warren and backcrossed for more than 10 generations on a C57BL/6 background. Food and water were provided ad libitum, and mice were kept on a 12 h light/dark cycle (7am-7pm light period). Pups were kept with their dams until weaning at postnatal day 21. After weaning, mice were group housed (maximum of 6 per cage) by sex. Cages were maintained in ventilated racks in temperature (20-21°C) controlled rooms.

extract_protocol:
Frozen, isolated CA1 hippocampal slices were thawed in ice-cold homogenization buffer (20mM Tris-HCl pH7.4, 5mM MgCl2, 100mM KCl, 1mM DTT, 100μg/ml CHX (cycloheximide), 25U/ml Turbo DNaseI (Ambion, #AM2238), 1X EDTA-free protease inhibitor (Roche), avoiding detergent in nuclease-free water) on ice for 5min. Wide orifice tips were used to transfer slices to a pre-chilled detergent-free Dounce homogenizer. Tissues were slowly homogenized by hand (20 strokes of loose pestle A, and 20 strokes of tight pestle B). Homogenates were carefully transferred to clean 1.5ml tubes with clean glass Pasteur pipets and bulbs. 1% NP-40 was added to the homogenates and incubated on ice for 10min. Homogenates were clarified by centrifugation at 2,000g 4 °C for 10min. The supernatants were collected and clarified again by centrifugation at 20,000g 4 °C for 10min. The supernatants were collected, and the amounts of nucleic acid were measured by Nanodrop (A260 units). For each sample, cytoplasmic RNA for RNA-seq was purified from one-fourth of the lysate with TRIzol LS reagent (Invitrogen, #10296028). The other three-fourths of the lysate was digested with 100ng RNase A (Sigma, # R4875) and 60U RNase T1 (Thermo Fisher Scientific, #EN0542) per A260 at 25°C for 30 min and stopped by chilling on ice and adding 50U SUPERase In RNase inhibitor (Ambion, #AM2694). Digested lysates were applied to 10%-50% (w/v) sucrose gradients prepared in 1X polysome buffer (20mM Tris-HCl pH7.4, 5mM MgCl2, 100mM KCl, 1mM DTT, 100μg/ml CHX in nuclease-free water). After the ultracentrifugation in a SW41Ti rotor (Beckman Coulter) at 35,000 rpm (avg 151,263g) 4°C for 2.5 hours, gradients were fractionated at 1.5 ml/min and 12 sec collection intervals through a fractionation system (Brandel) that continually monitored A260 values. Monosome fractions were identified, pooled, and extracted with TRIzol LS.
3' ligation based library construction, which is similar to miRNA-seq. Ribosome protected mRNA fragments were ligated to 3' adapters. RT was then performed and cDNA was circularized. PCR was performed to add adapters for Illumina sequencing. In parallel, input RNA samples were processed similarly as the ribosome footprints except the following steps. After rRNA depletion, input RNA mixed with an equal volume of 2x alkaline fragmentation solution (2 mM EDTA, 10 mM Na2CO3, 90 mM NaHCO3, pH ~ 9.3) and heated at 95°C for 15min to achieve an average fragment length of ~140nt. Fragmented RNA samples were separated on a 10% TBU gel and size-selected between the 100 and 150nt markers. RT products were separated on a 10% TBU gel and the 200-250nt region was selected. Antisense probe depletion was omitted for input RNA samples. 260-300bp final PCR products were size-selected on an 8% TBE gel.  The size distributions of final libraries were measured by Fragment Analyzer (Advanced Analytical, performed by Molecular Biology Core Labs at UMMS). The concentrations were quantified with KAPA Library Quantification Kit (Kapa Biosystems, #KK4835). Libraries were pooled with equal molar ratios, denatured, diluted, and sequenced with NextSeq 500/550 High Output Kit v2 (Illumina, 75bp single-end runs, #FC-404-2005) on a Nextseq500 sequencer (Illumina).

treatment_protocol: Briefly, mice were anesthetized with ketamine (125 mg/kg)/xylazine (25 mg/kg) and transcardially perfused with chilled (4°C) sucrose dissection buffer aerated with 95% O2/5% CO2. Transverse hippocampal slices (400µm) were obtained on a Leica VT1200S slicer. For ribosomal profiling experiments (Figure 1), CA3 was cut off to enrich for CA1 and for each biological replicate, 8-10 slices from 6-8 mice/genotype were pooled. Slices were recovered and maintained at 30°C for 3-4 hours in artificial cerebrospinal fluid (ACSF) aerated with 95%/O2/5% CO2 to pH 7.4. Slices were then treated with cycloheximide (100 µg/ml) in ACSF, 4°C, snap-frozen on dry ice/EtOH bath, and stored at -80°C.

tag: strain

value: brain

value: Male

value: post natal day 28-35

value: wild type

tag: experiment

value: ribosome profiling

tag: molecule subtype

value: ribosome protected RNA footprint


title: Chicken DRG E5 Brachial

description:
miRNA profile
2

source_name: Chicken Brachial DRG at embryonic day 5


title: S_122_PLB_T8

tag: visit

tag: treatment

tag: age


title: wt_ribo_rep4

tag: gender


title: S_97_PLB_T0

tag: response


title: S_93_PLB_T0


title: S_89_DLX_T8


title: S_100_DLX_T0


title: S_94_DLX_T8


title: S_92_PLB_T0


title: S_95_PLB_T8


title: S_99_PLB_T0


title: 48Q-Bcat-replicate-2

city: Duarte

first: Zijie

last: Sun

state: CA

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

description:
S7573
Processed ARQs-Bcat read_counts.txt

data_processing:
Real-time analysis (RTA)2.2.38 software was used to process the image analysis and base calling.
Reads were aligned against the mouse genome (mm10) using TopHat (v.2.0.14).
Read counts were tabulated using HTSeq-count (v0.6.0)
Genome_build: UCSC. The mouse genome (mm10).
Supplementary_files_format_and_content: Txt file with raw reads for each sample corresponding to each gene

source_name: Prostate tumor

extract_protocol:
RNA samples were extracted from fresh mouse prostate tumors or normal prostate using RNA-Bee (TEL-TEST, Inc.,Friendswood, TX, USA)
The library was prepared with Kapa RNA Hyperprep Kit (Kapa Biosystems, CatKK8581).

value: ArhAR48Q/Y  Ctnnb1(Ex3)L/wt PBCre-4

value: Prostate

tag: tumor/normal

value: Tumor


title: S_96_DLX_T8


title: WT-control-replicate-1

description:
S8126
Processed ARQs-Bcat read_counts.txt

source_name: Prostate tissue

value: Normal


title: S_98_DLX_T8

value: F


title: S_98_DLX_T0

value: whole blood


title: S_96_DLX_T0

value: DLX


title: S_89_DLX_T0


title: S_92_PLB_T8

value: PLB


title: S_91_PLB_T8


title: S_90_PLB_T8


title: S_93_PLB_T8


title: S_94_DLX_T0


title: S_90_PLB_T0


title: S_95_PLB_T0


title: S_91_PLB_T0


title: S_97_PLB_T8


title: wt_ribo_rep3

tag: genotype


title: S_88_DLX_T0


title: 12Q-Bcat-repilcate 2

description:
S7286
Processed ARQs-Bcat read_counts.txt

value: ArhAR12Q/Y  Ctnnb1(Ex3)L/wt PBCre-4


title: wt_ribo_rep2


title: wt_ribo_rep1


title: ko_ribo_rep5

value: Fmr1 KO


title: 48Q-Bcat-replicate-1

description:
S7329
Processed ARQs-Bcat read_counts.txt


title: g2-E18-5_3

city: Rochester

first: Andrew

last: McDavid

state: NY

address: 265 Crittenden Boulevard, CU 420630

institute: University of Rochester

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - Trimmomatic-0.36 "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15"
MAPPING - STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - subread-1.5.0p3, featurecounts, Unique   "-s 2 -t exon -g gene_name"

Genome_build: GRCm38.p5 + Gencode-M12
Supplementary_files_format_and_content: Gene counts, tab delimited

molecule: polyA RNA

source_name: Type II lung cells

growth_protocol: Mouse AT2 cells were isolated from SftpcEGFP mice using Dispase with agarose instillation via the trachea, followed by filtration and immunodepletion with anti-CD16/CD32 and CD45 antibodies.  AT2 cells collected from SftpEGFP mice were purified by sorting for green fluorescence using a 4-laser, 18-color FACSAria II flow cytometer (Becton Dickenson, San Jose, CA) in a Baker BioPROTECT hood (Baker, Sanford, ME) at the University of Rochester Medical Center flow facility.

