title: 50 μM MgCl2, immunopreciptated

city: Hershey

first: Mauricio

middle: Henriques

last: Pontes

state: PA

address: 500 University Drive

department: Pathology

institute: Penn State University

data_processing:
Assembly of sequenced fragments into Salmonella enterica 14028s genome (GenBank: CP001363.1) was carried out using CLC Genomics Workbench software.
For each assembly file, enrichment locations were determined using a Perl script that outputs a file with a column showing the coverage at each genomic base (Genome Res. 2011. 21:1487-1497). The output file of each assembly was visualized as user plot in Arthemis.
Genome_build: Salmonella enterica 14028s (GenBank: CP001363.1)
Supplementary_files_format_and_content: The output file of each assembly was visualized as user plot in Arthemis

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Whole cell

growth_protocol: After overnight growth in N-minimal medium (J Biol Chem. 1991. 266:824-829) containing 10 mM MgCl2, cells were washed twice in MgCl2-free medium, innoculated (1:50) in fresh N-minimal medium containing 10 or 50 μM MgCl2. Cells were grown to an optical density (OD600) of 0.34-0.4.

extract_protocol:
DNA was sheared and immunopreciptated using a protocol similar to (J. Biol. Chem. 2005. 280:4089-4094).
Libraries were prepared for multiplex by the Yale Center for Genomic Analysis.

treatment_protocol: Cells were cross-linked with 1% (v/v) formaldehyde. Sample were quenched and lysed using a protocol similar to (J. Biol. Chem. 2005. 280:4089-4094).

value: Bacteria

tag: chip antibody

value: E. coli RNA Polymerase beta prime Mouse Monoclonal Antibody (NeoClone, Cat#WP001; RRID:AB_2564515)


title: R6/2_HD_Heart_Male_Vehicle rep4

status: Public on Sep 23 2017

type: SRA

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

country: USA

institute: CHDI

library_source: transcriptomic

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omicsoft OSA 4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omicsoft: Trimming  /Mode=TrimByQuality /ReadTrimQuality=2;  Options  /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse.B37, gene models version Ensembl.R67
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Heart, Vehicle

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: background

tag: genotype

tag: tissue

value: Heart

tag: Sex

value: Male

tag: treatment

value: Vehicle

tag: treatment dose

tag: treatment administration route

value: Oral

tag: treatment frequency

value: Twice-Daily (b.i.d)


title: R6/2_HD_Heart_Female_Vehicle rep2

value: Female


title: input DNA

library_source: genomic

molecule: genomic DNA

tag: cell type

tag: strain


title: R6/2_HD_Heart_Female_Vehicle rep3


title: R6/2_HD_Heart_Female_CHDI-00390576_100mg/kg rep3

value: 100 mg/kg


title: R6/2_HD_Heart_Female_CHDI-00390576_30mg/kg rep3

value: 30 mg/kg


title: 10 μM MgCl2, immunopreciptated


title: R6/2_HD_Heart_Male_CHDI-00390576_30mg/kg rep3


title: R6/2_HD_Heart_Male_CHDI-00390576_100mg/kg rep3


title: WT_Liver_Male_Vehicle rep1

source_name: Liver, Vehicle

value: Wild Type

value: Liver


title: R6/2_HD_Heart_Female_CHDI-00390576_30mg/kg rep2


title: R6/2_HD_Heart_Female_CHDI-00390576_100mg/kg rep2


title: R6/2_HD_Heart_Male_Vehicle rep3


title: R6/2_HD_Heart_Female_CHDI-00390576_100mg/kg rep1


title: WT_Heart_Female_Vehicle rep2


title: R6/2_HD_Heart_Male_CHDI-00390576_30mg/kg rep2


title: R6/2_HD_Heart_Male_Vehicle rep2


title: R6/2_HD_Heart_Female_CHDI-00390576_30mg/kg rep1


title: WT_Heart_Male_Vehicle rep3


title: R6/2_HD_Heart_Male_CHDI-00390576_100mg/kg rep1


title: R6/2_HD_Heart_Female_Vehicle rep1


title: R6/2_HD_Heart_Male_CHDI-00390576_30mg/kg rep1


title: WT_Heart_Male_Vehicle rep1


title: WT_Heart_Male_Vehicle rep2


title: WT

city: Pozuelo de Alarcón (Madrid)

first: Daniel

last: Conde

address: Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo 28223

country: Spain

institute: Centre for Plant Biotechnology and Genomics U.P.M. – I.N.I.A

data_processing:
Pre-processing and assembly of sequence data were conducted using the web-based platform Galaxy at https://usegalaxy.org/which includes tools to remove reads containing N blurs, adapter sequences, and sequences shorter than 15 nucleotides. Quality control of reads was carried out with the FastQC Galaxy tool
Removal of rRNA, if needed, was performed locally with the SortMeRNA tool. The TopHat Galaxy tool was used to map clean reads to the Populus tremula x P. alba INRA clone 717-1B4 genome using the default settings
Differentially expressed gene (DEG) lists for CsDML OX versus WT were obtained using the function exactTest (edgeR package of R)
Genome_build: Populus tremula x P. alba INRA clone 717-1B4 at:
http://aspendb.uga.edu/s717
Please note that the "sPta717_v1.1.gene.gff3" (with coordinates) was used to analyze the data, similar to Populus trichocarpa available at:
https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa
Supplementary_files_format_and_content: xlsx file include log2FC in CsDMLOX respect to wild type

organism: Populus tremula x Populus alba

extract_protocol:
Libraries were prepared using 1 µg of RNA in the NEBNext® Ultra™ Directional RNA Library Prep Kit following the supplier's instructions (New England Biolabs, Ipswich, MA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: clone id

tag: genotype/variation

value: wild type

value: apices

tag: time point

value: after 28 days in SD


title: R6/2_HD_Heart_Male_Vehicle rep1


title: R6/2_HD_Tibialis_Female_CHDI-00390576_30mg/kg rep4

source_name: Tibialis, CHDI-00390576, 30  mg/kg

value: Tibialis


title: WT_Tibialis_Male_Vehicle rep4

source_name: Tibialis, Vehicle


title: R6/2_HD_Tibialis_Male_Vehicle rep3


title: WT_Tibialis_Female_Vehicle rep3


title: R6/2_HD_Tibialis_Male_CHDI-00390576_30mg/kg rep4


title: R6/2_HD_Tibialis_Male_CHDI-00390576_30mg/kg rep3


title: R6/2_HD_Tibialis_Male_CHDI-00390576_100mg/kg rep3

source_name: Tibialis, CHDI-00390576, 100  mg/kg


title: R6/2_HD_Tibialis_Female_Vehicle rep4


title: R6/2_HD_Tibialis_Female_CHDI-00390576_30mg/kg rep3


title: R6/2_HD_Tibialis_Male_CHDI-00390576_100mg/kg rep2


title: R6/2_HD_Tibialis_Female_Vehicle rep3


title: R6/2_HD_Heart_Male_CHDI-00390576_100mg/kg rep2


title: WT_Heart_Female_Vehicle rep1


title: WT_Tibialis_Male_Vehicle rep3


title: R6/2_HD_Tibialis_Female_CHDI-00390576_30mg/kg rep2


title: R6/2_HD_Tibialis_Female_CHDI-00390576_100mg/kg rep4


title: WT_Tibialis_Female_Vehicle rep1


title: R6/2_HD_Tibialis_Male_CHDI-00390576_30mg/kg rep2


title: R6/2_HD_Tibialis_Male_Vehicle rep2


title: R6/2_HD_Tibialis_Female_CHDI-00390576_100mg/kg rep3


title: R6/2_HD_Tibialis_Male_CHDI-00390576_30mg/kg rep1


title: WT_Tibialis_Female_Vehicle rep4


title: WT_Tibialis_Male_Vehicle rep2


title: R6/2_HD_Tibialis_Female_CHDI-00390576_30mg/kg rep1


title: R6/2_HD_Tibialis_Female_Vehicle rep2


title: R6/2_HD_Tibialis_Male_CHDI-00390576_100mg/kg rep4


title: WT_Tibialis_Female_Vehicle rep2


title: R6/2_HD_Tibialis_Female_CHDI-00390576_100mg/kg rep1


title: WT_Striatum_Male_Vehicle rep4

source_name: Striatum, Vehicle

value: Striatum


title: WT_Striatum_Male_Vehicle rep3


title: R6/2_HD_Striatum_Female_Vehicle rep4


title: WT_Tibialis_Male_Vehicle rep1


title: R6/2_HD_Tibialis_Female_CHDI-00390576_100mg/kg rep2


title: R6/2_HD_Striatum_Male_CHDI-00390576_100mg/kg rep3

source_name: Striatum, CHDI-00390576, 100  mg/kg


title: R6/2_HD_Tibialis_Male_Vehicle rep1


title: R6/2_HD_Striatum_Male_Vehicle rep3


title: R6/2_HD_Striatum_Female_CHDI-00390576_100mg/kg rep4


title: R6/2_HD_Striatum_Female_CHDI-00390576_30mg/kg rep3

source_name: Striatum, CHDI-00390576, 30  mg/kg


title: R6/2_HD_Striatum_Male_CHDI-00390576_100mg/kg rep1


title: R6/2_HD_Striatum_Male_CHDI-00390576_100mg/kg rep2


title: R6/2_HD_Striatum_Female_CHDI-00390576_100mg/kg rep3


title: R6/2_HD_Striatum_Male_CHDI-00390576_30mg/kg rep3


title: R6/2_HD_Striatum_Female_CHDI-00390576_30mg/kg rep4


title: R6/2_HD_Striatum_Female_CHDI-00390576_30mg/kg rep2


title: WT_Striatum_Male_Vehicle rep1


title: R6/2_HD_Striatum_Female_CHDI-00390576_100mg/kg rep2


title: R6/2_HD_Tibialis_Female_Vehicle rep1


title: R6/2_HD_Tibialis_Male_CHDI-00390576_100mg/kg rep1


title: R6/2_HD_Striatum_Female_CHDI-00390576_100mg/kg rep1


title: R6/2_HD_Striatum_Male_CHDI-00390576_30mg/kg rep2


title: WT_Striatum_Female_Vehicle rep3


title: R6/2_HD_Striatum_Male_CHDI-00390576_30mg/kg rep4


title: WT_Striatum_Female_Vehicle rep2


title: R6/2_HD_Striatum_Male_Vehicle rep2


title: R6/2_HD_Striatum_Male_Vehicle rep4


title: R6/2_HD_Striatum_Male_CHDI-00390576_100mg/kg rep4


title: WT_Striatum_Male_Vehicle rep2


title: R6/2_HD_Striatum_Female_CHDI-00390576_30mg/kg rep1


title: R6/2_HD_Striatum_Female_Vehicle rep1


title: R6/2_HD_Striatum_Female_Vehicle rep2


title: R6/2_HD_Striatum_Male_CHDI-00390576_30mg/kg rep1


title: WT_Striatum_Female_Vehicle rep1


title: R6/2_HD_Striatum_Male_Vehicle rep1


title: R6/2_HD_Cortex_Male_Vehicle rep4

source_name: Cortex, Vehicle

value: Cortex


title: 43713 PEA QS s4U+IAA Rep 3

city: Vienna

first: Brian

last: Reichholf

address: Doktor-Bohr-Gasse 3

country: Austria

institute: IMBA

description: synthetic RNA control oligo was subjected IAA reaction and preciptiated; reverse transcription was performed with QS, full length cDNA was gel purified, PCR amplified and sequenced

data_processing:
Basecalls performed using RTA V1.18.64.0
Cutadapt v1.7.1 was used to trim adapters (allowing for default 10% mismatch in adapter sequence) and sequences of 21nt length were filtered.
Adapter trimmed sequences were aligned to mature dme-let-7 sequence (TGAGGTAGTAGGTTGTATAGT) using bowtie v0.12.9 allowing for 3 mismatches and converted to bam using samtools v0.1.18.
“N” containing sequences were filtered from alignment. Remaining alignments were converted to pileup format. Finally, fraction of each mutation per position were extracted from pileup. Output table was analyzed and plotted in Excel v15.22 (Microsoft) and Prism v7.0a (GraphPad).
Supplementary_files_format_and_content: tab-delimited text files contain the coverage and mutation counts for each position along the dme-let-7 sequence.

organism: synthetic construct

source_name: PEA QS s4U+IAA

extract_protocol:
synthetic RNA control oligo were subjected to IAA-alkylation or control reactions, preciptiated and reverse transcribed; full length cDNA was gel purified, PCR amplified and sequenced
PCR amplification of full length cDNA products

treatment_protocol: template RNA oligonucleotides (5L-let-7-3L or 5L-let-7-s4Up9-3L; Dharmacon) were deprotected according to the instructions of the manufacturer and purified by denaturing polyacrylamide gel-elution.

