title: Female Gut Replicate 1 sRNAseq


title: Male Gut Replicate 3 sRNAseq

status: Public on Oct 16 2015

type: SRA

city: Singapore

first: Vivek

last: Tanavde

state: Singapore

address: 30 Biopolis Street, #07-01, Matrix

department: Genome and Gene Expression Data Analysis Division

country: Singapore

institute: Bioinformatics Institute, A*STAR, Singapore

library_source: transcriptomic

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
The sequenced reads were first subjected to adapter removal through the cutadapt program (Martin 2011). The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package (Friedländer et al. 2012).
The unique reads fasta file was then put through an elimination pipeline module (Vaz et al. 2010) comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database, finally culminating into an un-annotated pool of reads that served as a source of novel miRNAs and novel sRNAs.
The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl -p <zebrafish precursor miRNA fasta file> -m <zebrafish mature miRNA fasta file> -r <unique reads fasta file> -t Zebrafish
The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M-values (TMM) normalisation using the Bioconductor package edgeR (Robinson et al. 2010).
Genome_build: ZV9
Supplementary_files_format_and_content: 1. 'Danio-rerio-known-miRNA-Rel19-profile-Raw.txt': Tab-delimited text file that includes the raw counts for the known mature miRNA (miRBase Release 19).
Supplementary_files_format_and_content: 2. 'Danio-rerio-known-miRNA-Rel19-profile-Normalised.txt': Tab-delimited text file that includes the Trimmed Mean of M-values (TMM) normalised counts for the known mature miRNA (miRBase Release 19). One of the replicate of Heart (MZH008) failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.

molecule: total RNA

organism: Danio rerio

source_name: Male Gut

growth_protocol: Fishes were purchased from a local supplier and acclimatized before tissue extraction.

extract_protocol:
Total RNA were extracted using mirVana™ miRNA Isolation Kit (AM1560, Life Technologies). Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol.
Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit ( RS-200-0012, Illumina, Inc.). Libraries were prepared according to manufacturer instructions. Briefly, 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel (Life Technologies) and bands corresponding to adapter-ligated constructs derived from 22-30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser (Agilent Technologies) before sequencing.

tag: gender

value: Male

tag: tissue

value: Gut

tag: genetic background

value: Wild type - Singapore strain


title: Male Gut Replicate 2 sRNAseq


title: Male Gut Replicate 1 sRNAseq


title: Female Brain Replicate 2 sRNAseq

source_name: Female Brain

value: Female

value: Brain


title: Female Brain Replicate 3 sRNAseq


title: Testis Replicate 1 sRNAseq

source_name: Testis

value: Testis


title: Female Brain Replicate 1 sRNAseq


title: Male Brain Replicate 2 sRNAseq

source_name: Male Brain


title: Embryo Replicate 3 sRNAseq

description: gender: not specified

source_name: Embryo

value: Embryo


title: Male Brain Replicate 1 sRNAseq


title: Embryo Replicate 2 sRNAseq

description: gender: not specified


title: Embryo Replicate 1 sRNAseq

description: gender: not specified


title: Input_2__CD4+_Treg

city: Boston

first: R. Anthony

last: Barnitz

state: MA

address: 450 Brookline Ave.

department: Department of Pediatric Oncology

country: USA

institute: Dana-Farbert Cancer Institute, Harvard Medical School

library_source: genomic

data_processing:
Basecalls and demultiplexing were performed using CASAVA v1.8.2
ChIP-Seq reads were aligned to the mouse NCBI37/mm9 reference genome using bowtie (PubMed ID: 19261174) v0.12.7 using the following parameter: (-n 1 -m 1 --best --strata)
Reads were sorted using samtools (PMID: 19505943) and deduplicated using picard (http://picard.sourceforge.net/)
SPP (PMID: 19029915) and MACS2 (PMID: 18798982) were both used for peak finding.  Regions from both peak callers were combined with mergeBed (PMID: 20110278).  Quality rating for the merged regions was assigned based on the maximum significance from either source.
Genome_build: mm9
Supplementary_files_format_and_content: SPP was used to generated BigWig visualization tracks for ChIP reads corrected for background (ChIP Input DNA)

molecule: genomic DNA

organism: Mus musculus

source_name: In vitro activated CD4+ Treg

growth_protocol: CD4 (CD3+ CD4+ CD25+ ) and CD8 Treg (CD3+ CD8+ Ly49+ ) were purified from the spleen of WT B6 mice by fluorescence activated cell sorting (FACS).

extract_protocol:
In vitro activated CD4+ and CD8+ Tregs were fixed with 1% formaldehyde and flash frozen at -80°C.  The fixed cells were lysed and the chromatin was sheared using a Covaris E210 Ultrasonicator.  Transcription factor-DNA and histone-DNA complexes were immunoprecipitated and then eluted from magnetic beads.  The formaldehyde crosslinks were reversed, and the ChIP DNA fragments were purified.
ChIP DNA was prepared for high-throughput Illumina sequencing using the NEBNext ChIP-Seq Library Master Mix Set for Illumina kit and the NEBNext Multiplex Oligos for Illumina kit according to a modified manufacturer's protocol.  For each ChIP or input sample, 50 ng of DNA was used to prepare a sequencing library.  The DNA fragments were end-repaired, dA-tailed, and ligated to illumina adaptors according th the kit instructions.  DNA fragments of 150-600 bp in length were then selected using Pippin Prep 2% Agarose Gel Cassettes and the Pippin Prep DNA Size Selection System.  The ChIP DNA was then amplified with 12 PCR cycles using the NEBNext Multiplex Oligos.  Amplifed DNA was purfied using a 1:1 ratio of DNA to Agencort AMPure XP beads.

treatment_protocol: CD4 (CD3+ CD4+ CD25+ ) and CD8 Treg (CD3+ CD8+ Ly49+ ) were activated in vitro by incubating with microbeads coated with anti-CD3 and anti-CD28 Ab and supplemented with either IL-2 (CD4 Treg, 50 ng/ml) or IL-15 (CD8 Treg, 20 ng/ml) for 5 days.