extract_protocol:
AT2 cells isolated from SftpcEGFP mice were immediately in RLT Plus buffer (Qiagen). RNA extraction was performed with Qiagen RNeasy PLUS Micro kit following manufacturer recommendations and its concentration was determined with the NanopDrop 1000 spectrophotometer and RNA quality assessed with the Agilent Bioanalyzer.
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for Illumina sequencing library construction per manufacturer’s protocols.

treatment_protocol: SftpcEGFP mice obtained from Brigid Hogan (Duke Medical Center, Raleigh, NC). Newborn mice were exposed to room air or hyperoxia (100% oxygen) between postnatal days 0 and 4. Dams were rotated between room air and hyperoxia every 24 hours to reduce oxygen toxicity to their lungs.  Oxygen levels, humidity of 40%-70% and temperature of 37ºC were monitored at least twice per day. Mice were housed in micro-isolator cages in a specified pathogen-free environment, and were provided food and water ad libitum.  All experiments with mice were reviewed and approved by the University Committee on Animal Resources at the University of Rochester.

value: SftpcEGFP

value: Room air


title: WT-control-replicate-2

description:
S7722
Processed ARQs-Bcat read_counts.txt


title: g2-E18-5_1


title: ko_ribo_rep3

value: brain

value: Male


title: RA-pnd4-M2


title: ko_ribo_rep1

value: post natal day 28-35


title: g2-E18-5_2


title: RA-pnd4-M1


title: S_86_DLX_T0

value: M


title: S_83_DLX_T8


title: S_86_DLX_T8


title: S_83_DLX_T0


title: S_84_PLB_T8


title: S_85_PLB_T8


title: S_85_PLB_T0


title: S_87_PLB_T8


title: S_82_PLB_T8


title: S_82_PLB_T0


title: S_81_PLB_T8


title: S_80_DLX_T8


title: S_84_PLB_T0


title: ko_ribo_rep2

value: ribosome profiling

value: ribosome protected RNA footprint


title: S_80_DLX_T0


title: RA-pnd4-3


title: wt_rna_rep3

value: wild type

value: cytoplasmic fraction RNA-seq

value: random fragmented RNA


title: O2-pnd4-M2

value: 100percent Oxygen from birth until PND4


title: S_79_DLX_T8

value: F

value: whole blood


title: O2-pnd4-M1


title: wt_rna_rep1


title: wt_rna_rep2


title: O2-pnd4-3


title: injected_knockdown_Rep_6

city: Munich

first: Adam

last: Burton

address: Marchioninistr. 25

department: IES

country: Germany

institute: Helmholtz Munchen

data_processing:
Fastq reads were trimmed using  Bbduk software with the parameters: ktrim=r, k=23, mink=11, hdist=1, tbo, tpe. (version last modified May 30, 2018)
SAM: Trimmed reads were aligned using STAR (version 2.5.2b) with the following parameters: --outFilterType BySJout --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0 --outFilterMismatchNmax 33 --seedSearchStartLmax 12 --alignSJoverhangMin 15
BAM: SAM files were converted to BAM and sorted using samtools utilities.
Counts: HTSeq tool htseq-count (version 0.9.1) was used for read counting against the gene annotations downloaded from gencode (Release M12, GRCm38.p5) with reverse strand setting. SAM files were converted to BAM and sorted using samtools utilities.
Differential gene expression analysis between the three conditions was performed using DESeq2 (version 1.18.1). Spike-in normalisation factor was calculated from ERCC spike-in mix using the remove unwanted variation strategy from RUVseq (version 1.12.0). DESeq2 was run with the design: spike-in normalisation factor + conditions.
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2 output

source_name: 2-cell stage

growth_protocol: incubation KSOM

extract_protocol:
single embryo
Smartseq2

treatment_protocol: microinjection zygotes Suv39h1wt or mut mRNA

tag: injected with

value: dsSuv39h2 injected

value: 2-cell stage embryo

tag: strain background

value: Hybrid crosses  (paternal DBA/ maternal F1:C57BL/6J × CBA/H)


title: injected_knockdown_Rep_5


title: ko_rna_rep5

value: Fmr1 KO


title: ko_rna_rep4


title: ko_ribo_rep4


title: injected_control_Rep_6

value: dsLacz injected


title: ko_rna_rep3

value: brain


title: 12Q-Bcat-repilcate 1

description:
S5893
Processed ARQs-Bcat read_counts.txt

value: ArhAR12Q/Y  Ctnnb1(Ex3)L/wt PBCre-4

value: Prostate

value: Tumor


title: S_79_DLX_T0

value: DLX


title: S_78_PLB_T0

value: PLB


title: S_75_PLB_T8

value: M


title: S_77_DLX_T0


title: ko_rna_rep2

value: Male

value: post natal day 28-35

value: cytoplasmic fraction RNA-seq


title: S_76_DLX_T8


title: S_78_PLB_T8

value: F


title: S_76_DLX_T0

value: whole blood


title: S_73_DLX_T0


title: injected_control_Rep_5


title: S_74_DLX_T0


title: S_75_PLB_T0


title: S_72_PLB_T8


title: ko_rna_rep1

value: random fragmented RNA


title: S_77_DLX_T8


title: S_73_DLX_T8


title: injected_knockdown_Rep_3

value: dsSuv39h2 injected

value: 2-cell stage embryo


title: injected_knockdown_Rep_4

value: Hybrid crosses  (paternal DBA/ maternal F1:C57BL/6J × CBA/H)


title: wt_vehicle_heavy_rnaseq

data_processing:
RNA-seq
Fastq files were uploaded to the Dolphin platform at the UMMS Bioinformatics Core for mapping and quantification. 9nt molecular labels were trimmed from both 5’ends of the pair-end reads and quality-filtered with Trimmomatic (0.32). Reads mapped to  mouse rRNA by Bowtie2 (2.1.0) were filtered out. Cleaned reads were next mapped to the Refseq (V69) mouse transcriptome and quantified by RSEM (1.2.11).
Estimated counts on each gene were used for the differential gene expression analysis by DESeq2 (1.16.1). After the normalization by median of ratios method, only the genes with minimal 5 counts average across all samples were kept for the DEG analysis. Data were fit to a model of treatment+fraction+treatment:fraction+treatment:genotype:fraction and the treatmenthht.fractionheavy result was used to identify mRNA enriched or depleted in the heavy fractions after HTT treatment. P<0.05 and 2-fold change were used as the cut-offs.
For the medium fractions after HHT treatment, Fmr1 KO samples was directly compared to the WT samples and p<0.05 was used as the cut-off for identifying DEGs. Steady state ribosome profiling data of the decreased DEGs were compared to all the other genes to indepdently confirm whether these mRNAs indeed had fewer stalled ribosomes in Fmr1 KO.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count and tpm values for each Sample

extract_protocol:
Frozen cortical-hippocampal slices were thawed in ice-cold homogenization buffer on ice for 5min. Wide orifice tips were used to transfer slices to a pre-chilled detergent-free Dounce homogenizer. Tissues were gently homogenized by hand (3 strokes of loose pestle A, and 7 strokes of tight pestle B). Homogenates were carefully transferred to clean 1.5ml tubes with clean glass Pasteur pipets and bulbs. Homogenates were clarified by centrifugation at 2,000g 4 °C for 10min. The supernatants were collected and clarified again by centrifugation at 10,000g 4 °C for 10min. The supernatants were collected, and the amounts of nucleic acid were measured with Nanodrop (A260 units). 1% NP-40 was added to the homogenates and incubated on ice for 10min. ~1A260 unit of lysate was saved for the input RNA. ~5 A260 units of lysate were applied to 15%-45% (w/w) sucrose gradients prepared in 1X polysome buffer and with the lower block mark and long cap. After the ultracentrifugation in a SW41Ti rotor (Beckman Coulter) at 35,000 rpm (avg 151,263g) 4°C for 2 hours, gradients were fractionated at 1.5 ml/min and 20 sec collection intervals through a fractionation system (Brandel) that continually monitored A260 values. Some gradients were treated with RNase A prior to centrifugation.
Based on the FMRP signals in the immunoblotting of gradient fractions, medium and heavy fractions were identified, pooled, and extracted with TRIzol LS together with saved input lysates. RNA samples were quantified with Qubit HS RNA assay kit and the integrity was examined with Fragment Analyzer. 200ng RNA was used for BIOO Rapid directional qRNA-seq library preparation following the manufacturer’s instructions. 12 cycles were used for the final PCR amplification. The libraries were quantified with KAPA Library Quantification Kit and the quality was examined with Fragment Analyzer. Libraries were pooled with equal molar ratios, denatured, diluted, and sequenced with NextSeq 500/550 High Output Kit v2 (Illumina, 80bp pair-end runs for RNA-seq, #FC-404-2002) on a Nextseq500 sequencer (Illumina).