tag: molecule subtype

value: synthetic RNA control oligo containing dme-let7 sequence with s4U at position 9 flanked by 3' and 5' adapter sequences (5L-let-7-s4U-p9-3L)


title: R6/2_HD_Cortex_Female_Vehicle rep4


title: 43712 PEA QS s4U-IAA Rep 3

description: synthetic RNA control oligo was subjected -IAA control reaction and preciptiated; reverse transcription was performed with QS, full length cDNA was gel purified, PCR amplified and sequenced

source_name: PEA QS s4U-IAA


title: WT_Cortex_Female_Vehicle rep3


title: WT_Cortex_Male_Vehicle rep4


title: R6/2_HD_Cortex_Male_Vehicle rep3


title: 43711 PEA QS ctr+IAA Rep 3

source_name: PEA QS ctr+IAA

value: synthetic RNA control oligo containing dme-let7 sequence (no s4U) flanked by 3' and 5' adapter sequences (5L-let-7-3L)


title: R6/2_HD_Cortex_Male_CHDI-00390576_30mg/kg rep4

source_name: Cortex, CHDI-00390576, 30  mg/kg

value: Male


title: 43710 PEA QS ctr-IAA Rep 3

source_name: PEA QS ctr-IAA


title: WT_Cortex_Male_Vehicle rep3

value: Vehicle


title: R6/2_HD_Cortex_Female_Vehicle rep3

value: Oral


title: R6/2_HD_Cortex_Female_Vehicle rep2

value: Twice-Daily (b.i.d)


title: 43706 PEA SSIII s4U-IAA Rep 3

description: synthetic RNA control oligo was subjected -IAA control reaction and preciptiated; reverse transcription was performed with SSIII, full length cDNA was gel purified, PCR amplified and sequenced

source_name: PEA SSIII s4U-IAA


title: 43707 PEA SSIII s4U+IAA Rep 3

description: synthetic RNA control oligo was subjected IAA reaction and preciptiated; reverse transcription was performed with SSIII, full length cDNA was gel purified, PCR amplified and sequenced

source_name: PEA SSIII s4U+IAA


title: R6/2_HD_Striatum_Female_Vehicle rep3

value: Female


title: 43705 PEA SSIII ctr+IAA Rep 3

source_name: PEA SSIII ctr+IAA


title: R6/2_HD_Cortex_Male_CHDI-00390576_100mg/kg rep3

value: 100 mg/kg


title: R6/2_HD_Cortex_Male_CHDI-00390576_30mg/kg rep2

value: 30 mg/kg


title: R6/2_HD_Cortex_Male_Vehicle rep2


title: R6/2_HD_Cortex_Female_CHDI-00390576_30mg/kg rep4


title: R6/2_HD_Cortex_Male_CHDI-00390576_30mg/kg rep3


title: 43704 PEA SSIII ctr-IAA Rep 3

source_name: PEA SSIII ctr-IAA


title: R6/2_HD_Cortex_Female_CHDI-00390576_100mg/kg rep4


title: 43701 PEA SSII s4U+IAA Rep 3

description: synthetic RNA control oligo was subjected IAA reaction and preciptiated; reverse transcription was performed with SSII, full length cDNA was gel purified, PCR amplified and sequenced

source_name: PEA SSII s4U+IAA


title: R6/2_HD_Cortex_Female_CHDI-00390576_100mg/kg rep3


title: WT_Cortex_Female_Vehicle rep2

value: Wild Type


title: WT_Cortex_Male_Vehicle rep2


title: R6/2_HD_Cortex_Male_CHDI-00390576_100mg/kg rep4


title: R6/2_HD_Cortex_Female_CHDI-00390576_100mg/kg rep2


title: 43700 PEA SSII s4U-IAA Rep 3

description: synthetic RNA control oligo was subjected -IAA control reaction and preciptiated; reverse transcription was performed with SSII, full length cDNA was gel purified, PCR amplified and sequenced