tag: cell type

value: day 5 in vitro activated CD4+ Treg

tag: mouse strain

tag: chip antibody

value: none (input)


title: H3K27me3_ChIP_CD8+_Treg

description: H3K27me3 ChIP data; corrected with Input_1__CD8+_Treg

source_name: In vitro activated CD8+ Treg

value: day 5 in vitro activated CD8+ Treg

value: H3K27me3 (Millipore, 07-449)


title: Male Brain Replicate 3 sRNAseq


title: Input_1__CD8+_Treg


title: Linc-Yy1_Yy1_ChIP-seq

city: Shenzhen

first: Kun

last: Sun

address: Rm B505, No. 9 Duxue Road, Nanshan District

department: Cancer Research

country: China

institute: Shenzhen Bay Laboratory

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads by ChIP-seq were mapped to mm9 genome using SOAP2 with parameters: -v 2 -r 0 -m 0 -p 20
Peaks were called using MACS2 (v1.4.2), a p-value of 10^-5 is used as the cutoff
Annotations of the peaks were perfomed using in-house programs against the RefSeq gene annotation. Overlaping analysis was performed using in-house programs and the maximum distance limitation is set to 1000bp.
RNA-seq reads were first aligned to the mm9 genome using TopHat (v2.0.4) then merged with Others C2C12 RNA-seq data (GEO accession: GSE20846). Then ab initio assembly (for GM/DM RNA-seq) was conducted using Cufflinks (v2.1.1).
The assembled transcripts were then processed by Sebnif (v1.2.1) and annotated by Histone markers, EST Tags and MyoD bindings for novel lincRNA discovery.
Differentially expression between siNC and siLinc-Yy1 was conducted using Cuffdiff (v2.0.4) against RefSeq genes.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files were generated by MACS, scores represent -10*log(p)

source_name: C2C12 myoblasts

growth_protocol: C2C12 myoblasts were growed in gowth medium containing DMEM, 10% FBS and 1% pen/srep.

extract_protocol:
Chromatins from myoblasts and myotubes were isolated and sonicated to 100-300nt for immunoprecipitation with antibodies
Purified RNA was fragmented and the cDNA was synthesized by reverse transcription. The resulting double-stranded DNA fragments were end-repaired and A-nucleotide overhangs were added.
ChIP-seq libraries were constructed closely according to the standard illumina pair-end ChIP-seq procedure
After the attachment of anchor sequences, fragments were PCR-amplified using Illumina primers.

treatment_protocol: C2C12 myoblasts were induced to differentiate by culturing in differentiation medium (DMEM, 2% horse serum and 1% pen/strep)

tag: cell line

tag: developmental stage

value: Myoblast (MB)

tag: antibody

value: YY1 (Santa Cruz)


title: H3K27ac_ChIP_CD8+_Treg

description: H3K27ac ChIP data; corrected with Input_1__CD8+_Treg

value: H3K27ac (Abcam, ab4729)


title: DM_RNA-seq

description:
cDNA
PolyA+ selected

value: Myotube (MT)


title: H3K27ac_ChIP_CD4+_Treg

description: H3K27ac ChIP data; corrected with Input_1__CD4+_Treg


title: GM_RNA-seq

description:
cDNA
PolyA+ selected


title: Input_1__CD4+_Treg


title: wt (2) BAFF 6hr

city: Los Angeles

first: Alexander

last: Hoffmann

state: CA

address: 570 Boyer Hall

department: MIMG

institute: UCLA

data_processing: Illumina Hiseq 2000 with real time analysis version 1.13.48 was used for basecalling and Casava version 1.8.2 was used to extract reads

source_name: B cells

growth_protocol: Primary follicular B cells isolated from the spleen of mouse using Marginal Zone and Follicular B Cell Isolation Kit (MiltenyiBiotec)

extract_protocol:
RNA was extracted and purified as per the manufacturers protocol using the RNeasy kit (QIAGEN). 1 mg of the quantified RNA was reverse transcribed using superscript II RT system (Invitrogen) and poly-dT primers.
cDNA libraries were generated using theIllumina Truseq RNA LT Kit, 12-index SetA format and quantitation was performed using the Roche Light Cycler 480.

treatment_protocol: Follicular B cells were grown in complete media consisted of RPMI-1640, 10mM HEPES, 0.055mM Bme, Pen/Strep and L-glut and stimulated with 50ng/ml BAFF

tag: strain

tag: genotype/variation

value: wild type

tag: rna adapter index

tag: barcode

value: TGACCAA

tag: lane


title: wt (2) BAFF 27hr

value: ACAGTGA


title: wt (1) BAFF 6hr


title: Helios_ChIP_CD8+_Treg

description: Helios ChIP data; corrected with Input_1__CD8+_Treg

value: Helios (Santa Cruz, G-20, sc-9866)