treatment_protocol: Briefly, mice were anesthetized with ketamine (125 mg/kg)/xylazine (25 mg/kg) and transcardially perfused with chilled (4°C) sucrose dissection buffer aerated with 95% O2/5% CO2. Transverse hippocampal slices (400µm) were obtained on a Leica VT1200S slicer.WT or Fmr1KO mouse hippocampal slices were treated with DMSO vehicle or 20µM HHT for 30min at 30°C. Ten slices from 2-3 mice/genotype were pooled for each biological replicate.

value: wild type


title: wt_vehicle_medium_rnaseq

value: brain


title: wt_vehicle_input_rnaseq


title: injected_control_Rep_3

value: dsLacz injected


title: injected_control_Rep_2


title: S_70_PLB_T8


title: S_70_PLB_T0


title: S_71_PLB_T0


title: S_68_DLX_T8


title: wt_hht_rep2_heavy_rnaseq


title: S_69_PLB_T0


title: S_87_PLB_T0


title: injected_control_Rep_4


title: S_71_PLB_T8


title: S_74_DLX_T8


title: non_injected_Rep_3

value: non-injected


title: wt_hht_rep2_medium_rnaseq


title: S_68_DLX_T0


title: Chicken DRG E7 Thoracic

description:
miRNA profile
8

source_name: Chicken Thoracic DRG at embryonic day 7

value: wildtype

value: Thoracic


title: S_72_PLB_T0

value: PLB


title: wt_hht_rep1_medium_rnaseq


title: wt_hht_rep1_heavy_rnaseq


title: S_67_PLB_T8

value: M


title: non_injected_Rep_4


title: S_66_PLB_T8


title: S_67_PLB_T0


title: S_69_PLB_T8


title: wt_rna_rep4

value: Male


title: S_65_PLB_T0


title: injected_knockdown_Rep_2


title: S_66_PLB_T0


title: non_injected_Rep_2


title: wt_hht_rep2_input_rnaseq

value: post natal day 28-35


title: injected_knockdown_Rep_1


title: wt_hht_rep1_input_rnaseq

value: cytoplasmic fraction RNA-seq


title: S_81_PLB_T0


title: ko_vehicle_heavy_rnaseq

value: Fmr1 KO


title: injected_control_Rep_1


title: non_injected_Rep_1


title: ko_vehicle_medium_rnaseq


title: ko_vehicle_input_rnaseq


title: S_62_DLX_T0

value: DLX

value: whole blood


title: S_62_DLX_T8


title: ko_hht_rep1_heavy_rnaseq


title: S_64_PLB_T8

value: F


title: S_63_DLX_T8


title: S_64_PLB_T0


title: S_63_DLX_T0


title: S_61_PLB_T0


title: ko_hht_rep2_medium_rnaseq


title: S_59_DLX_T8


title: S_58_PLB_T8


title: S_58_PLB_T0


title: S_59_DLX_T0


title: ko_hht_rep1_medium_rnaseq


title: S_57_DLX_T8


title: ko_hht_rep2_input_rnaseq


title: ko_hht_rep1_input_rnaseq


title: slice_hrt_60

description: ribosome protected RNA footprint

data_processing:
Library strategy: Ribosome profiling
Ribosome protected footprints, 5nt UMI sequences
Individual samples were separated from the raw fastq files based on the barcode sequences. Adaptor sequences (TGGAATTCTCGGGTGCCAAGGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG) were removed with cutadapt (1.7.1). Trimmed fastq files were uploaded to the Dolphin platform (https://www.umassmed.edu/biocore/introducing-dolphin/) at the UMMS Bioinformatics Core for the mapping steps. Trimmed reads were quality filtered with Trimmomatic (0.32) and mapped to the mouse rRNA and then tRNA references with Bowtie2 (2.1.0). Unmapped reads were next mapped to the mm10 mouse genome with Tophat2 (2.0.9). Reads mapped to >1 loci of the genome were classified as “multimapped” reads and discarded. PCR duplicates were marked based on the UMI sequences with custom scripts and only uniquely mapped reads without duplicates were retained with Samtools (0.0.19) for the downstream analyses. RPF length distribution, P-site offsets, and frame preference were calculated with plastid (0.4.8). Counts at each nucleotide position were extracted using P-sites of RPFs and 5’end of mRNA reads with +11 offset, normalized to the library size, averaged across replicates, and plotted along mRNA positions with custom scripts.
To categorize and group genes with distinct ribosome run-off patterns, the RPF of each gene at each time point was first normalized to time point 0. The Euclidean distance matrix was then calculated, followed by hierarchical clustering using Ward’s agglomeration method. The clustering process was performed using the hclust, and the clustering heatmap was displayed using pheatmap in R. To test the reliability of clustering, analysis of group similarities (ANOSIM) test was performed using vegan in R with 1000 permutation times on both overall clusters and sub-clusters. The global pattern of each cluster was summarized using the corresponding median and standard deviation in each timepoint.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample and the ratio of 5,10,30,60 timepoints to 0 time sample.

extract_protocol:
Frozen cortical-hippocampal slices were thawed in ice-cold lysis buffer (20mM Tris-HCl pH7.4, 5mM MgCl2, 100mM KCl, 1mM DTT, 100μg/ml CHX, 25U/ml Turbo DNaseI, 1X EDTA-free protease inhibitor, 1% NP-40, in nuclease-free water) on ice for 5min. Tissues were dissociated by pipetting and further trituration through 25G needle for 10 times. Lysates were incubated on ice for 10min and then clarified by centrifugation at 2,000g 4 °C for 10min. The supernatants were collected and clarified again by centrifugation at 20,000g 4 °C for 10min. The supernatants were collected, and the amounts of nucleic acid were measured with Qubit HS RNA assays. Lysates containing ~40µg RNA were digested with 600ng RNase A (Ambion, #AM2270) + 75U RNase T1 (Thermo Fisher Scientific, #EN0542) /µg RNA in 0.3ml at 25°C for 30min and stopped by chilling on ice and adding 50U SUPERase In RNase inhibitor. Digested lysates were applied to 10%-50% (w/v) sucrose gradients similarly as above.
3' ligation based library construction, which is similar to miRNA-seq. Ribosome protected mRNA fragments were ligated to 3' adapters. RT was then performed. RT products were separated on a 10% TBU gel and the 200-250nt region was selected. cDNA was circularized. PCR was performed to add adapters for Illumina sequencing.   260-300bp final PCR products were size-selected on an 8% TBE gel.  The size distributions of final libraries were measured by Fragment Analyzer (Advanced Analytical, performed by Molecular Biology Core Labs at UMMS). The concentrations were quantified with KAPA Library Quantification Kit (Kapa Biosystems, #KK4835). Libraries were pooled with equal molar ratios, denatured, diluted, and sequenced with NextSeq 500/550 High Output Kit v2 (Illumina, 75bp single-end runs, #FC-404-2005) on a Nextseq500 sequencer (Illumina).

treatment_protocol: Briefly, mice were anesthetized with ketamine (125 mg/kg)/xylazine (25 mg/kg) and transcardially perfused with chilled (4°C) sucrose dissection buffer aerated with 95% O2/5% CO2. Transverse hippocampal slices (400µm) were obtained on a Leica VT1200S slicer. For homoharringtonine (HHT) experiments (Figures 3-5), cortical-hippocampal slices were recovered 3-4 hours in ACSF and then treated with HHT (20 µM) (Tocris) or 0.05% DMSO (vehicle) for different times (0, 5, 10, 30, 60 min). At the end of the incubation time, slices were snap/frozen on dry ice/EtOH bath and stored at -80 C. Ten slices from 2-3 mice/genotype were pooled for each biological replicate.

value: ribosome profiling


title: S_60_PLB_T0


title: S_57_DLX_T0


title: S_56_DLX_T8


title: S_56_DLX_T0


title: S_55_PLB_T0


title: slice_hrt_30

description: ribosome protected RNA footprint


title: slice_hrt_10

description: ribosome protected RNA footprint


title: S_53_PLB_T8


title: slice_hrt_5

description: ribosome protected RNA footprint


title: S_61_PLB_T8


title: S_54_DLX_T8


title: slice_hrt_0

description: ribosome protected RNA footprint


title: miR-17-5

city: Nantes

first: Frederic

last: Blanchard

address: 1 rue Gaston Veil

country: France

institute: INSERM

description:
10_TREATED_RNASEQ
processed data file: gene_matrix_fpkm.txt

data_processing:
Basecalls performed using bcl2fastq2 (v2.20).
The reads are mapped to the genome using the STAR algorithm (v2.5.2b) with default settings. Alignment information for each read is stored in the BAM format.
Read counts per gene were obtained using featureCounts program in Subread software packages (v1.5.2). Only read pairs that have both ends aligned were counted.
Differential expression analysis performed with DESeq2 (v1.14.1) at 10% adjusted P-value level.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_matrix_fpkm.txt: Tab-delimited text file with FPKM (Fragments Per Kilobase of transcript per Million mapped reads).