source_name: PEA SSII s4U-IAA


title: R6/2_HD_Cortex_Male_CHDI-00390576_100mg/kg rep2


title: R6/2_HD_Cortex_Female_CHDI-00390576_30mg/kg rep3


title: R6/2_HD_Cortex_Female_CHDI-00390576_100mg/kg rep1


title: 43699 PEA SSII ctr+IAA Rep 3

source_name: PEA SSII ctr+IAA


title: R6/2_HD_Cortex_Female_Vehicle rep1


title: 43698 PEA SSII ctr-IAA Rep 3

source_name: PEA SSII ctr-IAA


title: R6/2_HD_Cortex_Female_CHDI-00390576_30mg/kg rep2


title: Het(Q175)_Liver_Female_CHDI-00390576_100mg/kg_rep4

tag: background strain

value: Het(Q175) knock-in

value: Liver

tag: age

value: 6 months

tag: treatment duration

value: from 4 weeks to 6 months


title: 43689 PEA SSIII s4U+IAA Rep 2


title: R6/2_HD_Cortex_Male_Vehicle rep1

tag: background


title: R6/2_HD_Cortex_Male_CHDI-00390576_30mg/kg rep1

tag: genotype


title: 43688 PEA SSIII s4U-IAA Rep 2


title: WT_Cortex_Female_Vehicle rep1

tag: tissue


title: 43693 PEA QS ctr+IAA Rep 2


title: WT_Cortex_Male_Vehicle rep1

tag: Sex


title: 43692 PEA QS ctr-IAA Rep 2


title: 43694 PEA QS s4U-IAA Rep 2


title: Het(Q175)_Liver_Male_CHDI-00390576_100mg/kg_rep4

tag: treatment


title: Het(Q175)_Liver_Male_CHDI-00390576_30mg/kg_rep4

tag: treatment dose


title: R6/2_HD_Cortex_Male_CHDI-00390576_100mg/kg rep1

tag: treatment administration route


title: Het(Q175)_Liver_Female_Vehicle_rep4

source_name: Liver, Vehicle

tag: treatment frequency


title: Het(Q175)_Liver_Female_CHDI-00390576_100mg/kg_rep3


title: 43686 PEA SSIII ctr-IAA Rep 2


title: R6/2_HD_Cortex_Female_CHDI-00390576_30mg/kg rep1


title: 43683 PEA SSII s4U+IAA Rep 2


title: Het(Q175)_Liver_Male_CHDI-00390576_100mg/kg_rep2


title: Het(Q175)_Liver_Female_Vehicle_rep3


title: Het(Q175)_Liver_Male_CHDI-00390576_30mg/kg_rep3


title: Het(Q175)_Liver_Female_CHDI-00390576_30mg/kg_rep4


title: 43682 PEA SSII s4U-IAA Rep 2


title: 43687 PEA SSIII ctr+IAA Rep 2


title: Het(Q175)_Liver_Male_Vehicle_rep4


title: Het(Q175)_Liver_Female_CHDI-00390576_100mg/kg_rep2


title: 43695 PEA QS s4U+IAA Rep 2


title: Het(Q175)_Liver_Male_CHDI-00390576_100mg/kg_rep3


title: 43681 PEA SSII ctr+IAA Rep 2


title: 43680 PEA SSII ctr-IAA Rep 2


title: WT_Liver_Male_Vehicle_rep4


title: WT_Liver_Female_Vehicle_rep4


title: Het(Q175)_Liver_Male_CHDI-00390576_30mg/kg_rep2


title: Het(Q175)_Liver_Male_Vehicle_rep3


title: Het(Q175)_Liver_Female_Vehicle_rep1


title: 43674 PEA QS ctr-IAA Rep 1


title: 43677 PEA QS s4U+IAA Rep 1


title: Het(Q175)_Liver_Female_CHDI-00390576_30mg/kg_rep2


title: Het(Q175)_Liver_Female_CHDI-00390576_30mg/kg_rep3


title: WT_Liver_Male_Vehicle_rep3


title: 43670 PEA SSIII s4U-IAA Rep 1


title: 43671 PEA SSIII s4U+IAA Rep 1


title: Het(Q175)_Liver_Female_CHDI-00390576_100mg/kg_rep1


title: Het(Q175)_Liver_Male_CHDI-00390576_100mg/kg_rep1


title: WT_Liver_Male_Vehicle_rep2


title: 43676 PEA QS s4U-IAA Rep 1


title: WT_Liver_Female_Vehicle_rep2


title: Het(Q175)_Liver_Female_Vehicle_rep2


title: Het(Q175)_Liver_Male_Vehicle_rep2


title: 43669 PEA SSIII ctr+IAA Rep 1


title: WT_Liver_Female_Vehicle_rep3


title: WT_Liver_Female_Vehicle_rep1


title: WT_Liver_Male_Vehicle_rep1


title: Het(Q175)_Liver_Female_CHDI-00390576_30mg/kg_rep1


title: Het(Q175)_Liver_Male_CHDI-00390576_30mg/kg_rep1


title: 43668 PEA SSIII ctr-IAA Rep 1


title: 43675 PEA QS ctr+IAA Rep 1


title: Het(Q175)_Heart_Male_CHDI-00390576_100mg/kg_rep4

value: Heart


title: 43665 PEA SSII s4U+IAA Rep 1


title: Het(Q175)_Heart_Male_CHDI-00390576_30mg/kg_rep4


title: Het(Q175)_Heart_Female_CHDI-00390576_30mg/kg_rep4


title: 43662 PEA SSII ctr-IAA Rep 1


title: Het(Q175)_Heart_Female_CHDI-00390576_100mg/kg_rep4


title: WT_Heart_Male_Vehicle_rep4

source_name: Heart, Vehicle


title: Het(Q175)_Heart_Male_Vehicle_rep3


title: Het(Q175)_Heart_Female_CHDI-00390576_30mg/kg_rep1


title: Het(Q175)_Heart_Female_CHDI-00390576_100mg/kg_rep1


title: 43663 PEA SSII ctr+IAA Rep 1


title: Het(Q175)_Liver_Male_Vehicle_rep1


title: Het(Q175)_Heart_Female_CHDI-00390576_100mg/kg_rep3


title: 43664 PEA SSII s4U-IAA Rep 1


title: Het(Q175)_Heart_Female_Vehicle_rep3


title: Het(Q175)_Heart_Female_CHDI-00390576_100mg/kg_rep2


title: Het(Q175)_Heart_Female_CHDI-00390576_30mg/kg_rep2


title: Het(Q175)_Heart_Female_CHDI-00390576_30mg/kg_rep3


title: WT_Heart_Male_Vehicle_rep3


title: Het(Q175)_Heart_Male_Vehicle_rep4


title: Het(Q175)_Heart_Male_CHDI-00390576_100mg/kg_rep3


title: WT_Heart_Male_Vehicle_rep2


title: Het(Q175)_Heart_Male_CHDI-00390576_30mg/kg_rep2


title: Het(Q175)_Heart_Female_Vehicle_rep2


title: WT_Heart_Female_Vehicle_rep3


title: Het(Q175)_Heart_Female_Vehicle_rep1


title: WT_Heart_Male_Vehicle_rep1


title: Het(Q175)_Heart_Male_CHDI-00390576_100mg/kg_rep2


title: WT_Heart_Female_Vehicle_rep4


title: Het(Q175)_Heart_Male_CHDI-00390576_30mg/kg_rep3


title: Het(Q175)_Heart_Male_CHDI-00390576_30mg/kg_rep1


title: Het(Q175)_Heart_Male_Vehicle_rep2


title: Het(Q175)_Heart_Female_Vehicle_rep4


title: WT_Heart_Female_Vehicle_rep2


title: Het(Q175)_Heart_Male_CHDI-00390576_100mg/kg_rep1


title: Het(Q175)_Heart_Male_Vehicle_rep1


title: WT_Heart_Female_Vehicle_rep1


title: WT_Tibialis_Male_Vehicle_rep4

source_name: Tibialis, Vehicle

value: Tibialis


title: Het(Q175)_Tibialis_Male_Vehicle_rep4


title: Het(Q175)_Tibialis_Male_CHDI-00390576_30mg/kg_rep4

source_name: Tibialis, CHDI-00390576, 30 mg/kg


title: Het(Q175)_Tibialis_Male_CHDI-00390576_100mg/kg_rep4

source_name: Tibialis, CHDI-00390576, 100 mg/kg


title: Het(Q175)_Tibialis_Female_Vehicle_rep3


title: WT_Tibialis_Female_Vehicle_rep4


title: Het(Q175)_Tibialis_Male_CHDI-00390576_30mg/kg_rep3


title: Het(Q175)_Tibialis_Male_Vehicle_rep3


title: WT_Tibialis_Male_Vehicle_rep3


title: Het(Q175)_Tibialis_Female_Vehicle_rep2


title: Het(Q175)_Tibialis_Female_CHDI-00390576_30mg/kg_rep4


title: WT_Tibialis_Female_Vehicle_rep3


title: WT_Tibialis_Male_Vehicle_rep2


title: Het(Q175)_Tibialis_Female_Vehicle_rep4


title: Het(Q175)_Tibialis_Female_CHDI-00390576_30mg/kg_rep3


title: WT_Tibialis_Female_Vehicle_rep2


title: Het(Q175)_Tibialis_Female_CHDI-00390576_100mg/kg_rep4


title: Het(Q175)_Tibialis_Female_CHDI-00390576_30mg/kg_rep2


title: Het(Q175)_Tibialis_Female_CHDI-00390576_100mg/kg_rep3


title: Het(Q175)_Tibialis_Female_CHDI-00390576_100mg/kg_rep2


title: WT_Tibialis_Male_Vehicle_rep1


title: Het(Q175)_Tibialis_Male_CHDI-00390576_100mg/kg_rep3


title: Het(Q175)_Tibialis_Male_CHDI-00390576_100mg/kg_rep2


title: Het(Q175)_Tibialis_Male_CHDI-00390576_100mg/kg_rep1


title: Het(Q175)_Tibialis_Female_CHDI-00390576_100mg/kg_rep1


title: Het(Q175)_Tibialis_Male_Vehicle_rep1


title: Het(Q175)_Tibialis_Female_CHDI-00390576_30mg/kg_rep1


title: Het(Q175)_Tibialis_Female_Vehicle_rep1


title: WT_Tibialis_Female_Vehicle_rep1


title: Het(Q175)_Cortex_Male_Vehicle_rep4

source_name: Cortex, Vehicle

value: Cortex


title: Het(Q175)_Tibialis_Male_CHDI-00390576_30mg/kg_rep2


title: Het(Q175)_Tibialis_Male_CHDI-00390576_30mg/kg_rep1


title: Het(Q175)_Cortex_Female_Vehicle_rep3


title: Het(Q175)_Cortex_Female_CHDI-00390576_100mg/kg_rep4


title: Het(Q175)_Cortex_Female_Vehicle_rep4


title: WT_Cortex_Male_Vehicle_rep4


title: WT_Cortex_Male_Vehicle_rep3


title: Het(Q175)_Tibialis_Male_Vehicle_rep2


title: Het(Q175)_Cortex_Female_Vehicle_rep2


title: Het(Q175)_Cortex_Male_CHDI-00390576_100mg/kg_rep4


title: Het(Q175)_Cortex_Male_CHDI-00390576_30mg/kg_rep4

source_name: Cortex, CHDI-00390576, 30 mg/kg


title: Het(Q175)_Cortex_Female_Vehicle_rep1


title: Het(Q175)_Cortex_Male_Vehicle_rep3


title: Het(Q175)_Cortex_Female_CHDI-00390576_100mg/kg_rep3


title: Het(Q175)_Cortex_Male_CHDI-00390576_30mg/kg_rep3


title: Het(Q175)_Cortex_Male_CHDI-00390576_100mg/kg_rep3


title: Het(Q175)_Cortex_Female_CHDI-00390576_30mg/kg_rep3


title: Het(Q175)_Cortex_Female_CHDI-00390576_30mg/kg_rep2


title: Het(Q175)_Cortex_Male_CHDI-00390576_30mg/kg_rep2


title: Het(Q175)_Cortex_Female_CHDI-00390576_100mg/kg_rep2


title: WT_Cortex_Female_Vehicle_rep3


title: Het(Q175)_Cortex_Female_CHDI-00390576_30mg/kg_rep4


title: WT_Cortex_Male_Vehicle_rep2


title: WT_Cortex_Female_Vehicle_rep4


title: Het(Q175)_Cortex_Male_CHDI-00390576_100mg/kg_rep1


title: Het(Q175)_Cortex_Male_CHDI-00390576_30mg/kg_rep1


title: WT_Cortex_Female_Vehicle_rep1


title: WT_Cortex_Female_Vehicle_rep2


title: WT_Cortex_Male_Vehicle_rep1


title: Het(Q175)_Striatum_Female_CHDI-00390576_100mg/kg_rep4

source_name: Striatum, CHDI-00390576, 100 mg/kg

value: Striatum


title: Het(Q175)_Cortex_Female_CHDI-00390576_30mg/kg_rep1


title: Het(Q175)_Striatum_Female_Vehicle_rep4

source_name: Striatum, Vehicle


title: Het(Q175)_Striatum_Male_CHDI-00390576_30mg/kg_rep3

source_name: Striatum, CHDI-00390576, 30 mg/kg


title: WT_Striatum_Male_Vehicle_rep4


title: Het(Q175)_Striatum_Female_Vehicle_rep3


title: Het(Q175)_Striatum_Male_Vehicle_rep4


title: Het(Q175)_Cortex_Female_CHDI-00390576_100mg/kg_rep1


title: Het(Q175)_Striatum_Male_CHDI-00390576_30mg/kg_rep4


title: Het(Q175)_Striatum_Male_CHDI-00390576_100mg/kg_rep4


title: WT_Striatum_Female_Vehicle_rep4


title: Het(Q175)_Striatum_Female_CHDI-00390576_100mg/kg_rep3


title: Het(Q175)_Striatum_Female_CHDI-00390576_30mg/kg_rep3


title: Het(Q175)_Striatum_Female_CHDI-00390576_30mg/kg_rep4


title: WT_Striatum_Female_Vehicle_rep3


title: Het(Q175)_Cortex_Male_CHDI-00390576_100mg/kg_rep2


title: Het(Q175)_Striatum_Male_CHDI-00390576_100mg/kg_rep3


title: Het(Q175)_Cortex_Male_Vehicle_rep1


title: WT_Striatum_Female_Vehicle_rep2


title: WT_Striatum_Male_Vehicle_rep3


title: Het(Q175)_Striatum_Female_Vehicle_rep2


title: Het(Q175)_Striatum_Male_CHDI-00390576_100mg/kg_rep2


title: Het(Q175)_Striatum_Male_CHDI-00390576_100mg/kg_rep1


title: WT_Striatum_Male_Vehicle_rep2


title: Het(Q175)_Striatum_Male_CHDI-00390576_30mg/kg_rep2


title: Het(Q175)_Striatum_Female_CHDI-00390576_100mg/kg_rep2


title: Het(Q175)_Striatum_Male_Vehicle_rep3


title: Het(Q175)_Striatum_Male_CHDI-00390576_30mg/kg_rep1


title: Het(Q175)_Striatum_Female_CHDI-00390576_100mg/kg_rep1


title: Het(Q175)_Striatum_Male_Vehicle_rep2


title: Het(Q175)_Striatum_Female_CHDI-00390576_30mg/kg_rep2


title: Het(Q175)_Striatum_Female_CHDI-00390576_30mg/kg_rep1


title: WT_Striatum_Male_Vehicle_rep1


title: Het(Q175)_Striatum_Male_Vehicle_rep1


title: WT_Striatum_Female_Vehicle_rep1


title: Het(Q175)_Striatum_Female_Vehicle_rep1


title: YAP_ChIPseq_rep1

status: Public on Sep 22 2017

city: Shanghai

first: Weisheng

last: Zheng

address: Siping Road, No.1239

department: Department of Bioinformatics

country: China

institute: Tongji University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to hg19 genome assembly using Bowtie version 0.12.7 with default parameters. Only the concordant pairs with mapq > 3 were retained.
Wig files were generated from the filtered alignments. Briefly, the genome were divided into 10 bp windows. Reads Per Kilobase per Million mapped reads (RPKM) value was calculated in eary window and the adjacent windows were used for smooth the values.
The high-confidence sets of YAP and TFCP2 were obtained by using the IDR (Irreproducible Discovery Rate) pipeline2: Firstly, we used MACS2 version 2.1.03 to call peak sets on individual replicates, pseudo-replicates and pooled data. Then we run an IDR analysis on these peak sets and an IDR threshold of 0.01 was used to filter and obtain optimal sets of peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

organism: Homo sapiens

source_name: liver cancer cell

growth_protocol: Bel-7402 cells were were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Hyclone, Logan, UT, USA) supplemented with 10% fetal bovine serum (FBS) (GIBCO, Carlsbad, CA, USA) and penicillin/streptomycin (GIBCO).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

tag: cell line

tag: cell type

value: Hepatocellular carcinoma

tag: antibodies

value: anti-YAP (CST #14074)


title: TFCP2_ChIPseq_rep2

value: anti-TFCP2 (CST #80784)


title: YAP_ChIPseq_rep2


title: input_DNA_rep3


title: TFCP2_ChIPseq_rep1


title: input_DNA_rep2


title: input_DNA_rep1


title: YAP_kd_RNA_rep3

data_processing:
Basecalls performed using CASAVA version 1.4
Raw RNA-seq reads were trimmed for adapter sequences, and marked for low-quality sequence. Then the clean reads were aligned to hg19 genome assembly and known junctions using Tophat v2.0.13 with default parameters.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were caculated using Cufflinks v2.2.1 with known genes annotation.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM abundance measurements

extract_protocol:
RNA extraction was performed in Bojian Biotechnology, Ltd using routine protocols.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

value: hepatocellular carcinoma


title: YAP_ChIPseq_rep3


title: TFCP2_ChIPseq_rep3


title: TFCP2_kd_RNA_rep3


title: YAP_kd_RNA_rep1


title: YAP_kd_RNA_rep2


title: TFCP2_kd_RNA_rep2


title: Control_RNA_rep1


title: Control_RNA_rep2


title: Control_RNA_rep3


title: 2nd leaf, DAH20_Replicate2

city: Mainz

first: Hyobin

last: Jeong

state: Germany

address: Richard shirrmann Str 12.

country: Germany

institute: IMB

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences using Cutadapt v1.2.1, and then mapped to Oryza sativa IRGSP-1.0.22 genome using TopHat v2.0.10 with parameters -r 100 --library-type fr-firststrand --mate-std-dev 100 --solexa-quals -p 24 --bowtie-n.
After removing duplicate reads, the number of reads mapped to gene features were counted using HTSeq v0.6.1.
The number of reads counted by HTseq were normalized into count per million (CPM) by TMM normalization method using edgeR package.
Genome_build: Oryza sativa IRGSP-1.0.22
Supplementary_files_format_and_content: tab-delimited text file including normalized read counts for each sample

molecule: polyA RNA

organism: Oryza sativa Japonica Group

source_name: 2nd leaf, DAH20

extract_protocol:
Rice leaf tissue was ground using a mortar and pestle, and total RNA was extracted from ~100 mg of tissue using RNeasy Plant Mini Kit (Qiagen). Total RNA integrity was confirmed using the Agilent Technologies 2100 BioAnalyzer (RNA integrity number >8.0). Poly(A) mRNA isolation from total RNA and fragmentation were performed using the Illumina Truseq Stranded mRNA LT Sample Prep Kit with poly-T oligo-attached magnetic beads, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina Truseq Stranded mRNA LT Sample Prep Kit, according to the manufacturer’s protocol.

treatment_protocol: mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.

tag: cultivar

value: Asian rice cultivar, Dongjin

value: 2nd leaf

tag: time

tag: replicate


title: 2nd leaf, DAH36_Replicate2

source_name: 2nd leaf, DAH36


title: 2nd leaf, DAH36_Replicate3


title: 2nd leaf, DAH28_Replicate2

source_name: 2nd leaf, DAH28


title: 2nd leaf, DAH44_Replicate2

source_name: 2nd leaf, DAH44


title: 2nd leaf, DAH36_Replicate1


title: 2nd leaf, DAH28_Replicate3


title: 2nd leaf, DAH44_Replicate3


title: 2nd leaf, DAH44_Replicate1


title: 2nd leaf, DAH28_Replicate1


title: 2nd leaf, DAH12_Replicate3

source_name: 2nd leaf, DAH12


title: 2nd leaf, DAH12_Replicate1


title: 2nd leaf, DAH12_Replicate2


title: 2nd leaf, DAH4_Replicate2

source_name: 2nd leaf, DAH4


title: 2nd leaf, DAH4_Replicate1


title: 2nd leaf, DAH4_Replicate3


title: Flag leaf, DAH44_Replicate2

source_name: Flag leaf, DAH44

value: Flag leaf


title: Flag leaf, DAH44_Replicate3


title: Flag leaf, DAH44_Replicate1


title: Flag leaf, DAH36_Replicate3

source_name: Flag leaf, DAH36


title: Flag leaf, DAH36_Replicate2


title: Flag leaf, DAH28_Replicate3

source_name: Flag leaf, DAH28


title: Flag leaf, DAH36_Replicate1


title: 2nd leaf, DAH20_Replicate3


title: Flag leaf, DAH28_Replicate2


title: Flag leaf, DAH20_Replicate3

source_name: Flag leaf, DAH20


title: Flag leaf, DAH28_Replicate1


title: TFCP2_kd_RNA_rep1


title: 2nd leaf, DAH20_Replicate1


title: Flag leaf, DAH12_Replicate1

source_name: Flag leaf, DAH12


title: Flag leaf, DAH12_Replicate2


title: 1 strike male 24hours

city: Detroit

first: Douglas

last: Ruden

state: Michigan

address: 275 E. Hancock Ave., Room  291.1

department: Department of Obstetrics and Gynecology

institute: Wayne State University

description: 1 strike male 24hours

data_processing:
Illumina BaseSpace Sequence Hub was used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to dm3 whole genome using TopHat v2.1.0 with default alignment parameters.After alignment the mapped reads was further filtered by mappability score (MAPQ≥ 10).
The quality controlled .bam files were sorted by genomic position of the reads using samtools-0.1.19. PCR duplicate reads were processed and removed using rmdup function (options -S) in samtools.
Processed .bam files were converted to bed files. Platform-independent 'tag directory' was created using HOMER. Quality metrics GC% bias and Genomic Nucleotide Frequency relative to read positions was estimated using HOMER. Out of bound reads were removed and Normalized read coverage across the dm3 genome-build was outputted as .bedGraph.gz file using HOMER.
Genome_build: dm3
Supplementary_files_format_and_content: .bedGraph.gz files include Normalized coverage values for each sample. These files can be directly uploaded to UCSC genome browser.

organism: Drosophila melanogaster

source_name: whole heads

extract_protocol:
Heads from 50 male and 50 female flies for control and 1 strike  were pulled off manually one at a time and immediately transferred to RNAlater (500µl). Fly head collection was done at 2 time-points 4 hours and 24 hours post-TBI (after strike).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flies were collected in sturdy plastic vials and subjected to Traumatic brain injury using the High Impact trauma (HIT) device. The flies were subjected to TBI, at a spring deflection of approx. 45o to ameliorate the impact of trauma.