title: dbko (2) BAFF 0hr

value: relb-/-crel-/-

value: AGTCAAC


title: wt (2) BAFF 0hr

value: CGATGTA


title: wt (1) BAFF 27hr


title: H3K27me3_ChIP_CD4+_Treg

description: H3K27me3 ChIP data; corrected with Input_1__CD4+_Treg


title: cko (2) BAFF 6hr

value: crel-/-

value: CAGATCA


title: dbko (2) BAFF 6hr

value: AGTTCCG


title: cko (2) BAFF 0hr

value: GCCAATA


title: dbko (1) BAFF 6hr


title: dbko (1) BAFF 0hr


title: cko (1) BAFF 6hr


title: FKBP5_enh_TA_single_rep2

city: Nijmegen

first: Shuang-Yin

last: Wang

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: RIMLS

description: 4C PCR product. Barcode: TTACTGGGTCATGAGGATC

data_processing:
Library strategy: 4C-seq
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
Illumina RTA 1.6.47.1 used for basecalling of GAII data.
Library strategy: ChIP-seq. The reads were aligned to build version hg19 of the human genome using bwa (version 0.6.2) with default parameters. Only unique mapped reads were kept for downstream analysis. Reads from PCR duplicates were also removed. MACS (version 1.4.2), was used to identify regions of ChIP-seq enrichment over background using parameters -p 1e-9 –nomodel.
Library strategy: ChIA-PET. The first 72bp of each sequenced read carries the complete ChIA-PET ligation product (linker plus genomic DNA) was taken for the further analysis after trimming the ends of each read.  Subsequently, single end sequenced reads were split at the linker ligation junction (linkerA/B-|-linkerA/B) and flipped to make the data compatible (similar to paired end sequencing reads) for the ChIA-PET data analysis pipeline (doi:10.1186/gb-2010-11-2-r22).
Library strategy: 4C-seq. The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank DpnII sites (fragment ends). Repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse genome hg19.
Genome_build: hg19

organism: Homo sapiens

source_name: HeLa B2 cells

growth_protocol: HeLa B2 cells were maintained as described in previous study (doi:10.1101/gr.118042.110). Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% charcoal stripped fetal calf serum (FCS) for 72-96 hours before subsequent treatment and/or harvesting.

extract_protocol: Libraries were prepared according to Illumina's instructions.

value: HeLa

tag: treatment protocol

value: 1μM of Triamcinolonacetonide (T6501, Sigma-Aldrich)


title: Helios_ChIP_CD4+_Treg

description: Helios ChIP data; corrected with Input_2__CD4+_Treg

value: day 5 in vitro activated CD4+ Treg


title: MDA_MB_453_ARChIPseq_DHT1

city: Cambridge

first: Kerstin

last: Meyer

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Single-end 36bp reads were generated by the Illumina HiSeq 2000 and aligned against the Human Reference Genome (NCBI Build 36.6) using BWA version 0.5.5. Reads were filtered by removing those with a BWA alignment quality score less than 15 as well as duplicate reads.
Enriched regions of the genome were identified by comparing ChIP samples to input samples using MACS Version 1.3.7.1
Genome_build: GRCh36
Supplementary_files_format_and_content: Consensus peaks in TXT format

source_name: Mammary gland/breast metastatic carcinoma

growth_protocol: Cells were maintained in DMEM, 10% foetal calf serum, prior to harvesting cells were estrogen starved for three days with daily media changes.

extract_protocol:
ChIP-seq was carried out as described by Schmidt et al. Methods 48, 240-8 (2009)
Tru-seq libraries were prepared and sequenced by Illumina sequencing.

treatment_protocol: Cells were treated for 4 hours with vehicle control (ethanol), 5α-dihydrotestosterone (DHT; 10nM) or medroxyprogesterone acetate (MPA; 10nM).

value: female

value: AR (Santa Cruz Biotech, N-20, sc-816)


title: MDA_MB_453_ARChIPseq_MPA2


title: MDA_MB_453_ARChIPseq_Input

value: none (input)


title: Exp 3 Wk0 CD34+

city: Sydney

first: Jason

last: Wong

state: NSW

address: Level 2, Lowy Cancer Research Centre, University of New South Wales

country: Australia

institute: UNIVERSITY OF NEW SOUTH WALES

description: Untransduced control, expt 3

data_processing:
Base-calling: Illumina Real Time Analysis, scoring metric v1.5
Raw reads were prefiltered to remove all reads that have 3 or more bases with a quality score of less than Q13
All provided cleaned data have had adaptors clipped
Alignments were all made against hg19. mRNA-seq: tophat (version 1.3.1) -g 25 -r 20 --segment-length 45 -G "hg19_refseq.gtf" --solexa1.3-quals
Genome_build: hg19
Supplementary_files_format_and_content: Exon read counts in text format generated using analyzeRNA.pl from the HOMER package

molecule: polyA RNA

source_name: Human cord blood derived CD34+ cells

extract_protocol:
Cord blood cells were retrovirally transduced then flow sorted to select GFP+ CD34+ cells. Total RAN was extracted using Qiagen miRNeasy kit and 200ng of total RNA used for library construction.
Illumina TruSeq

tag: treatment

value: Untransduced control


title: MDA_MB_453_ARChIPseq_MPA1


title: MDA_MB_453_ARChIPseq_Vehicle2


title: Exp 3 Wk0 CD34+ GFP+ ERG WT

description: ERG3 overexpressing, expt 3

value: ERG3 overexpressing


title: Exp 3 Wk0 CD34+ GFP+ ERG 283A

description: ERG3 S283A overexpressing, expt 3

value: ERG3 S283A overexpressing


title: Exp 3 Wk0 CD34+ GFP+ ERG 283D

description: ERG3 S238D overexpressing, expt 3

value: ERG3 S238D overexpressing


title: MDA_MB_453_ARChIPseq_DHT2


title: Exp 2 Wk0 CD34+ GFP+ ERG 283D

description: ERG3 S238D overexpressing, expt 2


title: wt (1) BAFF 0hr

value: wild type


title: Exp 2 Wk0 CD34+ GFP+ ERG 283A

description: ERG3 S283A overexpressing, expt 2


title: Linc-Yy1_H3K27me3_ChIP-seq

value: Myoblast (MB)

value: H3K27me3 (Milipore)


title: Linc-Yy1_IgG_control

value: IgG (Santa Cruz)


title: Exp 2 Wk0 CD34+

description: Untransduced control, expt 2


title: Linc-Yy1_Eed_ChIP-seq

value: Eed (Milipore)


title: Linc-Yy1_Ezh2_ChIP-Seq

value: Ezh2 (Active Motif)


title: Exp 2 Wk0 CD34+ GFP+ ERG WT

description: ERG3 overexpressing, expt 2


title: vector_IgG_control


title: vector_Eed_ChIP-seq


title: vector_H3K27me3_ChIP-seq


title: cko (1) BAFF 0hr

value: crel-/-

value: GCCAATA


title: MDA_MB_453_ARChIPseq_Vehicle1


title: vector_Ezh2_ChIP-Seq


title: EHF_Nkx25Tbx5_1

city: London

first: Kenta

last: Yashiro

address: Charterhouse Square

department: Willaim Harvey research Institute

institute: Barts and The London School of Medicine and Dentistry, Queen Mary University of London

description: The data is dividede into the four fastq files.