source_name: ankle

extract_protocol:
Ankles were dissected (skin was removed), flash frozen on dry ice, and RNA was harvested using QIAzol lysis reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Ankles of DBA1 mice with collagen-induced arthritis were injected intra-articularly with miR-17-5p mimic lipoplex or irrelevant miR lipolex.

tag: joint

value: ankle

tag: induction

value: collagen-induced arthritis

tag: miRNA


title: S_52_PLB_T8

tag: tissue


title: ko_hht_rep2_heavy_rnaseq

value: brain


title: S_54_DLX_T0


title: S_51_DLX_T0


title: miR-17-2

description:
07_TREATED_RNASEQ
processed data file: gene_matrix_fpkm.txt


title: S_60_PLB_T8


title: S_49_DLX_T8


title: S_55_PLB_T8


title: S_51_DLX_T8


title: miR-17-4

description:
09_TREATED_RNASEQ
processed data file: gene_matrix_fpkm.txt


title: miR-17-1

description:
06_TREATED_RNASEQ
processed data file: gene_matrix_fpkm.txt


title: miR-control-5

description:
05_CONTROL_RNASEQ
processed data file: gene_matrix_fpkm.txt

value: miR-control


title: S_52_PLB_T0


title: S_50_PLB_T8


title: miR-control-3

description:
03_CONTROL_RNASEQ
processed data file: gene_matrix_fpkm.txt


title: S_53_PLB_T0


title: S_48_PLB_T8


title: S_50_PLB_T0


title: miR-control-2

description:
02_CONTROL_RNASEQ
processed data file: gene_matrix_fpkm.txt


title: S_47_DLX_T8


title: S_49_DLX_T0


title: S_47_DLX_T0


title: S_46_PLB_T0


title: S_44_PLB_T0


title: S_45_DLX_T0


title: S_43_DLX_T0


title: S_48_PLB_T0


title: S_43_DLX_T8


title: S_44_PLB_T8


title: microglia_M689

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
FACS isolated using EMBRACE technique
microglia_mof_vs_cre_DEseq_basic_counts_DESeq2.normalized.tsv
microglia_mof_vs_cre_DEseq_basic_DEresults.tsv

data_processing:
RNA-seq: Raw sequencing data controlled for quality, trimmed and mapped to the reference mm10 genome using STAR (Dobin et al., 2013).
RNA-seq: The identity of reads was identified through FeatureCount (Liao et al., 2014).
RNA-seq: Differentially expressed genes were identified using DESeq2 (Love et al., 2014).
ChIP seq: Raw sequencing data controlled for quality, trimmed and mapped to the reference mm10 genome using Bowtie2 (Langmead B et al., 2012).
ChIP-seq: PCR duplicates were removed using sambamba (Tarasov et al., 2015)
ChIP-seq: coverage of ChIP and input was calculated and compared using deeptools bamCoverage and bamCompare (Ramirez et al., 2016)
Genome_build: mm10

growth_protocol: pericytes were extracted from the adult brain and maintained in Pericyte medium (ScienCell 1201) with the appropriate growth factors

extract_protocol:
RNA from cultured pericytes, whole E14.5 brains and from neural cells was isolated using the Qiagen mini kit (#74104), while RNA from pericytes, endothelial cells and microglia was extracted using the Qiagen miRNeasy Micro kit (#1071023).
Libraries for RNA-seq of cultured pericytes, whole E14.5 brains and the neural population were prepared using the Illumina TruSeq library preparation kit. For pericytes, endothelial cells and microglia, cDNA was prepared from isolated RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech 634891). Libraries were prepared using the Nextera XT DNA library preparation kit (Illumina FC-131-1096) and sequenced on the HiSeq Hiseq 3000 or NextSeq 500.
ChIP and library preparation for IP DNA was undertaken using the RELACS protocol (Arrigoni et al. 2018 Communications Biology)

treatment_protocol: FA treatment (FA were conjugated with BSA before application): 200 μM C14:0, 200 μM C16:0, 20 μM C20:0 and 10 μM C24:0. Vehicle: ethanol + BSA.

value: microglia

tag: genotype/variation

value: Mof nKO


title: microglia_M646


title: microglia_M643


title: S_42_PLB_T0


title: microglia_Cre206

value: Cre control


title: S_41_PLB_T0

value: PLB


title: S_41_PLB_T8

value: M


title: microglia_Cre204


title: S_40_PLB_T8


title: microglia_Cre203


title: S_40_PLB_T0


title: S_46_PLB_T8


title: S_39_PLB_T0


title: S_42_PLB_T8


title: whole_brain_K3_149

description:
whole_brain_geneCounts.txt
whole_brain_kansl3_differential_genes.txt

value: whole E14.5 brain

value: Kansl3 nKO


title: S_38_PLB_T0


title: S_38_PLB_T8


title: S_37_DLX_T0


title: whole_brain_K3_119


title: whole_brain_K3_117


title: S_36_PLB_T8


title: whole_brain_K2_63

description:
whole_brain_geneCounts.txt
whole_brain_kansl2_differential_genes.txt

value: Kansl2 nKO


title: whole_brain_K2_68


title: whole_brain_K2_70


title: whole_brain_Mof_197

description:
whole_brain_geneCounts.txt
whole_brain_mof_differential_genes.txt


title: whole_brain_Mof_200


title: S_36_PLB_T0


title: S_33_DLX_T8


title: S_32_DLX_T0


title: S_32_DLX_T8


title: S_31_DLX_T0


title: S_31_DLX_T8


title: ∆swr-1 H3K27me2/3 ChIP-seq rep 2

city: Athens

first: Zachary

middle: A

last: Lewis

state: GA

address: 1000 Cedar St. Biosciences Bldg

department: Microbiology

institute: University of Georgia

data_processing:
Trimmed with TrimGalore! Version version 4.0 parameters --length 20 --fastqc
alignment with bwa mem version 0.7.15/ parameters -M
conversion to bam and sorted and indexed with samtools version 1.3.1/
create tag directory with HOMER version 4.8/ parameters -keepOne
bigwigs made with DeepTools 3.3.1/ parameters --normalizeUsing CPM
Deeptools for creation of heatmaps and metaplots
Genome_build: GCA_000182925.2 (NC12)
Supplementary_files_format_and_content: CPM normalized bigwigs

organism: Neurospora crassa

source_name: ∆swr-1 H3K27me2/3 ChIP-seq

extract_protocol:
Cells lysed in lysis buffer using probe sonicator
Illumina TruSeq

tag: strain info.

tag: developmental stage/tissue

value: mycelium

tag: chip antibody

tag: growth protocol

value: overnight in VMM + 1.5% sucrose, 25˚C

tag: library strategy

value: Illumina TruSeq ChIP


title: ∆swr-1 input ChIP-seq rep 2

source_name: ∆swr-1 input ChIP-seq


title: S_34_DLX_T8

tag: visit

tag: treatment

value: DLX

tag: age

value: F

value: whole blood


title: S_33_DLX_T0

tag: gender

tag: response


title: S_34_DLX_T0


title: S_35_DLX_T8


title: S_35_DLX_T0


title: S_29_DLX_T8


title: S_29_DLX_T0


title: ∆swr-1 H3K27me2/3 ChIP-seq rep 1

description: 103-92_ChIP_NCU09993_dswr-1_K27me2me3_Rep1_Nc_ON-56985988

value: overnight in VMM + 1.5% sucrose, 32˚C


title: S_28_DLX_T8


title: whole_brain_Mof_193


title: S_28_DLX_T0


title: S_30_PLB_T8


title: S_65_PLB_T8


title: whole_brain_Cre_19


title: ∆swr-1 input ChIP-seq rep 1

description: 103-91_ChIP_NCU09993_dswr-1_input_Rep1_Nc_ON-56979017


title: whole_brain_Cre_18


title: ∆hH2az;∆eed;his-3::Pccg-1-3xflag-eed H3K27me2/3 ChIP-seq rep 2

description: 112_34_ChIP_deed_dhh2az_Flag_eed_H3K27me2_3_rep2_S27


title: S_37_DLX_T8


title: S_27_PLB_T8


title: whole_brain_Cre_16


title: ∆eed;his-3::Pccg-1-3xflag-eed input ChIP-seq rep 1

description: 112_31_ChIP_deed_Flag_eed_input_rep2_S24


title: dsSuv39h2 03-07 [D2]