tag: strain

value: whole heads

value: 0-5 days

value: male

tag: group

value: Traumatic brain injury


title: Flag leaf, DAH4_Replicate1

source_name: Flag leaf, DAH4


title: 1 strike female 4hours

description: 1 strike female 4hours

tag: age

value: female


title: 1 strike male 4hours

description: 1 strike male 4hours


title: control female 24hours

description: control female 24hours

value: control


title: Flag leaf, DAH20_Replicate1


title: Flag leaf, DAH4_Replicate3


title: Flag leaf, DAH4_Replicate2


title: TH2cre

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

description:
Th2 cells were generated by adding IL-2 (1 ng/mL), IL-4 (2 ng/ml) and neutralizing IFN- antibody (clone R4.6A2, 5 μg/mL) into the culture.
genotype: EGFRΔCD4

data_processing:
Libraries were sequenced using the Nextseq500 platform (Illumina), producing single end reads of 75bp (Utrecht Sequencing Facility). Reads were aligned to the human reference genome GRCh37 using STAR version 2.4.2a. Picard’s AddOrReplaceReadGroups (v1.98) was used to add read groups to the BAM files, which were sorted with Sambamba v0.4.5 and transcript abundances were quantified with HTSeq-count version 0.6.1p1 using the union mode.
Genome_build: GRCm38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: [.txt] Raw read counts per gene

source_name: CD4+ CD25− CD45Rbhi spleen

growth_protocol: CD4+ CD25− CD45Rbhi cells were FACS-sorted from spleens of wt and EGFRΔCD4 mice and cultured in IMDM medium supplemented with 10% FCS, 1% l-glutamine, 1% penicillin/streptomycin and 5 × 10−5 M 2-mercaptoethanol.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (QUIAGEN Cat. No. 74104).
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)


title: control female 4hours

description: control female 4hours


title: 1 strike female 24hours

description: 1 strike female 24hours


title: naivewt

value: naive

value: WT


title: Flag leaf, DAH12_Replicate3


title: control male 24hours

description: control male 24hours


title: Long projecting cells from WT mouse brain (LPC-7)

first: Anirban

last: Paul

department: Neural and Behavioral Sciences

institute: Penn State College of Medicine

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads from read2 were mapped to mm9 whole genome using bowtie v0.12.7 with parameters -p 7 -o
random unique tags from read1 were matched to mapped reads from read2
duplicate tags for each matched mapped reads were discarded
mapped reads with unique tags retained and aggregated
Genome_build: mm9
Supplementary_files_format_and_content: paul2016.processed.data.txt includes absolute unique tag count values for each single cell

growth_protocol: mouse housed in 12hr day light cycle, fed ad libitum

extract_protocol:
fresh intact brain sliced in ACSF, dissected, triturated to isolate single RFP neurons
2 round linear amplification with MessageAmp-II aRNA kit followed by cDNA lib preparation with Illumina TrueSeq smallRNA kit
polyA based library preparation with each aRNA containing unique random tag

treatment_protocol: no experimental treatment; Nkx2.1-CreER mouse induced at E17.5 w/ 150ul 20mg/ml Tamoxifen to express RFP

value: Sst-Flp; Nos1-Cre; Ai65

value: frontal cortex

value: Long projecting cells

tag: animal

value: postnatal 28

tag: library batch

tag: flowcell

tag: lane


title: Long projecting cells from WT mouse brain (LPC-8)

tag: tissue

value: postnatal 29

tag: Sex


title: Long projecting cells from WT mouse brain (LPC-6)


title: Long projecting cells from WT mouse brain (LPC-5)


title: Long projecting cells from WT mouse brain (LPC-9)


title: Long projecting cells from WT mouse brain (LPC-3)


title: Long projecting cells from WT mouse brain (LPC-1)


title: TH2wt

description: Th2 cells were generated by adding IL-2 (1 ng/mL), IL-4 (2 ng/ml) and neutralizing IFN- antibody (clone R4.6A2, 5 μg/mL) into the culture.

tag: genotype


title: naivecre

description: genotype: EGFRΔCD4


title: Flag leaf, DAH20_Replicate2


title: Chandelier cells upper layer from WT brain (CHC1-3)

value: Nkx2.1-CreER; Ai15

value: frontal cortex, infralimbic, prelimbic area, L1 L2/3 border

value: Chandelier cells upper layer

value: postnatal 58


title: Chandelier cells upper layer from WT brain (CHC1-1)

value: Nkx2.1-CreER; Ai14

value: postnatal 50


title: Het(Q175)_Cortex_Male_Vehicle_rep2

source_name: Cortex, Vehicle

tag: background strain

value: Het(Q175) knock-in

value: Cortex

value: Male

value: 6 months

tag: treatment duration

value: from 4 weeks to 6 months

tag: treatment

value: Vehicle

tag: treatment administration route

value: Oral

tag: treatment frequency

value: Twice-Daily (b.i.d)


title: control male 4hours

description: control male 4hours

value: whole heads

value: 0-5 days

value: male

value: control


title: Chandelier cells upper layer from WT brain (CHC1-4)

value: frontal cortex, infralimbic, prelimbic area, L1 L2/3 border

tag: cell type

value: postnatal 40

value: female


title: Chandelier cells upper layer from WT brain (CHC1-2)

value: Nkx2.1-CreER; Ai14

value: Chandelier cells upper layer


title: Chandelier cells deep layer from WT brain (CHC2-2)

value: frontal cortex layers 5 & 6

value: Chandelier cells deep layer

value: postnatal 34


title: Chandelier cells deep layer from WT brain (CHC2-4)


title: PV basket cells from WT mouse brain (PVC-13)

source_name: PV basket cells from WT mouse brain

value: Pv-iresCre; Ai14

value: frontal cortex, all layers

value: PV basket cells

value: postnatal 83


title: Chandelier cells deep layer from WT brain (CHC2-1)


title: PV basket cells from WT mouse brain (PVC-14)


title: PV basket cells from WT mouse brain (PVC-16)


title: PV basket cells from WT mouse brain (PVC-12)


title: PV basket cells from WT mouse brain (PVC-10)


title: Long projecting cells from WT mouse brain (LPC-4)

value: Sst-Flp; Nos1-Cre; Ai65

value: frontal cortex

value: Long projecting cells

value: postnatal 28


title: PV basket cells from WT mouse brain (PVC-7)

value: postnatal 81

value: male


title: PV basket cells from WT mouse brain (PVC-8)

value: postnatal 58


title: PV basket cells from WT mouse brain (PVC-4)


title: PV basket cells from WT mouse brain (PVC-9)


title: Long projecting cells from WT mouse brain (LPC-2)


title: PV basket cells from WT mouse brain (PVC-3)

value: female


title: PV basket cells from WT mouse brain (PVC-6)


title: PV basket cells from WT mouse brain (PVC-5)


title: PV basket cells from WT mouse brain (PVC-1)


title: CCK-basket cell from WT mouse brain (CCKC-4)

source_name: CCK-basket cell from WT mouse brain

value: Vip-Flp; CCK-Cre; Ai65

value: frontal cortex, layer 2+3

value: CCK-basket cells

value: postnatal 40


title: PV basket cells from WT mouse brain (PVC-2)


title: Chandelier cells upper layer from WT brain (CHC1-5)

value: Nkx2.1-CreER; Ai14

value: frontal cortex, infralimbic, prelimbic area, L1 L2/3 border

value: Chandelier cells upper layer


title: Chandelier cells deep layer from WT brain (CHC2-3)

value: frontal cortex layers 5 & 6

value: Chandelier cells deep layer

value: postnatal 34


title: PV basket cells from WT mouse brain (PVC-15)

value: Pv-iresCre; Ai14

value: frontal cortex, all layers

value: PV basket cells

value: postnatal 83


title: CCK-basket cell from WT mouse brain (CCKC-1)

value: postnatal 39

value: male


title: PV basket cells from WT mouse brain (PVC-11)

value: female


title: CCK-basket cell from WT mouse brain (CCKC-2)

value: Vip-Flp; CCK-Cre; Ai65


title: CCK-basket cell from WT mouse brain (CCKC-3)

value: frontal cortex, layer 2+3


title: Interneuron selective cell from WT mouse brain (ISC-4)

value: Vip-Flp; CR-Cre; Ai65

value: frontal cortex, layer 2/3

value: Interneuron selective cells

value: postnatal 32


title: Interneuron selective cell from WT mouse brain (ISC-2)


title: Interneuron selective cell from WT mouse brain (ISC-1)


title: P15_0

city: Wuhan

first: Yan

last: Wu

address: Bayi Street

institute: Wuhan University

data_processing:
All six samples that were named as P15-0, P15-6, P15-48, PC-0, PC-6 and PC-48, sequenced by high throughput Illumina Solexa system.
Removing the sequence of low quality, poly A, incorrect adaptor and smaller than 18nt, clean reads were obtained.
Then by comparing to genebank, rfam and genome sequence of exons and introns, other types of RNA (rRNA, snRNA, snoRNA and tRNA), repeat sequence and genomic degradation products were all excluded, the rest of the sequences were miRNAs
The remaining reads were compared to the miRNA database in miRBase (release 21, http://www.mirbase.org/).
The differential expression analysis of miRNA expression was operated by edgeR.

organism: Oryza sativa

source_name: BPH15 introgression line leaf shealth without BPH infestaion (at 0h)

growth_protocol: Plants were grown in a controlled growth chamber. The fourth leaf of 3-week-old young plants were used as the material in all experiments.

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad,CA, US)following the manufacturer’s instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treat plants with BPH in different time points (as indicated) then sampled in the same time points.

value: leaf shealth

value: Resistant to BPH

value: four-leaf stage


title: P15_6

source_name: BPH15 introgression line leaf shealth with BPH infestaion (at 6h)


title: Martinotti cells from WT mouse brain (MNC-3)

source_name: Martinotti cells from WT mouse brain

value: Sst-Flp; CR-Cre; Ai65

value: frontal cortex, layer2/3

value: Martinotti cells

value: postnatal 35


title: PC_48

source_name: 9311 leaf shealth witht BPH infestaion (at 48h)

value: Susceptible to BPH


title: Martinotti cells from WT mouse brain (MNC-4)


title: PC_6

source_name: 9311 leaf shealth with BPH infestaion (at 6h)


title: PC_0

source_name: 9311 leaf shealth without BPH infestaion (at 0h)


title: Martinotti cells from WT mouse brain (MNC-2)


title: Martinotti cells from WT mouse brain (MNC-1)


title: RNA-Seq control

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

country: South Korea

institute: Yonsei University

data_processing:
Reads were quality trimmed and filtered using the NGS QC toolkit v2.3 to remove reads containing low-quality bases.
After preprocessing, the RNA sequenced reads were mapped to hg19 genome using RSEM with bowtie2 v2.0.0-beta7.
ChIP sequence reads were mapped to T.vaginalis genome using bowtie2 v2.0.0-beta7.
FPKM (fragments per kilobase of exon per million fragments mapped) for RNA-Seq were calculated using RSEM.
genome build: hg19
processed data files format and content: RNA-Seq wig files were generated using RSEM.

source_name: Breast cancer cell line

growth_protocol: MDA-MB-231 breast cancer cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% heat-inactivated fetal bovine serum and 100 U/ml penicillin/streptomycin.

extract_protocol:
Total RNA was isolated using RiboEx column (GeneAll Biotechnology).
RNA-seq and ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-231 cells were infected with lentiviruses expressing shRNA against SATB1 or containing empty pLKO.1 vector; drug-resistant cells were selected.

tag: cell line

value: Control cells

tag: chip antibody


title: ChIP-Seq control H3K4me3

data_processing:
Reads were quality trimmed and filtered using the NGS QC toolkit v2.3 to remove reads containing low-quality bases.
ChIP-Seq read counts were calculated for each gene using HTSeq v0.6.1 and were converted log2 CPM (count per million) values using Bioconductor package edgeR v3.6.8
We called peaks for each experiment using HOMER with the default options.
genome build: hg19
processed data files format and content: ChIP-Seq bedGraphs were generated using BEDtools

extract_protocol:
Chromatin lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
RNA-seq and ChIP-seq libraries were prepared for sequencing using standard Illumina protocols


title: RNA-Seq shSATB1

value: SATB1-depleted cells


title: ChIP-Seq shSATB1 H3K27me3


title: ChIP-Seq control H3K27me3


title: ChIP-Seq shSATB1 H3K4me3


title: P15_48

source_name: BPH15 introgression line leaf shealth witht BPH infestaion (at 48h)


title: mOSN-Lhx2KO_ATACseq_rep2

city: Piscataway

first: Kevin

last: Monahan

state: NJ

address: 604 Allison Rd

department: Molecular Biology and Biochemistry

institute: Rutgers University

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.2.6) with default parameters. ATAC-Seq and Native ChIP-Seq samples were aligned with Bowtie2 (2.2.6) using -X 1000.
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ATACseq, reads mapping to mitochondrial DNA were also removed. For ATAC and ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq and ATAC-Seq, bigWig files were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). ATAC-seq fragments were shifted 4bp upstream (- adjust 4) during bigWig generation. For RNA-Seq, bigWig files were generated with RSeQC (2.6.4) using -t 10000000.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files at base pair resolution. ChIP-Seq and ATAC-Seq files normalized to a library size of 10,000,000 reads. RNA-seq files normalized to a library size of 1,000,000 reads.

source_name: mature olfactory sensory neurons

extract_protocol:
Crosslinked-ChIP: Chromatin from formaldehyde cross-linked cells was sheared on a Covaris S220 Focused-ultrasonicator to a size range of 200-500bp. Approximately 1-2ug of sheared chromatin was used for immunoprecipitation with antibodies, and precipitated DNA was column purified. Native-ChIP: Native chromatin was digested with Micrococal Nuclease to predominantly mono and di-nucleosome sized fragments. Nucleosomal DNA was immunoprecipitated with antibodies and column purified. ATAC: Cells were lysed and then transposed with Nextera Tn5 transposase (Illumina). Transposed DNA was column purified using a Qiagen MinElute PCR cleanup kit. RNA: Cells were lysed in Trizol-LS (ThermoFisher) then RNA was extracted and treated with Turbo-DNase (ThermoFisher).
Crosslinked-ChIP: ChIP-seq Libraries were prepared using a Nugen Ultralow V2 kit. Native-ChIP: ChIP-seq Libraries were prepared using a Nugen Ultralow V2 kit. ATAC: Transposed DNA was amplified using barcoded primers and NEBNext High-Fidelity PCR Master Mix. RNA: RNA-seq libraries were prepared using a TruSeq Stranded Total RNA with Ribo-Zero Gold Set B kit (Illumina RS-1222302).