data_processing:
Illumina Pipeline RTA 1.8.70.0 / BCL Converter 1.7.1 / CASAVA 1.7.0 was used for image analysis and base calling.
Reads were aligned to the mouse mm10 genome and RefSeq transcripts using Partek Flow. Up to 2 mismatches in 28 bases in the seed was allowed.
Aligned reads were mapped to RefSeq gene definitions and annotated by Partek Genomics Suite.
RPMs were calculated by Partek Genomics Suite.
Reads mapped to multiple sites were allocated according to the relative distribution of reads mapped to unique locations.
Genome_build: mm10
Supplementary_files_format_and_content: RPM

source_name: mouse embryonic precursor cells

extract_protocol: Single cell level was lysed in lysis buffer and subjected to 1st strand cDNA synthesis with Oligo (dT) tagged by V1 primer. After the addition of poly (A) tail to the 3'-end of the 1st strand, the 2nd strand was synthesized with Oligo (dT) tagged by V3 primer. The single-cell level cDNA was amplified by 20 cycles of PCR with V1 and V3 primers. The libraries were prepared with the Nextera DNA preparation kit (Illumina compatible) (Epicentre, an Illumina company) with some modification. 100 ng of single cell cDNA was suspended in HMW buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (hyperactive Tn5 transposase), incubating at 55C for 5 min. Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research), and then the libraries were prepared by PCR with Nextera PCR enzyme, Nextera primer cocktail, and Nextera adaptor 2 according to the following program: one cycle of 72C for 3 min and 95 C for 30 s (one cycle), 13 cycles of 95C for 10s, 62C for 30s, 72C for 3min.

value: mouse embryonic precursor cells

value: Early Headfold stage

value: Nkx2-5/Tbx5 double positive

value: CD1 strain


title: EHF_Nkx25Tbx5_2


title: EHF_Nkx25Tbx5_3


title: EHF_Nkx25_2

value: Nkx2-5 single positive


title: Exp 3 Wk0 CD34+ GFP+

description: Empty vector transduced, expt 3

value: Empty vector transduced


title: EB_Tbx5_3

value: Early Allantoic bud stage

value: Tbx5 single positive


title: Exp 2 Wk0 CD34+ GFP+

description: Empty vector transduced, expt 2


title: EB_Nkx25_1

description: The data is dividede into the three fastq files.


title: EB_Nkx25_3


title: EB_Nkx25_2


title: EB_Tbx5_1


title: EB_Tbx5_2


title: siNC_RNA-seq

description:
cDNA
PolyA+ selected


title: siLinc-Yy1_RNA-seq

description:
cDNA
PolyA+ selected


title: EHF_Nkx25_3

description: The one file contains all data relevant to this specimen.


title: Co_P1_FA_GFP_75

status: Public on Oct 15 2015

city: Bethesda

first: Michael

middle: C

last: Kelly

state: MD

address: 41 Center Drive

department: Center for Cancer Research

institute: NCI

description: Single cell

data_processing:
Basecalling and sample demultiplexing by Illumina HAS 0.9
We prepared a Bowtie2_2.2.3 index from the NCBI whole genome mm10 reference transcriptome using default rsem1.2.19 parameters
Paired-end reads were aligned to transcriptome using rsem1.2.19 command rsem-calculate-expression -p 16 --calc-pme --calc-ci --ci-memory 20000 --bowtie2 --bowtie-chunkmbs 512 --no-bam-output --time --paired-end --forward-prob 0.5 --estimate-rspd *R1_001.fastq *R2_001.fastq /ReferenceLocation ./OutputLocation 2>./*.Log.txt 1>./*.Console.txt
Genome_build: NCBI GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file with the estimated expression (TPM) for each gene for each Sample as calculated by RSEM1.2.19. Tab-delmited text file with the estimated count for each gene for each Sample as calculated by RSEM1.2.19.

source_name: Cochlear epithelium

growth_protocol: All cells used were from acute isolations from postnatal day 1 mice that carry transgenic alleles to fluorescently mark the supporting cells and hair cells of the inner ear.

extract_protocol:
Following dissociation of tissue into a single-cell suspension, target cells were enriched by purification as described, cells were lysed, polyA RNA reverse-transcribed, and cDNA amplified using SMARTer ultra-low input cDNA synthesis (Clontech) on the C1 microfluidics platform (Fluidigm).
cDNA libraries were prepared for sequencing using Nextera XT tagmentation and 96-barcode indexing (Illumina). Barcoded samples were pooled, cleaned with Agencourt AMPure XP magnetic bead isolation (Beckman Coulter).

treatment_protocol: All cells are untreated.