description:
Embryo_D2
processed data file: Mutant.bw

data_processing:
library strategy: NicE-Seq (nicking enzyme assisted sequencing)
Adaptor and low-quality sequences were trimmed from paired-end sequencing reads using Trim Galore v 0.5.0
Trimmed read pairs were mapped to the reference genome (mouse: mm10) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools.
Peak calling was done with MACS2 v. 2.1.2
Genome_build: mm10
Supplementary_files_format_and_content: Bigwigs were generated using 100bp bins using deeptools bamCoverage with the following parameters: --normalizeUsing RPKM

source_name: Suv39h2 knockdown_8-cell stage

extract_protocol:
nuclear isolation of fixed embryos, phenol-chloroform for DNA extraction, streptavidin beads capture of biotin labelled accessible regions
NEB Ultra II kit

treatment_protocol: microinjection zygotes 500 ng/ul dsSuv39h2 or dsLacz RNA

value: Hybrid crosses  (paternal DBA/maternal F1:C57BL/6J × CBA/H)

value: dsSuv39h2 injected

tag: developmental stage

value: 8-cell stage


title: Control 05-07 [C3]

description:
Embryo_C3
processed data file: Control.bw

source_name: control_8-cell stage

tag: strain background

value: dsLacz injected


title: S_27_PLB_T0


title: S_26_DLX_T0


title: ∆hH2az;∆eed;his-3::Pccg-1-3xflag-eed input ChIP-seq rep 2

description: 112_33_ChIP_deed_dhh2az_Flag_eed_input_rep2_S26


title: Control 03-07 [C2]

description:
Embryo_C2
processed data file: Control.bw


title: S_24_DLX_T8


title: dsSuv39h2 08-06 [D1]

description:
Embryo_D1
processed data file: Mutant.bw


title: S_25_DLX_T0


title: dsSuv39h2 05-07 [D3]

description:
Embryo_d3
processed data file: Mutant.bw


title: ∆cac-3 input ChIP-seq rep 2

source_name: ∆cac-3 input ChIP-seq


title: S_26_DLX_T8


title: S_25_DLX_T8


title: S_23_PLB_T0


title: S_22_DLX_T8


title: S_24_DLX_T0


title: S_22_DLX_T0


title: ∆cac-3 H3K27me2/3 ChIP-seq rep 2

source_name: ∆cac-3 H3K27me2/3 ChIP-seq


title: ∆eed;his-3::Pccg-1-3xflag-eed H3K27me2/3 ChIP-seq rep 1

description: 112_32_ChIP_deed_Flag_eed_H3K27me2_3_rep2_S25


title: Control 08-06 [C1]

description:
Embryo_C1
processed data file: Control.bw


title: ∆set-7 H3K27me2/3 ChIP-seq rep 2

source_name: ∆set-7 H3K27me2/3 ChIP-seq


title: S_23_PLB_T8


title: ∆set-7 input ChIP-seq rep 2

source_name: ∆set-7 input ChIP-seq


title: Wild type input ChIP-seq rep 4

source_name: Wild type input ChIP-seq

value: Wild type


title: Capture3_Drop-seq

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description:
DropSeq_counts.txt
read1 contains the cell barcode in bases 1-12, and the UMI in bases 13-20. read2 is cDNA.  Please see the file cell_barcodes.txt (available on series record) for cell barcode for each cell ID.

data_processing:
Drop-Seq data was processed using Drop-Seq_tools_1.13. The alignment and QC pipeline used is available at http://mccarrolllab.com/dropseq/ (Macosko et al., 2015). Base calls were performed with bcl2fastq. Reads were aligned to reference genome mm9 with STAR aligner. Aligned reads were tagged with its mate-pair UMI and cell barcode. Then aligned exon reads were tagged with the corresponding gene name. This pipeline produced a single cell Digital Gene Expression (DGE) matrix that was used for downstream analysis.
genome build: mm9
Supplementary_files_format_and_content: peak bed file: Counts table: raw counts per gene for RNA-seq

source_name: Germinal center B cells_CXCR4-/loCD83+

extract_protocol: Drop-Seq was performed on single-cell GC B cell suspensions to generate single-cell cDNA libraries attached to microbeads. Microbeads were counted, amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.

treatment_protocol: Mice were immunized intraperitoneally with 10^9 sheep red blood cells in PBS, then boosted with 10^9 SRBC 5 days later. On day 14, germinal center B cells were isolated from spleens for downstream applications.

tag: cell type

value: Germinal center B cells

tag: sorting strategy

value: Total B220+GL7+CD95+ GC B cells were isolated by FACS for Drop-Seq captures and downstream single cell RNA-Seq. To detect a balanced distribution of GC B subpopulations contained within the total GC B cell population, three Drop-Seq captures were performed. Capture 1 corresponds to GC B cells broadly gated as CXCR4+CD83-/lo, capture 2 as CXCR4+CD83+, and capture 3 as CXCR4-/loCD83+.


title: Capture2_Drop-seq

source_name: Germinal center B cells_CXCR4+CD83+


title: Wild type H3K27me2/3 ChIP-seq rep 4

description: 112_24_ChIP_wildtype_H3K27me2_3_rep2_S17

source_name: Wild type H3K27me2/3 ChIP-seq


title: S_21_PLB_T8

value: PLB


title: ∆hH2az;∆eed;his-3::Pccg-1-3xflag-eed H3K27me2/3 ChIP-seq rep 1


title: Capture1_Drop-seq

source_name: Germinal center B cells_CXCR4+CD83-/lo


title: ∆hH2Az H3K27me2/3 ChIP--seq rep 5

source_name: ∆hH2Az H3K27me2/3 ChIP--seq


title: S_21_PLB_T0


title: S_19_DLX_T8


title: S_20_PLB_T0


title: S_20_PLB_T8


title: S_39_PLB_T8


title: ∆hH2Az input ChIP--seq rep 1

source_name: ∆hH2Az input ChIP--seq


title: ∆set-7 H3K27me2/3 ChIP-seq rep 1


title: S_18_DLX_T0


title: S_18_DLX_T8


title: S_45_DLX_T8

value: M


title: S_19_DLX_T0


title: S_30_PLB_T0


title: Wild type H3K27me2/3 ChIP-seq rep 3


title: S_17_PLB_T0


title: Wild type input ChIP-seq rep 3


title: S_17_PLB_T8


title: S_16_PLB_T8


title: hH2Az-gfp input ChIP-seq rep 2

description: 103-42_ChIP_S493_hH2Az-gfp_input_Rep1_Nc_ON-56987956

source_name: hH2Az-gfp input ChIP-seq


title: ∆cac-3 H3K27me2/3 ChIP-seq rep 1

description: 102-79_ChIP_NCU06679_dcac3_K27me2me3_Rep1_Nc_ON-51568623


title: S_88_DLX_T8


title: MN_Col: genomic DNA of saliva (for pre-test) from MN via Oragene with column treatment

type: genomic

city: Kumamoto

first: Kazuya

last: Iwamoto

address: 1-1-1 Honjo, Chuo-ku

department: Faculty of Life Sciences

institute: Kumamoto University

description: genomic DNA (pre-test) of human saliva sample, extracted by Ora-kit with column treatment

hyb_protocol: Bisulfite converted DNA was amplified, processed and hybridized to Illumina HumanMethylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: BeadStudio.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol was used.

extract_protocol: Genomic DNA of blood was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions. Genomic DNA of saliva was extracted rom saliva samples using Ora-kit according to standard instructions and purified by precipitation with EtOH.

value: saliva

tag: test series

value: pre-test


title: S_16_PLB_T0

data_processing: All array probes and samples were subjected to quality control using Flexarray® package implemented in R (version 1.6.3). Data were normalized using background adjustment and log2 transformation, variance stabilization transformation (VST) correction, and quantile normalization.

extract_protocol: Whole blood samples were collected using PAXgene Blood RNA Tubes (PreAnalytix®). Total RNA was extracted using the Qiagen miRNeasy Micro Kit, with DNase treatment.