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For horizontal basal cells, dissociated cells were resuspended in 800uL PBS with 1:80 CD54-PE antibody (BioLegend, Cat# 116107), incubated for 30 minutes at 4oC with rotation, and then washed twice with PBS. Labeled cells were then resuspended in sort media (PBS with 2% Fetal Bovine Serum) supplemented with 100 U/mL DNase I (Worthington Biochemical), 4mM MgCl2, and 500ng/mL DAPI (Invitrogen). For all other ATAC and Native-ChIP samples, dissociated cells were washed once with sort media and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical), 4mM MgCl2, and 500ng/mL DAPI (Invitrogen). For Crosslinked-ChIP samples, cells were fixed prior to sorting. Dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 5 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.

value: mature olfactory sensory neurons

value: OMPcre; Lhx2fl/fl

value: ATAC


title: mOSN-Lhx2KO_Ebf_ChIPseq_Rep2

value: anti-Ebf (Aviva, ARP32960_P050)

value: Crosslinked-ChIP


title: mOSN-Lhx2KO_Lhx2_ChIPseq_Rep2

value: anti-Lhx2 (Roberson et al., 2001)


title: S.aureus_mouse_B

city: Toronto

last: De Carvalho

state: ON

address: 101 College St

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
RNA-seq reads were aligned to the transcriptome of mouse genome GRCm38/mm10 using the Kallisto package with the quant command
with parameters -t 1 --plaintext --bias -l 200 -s 20 --single --pseudobam
For each sample, BAM files, containing all the alignments, were obtained along with the estimated counts for each transcript; these were then summed up for each gene
The genic counts for all the samples were assembled and quantile normalized using the R function normalize.quantiles
before getting the counts per million to account for the library sizes.   These normalized counts were log2 transformed with: t(log2(t(CountsMatrix_QNorm + 0.5)/(lib.size + 1) * 1e+06)); lib.size <- colSums(CountsMatrix_QNorm)
These transformed counts were input to the R package limma’s lmFit function -  and using empirical Bayes methods to borrow information between genes along with correcting for mean-variance trend - to get Differentially Expressed Genes (DEGs) for SA vs NS (S. aureus vs Non Stimulated) and GAS vs NS.
The p-values obtained using t-tests were adjusted using the Benjamini-Hochberg procedure.  Log 2 Fold Changes (FCs) were also returned, with positive values indicating over-expression compared to the Non Stimulated condition, and negative values indicating under-expression with SA or GAS.
DEGs were called using adjusted p-value < 0.05 and actual FCs > 2 in either direction.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: TSV files containing the estimated counts for each transcript, along with other metrics

source_name: bone marrow-derived dendritic cells (BMDC)

growth_protocol: BM-derived dendritic cells (BMDC)  were routinely generated by incubating murine bone marrow cells with 20ng/mL of mGMCSF.  After 9 days, the differentiated cells were used for in vitro stimulation assays. BMDC were plated in 48-well plates at a density of 2 x 105/ml

extract_protocol:
Total RNA was isolated using an RNeasy Mini-kit (Qiagen, Valencia, CA) according to the manufacturer's protocol.
mRNA was purified from one microgram of total RNA with the use of Ambion Dynabeads® mRNA DIRECT™ Micro Purification Kit
Purified mRNA was fragmented, adapters ligated, reverse transcribed to make cDNA, and cDNA amplified with Ion Total RNA-Seq Kit v2, Ion Torrent™, per manufacturer’s recommendations. Samples were individually barcoded using Ion Xpress™ RNA-Seq Barcode 1-16 Kit, Ion Torrent™, before their cDNA was amplified. RNAseq libraries were assessed for concentration and length using Invitrogens Qubit® dsDNA HS Assay Kit (Carlsbad, CA) and Agilent DNA 1000 Kit respectively

treatment_protocol: BMDCs were plated in 48-well plates at a density of 2 x 105/ml and infected with S. aureus or GAS at MOI of 3. Infected DC were incubated for 1 h in antibiotic-free medium, washed twice to remove unbound bacteria and further incubated in RPMI media supplemented with 10% FBS and 100 μg/ml of Gentamicin for 12 hr

tag: strain

value: wild-type

tag: agent

value: S. aureus LAC MOI 3


title: mOSN-Lhx2KO_Input_ChIPseq


title: Interneuron selective cell from WT mouse brain (ISC-3)

value: Vip-Flp; CR-Cre; Ai65

value: frontal cortex, layer 2/3

value: Interneuron selective cells

tag: animal

tag: age

value: postnatal 32

value: female


title: mOSN_RNAseq_rep3

value: OMPiresGFP

value: RNA


title: S.aureus_mouse_C

value: bone marrow-derived dendritic cells (BMDC)


title: mOSN-Lhx2KO_RNAseq_rep2


title: Group_A._Streptococcus_mouse_B

value: S. pyogenes M49 MOI 3


title: Group_A._Streptococcus_mouse_A


title: Group_A._Streptococcus_mouse_C


title: S.aureus_mouse_A


title: No_stimulation_mouse_C


title: No_stimulation_mouse_A


title: No_stimulation_mouse_B


title: P0 Vestibule, rep2

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
Alignment to the mm10 genome assembly using STAR
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files generated by STAR during the alignment process

source_name: P0 Vestibule

growth_protocol: C57BL/6J mice, including newborns, adult and time-mated pregnant females, were purchased from Envigo, Jerusalem, Israel.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen). The integrity of the total RNA was estimated using the 2100 Bioanalyzer (Agilent Technologies).
400ng of total RNA was used to prepare twelve paired-end (PE) cDNA libraries using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) at the Tel Aviv University Genome Analysis Laboratory (https://en-med.tau.ac.il/Genomic-Analysis-Lab).

tag: strain background

tag: developmental stage

value: vestibute

tag: replicate


title: P0 Vestibule, rep3

tag: tissue


title: P0 Vestibule, rep1


title: E16.5 Vestibule, rep3

source_name: E16.5 Vestibule


title: P0 Cochlea, rep1

source_name: P0 Cochlea

value: cochlea


title: E16.5 Vestibule, rep1


title: E16.5 Vestibule, rep2


title: E16.5 Cochlea, rep3

source_name: E16.5 Cochlea


title: E16.5 Cochlea, rep2


title: E16.5 Cochlea, rep1


title: P0 Cochlea, rep3


title: mOSN_H3K9me3_Mnase-ChIP_rep2

value: mature olfactory sensory neurons

tag: genotype

value: OMP-IRES-GFP

value: anti-H3K9me3 (abcam, ab8898)

value: Native-ChIP


title: mOSN_H3K27ac_Mnase-ChIP_rep2

value: anti-H3K27ac (Active Motif, AM39133)


title: mOSN_H3K9me3_Mnase-ChIP_rep1


title: mOSN+Fusion_ATACseq_rep2

value: OMP-IRES-tTA; tetO-Fusion-2a-mCherry

value: ATAC


title: mOSN_H3K79me3_Mnase-ChIP

value: anti-H3K79me3 (abcam, ab2621)


title: mOSN_H3K27ac_Mnase-ChIP_rep1


title: Olfr17_ATACseq_rep1

source_name: Olfr17+ mature olfactory sensory neurons


title: Olfr17_ATACseq_rep2

value: Olfr17+ mature olfactory sensory neurons


title: mOSN_input_Mnase-ChIP


title: Olfr1507iGFP_ATACseq_rep2

source_name: Olfr1507+ mature olfactory sensory neurons


title: mOSN+Fusion_ATACseq_rep1


title: mOSN-Lhx2KO_ATACseq

value: OMP-IRES-Cre; Lhx2fl/fl


title: Olfr1507iGFP_ATACseq_rep1

value: Olfr1507+ mature olfactory sensory neurons


title: mOSN_ATACseq_rep4


title: mOSN_ATACseq_rep3


title: P0 Cochlea, rep2


title: Challenged 108h

city: Guangzhou

first: Jie

last: Li

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

institute: Sun Yat-Sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
The SAPAS-generated raw reads were filtered and trimmed for quality control utilizing Perl script, and then mapped to the chicken genome galGal4 assembly and Marek’s disease virus genome MD5 respectively by applying Bowtie.
After internal priming filtering, the resulting uniquely mapped reads were clustered to define poly(A) sites as described previously (Fu et al., 2011).
Genome_build: galGal4
Supplementary_files_format_and_content: tab-delimited text files including poly(A) sites information for each Sample

organism: Gallus

source_name: embryo fibroblasts cells_challenged

extract_protocol:
Total RNA was extracted from samples using TRIzol (Invitrogen) according to manufacturer’s instruction.
Approximately 2 μg total RNA was randomly fragmented by heating. First-strand cDNA was synthesized by reverse transcription with an anchored oligo d(T) primer and a 5’ template switching adaptor. PCR was then performed to amplify the cDNA, and the number of cycles was optimized to ensure that the double-strand cDNA remained in the exponential phase of amplification. Then fragments of 250–500 bp in size were excised and purified by Agencourt Ampure magnetic bead (Beckman Coulter) according to manufacturer’s instruction. The average size was determined by Agilent 2100 bioanalyzer (Agilent Genomics).

value: embryo fibroblasts cells

tag: challenged with

value: Marek’s Disease Virus

tag: time point

value: 108h post-infection


title: mOSN_ATACseq_rep1


title: Control 108h

source_name: embryo fibroblasts cells_control

value: none (control)


title: mOSN-Lhx2KO_Ebf_ChIPseq

value: anti-Ebf (Aviva, ARP32960_P050)

value: Crosslinked-ChIP


title: mOSN-Lhx2KO_Lhx2_ChIPseq

value: mature olfactory sensory neurons

value: anti-Lhx2 (Roberson et al., 2001)


title: Challenged 72h

value: 72h post-infection


title: Challenged 54h

value: 54h post-infection


title: Olfr151iGFP_ATACseq_rep2

source_name: Olfr151+ mature olfactory sensory neurons


title: mOSN_input_ChIPseq_rep2

value: OMP-IRES-GFP


title: Olfr151iGFP_ATACseq_rep1

value: Olfr151+ mature olfactory sensory neurons


title: mOSN_input_ChIPseq_rep1


title: Control C

city: Qingdao

first: Lina

last: Sun

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of Sciences

data_processing:
The original image data was transferred into sequence data by base calling(using CASAVA version 1.5+), (defined as ‘raw reads’) and saved as fastq files that include the detailed reads sequences and the reads quality information.
The raw reads obtained from Solexa sequencing were processed by trimming poor quality reads, 5’ adapter pollution reads, reads without 3’ adapters, reads without insert fragments, reads containing poly(A) stretches, and reads less than 18nt. rRNA, tRNA, snRNA and snoRNA were removed by blasting against the GenBank database (http://blast.ncbi.nlm.nih.gov) and the Rfram database (http://sanger.ac.uk/software/Rfam).
Considering that no miRNA information of the sea cucumber was in miRBase19.0, the remaining clean reads were aligned to search all known precursor/mature miRNAs of all animal species in miRBase 19.0 with perfect matches.
Chose the highest expression miRNA for each mature miRNA family which was regarded as a temporary miRNA database. Clean data was aligned to the above temporary miRNA database and the expression of miRNA is generated by summing the count of reads which can align to the temporary miRNA database without mismatches.
Potentially novel miRNAs were identified using MIREAP (http://sourceforge.net/projects/mireap/) with stem-loop structure prediction
processed data files format and content: count of reads

organism: Apostichopus japonicus

source_name: Apostihopus japonicus intestine

extract_protocol:
Total RNA was extracted from an individual intestine using the RNAeasy mini kit (Qiagen, USA) according to the manufacturer’s instructions.
The quality and concentration of RNA were measured by NanoDrop 1000 (Thermo) after which the mRNA in total RNA was enriched by using the oligo(dT) magnetic beads. After the addition of fragmentation buffer, the mRNA was interrupted and formed short fragments (~200 bp). The first strand cDNA was then synthesized by the random hexamer-primer, using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified using the QiaQuick PCR extraction kit, and washed with EB buffer so as to facilitate end repair and the addition of a single nucleotide A (adenine). Finally, sequencing adaptors were ligated to the fragments. The required fragments were purified by means of agarose gel electrophoresis and enriched by PCR amplification.