tag: purification

value: FACS

tag: c1 ifc #

value: IFC 9

tag: gfp (i)

tag: tdtomato (i)

tag: classifications

value: Lat SC (ii)


title: Co_P1_FA_GFP_77

description: Single cell

value: Med SC


title: Co_P1_FA_GFP_72

description: Single cell


title: Co_P1_FA_GFP_69

description: Single cell


title: Co_P1_FA_GFP_71

description: Single cell

value: Lat SC (i)


title: Co_P1_FA_GFP_78

description: Single cell


title: Co_P1_FA_GFP_76

description: Single cell


title: Co_P1_FA_GFP_73

description: Single cell


title: Co_P1_FA_GFP_68

description: Single cell


title: Co_P1_FA_GFP_70

description: Single cell


title: Co_P1_FA_GFP_74

description: Single cell


title: Co_P1_FA_GFP_67

description: Single cell


title: Co_P1_FA_GFP_63

description: Single cell


title: Co_P1_FA_GFP_64

description: Single cell


title: Co_P1_FA_GFP_65

description: Single cell


title: Co_P1_FA_GFP_66

description: Single cell


title: EHF_Nkx25_1

tag: cell type


title: Co_P1_FA_GFP_61

description: Single cell

value: SINGuLAR Outlier


title: Co_P1_FA_GFP_60

description: Single cell


title: Co_P1_FA_GFP_62

description: Single cell


title: Co_P1_FA_GFP_59

description: Single cell


title: Co_P1_FA_GFP_56

description: Single cell


title: Co_P1_FA_GFP_54

description: Single cell


title: Co_P1_FA_GFP_53

description: Single cell


title: Co_P1_FA_GFP_57

description: Single cell


title: Co_P1_FA_GFP_52

description: Single cell


title: Co_P1_FA_GFP_55

description: Single cell


title: Co_P1_FA_GFP_51

description: Single cell


title: Co_P1_FA_GFP_58

description: Single cell


title: Co_P1_FA_GFP_50

description: Single cell

value: Downsample Outlier


title: Co_P1_FA_GFP_49

description: Single cell


title: Co_P1_FA_GFP_48

description: Single cell


title: Co_P1_Ep_tdTom_9

description: Single cell

value: Enzymatic/mechanical

value: IFC 8

value: HC


title: Co_P1_FA_GFP_47

description: Single cell


title: Co_P1_Ep_Neg_53

description: Single cell

value: NSC (ii)


title: Co_P1_Ep_Neg_54

description: Single cell


title: Co_P1_Ep_tdTom_6

description: Single cell


title: Co_P1_Ep_tdTom_5

description: Single cell


title: Co_P1_Ep_tdTom_8

description: Single cell


title: Co_P1_Ep_Neg_50

description: Single cell


title: Co_P1_Ep_Neg_52

description: Single cell

value: NSC (i)