tag: tissue


title: MN_Ora: genomic DNA of saliva (for pre-test) from MN via Oragene

description: genomic DNA (pre-test) of human saliva sample, extracted by Ora-kit without column/RNase treatment


title: ∆set-7 input ChIP-seq rep 1

value: mycelium


title: MN_Col_Rna: genomic DNA of saliva (for pre-test) from MN via Oragene with column/RNase treatment

description: genomic DNA (pre-test) of human saliva sample, extracted by Ora-kit with column/RNase treatment


title: MN_Ora_Rna: genomic DNA of saliva (for pre-test) from MN via Oragene with Rnase treatment

description: genomic DNA (pre-test) of human saliva sample, extracted by Ora-kit with RNase treatment


title: S_15_PLB_T0


title: S_15_PLB_T8


title: ∆cac-3 input ChIP-seq rep 1

description: 102-78_ChIP_NCU06679_dcac3_input_Rep1_Nc_ON-51573552

value: Illumina TruSeq ChIP


title: hH2az complementation strain 2 H3K27me2/3 ChIP-seq rep 1

description: 102-75_ChIP_ACt9-3_dH2Az_H2Az_K27me2me3_Rep1_Nc_ON-51564635

source_name: hH2az complementation strain H3K27me2/3 ChIP-seq

value: hH2az complementation strain


title: S_14_DLX_T0

value: DLX


title: hH2az complementation strain 2 input ChIP-seq rep 1

description: 102-74_ChIP_ACt9-3_dH2Az_H2Az_input_Rep1_Nc_ON-51557731

source_name: hH2az complementation strain input ChIP-seq


title: S_14_DLX_T8

value: whole blood


title: hH2az complementation strain 1 H3K27me2/3 ChIP-seq rep 1

description: 102-73_ChIP_ACt12-1_dH2Az_H2Az_K27me2me3_Rep1_Nc_ON-51570611

value: overnight in VMM + 1.5% sucrose, 32˚C


title: S_13_DLX_T8


title: hH2az complementation strain 1 input ChIP-seq rep 1

description: 102-72_ChIP_ACt12-1_dH2Az_H2Az_input_Rep1_Nc_ON-51565668


title: FS_Ora_Rna: genomic DNA of saliva (for pre-test) from FS via Oragene with Rnase treatment


title: FS_Ora: genomic DNA of saliva (for pre-test) from FS via Oragene


title: Wild type H2A.Z 5ul ChIP-seq rep 1

description: 102-59_ChIP_S2_wt_H2A_Z_5ul_Nc_ON-51560716

source_name: Wild type H2A.Z 5ul ChIP-seq

value: N. crassa H2A.Z


title: FS_Col: genomic DNA of saliva (for pre-test) from FS via Oragene with column treatment


title: FS_Col_Rna: genomic DNA of saliva (for pre-test) from FS via Oragene with column/RNase treatment


title: S_13_DLX_T0


title: S_12_DLX_T8

value: F


title: hH2Az-gfp GFP ChIP-seq rep 2

description: 103-44_ChIP_S493_hH2Az-gfp_GFP_Rep1_Nc_ON-56981971

source_name: hH2Az-gfp GFP ChIP-seq


title: Wild type H2A.Z 2.5ul ChIP-seq rep 1

description: 102-58_ChIP_S2_wt_H2A_Z_2_5ul_Nc_ON-51568620

source_name: Wild type H2A.Z 2.5ul ChIP-seq


title: S_12_DLX_T0


title: CT541_s: genomic DNA of saliva from CT541

description: saliva sample

value: test


title: Wild type H2A.Z 1ul ChIP-seq rep 1

description: 102-24_ChIP_S2_wt_H2A_Z_1ul_Nc_ON-51573547

source_name: Wild type H2A.Z 1ul ChIP-seq


title: Wild type input ChIP-seq rep 2

description: 102-23_ChIP_S2_wt_input_Rep2_Nc_ON-51558724


title: MB_Ora: genomic DNA of saliva (for pre-test) from MB via Oragene


title: MB_Col_Rna: genomic DNA of saliva (for pre-test) from MB via Oragene　with column/RNase treatment


title: CT541_b: genomic DNA of blood from CT541

description: blood sample

value: blood


title: hH2Az-gfp H3K27me2/3 ChIP-seq rep 1

source_name: hH2Az-gfp H3K27me2/3 ChIP-seq


title: S_10_PLB_T8


title: hH2Az-gfp input ChIP-seq rep 1


title: S_11_PLB_T0


title: CT539_b: genomic DNA of blood from CT539

description: blood sample


title: MB_Col: genomic DNA of saliva (for pre-test) from MB via Oragene with column treatment


title: S_9_DLX_T8


title: ∆hH2Az H3K27me2/3 ChIP--seq rep 4


title: hH2Az-gfp GFP ChIP-seq rep 1


title: CT537_s: genomic DNA of saliva from CT537

description: saliva sample


title: S_11_PLB_T8


title: CT539_s: genomic DNA of saliva from CT539

description: saliva sample


title: S_10_PLB_T0


title: ∆hH2Az H3K27me2/3 ChIP--seq rep 3


title: CT540_s: genomic DNA of saliva from CT540

description: saliva sample


title: ∆hH2Az H3K27me2/3 ChIP--seq rep 2


title: S_9_DLX_T0


title: CT540_b: genomic DNA of blood from CT540

description: blood sample


title: CT535_s: genomic DNA of saliva from CT535

description: saliva sample


title: CT535_b: genomic DNA of blood from CT535

description: blood sample


title: S_7_PLB_T8


title: ∆hH2Az H3K27me2/3 ChIP--seq rep 1


title: MB_Ora_Rna: genomic DNA of saliva (for pre-test) from MB via Oragene with Rnase treatment


title: Wild type H3K27me2/3 ChIP-seq rep 2

value: Wild type


title: Wild type H3K27me2/3 ChIP-seq rep 1


title: S_6_PLB_T8


title: S_8_DLX_T0


title: ∆set-7 RNA-seq rep 3

description:
processed data file: NC_Run104.countsNoName.txt
104_R12_RNA_S238_4_927_Dset7_polyA_rep3_Nc_MycelialDisks_S12

source_name: ∆set-7 RNA-seq

value: 12 hours in VMM + 2% glucose, constant light, 30˚C

value: Illumina TruSeq stranded mRNA


title: CT533_b: genomic DNA of blood from CT533

description: blood sample


title: S_7_PLB_T0

value: PLB


title: ∆set-7 RNA-seq rep 2

description:
processed data file: NC_Run104.countsNoName.txt
104_R11_RNA_S238_3_920_Dset7_polyA_rep2_Nc_MycelialDisks_S11


title: ∆set-7 RNA-seq rep 1

description:
processed data file: NC_Run104.countsNoName.txt
104_R10_RNA_S238_2_920_Dset7_polyA_rep1_Nc_MycelialDisks_S10


title: CT533_s: genomic DNA of saliva from CT533

description: saliva sample


title: S_5_PLB_T8

value: M


title: S_6_PLB_T0


title: ∆hH2Az;∆set-7 RNA-seq rep 3

description:
processed data file: NC_Run104.countsNoName.txt
104_R9_RNA_ACx36_1_2_927_Dh2azDset7_polyA_rep3_Nc_MycelialDisks_S9

source_name: ∆hH2Az;∆set-7 RNA-seq


title: CT537_b: genomic DNA of blood from CT537

description: blood sample


title: S_4_DLX_T8


title: CT534_s: genomic DNA of saliva from CT534

description: saliva sample

value: saliva


title: CT531_b: genomic DNA of blood from CT531

description: blood sample


title: CT532_b: genomic DNA of blood from CT532

description: blood sample


title: CT532_s: genomic DNA of saliva from CT532

description: saliva sample


title: ∆hH2Az;∆set-7 RNA-seq rep 2

description:
processed data file: NC_Run104.countsNoName.txt
104_R8_RNA_ACx36_1_3_920_Dh2azDset7_polyA_rep2_Nc_MycelialDisks_S8


title: ∆hH2Az;∆set-7 RNA-seq rep 1

description:
processed data file: NC_Run104.countsNoName.txt
104_R7_RNA_ACx36_1_1_920_Dh2azDset7_polyA_rep1_Nc_MycelialDisks_S7


title: S_4_DLX_T0


title: 252800519299_S01_GE1_107_Sep09_1_3

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min.

scan_protocol: Detection of fluorescence signals was done using the Agilent`s Microarray Scanner System (Agilent Technologies).

data_processing: Agilent’s Feature Extraction software version 11 is used to read and process the TIFF file..The raw data was pre-processed in Partek Genomic Suite

source_name: WT mice 3h

label_protocol: For the linear T7-based amplification step, 20 ng total RNA of sample 1 0h and 40 ng total RNA of all other samples was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: RNA was prepared from sorted splenic Treg cells using the NucleoSpin® RNA kit (Macherey-Nagel) according to the manufacturers instructions. RNA quality was checked using the 2100 Bioanalyzer (Agilent Technologies) with the RNA 6000 Pico Kit for total RNA samples.

tag: genotype/variation

value: CD83 WT

value: 9 weeks

value: female

value: 3h activated splenic sorted Treg cells

tag: array

tag: position of subarray


title: CT531_s: genomic DNA of saliva from CT531

description: saliva sample


title: CT530_s: genomic DNA of saliva from CT530

description: saliva sample


title: S_8_DLX_T8

value: DLX


title: S_3_DLX_T8

value: whole blood


title: 252800519299_S01_GE1_107_Sep09_1_2


title: S_3_DLX_T0


title: ∆hH2Az RNA-seq rep 3

description:
processed data file: NC_Run104.countsNoName.txt
104_R6_RNA_ACx11_19_4_927_Dh2az_polyA_rep3_Nc_MycelialDisks_S6

source_name: ∆hH2Az RNA-seq

tag: strain info.