value: intestine

tag: group

value: control


title: Control 54h


title: mOSN_ATACseq_rep2

value: ATAC


title: Challenged 36h

value: 36h post-infection


title: Control A


title: Control B


title: mOSN_Lhx2_ChIPSeq_rep2


title: Control 18h

value: 18h post-infection


title: mOSN+Fusion_RNAseq_rep1

value: OMP-IRES-tTA; tetO-Fusion-2a-mCherry

value: RNA


title: mOSN_Lhx2_ChIPSeq_rep1


title: Challenged 18h

value: embryo fibroblasts cells

value: Marek’s Disease Virus


title: mOSN_Ebf_ChIPSeq_rep1

value: anti-Ebf (Aviva, ARP32960_P050)


title: 3dpeB

value: 3 days post evisceration (dpe)


title: mOSN_Ebf_ChIPSeq_rep2

value: mature olfactory sensory neurons

value: Crosslinked-ChIP


title: mOSN+Fusion_RNAseq_rep2


title: mOSN_RNAseq_rep2


title: Control 36h

value: none (control)


title: HTS-3 [miRNA]

city: Wuxi

first: Jun

last: Qiang

state: Jiangsu

address: 9 Shanshi East road

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

description:
miRNA sequencing
Processed data file: miRNA_sequences_expression_data.txt

data_processing:
Following normalized deep-sequencing counts, DE miRNA was identified by using of Student's T-tests. The threshold of less than 0.05 was significance in analysis. The aligned reads were analyzed by Cufflinks, which uses the normalized RNA-seq fragment counts to measure the relative abundances of the transcripts. The unit of measurement is Fragment Per Kilobase of exon per Million fragments mapped (FPKM). We used Student's T-tests to analyze the DE mRNAs.
To predict the target genes by DE miRNAs, we employed TargetScan 5.2 (http://www.targetscan.org/vert_50/) and miRanda v3.3a toolbox (http://www.microrna.org/microrna/home.do) were used to analyze miRNA binding sites. Finally, these data predicted by both algorithms were combined and the overlaps were calculated. The GO (http://www.geneontology.org) databases was used to assign terms and pathways to the target genes to determine their potential downstream biological functions. The GO (http://www.geneontology.org) and KEGG (http://www.genome.jp/kegg/pathway.html) databases were used to assign terms and pathways to the DE genes to determine their potential downstream biological functions. Significantly enriched KEGG terms were determined by using of the corrected P-values (P<0.05).
We employed ACGT101-CORR1.1 to predict all possible positive and negative miRNA-mRNA pairs following the LC-BIO (Hangzhou, China) recommended protocol. Based on integrated analysis of DE miRNAs (P<0.05, fold-change ≥ 1.5 or ≤ 0.67 and RPM ≥ 5) and DE mRNAs (P<0.05, fold-change ≥ 2 or ≤ 0.5 and FPKM ≥ 10), and the principle of miRNA-mRNA pairs in animals, negative relationship of DE miRNA-DE mRNA pairs were screened. We used Cytoscape software (http://www.cytoscape.org/) to construct interaction network of negative DE miRNA-DE mRNA pairs.
Genome_build: Orenil1.0
Supplementary_files_format_and_content: miRNA_sequences_expression_data.txt: Tab-delimited text file includes expression profiles.
Supplementary_files_format_and_content: Gene_sequences_expression_data.txt: Tab-delimited text file includes expression profiles.

organism: Oreochromis niloticus

source_name: genetically improved farmed tilapia (GIFT), liver, 37.5 °C

growth_protocol: In this study, the GIFT used were 16th generation. The 16thGIFT was registered as a new aquaculture variety in 2014 in China. The breeding base was imported from the world fish Center (WorldFish Center) in 2006, 60 families of 10th generation genetically improved farmed tilapia (GIFT, Oreochromis niloticus) using comprehensive breeding methods combined with quantitative genetics BLUP analysis and family selection. After six generations of breeding, the 16th generation GIFT were successfully bred, these possessed rapid growth, increased size, and strong stress resistance. The experimental fish were of the same genetic background as the offspring from the same family and were obtained from the Yixing tilapia farm at the Freshwater Fisheries Research Center of the Chinese Academy of Fishery Sciences (Wuxi, China). The same batch of breeding fry were selected and cultured in outdoor cement pond for 50d, and then transported into the indoor water circulation system. The fish were acclimatized in indoor concrete tanks containing 29 °C water under a natural photoperiod with continuous aeration for 2 weeks prior to the experiment. The fish were conditioned to accept floating pellets feed (NingboTech-Bank Co., Ltd, Yuyao, China; crude protein 28%; crude lipid 6%).

extract_protocol:
The samples were used for further processing. About 1 ug total RNA of each sample was employed for constructing small RNA library based on protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA). Subsequently, we used the Illumina HiSeq 2500 and single-end sequencing (50 bp) to analyze small RNA library according to standard methods at the LC-BIO (Hangzhou, China).
Following the manufacturer's procedure, total RNA of liver samples was extracted by using of Trizol reagent (Invitrogen, CA, USA).

treatment_protocol: Before the formal experiment, the 48h LT50 of GIFT was determined by pre-experiment. The pre-experiment was set for a total of eight temperature gradients, including 35.5, 36, 36.5, 37, 37.5, 38, 38.5 and 39 °C. The temperatures reached the experimental temperature in 30 min by using of heater. Eight treatments with three replicates each 10 fish were set up for pre-experiment. The cumulative mortality of each treatment group within 48 h was counted and 48h LT50 of GIFT was obtained by linear interpolation. The 48h LT50 was 37.49 °C. Therefore, we chose 37.5°C as heat-stress temperature for the present study. The average weight of the experimental GIFT was 105±5g. The experiment was stocked into six 600-L tanks (25 fish per tank) with two replicate tanks at an initial temperature of 29 °C. The control GIFT livers (CO-1, CO-2 and CO-3) from three tanks at 29 °C were immediately removed and stored at liquid nitrogen. While the temperature of the another three treatments were rapidly increased to 37.5 °C using heaters. The liver tissues of heat-stressed groups (HTS-1, HTS-2 and HTS-3) were sampled at 24 h of stress and stored at liquid nitrogen. Sampled livers of CO and HTS groups contained three biological replicates. The liver tissues of three fish in each tank were mixed and pooled to construct one library, and six libraries (CO-1, CO-2, CO-3, HTS-1, HTS-2 and HTS-3) were built in this study. Additionally, the another five livers in each tank from control groups or the heat-stress groups at 24h were randomly selected, that were further used to verify experiment for miRNA and mRNA expression.

value: liver

tag: treatment

value: heat-stressed at 37.5 °C


title: HTS-2 [miRNA]


title: CO-3 [miRNA]

source_name: genetically improved farmed tilapia (GIFT), liver, 29 °C

value: stocked at 29 °C


title: mOSN_RNAseq_rep1

value: OMP-IRES-GFP


title: NPCrep2

city: Athens

first: Stephen

last: Dalton

state: GA

address: 500 D.W. Brooks Dr

department: Biochemistry and Molecular Biology Department

institute: Univeristy of Georgia

description: NPC-hESC FPKM

data_processing:
Basecalls were performed on the illumina Hiseq 2500 v4 platform
Processed reads were mapped to hg19 using tophat 2.0.13 (--no-novel-juncs --max-multihits 1 --solexa-quals --no-coverage-search)
Reads over ENSEMBL genes were counted using Subread 1.5.2 with the following parameters featureCounts -p -t exon -g gene_id
Differential gene expression was performed using Cufflinks 2.2.1 with default setting.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: Human Embryonic Stem Cells

growth_protocol: WA09 hESCs were seeded on matrigel coated plates at 50,000 cells/cm2 in DMEM/F-12 supplemented with 8 ng/mL FGF, 200 ng/mL IGF-I, 10 ng/mL Activin A and 10 ng/mL Heregulinβ-1 for 4 days.  Definitve endoderm (DE) was derived from WA09 cells seeded on matrigel coated plates at 50,000 cells/cm2 in DMEM/F-12 supplemented with 8 ng/mL FGF and 100 ng/mL Activin A for 4 days.  Wnt-3a at 25 ng/mL was added to the media for the first day of DE differentiation only.  Splanchnic mesoderm  (MESO) was derived from WA09 cells seeded on matrigel coated plates at 50,000 cells/cm2 in DMEM/F-12 supplemented with 8 ng/mL FGF, 200 ng/mL IGF-I, 10 ng/mL Activin A, 10 ng/mL Heregulinβ-1, 25 ng/mL Wnt-3a, and 100 ng/mL BMP-4 for 4 days.  Neural progenitor cells (NPC) were derived from WA09 cells seeded on matrigel coated plates at 90,000 cells/cm2 in DMEM/F-12 supplemented with 200 ng/mL IGF-I, 10 ng/mL Heregulinβ-1, 20 mM SB431542, and 500 nM LDN for 6 days.  Pre-neural crest cells (NCSC) were derived from WA09 cells seeded on matrigel coated plates at 90,000 cells/cm2 in DMEM/F-12 supplemented with 8 ng/mL FGF, 200 ng/mL IGF-I, 10 ng/mL, Heregulinβ-1, 20 mM SB431542, and 0.2 mM BIO for 6 days.

extract_protocol:
Cells were collected using Accutase (STEMCELL, 07920), homogenized with Omega Homogenizer Columns (HCR003). Total RNA were extracted using E.Z.N.A. Total RNA kit I (Omega, R6834), according to manufacture's protocol.
Samples with an RNA integrity number (RIN) above 0.9 were selected and sent out for standard RNA-Seq application, including poly A enrichment, adaptor ligation, bar-coding, library amplification, etc (Hudsonalpha, AL, US).

tag: passages

value: neural progenitor cells


title: NCSCrep1

description: NCSC-hESC FPKM

tag: cell type

value: pre-neural crest cells


title: NPCrep1

description: NPC-hESC FPKM

tag: cell line


title: NCSCrep2

description: NCSC-hESC FPKM


title: CO-2 [miRNA]


title: MESOrep2

description: MESO-hESC FPKM

value: splanchnic mesoderm


title: delete BvgAS+MgSO4 1

city: BETHESDA

first: Deborah

middle: M

last: Hinton

state: MD

address: 8 center Dr., Building 8, Rm 2A21

institute: NIH

data_processing:
Sequenced reads were trimmed for adaptor sequence.
CLC Biomedical Genomic Workbench version 3.5.4 with default parameters was used for mapping and differential expression analysis.
For differential expression analysis, Empirical DGE statistical test was performed after normalization with total reads.  At least a 1.6-fold change in gene expression with a FDR corrected p-value of ≤ 0.05 was considered significant.
Genome_build: NC_002929.2
Supplementary_files_format_and_content: Tab-delimited text files include: 1) the expression level of genes for each sample after normalization with total reads; 2)the fold change of each gene in two different samples from EDGE test; 3) FDR p-value.

organism: Bordetella pertussis

source_name: bacteria

growth_protocol: B. pertussis Tohama I BP536 and its ΔbvgAS derivative were grown on BG agar containing streptomycin (50 μg /ml) at 37 °C in the absence (nonmodulating condition) or presence (modulating condition) of 50 mM MgSO4.  After 3 days, cells were scrapped from the plates and resuspended in PLB medium with or without MgSO4 to obtain an initial OD600 between 0.1 and 0.2.  Cells were incubated at 37 °C with shaking at 250 rpm until the OD600 reached a value between 0.5 and 0.6.

extract_protocol:
Total RNA was isolated by a modified hot phenol extraction. After DNase treatment, rRNAs were removed using the RiboZero (Illumina).
Strand specific cDNA libraries were prepared using standard Illumina protocols for the Illumina ScriptSeq 2.0 kit.

treatment_protocol: Cells were treated by growth in the presence (modulating condition) or absence (non-modulating condition) of 50 mM MgSO4.