title: Co_P1_Ep_Neg_51

description: Single cell


title: Co_P1_Ep_Neg_49

description: Single cell


title: Co_P1_Ep_Neg_48

description: Single cell


title: Co_P1_Ep_Neg_46

description: Single cell


title: Co_P1_Ep_Neg_45

description: Single cell


title: Co_P1_Ep_Neg_47

description: Single cell


title: Co_P1_Ep_Neg_44

description: Single cell


title: Co_P1_Ep_Neg_39

description: Single cell


title: Co_P1_Ep_Neg_38

description: Single cell


title: Co_P1_FA_GFP_46

description: Single cell


title: Co_P1_Ep_tdTom_7

description: Single cell


title: Co_P1_Ep_Neg_40

description: Single cell


title: Co_P1_Ep_Neg_34

description: Single cell


title: Co_P1_Ep_GFP_40

description: Single cell

value: SC


title: Co_P1_Ep_GFP_39

description: Single cell


title: Co_P1_FA_GFP_79

description: Single cell


title: Co_P1_Ep_GFP_35

description: Single cell


title: Co_P1_Ep_GFP_38

description: Single cell


title: Co_P1_Ep_Neg_35

description: Single cell


title: Co_P1_Ep_GFP_37

description: Single cell


title: Co_P1_Ep_Neg_43

description: Single cell


title: Co_P1_Ep_GFP_34

description: Single cell


title: Co_P1_Ep_Neg_42

description: Single cell


title: Co_P1_Ep_GFP_33

description: Single cell


title: Co_P1_Ep_GFP_32

description: Single cell


title: Co_P1_Ep_Neg_41

description: Single cell


title: Co_P1_Ep_GFP_26

description: Single cell


title: Co_P1_FA_GFP_93

description: Single cell

value: IFC 7


title: Co_P1_Ep_GFP_31

description: Single cell


title: Co_P1_Ep_Neg_37

description: Single cell


title: Co_P1_Ep_GFP_28

description: Single cell


title: Co_P1_Ep_Neg_36

description: Single cell


title: Co_P1_Ep_GFP_25

description: Single cell


title: Co_P1_Ep_GFP_27

description: Single cell


title: Co_P1_Ep_GFP_29

description: Single cell


title: Co_P1_FA_GFP_91

description: Single cell


title: Co_P1_FA_HC_94

description: Single cell

value: FACs HC


title: Co_P1_FA_GFP_90

description: Single cell


title: Co_P1_FA_GFP_89

description: Single cell


title: Co_P1_Ep_GFP_36

description: Single cell


title: Co_P1_FA_GFP_88

description: Single cell


title: Co_P1_FA_GFP_92

description: Single cell


title: Co_P1_Ep_GFP_30

description: Single cell


title: Co_P1_FA_GFP_84

description: Single cell


title: Co_P1_FA_GFP_82

description: Single cell


title: Co_P1_Ep_tdTom_4

description: Single cell

value: IFC 6


title: Co_P1_FA_GFP_87

description: Single cell


title: Co_P1_FA_GFP_86

description: Single cell


title: Co_P1_FA_GFP_83

description: Single cell


title: Co_P1_FA_GFP_80

description: Single cell


title: Co_P1_FA_GFP_85

description: Single cell


title: Co_P1_Ep_tdTom_1

description: Single cell


title: Co_P1_FA_GFP_81

description: Single cell


title: Co_P1_Ep_Neg_8

description: Single cell


title: Co_P1_Ep_tdTom_2

description: Single cell


title: Co_P1_Ep_tdTom_0

description: Single cell


title: Co_P1_Ep_tdTom_3

description: Single cell


title: Co_P1_Ep_Neg_3

description: Single cell


title: Co_P1_Ep_Neg_6

description: Single cell


title: Co_P1_Ep_Neg_5

description: Single cell


title: Co_P1_Ep_Neg_28

description: Single cell


title: Co_P1_Ep_Neg_26

description: Single cell


title: Co_P1_Ep_Neg_25

description: Single cell


title: Co_P1_Ep_Neg_30

description: Single cell


title: Co_P1_Ep_Neg_32

description: Single cell


title: Co_P1_Ep_Neg_4

description: Single cell


title: Co_P1_Ep_Neg_31

description: Single cell


title: Co_P1_Ep_Neg_29

description: Single cell


title: Co_P1_Ep_Neg_27

description: Single cell


title: Co_P1_Ep_Neg_22

description: Single cell


title: Co_P1_Ep_Neg_24

description: Single cell


title: Co_P1_Ep_Neg_21

description: Single cell


title: Co_P1_Ep_Neg_18

description: Single cell


title: Co_P1_Ep_Neg_20

description: Single cell


title: Co_P1_Ep_Neg_19

description: Single cell


title: Co_P1_Ep_Neg_16

description: Single cell


title: Co_P1_Ep_GFP_6

description: Single cell


title: Co_P1_Ep_GFP_7

description: Single cell


title: Co_P1_Ep_GFP_5

description: Single cell


title: Co_P1_Ep_GFP_3

description: Single cell


title: Co_P1_Ep_Neg_15

description: Single cell


title: Co_P1_Ep_GFP_9

description: Single cell


title: Co_P1_Ep_Neg_0

description: Single cell


title: Co_P1_Ep_Neg_1

description: Single cell


title: Co_P1_Ep_GFP_19

description: Single cell


title: Co_P1_Ep_GFP_23

description: Single cell


title: Co_P1_Ep_GFP_24

description: Single cell


title: Co_P1_Ep_GFP_15

description: Single cell


title: Co_P1_Ep_GFP_22

description: Single cell


title: Co_P1_Ep_GFP_2

description: Single cell


title: Co_P1_Ep_GFP_16

description: Single cell


title: Co_P1_Ep_Neg_23

description: Single cell


title: Co_P1_Ep_GFP_20

description: Single cell


title: Co_P1_FA_GFP_9

description: Single cell

value: IFC 5


title: Co_P1_Ep_GFP_0

description: Single cell


title: Co_P1_Ep_GFP_13

description: Single cell


title: Co_P1_FA_GFP_8

description: Single cell

value: FACS


title: Co_P1_Ep_GFP_14

description: Single cell


title: Co_P1_Ep_GFP_11

description: Single cell


title: Co_P1_Ep_GFP_10

description: Single cell


title: Co_P1_FA_GFP_95

description: Single cell


title: Co_P1_FA_GFP_5

description: Single cell


title: Co_P1_Ep_GFP_1

description: Single cell


title: Co_P1_FA_GFP_4

description: Single cell


title: Co_P1_Ep_GFP_18

description: Single cell


title: Co_P1_FA_GFP_7

description: Single cell


title: Co_P1_FA_GFP_1

description: Single cell


title: Co_P1_FA_GFP_0

description: Single cell


title: Co_P1_FA_GFP_6

description: Single cell


title: proliferative fibroblast 1

city: Saskatoon

first: Christopher

middle: H.

last: Eskiw

state: SK

address: 51 Campus Drive

department: Food and Bioproduct Science

country: Canada

institute: University of Saskatchewan

data_processing:
TOPHAT/CUFFLINK 2.0 was used with parameters --bowtie1 -p 8 -r 20 --solexa-quals --coverage-search --microexon-search--library-type fr-unstranded
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the Seqmonk tool http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each of six samples

source_name: normal foreskin fibroblast

growth_protocol: 10 % FBS DMEM

extract_protocol:
MP24 Fast Prep green kit
polyA purified mRNAs

treatment_protocol: 0.5% FBS (Quiescence); 500nM Rapamycin 5 days

value: proliferative fibroblast

tag: source

value: foreskin 2DD


title: queiscent fibroblast 2

value: queiscent fibroblast


title: queiscent fibroblast 1


title: Rapamycin treated fibroblast 1

value: Rapamycin treated fibroblast


title: Rapamycin treated fibroblast 2


title: Resistant line ChIP input

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the mm10 mouse genome using bwa 0.6.2-r126
Peak-calling was performed using MACS2
Genome_build: mm10

source_name: Resistant line

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with murine IL-3 (10 ng/mL), 20% fetal calf serum, penicillin (100 units/mL), streptomycin (100 ug/mL), amphotericin B (250ng/mL) and gentamycin (50 ug/mL)

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)

treatment_protocol: Cell lines were grown in 0.1% DMSO or 600nM of I-BET151

tag: tissue

value: haematopoietic progenitors

tag: condition

value: Resistant

tag: chip antibody

value: none (input)


title: Ute_P1_tdTom_66

description: Single cell

source_name: Vestibular epithelium

value: Enzymatic/mechanical

value: IFC 4

value: HC (i)


title: Ute_P1_tdTom_63

description: Single cell


title: Co_P1_FA_GFP_3

description: Single cell

value: Lat SC (i)


title: Sensitive line ChIP input

source_name: Sensitive line

value: Sensitive

tag: strain


title: Co_P1_FA_GFP_2

description: Single cell

value: Med SC


title: HiSeq_Retina

city: St. Louis

first: Joseph

last: Corbo

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

description:
Amplicon-seq
Total RNA and DNA were extracted with TRIzol. mRNA was reverse-transcribed to cDNA. cDNA and DNA were enriched for barcode-derived molecules and adapter-ligated for sequencing. Three biological replicates (each derived from 5 retinas) were prepared. All six samples (RNA and DNA for each replicate) were indexed and run on a single lane.
Loading concentration of 8 pM with 10% Phi-X