tag: developmental stage/tissue

value: mycelium


title: 252800519299_S01_GE1_107_Sep09_1_1


title: 252800519298_S01_GE1_107_Sep09_1_3

source_name: WT mice 0h

value: non-activated splenic sorted Treg cells


title: ∆hH2Az RNA-seq rep 2

description:
processed data file: NC_Run104.countsNoName.txt
104_R5_RNA_ACx11_19_3_920_Dh2az_polyA_rep2_Nc_MycelialDisks_S5

tag: growth protocol

tag: library strategy


title: ∆hH2Az RNA-seq rep 1

description:
processed data file: NC_Run104.countsNoName.txt
104_R4_RNA_ACx11_19_1_920_Dh2az_polyA_rep1_Nc_MycelialDisks_S4


title: S_5_PLB_T0

tag: visit

tag: treatment


title: S_2_PLB_T8

tag: age

tag: gender


title: 252800519298_S01_GE1_107_Sep09_1_2


title: CT528_b: genomic DNA of blood from CT528

description: blood sample


title: S_2_PLB_T0

tag: response


title: Wild type RNA-seq rep 3

description:
processed data file: NC_Run104.countsNoName.txt
104_R3_RNA_S1_1_927_WT_polyA_rep3_Nc_MycelialDisks_S3

source_name: Wild type RNA-seq


title: CT529_s: genomic DNA of saliva from CT529

description: saliva sample


title: Wild type RNA-seq rep 2

description:
processed data file: NC_Run104.countsNoName.txt
104_R2_RNA_S1_2_920_WT_polyA_rep2_Nc_MycelialDisks_S2


title: S_1_PLB_T0


title: S_1_PLB_T8


title: CT534_b: genomic DNA of blood from CT534

description: blood sample


title: 252800519298_S01_GE1_107_Sep09_1_1

tag: strain background


title: CT530_b: genomic DNA of blood from CT530

description: blood sample


title: 252800519297_S01_GE1_107_Sep09_2_2

source_name: KO mice 3h

value: 21 weeks

tag: cell type


title: RNA_LZ.2

data_processing:
Raw reads were aligned to reference genome mm9 in a splice-aware manner using the STAR aligner (Dobin, et al., 2013). ENSEMBL mm9 genes were supplemented with ENSEMBL IG annotations from mm10 with coordinates coverted to mm9 by liftOver. Expression level of genes was quantified using FeatureCounts (Liao, et al., 2014).
genome build: mm9
Supplementary_files_format_and_content: peak bed file: Counts table: raw counts per gene for RNA-seq

source_name: Germinal center B cells

extract_protocol: RNA was isolated from the indicated flow sorted GC B cell populations with the Qiagen RNeasy kit (Qiagen). Concentration and purity was analyzed on a Nanodrop 1000 Spectrophotometer. mRNA was isolated by oligo-dT beads and library was prepared using standard Illumina library protocol (Kit: RS-122-2101 TruSeq® Stranded mRNA LT-SetA). Libraries were sequenced on the Illumina Hiseq4000.

value: Germinal center B cells

tag: sorting strategy

value: GC B cells FACS isolated by the new three population strategy were defined as follows. Total GC B cells were defined as B220+GL7+CD95+, then subsets were defined based on CXCR4 and CD83 expression. Proliferative DZ B cells (DZp) were defined as CXCR4+CD83+ (also described as gray zone [GZ] B cells), differentiating DZ B cells were CXCR4+CD83-, and LZ cells were defined as CXCR4-CD83+ GC B cells.


title: CT529_b: genomic DNA of blood from CT529

description: blood sample

value: blood

tag: test series

value: test


title: 80 mM mir-7 sample 4

city: Padova

first: Natascia

last: Tiso

address: via Ugo Bassi 58/B

department: Department of Biology

country: Italy

institute: University of Padova

description: replicate 4

hyb_protocol: Hybridization was performed on a human HT-12 v4 BeadChip according to the manufacturer's instructions

scan_protocol: Target Scan 6.2, mirBASE target, microcosm (EBI)

data_processing: Respective backgrounds were subtracted from all raw data using Bead Studio (Illumina) and the normalized using the cross-correlation method. Minimal intensity value of 30 was used to replace all negative and small intensities in the normalized data.

label: biotin

source_name: neural progenitors

label_protocol: Streptavidin-cy3 -based labeling was performed according to the Illumina® TotalPrep™-96 RNA Amplification Kit protocol

growth_protocol: Differentiation medium (N2B27) for the ReNVM cells comprised of DMEM/F12: Neurobasal (1:1), 0.5x N2, 0.5x B27, 1% L-Glutamine, 1% NEAA.  Neurobasal (1:1), 0.5x N2, 0.5x B27, 1% L-Glutamine, 1% NEAA.  Neurobasal (1:1), 0.5x N2, 0.5x B27, 1% L-Glutamine, 1% NEAA.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) and column-purified with RNeasy kits (Qiagen)

treatment_protocol: Cells were trasfected using 4 ul Lipofectamine RNAimax (Invitrogen) and one of the following RNA oligonucleotides: scrambled duplex (negative control), mir-7 at 50 mM and mir-7 at 80 mM

tag: type

value: ReNVM cells

tag: transfection

value: 80 mM mir-7 PremiR


title: 252800519297_S01_GE1_107_Sep09_2_1

tag: genotype/variation

value: 10 weeks

tag: array


title: CT527_s: genomic DNA of saliva from CT527

description: saliva sample

tag: tissue

value: saliva


title: 252800519297_S01_GE1_107_Sep09_1_4

tag: position of subarray


title: CT527_b: genomic DNA of blood from CT527

description: blood sample


title: 80 mM mir-7 sample 2

description: replicate 2


title: 80 mM mir-7 sample 1

description: replicate 1


title: 80 mM mir-7 sample 3

description: replicate 3


title: CT526_s: genomic DNA of saliva from CT526

description: saliva sample


title: RNA_LZ.1


title: 252800519297_S01_GE1_107_Sep09_1_3

source_name: KO mice 0h


title: RNA_DZp.2


title: Mouse DRG 11.5 TrkC -/- Brachial

description:
miRNA profile in trkC mutant
38

data_processing:
Illlumina software used for base calling
Adaptor removel and barcode extraction was used Mirprof tool by defalt settings.  http://srna-workbench.cmp.uea.ac.uk/mirprof-tutorial/
Data are then loaded to The Small RNA workbench software for aligment, normalisation and comparsion analysis. ( Bioinformatics. 2012 Aug 1; 28(15): 2059–2061.)
Genome_build: mm9, galgal4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Brachial DRG at embryonic day 11.5 in mouse TRkC mutant mouse

extract_protocol:
DRG has dissected and immediately disolved in Extraction buffer and proceed as Thermoscientific miRNA extraction kit (PureLink® miRNA Isolation Kit, K157001)
Using illumina standard protocols

value: trkC mutant

value: brachical

tag: developmental stage


title: CT528_s: genomic DNA of saliva from CT528

description: saliva sample


title: CT525_s: genomic DNA of saliva from CT525

description: saliva sample


title: Mouse DRG 14.5 TrkC -/- Brachial

description:
miRNA profile in trkC mutant
37

source_name: Brachial DRG at embryonic day 14.5 in mouse TRkC mutant mouse


title: RNA_DZp.1


title: Mouse DRG E12.5 Thoracic PDBU

description:
miRNA profile after treatment
36

source_name: Mouse Thoracic DRG at embryonic day 12.5 treated with PDBU

tag: agent

value: PDBU

value: wildtype

value: thoracic


title: 50 mM mir-7 sample 3

description: replicate 3

value: 50 mM mir-7 PremiR


title: CT524_b: genomic DNA of blood from CT524

description: blood sample


title: 252800519297_S01_GE1_107_Sep09_1_2

value: female


title: RNA_DZd.1


title: 50 mM mir-7 sample 4

description: replicate 4


title: RNA_DZd.2


title: Mouse DRG E12.5 Thoracic bFGF

description:
miRNA profile after treatment
35

source_name: Mouse Thoracic DRG at embryonic day 12.5 treated with bFGF

value: bFGF


title: CT526_b: genomic DNA of blood from CT526

description: blood sample


title: RNA_Classic_GC_LZ.2

value: Classic GC DZ and LZ B cells were sorted using FACS. Classic GC DZ B cells were defined as B220+GL7+CD95+CXCR4+CD83lo, and classic GC LZ B cells were defined as B220+GL7+CD95+CXCR4loCD83+.