value: Tohama I  BP536

value: deletion of bvgAS

value: with MgSO4


title: 3dpeA

value: intestine


title: 3dpeC


title: delete BvgAS+MgSO4 2


title: mOSN-Lhx2KO_RNAseq

value: OMP-IRES-Cre; Lhx2fl/fl

tag: chip antibody

value: RNA


title: MESOrep1

description: MESO-hESC FPKM


title: CO-1 [miRNA]


title: delete BvgAS-MgSO4 2

tag: strain

value: without MgSO4


title: Batch 2 CcI6 +200 mM sucrose

city: Durham

first: Louis

middle: S

last: Tisa

state: NH

address: 46 College Rd

department: MCBS

institute: University of New Hampshire

description: Barcode: GAGTGG

data_processing:
Illumina Casava 1.8.3 software used for base calling
Sequence reads were trimmed for adapter sequence and mapped to Frankia sp.strain CcI3 genome using CLC Genomics workbench
Genome_build: CcI6
Supplementary_files_format_and_content: tab-delimited tex files include RPKM values for each sample

organism: Frankia sp. CcI6

source_name: culture

growth_protocol: 7 days at 28 degrees in BAP medium

extract_protocol:
Rneasy kit
Stable RNA removal via the Microbeexpress kit. RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: growth under salt stress (+200 mM NaCl) or osmotic stress (+200 mM sucrose)

tag: stress

value: osmotic-stressed

tag: temperature

value: 28 o C

tag: time (days incubation)

value: 7 days


title: DErep2

description: DE-hESC FPKM

value: definitive endoderm


title: HTS-3 [mRNA]

description:
mRNA sequencing
Processed data file: Gene_sequences_expression_data.txt

extract_protocol:
About 10 ug total RNA of each liver sample was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Six cDNA libraries were created by reverse-transcription (RT) based on the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA). Finally, we performed the paired-end sequencing (300 ± 50 bp) on an Illumina HiSeq 2500 at the (LC Sciences, USA) according to standard methods. We aligned reads of CO-1, CO-2, CO-3, HTS-1, HTS-2 and HTS-3 groups to O. niloticus (http://www.ncbi.nlm.nih.gov/genome/?term=Oreochromis%20niloticus) reference genome by using of Tophat package. The methods of alignments and annotation were based on.
Following the manufacturer's procedure, total RNA of liver samples was extracted by using of Trizol reagent (Invitrogen, CA, USA).

value: liver

value: heat-stressed at 37.5 °C


title: WT+MgSO4 2

value: WT


title: Batch 2 CcI6 + 200 mM NaCl

description: Barcode: ATGTCA

value: salt-stressed


title: HTS-1 [miRNA]


title: delete BvgAS-MgSO4 1


title: DErep1

description: DE-hESC FPKM


title: Batch 2 CcI6 control

description: Barcode: TAGCCT

value: control


title: HTS-1 [mRNA]


title: HTS-2 [mRNA]


title: WT+MgSO4 1


title: WA09rep2

description:
NCSC-hESC FPKM
DE-hESC FPKM
MESO-hESC FPKM
NPC-hESC FPKM

value: human embryonic stem cells


title: CO-3 [mRNA]

value: stocked at 29 °C


title: Batch 1 CcI6 + 200 mM sucrose

description: Barcode: GTGGCC


title: WA09rep1


title: WT-MgSO4 2

value: Tohama I  BP536


title: CO-2 [mRNA]


title: Hepatocyte with Bim wild-type rep 2

status: Public on Sep 21 2017

city: Fitzroy

first: Esteban

middle: N

last: Gurzov

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent’s Institute of Medical Research

data_processing:
Sequencing reads were mapped to the mouse genome version GRCm38/mm10 using the program Tophat version 2
Gene quantification and abundance estimation from the mapped reads was performed using the FluxCapacitor program version 1.6.1. All genes have been assigned a relative coverage rate as measured in RPKM
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: The processed data files are in standard transcript GTF format (for the full format description see http://www.ensembl.org/info/website/upload/gff.html). The attributes column contains informations on the transcript length, transcript abundance quantification RPKM (reads per kilobase per million mapped reads) and the number of read that mapped to it.

source_name: Hepatocyte

growth_protocol: Tissue-specific deletion of BIM was generated by crossing Bim(lox/lox) mice with Alb-Cre (C57BL/6) mice (JAX). Male mice were kept on regular chow (20% protein, 6% fat and 3.2% crude fibre) or placed at 8-10 weeks of age on a high fat diet (SF04-027 Speciality Feeds, Perth, Western Australia) for 14-20 weeks

extract_protocol:
Hepatocytes were isolated by a two-step collagenase A (0.05% w/v; Roche Diagnostics) perfusion method (see article material and method)
Single-end RNA-seq library

tag: genotype/variation

value: wild-type


title: Hepatocyte with Bim wild-type rep 3


title: Batch 1 CcI6 + 200 mM NaCl

description: Barcode: GTTTCG


title: Hepatocyte with Bim knock-out rep 3

value: Bim knock-out


title: CO-1 [mRNA]


title: OKM_Obox1_D3_rep2

city: shanghai

first: You

address: 1239 siping road

department: school of life science and technology

institute: tongji university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 reference genome using tophat v2.1.1 with default parameters.
Gene expression for each sample was quantified to FPKM using Cufflinks(v 2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript.

growth_protocol: The OG2 MEFs were cultured in DMEM supplemented with 10% fetal bovine serum and Glutamine. The reprogramming cells were induced with doxycycline (Dox) (1ug/ml) for 3 days in ES medium consisted of DMEM supplemented with 15% fetal bovine serum,  nonessential amino acids, Glutamine, Nucleosides, 2-mercaptoethanol, LIF.

extract_protocol:
For RNA-seq, the cells were lysed using RLT buffer supplemented with β-mercaptoethanol and processed using the RNeasy mini kit (Cat. 74104).
KAPA Stranded mRNA-Seq Kit (KK8420)

treatment_protocol: The OG2 MEFs ( 3 days post-Dox induction with OSKM, OKM+Obox1 or OKM+empty vector overexpression) were digested to single cell and harvested to performed RNA-seq.

tag: strain background

value: reprogrammable mouse embryonic fibroblasts (MEFs)

tag: induced with

value: doxycycline (Dox) (1ug/ml) for 3 days

tag: reprogramming stage

tag: dox-induced genes


title: OKM_Obox1_D3_rep1


title: Batch 1 CcI6 control

description: Barcode: GATCAG


title: Hepatocyte with Bim wild-type rep 1


title: WT-MgSO4 1

tag: genotype

value: without MgSO4


title: Hepatocyte with Bim knock-out rep 1


title: Control 72h

value: embryo fibroblasts cells

tag: challenged with

value: none (control)

tag: time point

value: 72h post-infection


title: OSKM_D3_rep1

value: OSKM


title: S79_FGF23_tumour

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

description: Small RNA-seq

data_processing:
The original fastq files were converted to fasta format and reads without Ns were kept for further analysis.
The 3' adapter and HD signatures [Sorefan et al. 2012] were trimmed and the files were converted from redundant to non-redundant format.
The reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al. 2008].
The reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRBase, release 21.
The abundances of the reads were normalized using the RPM method [Mortazavi et al. 2008].
The differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20.
Genome_build: GRCh38
Supplementary_files_format_and_content: *csv: Comma-separated text files include sequences and raw abundances.

source_name: FGF23-producing benign tumour

extract_protocol:
Resected tissue was used for RNA extraction before small RNA library construction.
Illumina compatible method using HD adapters.

tag: disease state

value: phosphaturic mesenchymal tumour

tag: tissue

value: benign tumour


title: Hepatocyte with Bim knock-out rep 2


title: OSKM_D3_rep2

tag: cell type


title: OKM_D3_rep2

value: OKM


title: OKM_D3_rep1


title: SP_WR_5d_M109_exp1

city: Chicago

first: Nicolas

last: Chevrier

state: Illinois

address: 5640 South Ellis Avenue

department: Pritzker School of Molecular Engineering

institute: The University of Chicago

description:
Whole tissue
raw_counts_exp1_day7_day21.txt

data_processing:
Fastq files were demultiplexed with custom scripts and quality checked with FastQC.
Read mapping using STAR aligner with mm10 genome.
FeatureCounts was used to count mapped reads for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample. Rows = genes, and columns = whole-tissue or sorted CD8+ cell samples.

source_name: Spleen

extract_protocol:
For whole organs, samples were lysed in Trizol and total RNA was extracted by phenol-chloroform extraction followed by purification with Dynabeads MyOne Silane beads (Thermoscientific). For sorted cell populations, CD8+ T cell populations (5,000-10,000 cells per sample) were lysed in RLT buffer (Qiagen) containing 1% beta-mercaptoethanol and total RNA was extracted with Dynabeads MyOne Silane beads. After bead-based enrichment, total RNA samples were purified by on-bead DNase I treatment followed by cleanup with 80% ethanol. RNA concentration was normalized across samples prior library construction.
Total RNA was heat-fragmented to an average size of 500 bp fragments and reverse transcribed with barcoded oligo(dT) primers containing an Illumina-compatible adapter sequence. After RNA degradation, barcoded, single-stranded cDNA samples were pooled and flanked by an Illumina-compatible adapter sequence in their 3’ end using a ‘primer extension’ method with DNA Pol I, Large Klenow Fragment exo minus. cDNA pools flanked on both ends with illumina sequences were then amplified by PCR and sequenced on Illumina sequencers.

tag: cohort

value: WR

tag: days post infection

tag: mouse id

tag: experiment id

tag: sequencing batch


title: SP_WR_3d_M82_exp1

tag: strain


title: SP_WR_0_5d_M23_exp1


title: SP_MVA_WR_5d_M113_exp1


title: SP_WR_5d_M108_exp1


title: SP_WR_1_5d_M60_exp1


title: SP_WR_1_5d_M57_exp1


title: SP_MVA_WR_1_5d_M63_exp1


title: SP_WR_3d_M83_exp1


title: SP_MVA_WR_0_5d_M27_exp1


title: SP_MVA_WR_5d_M112_exp1


title: SP_WR_0_5d_M24_exp1


title: SP_MVA_5d_M105_exp1

value: MVA


title: SP_MVA_3d_M80_exp1


title: SP_MVA_3d_M78_exp1


title: SP_MVA_1_5d_M56_exp1


title: SP_MVA_5d_M103_exp1


title: SP_MVA_0_5d_M19_exp1


title: SP_MVA_1_5d_M53_exp1


title: SP_MVA_WR_3d_M88_exp1


title: SP_control_M139_exp1

value: Uninfected


title: SP_MVA_0_5d_M20_exp1


title: Sk_d_MVA_0_5d_M19_exp1

source_name: Skin


title: Sk_d_MVA_0_5d_M17_exp1


title: PB_WR_5d_M108_exp1

source_name: Peripheral blood mononuclear cells


title: SP_MVA_WR_3d_M85_exp1


title: SP_MVA_WR_1_5d_M64_exp1


title: PB_WR_5d_M107_exp1


title: PB_WR_3d_M84_exp1


title: PB_WR_3d_M83_exp1


title: PB_WR_1_5d_M60_exp1


title: PB_WR_0_5d_M24_exp1


title: PB_WR_0_5d_M22_exp1


title: PB_MVA_WR_5d_M111_exp1


title: PB_WR_1_5d_M59_exp1


title: PB_MVA_WR_3d_M86_exp1


title: PB_MVA_WR_3d_M87_exp1


title: PB_MVA_WR_3d_M85_exp1


title: PB_MVA_WR_5d_M112_exp1


title: SP_control_M1_exp1


title: PB_MVA_WR_1_5d_M62_exp1


title: PB_MVA_WR_1_5d_M61_exp1


title: PB_MVA_WR_1_5d_M63_exp1


title: PB_MVA_WR_0_5d_M26_exp1


title: PB_MVA_5d_M105_exp1


title: PB_MVA_3d_M80_exp1


title: PB_MVA_3d_M79_exp1


title: PB_MVA_5d_M104_exp1


title: PB_MVA_5d_M102_exp1


title: PB_MVA_3d_M78_exp1


title: PB_MVA_WR_5d_M110_exp1


title: PB_WR_3d_M82_exp1


title: PB_MVA_1_5d_M56_exp1


title: PB_MVA_3d_M77_exp1


title: PB_MVA_1_5d_M55_exp1


title: PB_MVA_WR_3d_M88_exp1


title: PB_MVA_WR_1_5d_M64_exp1


title: PB_MVA_1_5d_M54_exp1


title: PB_MVA_1_5d_M53_exp1


title: PB_MVA_WR_0_5d_M27_exp1


title: PB_MVA_0_5d_M20_exp1


title: PB_control_M3_exp1


title: PB_MVA_0_5d_M19_exp1


title: PB_control_M140_exp1


title: PB_MVA_0_5d_M17_exp1


title: PB_control_M139_exp1


title: PB_MVA_5d_M103_exp1


title: PB_control_M1_exp1


title: RNA_Vector_D3_RNA-seq_rep1

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq: Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v2.1.1 with default parameters.
RNA-seq: Gene expression for each sample was quantified to FPKM using Cufflinks(v 2.2.1).
ChIP-seq: Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using bowtie2 (v 2.2.9) with default parameters.
ChIP-Seq: peaks were called using macs14 (v 1.4.2 20120305) with the parameters(macs14 -t Sample.bam -c input.bam -g mm -n name -B -S).
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Tab-delimited text files include FPKM values for each transcript.
Supplementary_files_format_and_content: ChIP-seq: Bigwiggle files are generated through MASC14 with parameters(macs14 -t Sample.bam -c input.bam -g mm -n name -B -S).

growth_protocol: The reprogrammable MEFs were cultured in DMEM supplemented with 10% fetal bovine serum and Glutamine. The reprogramming cells were induced with doxycycline (Dox) (1ug/ml) for 3 days in ES medium consisted of DMEM supplemented with 15% fetal bovine serum,  nonessential amino acids, Glutamine, Nucleosides, 2-mercaptoethanol, LIF.