data_processing:
For MiSeq data: FastQC was run to check for sequencing quality. Read pairs were required to perfectly match an index (GCTCGA, TAGACTA, CGCTACCC, or ATAGTGGACA) and adapter sequence (AGACGTGTGCTCTTCCGATCT or TACACGACGCTCTTCCGATCT). The barcode sequence was extracted based on 6 flanking bases on either side (CGGTTT-barcode-GGGACG). The captured-and-cloned fragment was extracted based on the adjacent adapter sequence.
For MiSeq data: Captured-and-cloned fragment portion of reads were aligned to mm9 using Bowtie2 v2.1.0 with -X 1000 setting.
For MiSeq data: SAM file was converted to sorted BAM using samtools v0.1.19, and then to sorted BED using bedtools v2.22.1.
For MiSeq data: Captured-and-cloned fragments were examined for overlap with the 4,000 target regions. Only paired reads were used that mapped concordantly by Bowtie2, and with forward and reverse reads mapping to opposite strands of DNA (since the same fragment of DNA was sequenced from opposite directions for a given pair of reads). The number of reads for a given CRE-barcode association were tabulated. If a fragment overlapped two target regions, the target region with the most bases of overlap with the fragment was assigned.
For MiSeq data: Barcodes were required to be 14-16 bp in length. To account for a barcode being associated with multiple fragments (as a result of either sequencing error, or multiple fragments being cloned onto vectors with the same barcode), the following criteria were imposed. Each barcode was examined for the "top species" (the fragment with the highest number of paired reads for the barcode) and the "2nd species" (the fragment with the second-highest number of paired reads for the barcode). Let read_top = number of paired reads for the top species, read_2nd = number of paired reads for the 2nd species, and top_fraction = read_top/total number of paired reads for the barcode. Barcodes were included only if: (1) read_top ≥ 20 and top_fraction >0.95, or (2) read_top ≥ 10 and read_2nd ≤ 2 and top_fraction > 0.5. Barcodes present in both library preps were excluded.
For MiSeq data: For fragments associated with multiple barcodes (e.g., due to PCR amplification of the fragment), only the barcode with the greatest number of reads was included.
For HiSeq data: FastQC was run to check for sequencing quality. After trimming the first base, reads were required to begin with a perfect 10 bp match to a sample index plus additional bases of flanking sequence (GCTACGGCCG, CTCGATGGCC, AGACTATGGC, ATCGTCATGG, TAGTGGACAG, or CAGACTCAGT). These sample indices corresponded to RNA #1, RNA #2, RNA #3, DNA #1, DNA #2, and DNA #3 for each lane of HiSeq.
For HiSeq data: The barcode sequence was extracted based on 6 flanking bases on either side (CGTCCC-barcode-AAACCG). Barcodes (with known CRE correspondences, based on the MiSeq data) were tabulated for each sample. This gave the "raw counts".
For HiSeq data: For each tissue, barcodes that did not have at least 10 raw DNA counts for all 3 DNA samples were excluded from the subsequent analysis. Let r = the raw RNA count for a given barcoded construct, and let R be the total RNA counts for a given replicate. Let d be the raw DNA counts for a given barcoded construct, and let D be the total DNA counts for a given replicate. The expression (in log2 units) of a given barcoded construct is log base 2 of [0.001 + (r/R)/(d/D)], i.e., the ratio of normalized RNA to normalized DNA, plus a pseudocount of 0.001.
Genome_build: mm9

molecule: other

source_name: Retina

extract_protocol:
MiSeq: maxiprep; HiSeq: TRIzol extraction
PCR amplification and ligation of sequencing adapters

value: retina

value: Ex vivo electroporation at age P0

tag: harvest

value: Cultured for 8 days


title: Ute_P1_tdTom_67

description: Single cell

value: HC (ii)


title: proliferative fibroblast 2

value: proliferative fibroblast


title: Ute_P1_tdTom_68

description: Single cell

value: HC (iii-iv), Extrastriola


title: Ute_P1_tdTom_61

description: Single cell


title: Ute_P1_tdTom_64

description: Single cell


title: HiSeq_Cortex

description:
Amplicon-seq
Total RNA and DNA were extracted with TRIzol. mRNA was reverse-transcribed to cDNA. cDNA and DNA were enriched for barcode-derived molecules and adapter-ligated for sequencing. Three biological replicates (each derived from one animal) were prepared. All six samples (RNA and DNA for each replicate) were indexed and run on a single lane.
Loading concentration of 8 pM with 10% Phi-X

source_name: Cerebral cortex

value: cerebral cortex

value: In vivo stereotactic AAV injection at age 4-6 weeks

value: Harvested 4-5 weeks after injection. GFP-positive regions were microdissected.


title: Co_P1_FA_GFP_11

description: Single cell

value: FACS

value: IFC 5


title: Dox_plus_Yap

city: Worcester

first: Yu

last: Liu

address: AS5-1018, 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School

description: Sample 4

data_processing:
The fastq files were obtained using Illumina CASAVA v1.8
The quality of fastq reads was examined by FASTQC and low quality 5' nucleotides were removed before mapping
The fastq read were mapped on human geneome (mm9) using Tophat 1.4.1
The read counts were calculated using customed R scripts to calculate exon union reads per million reads per kb gene Model(RPKMs)
Genome_build: mm9
Supplementary_files_format_and_content: text file was provided for coding gene expression of all the samples in this study

source_name: Yaptg mouse intestinal organoids with doxycyclin

growth_protocol: Gut organoids were cultured according to a previously described protocol established by Sato and Clevers (Nature, 2009). Briefly, crypts were harvested by incubating opened small intestines in PBS containing 2mM EDTA. The epithelium was released by vigorous shaking and crypts separated using a 70mm cell strainer. Crypts were seeded in growth factor reduced Matrigel (BD Biosciences) and grown in Advanced DMEM/F12 (Invitrogen) supplemented with 2mM GlutaMax (Invitrogen), 100U/ml Penicillin/ 100ug/ml Streptomycin (Invitrogen), N2 Supplement (Invitrogen), B-27 Supplement (Invitrogen Cat), Mouse Recombinant Egf (R&D Systems), 100ng/ml Mouse Recombinant Noggin (Peprotech), 150ng/ml human Rsp1 (R&D Systems). To induce Yap expression in YapTg organoids, 1.5mg/ml doxycycline was added to the culture medium upon seeding crypts in Matrigel.