title: CT525_b: genomic DNA of blood from CT525

description: blood sample


title: 50 mM mir-7 sample 2

description: replicate 2


title: CT524_s: genomic DNA of saliva from CT524

description: saliva sample


title: 252800519297_S01_GE1_107_Sep09_1_1

value: non-activated splenic sorted Treg cells


title: 50 mM mir-7 sample 1

description: replicate 1


title: Mouse DRG E12.5 Thoracic NGF

description:
miRNA profile after treatment
34

source_name: Mouse Thoracic DRG at embryonic day 12.5 treated with NGF

value: NGF


title: RNA_Classic_GC_LZ.1

value: Germinal center B cells


title: neg-transfected ctrl 4

description: replicate 4

value: PremiR negative ctrl


title: CT522_s: genomic DNA of saliva from CT522

description: saliva sample

value: test


title: Mouse DRG E12.5 Thoracic Thyroid hormones 3

description:
miRNA profile after treatment
33

source_name: Mouse Thoracic DRG at embryonic day 12.5 treated with Thyroid hormone 3

value: Thyroid hormone 3


title: neg-transfected ctrl 3

description: replicate 3

value: ReNVM cells


title: CT523_s: genomic DNA of saliva from CT523

description: saliva sample

value: saliva


title: Wild type RNA-seq rep 1

description:
processed data file: NC_Run104.countsNoName.txt
104_R1_RNA_S1_1_920_WT_polyA_rep1_Nc_MycelialDisks_S1

tag: strain info.

value: Wild type

tag: developmental stage/tissue

value: mycelium

tag: growth protocol

value: 12 hours in VMM + 2% glucose, constant light, 30˚C

tag: library strategy

value: Illumina TruSeq stranded mRNA


title: INPUT_GCB.1

data_processing:
Raw reads were be aligned to reference genome mm9 using BWA MEM (Li, 2013). Apparent PCR duplicates were removed using Picard MarkDuplicates (Wysoker, et al., 2013). Peaks were called against inputs using Macs2 (Zhang, et al., 2008). Peaks with a score >5 were retained.
genome build: mm9
Supplementary_files_format_and_content: peak bed file: peak calls from Macs2 in bed format

extract_protocol: Chromatin from the indicated flow sorted GC B cell population (1-2 million cells) was used for each ChIP experiment with anti-H3K4me1 (Millipore 07-436) or anti-H3K27Ac (Abcam ab4729) antibody. DNA libraries were prepared by tagmentation from the sheared chromatin (200–600 bp). Libraries were sequenced on the Illumina Hiseq4000.

value: B220+GL7+CD95+ GC B cells were isolated by FACS.

tag: chip antibody

value: none (input)


title: RNA_Classic_GC_DZ.2


title: Mouse DRG E12.5 Thoracic Wnt3a

description:
miRNA profile after treatment
31

source_name: Mouse Thoracic DRG at embryonic day 12.5 treated with Wnt3a

value: wildtype

value: thoracic


title: neg-transfected ctrl 2

description: replicate 2


title: CT521_s: genomic DNA of saliva from CT521

description: saliva sample


title: neg-transfected ctrl 1

description: replicate 1


title: CT523_b: genomic DNA of blood from CT523

description: blood sample

value: blood


title: Mouse DRG E12.5 Thoracic Shh

description:
miRNA profile after treatment
32

source_name: Mouse Thoracic DRG at embryonic day 12.5 treated with Shh

value: Shh


title: CT522_b: genomic DNA of blood from CT522

description: blood sample


title: Mouse DRG E12.5 Thoracic Ctrl

description:
miRNA profile
28

source_name: Mouse Thoracic DRG at embryonic day 12.5 control

value: control


title: VCAF CO-CULTURE Rep1

city: London

first: Erik

last: Sahai

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description:
VCAF CO-CULTURE 0712
replicate11
gene expression data for VCAF cells in direct co-culture with A431

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with the lumi package in R

source_name: VCAF CO-CULTURE

label_protocol: Standard Illumina protocol

growth_protocol: DMEM with 10% FCS

extract_protocol: RNEasy mini kit Qiagen

treatment_protocol: Mono-culture vs Co-culture separated by 0.4micron filter vs direct co-culture followed by flow cytometry to sort GFP-labelled A431 cancer cells from mCherry-labelled CAFs

value: Stromal Fibroblast

tag: sample type

value: VCAF direct co-culture


title: VCAF CO-CULTURE Rep2

description:
VCAF CO-CULTURE 0801
replicate12
gene expression data for VCAF cells in direct co-culture with A431

tag: cell type


title: Mouse DRG E12.5 Thoracic Wnt5a

description:
miRNA profile after treatment
30

source_name: Mouse Thoracic DRG at embryonic day 12.5 treated with Wnt5a


title: Mouse DRG E18.5 Brachial

description:
miRNA profile
25

source_name: Mouse Brachial DRG at embryonic day 18.5

value: brachical


title: CT520_b: genomic DNA of blood from CT520

description: blood sample

value: test


title: VCAF SOLUBLE Rep1

description:
VCAF SOLUBLE 0712
replicate7
gene expression data for VCAF cells in co-culture with exchange of soluble factors with A431

source_name: VCAF SOLUBLE

value: VCAF soluble co-culture


title: CT520_s: genomic DNA of saliva from CT520

description: saliva sample

value: saliva


title: Mouse DRG E12.5 Thoracic NT3

description:
miRNA profile after treatment
29

source_name: Mouse Thoracic DRG at embryonic day 12.5 treated with NT3


title: Mouse DRG P16 Brachial

description:
miRNA profile
24

source_name: Mouse Brachial DRG at postnatal day 16


title: RNA_Classic_GC_DZ.1

source_name: Germinal center B cells

value: Germinal center B cells

tag: sorting strategy

value: Classic GC DZ and LZ B cells were sorted using FACS. Classic GC DZ B cells were defined as B220+GL7+CD95+CXCR4+CD83lo, and classic GC LZ B cells were defined as B220+GL7+CD95+CXCR4loCD83+.


title: CT521_b: genomic DNA of blood from CT521

description: blood sample

tag: test series


title: Mouse DRG P16 Lumbar

description:
miRNA profile
27

source_name: Mouse Lumbarl DRG at postnatal day 16

value: lumbar


title: Mouse DRG P16 Thoracic

description:
miRNA profile
26

source_name: Mouse Thoracic DRG at postnatal day 16


title: A431 SOLUBLE Rep2

description:
A431 SOLUBLE 0801
replicate6
gene expression data for A431 cells in co-culture with exchange of soluble factors with VCAF

source_name: A431 SOLUBLE

value: Epithelial Cancer

value: A431 soluble co-culture


title: Mouse DRG E18.5 Thoracic

description:
miRNA profile
22

source_name: Mouse Thoracic DRG at embryonic day 18.5


title: CT519_s: genomic DNA of saliva from CT519

description: saliva sample


title: VCAF SOLUBLE Rep2

description:
VCAF SOLUBLE 0801
replicate8
gene expression data for VCAF cells in co-culture with exchange of soluble factors with A431


title: Mouse DRG E18.5 Lumbar

description:
miRNA profile
23

source_name: Mouse Lumbar DRG at embryonic day 18.5


title: Mouse DRG E14.5 Brachial

description:
miRNA profile
21

source_name: Mouse Brachial DRG at embryonic day 14.5


title: Mouse DRG E13.5 Lumbar

description:
miRNA profile
20

source_name: Mouse Lumbar DRG at embryonic day 13.5


title: CT518_s: genomic DNA of saliva from CT518

description: saliva sample


title: m8V

city: Los Angeles

first: Dan

last: Theodorescu

address: 8700 Beverly Blvd., Davis Building, Rm 3057

institute: Cedars Sinai Medical Center

description: AGL full body KO mouse bladder

data_processing:
Illumina CASAVA used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads were mapped to refernce genome using TopHat2 and Fragments Per Kilobases per Million Reads (FPKM) determined
Genome_build: mm9
Supplementary_files_format_and_content: xls files including mapped read counts and FPKM per sample

source_name: BBN induced bladder cancer

extract_protocol:
Bladders were removed and flash frozen with liquid nitrogen.  Tumors were weighed, crushed, and RNA purified by Rneasy Plus Mini-Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with 0.05% BBN carcinogen for 12 weeks

tag: strain

value: Bladder

tag: genotype

value: AGL-FBKO


title: Mouse DRG E13.5 Brachial

description:
miRNA profile
18

source_name: Mouse Brachial DRG at embryonic day 13.5

tag: genotype/variation

value: wildtype


title: m7V

description: AGL full body KO mouse bladder


title: Mouse DRG E13.5 Thoracic

description:
miRNA profile
19

source_name: Mouse Thoracic DRG at embryonic day 13.5

value: thoracic