extract_protocol:
For RNA-seq, the cells were lysed using RLT buffer supplemented with β-mercaptoethanol and processed using the RNeasy mini kit (Cat. 74104).For ChIP-seq, the cells were cross-linked with 37% formaldehyde in serum-free medium at room temperature for 10 min in room temperature (RT). Glycine was added to stop the cross-linking at final concentration of 0.125 M and the cells were rinsed in PBS. Then the cells were re-suspended in lysis buffer containing protease inhibitors and chromatin was sonicated to 100-400 bp with Covaris M220 system.
RNA-seq: KAPA Stranded mRNA-Seq Kit (KK8420)
ChIP-seq: KAPA HyperPlus Library Preparation kit (KAPA KK8510)

treatment_protocol: The reprogrammable MEFs (0 day and 3 days post-Dox induction with or without Obox1’s overexpression) were digested to single cell and harvested to performed RNA-seq and ChIP-seq.

tag: genotype/variation background

value: transgenic carrying the tetO-OSKM transgene and Oct4-GFP/Rosa26-M2rtTA

value: OSKM+Vector


title: PB_control_M141_exp1


title: RNA_Vector_D3_RNA-seq_rep2

tag: strain background


title: RNA_Obox1_D3_RNA-seq_rep2

tag: induced with


title: RNA-seq brain macrophage 6m old sc6mVE_vehYFP2

city: New York

first: Frederic

last: Geissmann

state: NY

address: 1275 York Ave

department: Immunology Program

institute: Memorial Sloan Kettering Cancer Center (MSKCC)

data_processing:
An average of 54 million paired reads were generated per sample and the percent of mRNA bases was closed to 77% on average. FASTQ files were mapped to the Mouse genome mm10 using the Star aligner that maps reads gnomically and resolves reads across splice junctions. We used several QC metrics for the RNA-seq library, including intron–exon ratio, intragenic reads fraction, GC bias. We quantified exon and gene expression using Sailfish against the Mus musculus transcriptome GRCh38.
Genome_build: GRCh38
Supplementary_files_format_and_content: tpm

source_name: BRAFV600E microglia YFP+

growth_protocol: Csf1rMeriCreMer; BRAFLSL-V600E; Rosa26LSL-YFP mice

extract_protocol: Sorted cells underwent amplification (14 cycles) using the SMART-seq V4 (Clonetech) ultra low input RNA kit for sequencing. 10 ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).

treatment_protocol: sorted YFP+ F4/80+ cells in in indicated organs

value: brain macrophage


title: RNA-seq brain macrophage 6m old sc6mVE_vehYFP1


title: RNA-seq brain macrophage 6m old sc6mWT_veh1

source_name: BRAFWT microglia


title: RNA-seq brain macrophage 6m old sc6mWT_veh2


title: MEF_RNA-seq_rep2

source_name: MEF

tag: reprogramming stage


title: RNA_Obox1_D3_RNA-seq_rep1

tag: dox-induced genes


title: RNA-seq brain macrophage 1m old brain1VE5


title: MEF_RNA-seq_rep1


title: RNA-seq brain macrophage 1m old brain1VE4


title: ChIP_Obox1_D3

tag: chip antibody

value: Flag antibody (Sigma, F1804, SLBB7188)


title: RNA-seq liver macrophage 1m old liver1mVE5

source_name: BRAFV600E liver macrophage YFP+

value: liver macrophage


title: ChIP_input_D3

value: reprogrammable mouse embryonic fibroblasts (MEFs)

value: doxycycline (Dox) (1ug/ml) for 3 days


title: RNA-seq brain macrophage 1m old brain1WT5


title: RNA-seq liver macrophage 1m old liver1mVE4


title: RNA-seq brain macrophage 1m old brain1WT4


title: RNA-seq brain macrophage 1m old brain1VE3


title: RNA-seq liver macrophage 1m old liver1mWT5

source_name: BRAFWT liver macrophage


title: RNA-seq liver macrophage 1m old liver1mWT3


title: RNA-seq liver macrophage 1m old liver1mWT4


title: WT rep3

city: Daejeon

first: Yukyung

last: Jun

address: 245 Daehak-ro, Yuseong-gu

department: Center for Supercomputing Applications

institute: Korea Institute of Science and Technology Information

data_processing:
RNA sequencing was performed on Illumina HiSeq 2500 platform using 101 bp paired-end runs.
Sequencing reads were aligned to the mouse genome (mm10 from the UCSC genome database) using Mapsplice2 (version 2.1.7) after standard quality check and trimming with FastQC and Fastx-toolkit (version 0.0.13.2), respectively.
RSEM (version 1.2.12) was used to quantify the mRNA abundance.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include expected count, FPKM, and TPM values for each sample

source_name: WT mouse telencephalon

extract_protocol: none provided by submitter

value: telencephalon

tag: age

value: postnatal day 0

tag: genotype

value: TSC1 flox/flox;Emx1 +/+


title: WT rep1


title: TSC1-KO rep1

source_name: TSC1 detected mouse telencephalon

value: TSC1 flox/flox;Emx1-cre/+


title: TSC1-KO rep3


title: WT rep2


title: C9.9 (RNA-Seq)

city: London

first: Kathy

last: Niakan

address: Mill Hill

institute: The Francis Crick Institute

data_processing:
TopHat2
Samtools
Htseq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: RPKM values in csv document

source_name: Human Embryo

extract_protocol:
Single cells were isolated from blastocyst stage embryos (6-7 days post fertilisation) for subsequent analysis by micromanipulation, with a duration of less than 20 minutes. Embryos were placed in drops of G-MOPS solution (Vitrolife) on a petri dish overlaid with mineral oil. The plate was placed on a microscope stage (Olympus IX70) and the embryos were held with an opposing holding pipette and blastomere biopsy pipette (Research Instruments) using Narishige micromanipulators (Narishige, Japan). The biopsy mode of a Saturn 5 laser (Research Instruments) was used to separate the majority of the mural TE from the ICM and polar TE. The ICM and polar TE were washed quickly in PBS without Ca2+ and Mg2+ (Invitrogen) then placed in 0.05% trypsin/EDTA (Invitrogen) for 5 minutes at room temperature. Trypsin was quenched using Global Media supplemented with 5 mg/mL LifeGlobal Protein Supplement. After quenching, the cell clump was placed back on the stage in a drop of G-MOPS solution and pipetted up and down several times using the blastomere biopsy pipette.Single cells were picked using 100 μm inner diameter Stripper pipette (Origio) and transferred to individual low bind RNAse-free tubes containing 2.5 µl RLP plus buffer.
Samples were processed using a previously published protocol that was adapted where indicated (Macaulay et al. 2016).To separate RNA from gDNA 50 µl of Dynabeads were washed and incubated with 100 uM biotinylated poly-dT oligonucleotide (IDT). 10 µl of oligo-dT beads were added to each tube containing the single cell. Samples were incubated in a thermomixer for 20 min at room temperature at 2000 rpm. Tubes were put on a magnet until the beads collected into a pellet and the supernatant went clear. The supernatant containing the gDNA was transferred to a new collection tube. Beads were washed three times to collect any residual gDNA.cDNA was generated from the RNA captured on the bead using the SMARTer v4 Ultra Low Input kit. First strand cDNA was synthesised by adding 2 µl 5X Ultra low First strand buffer, 0.5 ul SMART-Seq v4 Oligo, 0.25 µl RNase Inhibitor, 6.25 µl Nuclease free water and 1 µl SMARTScribe Reverse Transcriptase to each sample. Reverse transcription was performed on the thermomixer using the settings 2 min at 42oC at 2000 rpm,  60 min at 42oC at 1500 rpm, 30 min at 50oCat 1500 rpm and 10 min at 60oCat 1500 rpm. cDNA was amplified by adding 12.5 μl 2X SeqAmp PCR buffer, 0.5 μl  PCR Primer II A (12µM), 0.5 µl SeqAmp DNA polymerase, 1.5 μl Nuclease free water. Beads were mixed on thermomixer for 60 sec at room temperature at 2000 rpm and then were incubated on a PCR machine using the following settings: 95oC for 1 min, 24 cycles of 98oC for 10 sec, 65oC for 30 sec and 68oC for 3 min, before a final extension for 10 min at 72oC. Amplified cDNA was purified by adding 25 μl SPRI Ampure XP beads, mixing well and incubating at room temperature for 8 min to allow amplified cDNA to bind to the beads. Sample tubes were placed on the magnet and allowed to stand until all beads had been immobilised. Supernatant was removed and discarded and beads were washed twice by adding 200 µl freshly prepared 80% ethanol and leaving for 30 sec before discarding the supernatant. Tubes were spun briefly to collect residual liquid. The bead pellet was allowed to air dry. 12 µl of purification buffer was added to rehydrate the pellet and incubated for 2 min at room temperature. cDNA was eluted by pipetting up and down 10 times before returning the tube to the magnet. The clear supernatant containing the cDNA was removed from the immobilised beads and transferred to a new low-bind tube. cDNA was stored at -80°C until library preparation. cDNA quality was assessed by High Sensitivity DNA assay on an Agilent 2100 Bioanalyser with good quality cDNA showing a broad peak from 300 to 9000 bp. cDNA concentration was measured using QuBit dsDNA HS kit (Life Technologies UK Ltd.).Libraries with a molar concentration greater than 2nM were submitted for 100-bp paired-end sequencing on Illumina HiSeq 2000.

treatment_protocol: Human embryo microinjections were performed in Global Total media with HEPES under mineral oil on a heated stage with a holding pipet (Research Instruments) and a Femtojet 4i microinjection manipulator set at approximately 40 injection pressure and 20 constant pressure. Embryos were microinjected with a mixture of Cas9  protein plus sgRNA back-filled into microfilament glass capillary injection needles (World Precision Instruments #TW100F-6) pulled using a pipet puller (Suter P-97 micropipette puller). Control embryos were injected with Cas9 protein. Human embryos were cultured in drops of pre-equilibrated Global media (LifeGlobal # LGGG-20) supplemented with 5 mg/mL protein supplement (LifeGlobal # LGPS-605) and overlaid with mineral oil (Origio #ART-4008-5P). Pre-implantation embryos were incubated at 37oC and 5.5% CO2 in an EmbryoScope+ (Vitrolife) time-lapse incubator for  5-6 days (human).

tag: developmental stage

value: Blastocyst

tag: embryo number

value: CRISPR 9

tag: sample type

value: Single cell


title: C9.7 (RNA-Seq)


title: C9.8 (RNA-Seq)


title: C9.6 (RNA-Seq)


title: C8.TE (RNA-Seq)

value: CRISPR 8

value: Trophectoderm biopsy


title: C9.5 (RNA-Seq)


title: C9.2 (RNA-Seq)


title: C9.1 (RNA-Seq)


title: C8.TEb (RNA-Seq)


title: C9.4 (RNA-Seq)


title: C8.9 (RNA-Seq)


title: C8.7 (RNA-Seq)


title: C8.6b (RNA-Seq)


title: C8.TE.2 (RNA-Seq)


title: RNA-seq liver macrophage 1m old liver1mVE3

tag: cell type


title: C8.8 (RNA-Seq)


title: C8.6 (RNA-Seq)


title: TSC1-KO rep2

tag: tissue


title: C8.5 (RNA-Seq)


title: C8.2 (RNA-Seq)


title: C8.3 (RNA-Seq)


title: C8.4 (RNA-Seq)


title: C8.14 (RNA-Seq)


title: C8.12 (RNA-Seq)


title: C8.13 (RNA-Seq)


title: C8.11 (RNA-Seq)


title: C8.10 (RNA-Seq)


title: C24.5 (RNA-Seq)

value: CRISPR 24


title: C8.1 (RNA-Seq)


title: C24.4 (RNA-Seq)


title: C24.3 (RNA-Seq)


title: C24.2 (RNA-Seq)


title: C16.9 (RNA-Seq)

value: CRISPR 16


title: C16.3 (RNA-Seq)


title: C16.6 (RNA-Seq)


title: C16.22 (RNA-Seq)


title: C16.18 (RNA-Seq)


title: C16.7 (RNA-Seq)


title: C16.21 (RNA-Seq)


title: C16.2 (RNA-Seq)


title: C16.11 (RNA-Seq)


title: C16.19 (RNA-Seq)


title: C16.5 (RNA-Seq)


title: C16.4 (RNA-Seq)


title: C16.15 (RNA-Seq)


title: C16.10 (RNA-Seq)


title: C12.TE (RNA-Seq)

value: CRISPR 12


title: C16.1 (RNA-Seq)


title: C12.6 (RNA-Seq)


title: C12.4 (RNA-Seq)


title: C12.7 (RNA-Seq)


title: C16.8 (RNA-Seq)


title: C12.3 (RNA-Seq)


title: C16.20 (RNA-Seq)


title: C12.2 (RNA-Seq)


title: C12.15 (RNA-Seq)


title: C12.14 (RNA-Seq)


title: C16.12 (RNA-Seq)


title: C12.13 (RNA-Seq)


title: C12.12 (RNA-Seq)


title: C12.5 (RNA-Seq)


title: C12.11 (RNA-Seq)


title: 8.5 (RNA-Seq)

value: Cas9 Injected control 8


title: C12.10 (RNA-Seq)


title: 7TE.2 (RNA-Seq)

value: Cas9 Injected control 7


title: C12.1 (RNA-Seq)


title: 8.4 (RNA-Seq)


title: 8TE.2 (RNA-Seq)


title: 5TE.2 (RNA-Seq)

value: Cas9 Injected control 5


title: 5TE.1 (RNA-Seq)


title: 8TE.1 (RNA-Seq)


title: 8.6 (RNA-Seq)


title: C12.3b (RNA-Seq)


title: 8.1b (RNA-Seq)


title: 7.1 (RNA-Seq)