extract_protocol:
Total RNA extracted with Qiagen Rneasy Miniprep columns
The sequencing libraries were constructed using Illumina TruSeq RNA preparation kit following the kit instructions.

treatment_protocol: see above

tag: developmental stage

value: organoids cultured from 24 hours following seeding

value: intestine

tag: genotype

value: YapTg


title: Dox_minus_Yap

description: Sample 3

source_name: Yaptg mouse intestinal organoids without doxycyclin


title: Ute_P1_tdTom_65

description: Single cell

value: Enzymatic/mechanical

value: IFC 4


title: Ute_P1_tdTom_60

description: Single cell

value: HC (i)


title: Ute_P1_tdTom_59

description: Single cell


title: Ute_P1_tdTom_54

description: Single cell

value: HC (iii-iv), Striola


title: Ute_P1_tdTom_55

description: Single cell


title: Ute_P1_tdTom_56

description: Single cell


title: Ute_P1_tdTom_57

description: Single cell


title: Ute_P1_tdTom_53

description: Single cell


title: CG9754_mut_asterix_mut_rep2_RNAseq

city: Cold Spring Harbor

first: Yang

last: Yu

state: NY

address: One Bungtown Road

institute: Cold Spring Harbor Laboratory

description: NSR RNAseq

data_processing:
The RNA-seq data were mapped using the STAR software package (version 2.3.0) with allowing up to 100 multi-alignment per read to get reads mapped to transposons.
Feature abundance estimations and the differential analysis were conducted using the TEtranscripts software package (http://hammelllab.labsites.cshl.edu/software/) . TEtranscripts distributes multi-mapped reads evenly among all potential matches at the initial step and using Expectation-Maximization approach to optimize the distribution of multi-mapped reads. TEtranscripts computes the gene abundances and transposon abundances at the same time, and integrates the gene count table and transposon count table into one count table and input to the DESeq package for the differential analsyis.
We used the DESeq package with suggested parameters as described above, accepting only changes greater than twofold, with adjusted p-values < 0.05 and counts per feature >20.
Genome_build: dm3/2006
Supplementary_files_format_and_content: results of DESeq analysis for transposons or genes which are deferentially expressed under the indicated experimental conditions include fold change in raw counts normalized according to DESeq protocol (Anders and Huber 2010, Genome Biol 11:R106) and p-values.

organism: Drosophila melanogaster

source_name: adult fly ovaries

growth_protocol: All fly stocks were maintained at 25°C on standard diet.

extract_protocol:
Total RNA was prepared with Trizol reagent (Invitrogen)
Transcriptome libraries were prepared according  (Armour et al. 2009, Nat Methods) using not-so-random priming (NSR). 1 ug total RNA was revere transcribed using SuperScript III enzyme with first-strand NSR primer. RNA template was removed with RNase H (Invitrogen) Then cDNA was mixed with exo− Klenow fragment (NEB) second-strand NSR primer to synthesize the second strand. For PCR amplification, purified second-strand synthesis reaction were mixed with ExpandPLUS enzyme (Roche) and PE-P5-SBS3 and PE-P7-SBS8 primers. Products were run on a 2% low-melt agarose gel, and the 200–500 bp. range were purified.

treatment_protocol: Flies were fed with yeast paste. Germline specific knockdowns were done as described (Czech et al., 2013 Mol Cell). CRISPR/Cas9 mediated generation of CG9754 mutants were done as described (Port et al., 2014 PNAS).

tag: age

value: 3-5 old

value: Ovary


title: CG9754_het_asterix_mut_rep2_RNAseq

description: NSR RNAseq


title: Day1_Het

description: Sample 1

source_name: Yap+/fl;VillinCre (Yap +/-) mouse intestinal organoids

value: Yap+/-


title: CG9754_mut_asterix_mut_rep1_RNAseq

description: NSR RNAseq


title: Ute_P1_tdTom_62

description: Single cell

value: HC (ii)


title: Ute_P1_tdTom_51

description: Single cell

value: HC (iii-iv), Extrastriola


title: Ute_P1_tdTom_52

description: Single cell


title: Ute_P1_tdTom_49

description: Single cell


title: CG9754_mut_asterix_het_rep2_RNAseq

description: NSR RNAseq


title: Day1_KO

description: Sample 2

source_name: Yapfl/fl;VillinCre (Yap -/-) mouse intestinal organoids

value: Yap-/-


title: Ute_P1_tdTom_47

description: Single cell


title: CG9754_het_asterix_mut_rep1_RNAseq

description: NSR RNAseq


title: Ute_P1_tdTom_50

description: Single cell


title: CG9754_het_rep2_smRNAseq

description: small RNA sequencing

data_processing:
Demultiplexed, concatenated files with the 50nt or 76nt Illumina reads were stripped of the 3’ linker, collapsed, and the resulting small RNA sequences were matched without mismatches to the Drosophila release 5 genome (dm3) using nexalign. Only reads that met these conditions were subjected to further analyses.
For annotations we used a combination of UCSC [dm3], miRBase [release 14], and Flybase [r5.26] tracks for protein coding genes, repeats/transposons, non-coding RNAs and microRNAs, as well as custom tracks (for synthetic markers, endo-siRNAs from structured loci, miR and miR* strands) with different priorities (annotation priority list available upon request). For comparison of small RNA counts between samples, libraries of dsRNA-white samples were set to one million reads. Next, all libraries were normalized based on unique mappers to the flamenco (for nos-GAL4 knockdowns) piRNA clusters.
Genome_build: dm3/2006
Supplementary_files_format_and_content: Excel file contains read counts of small RNAs (24 nt to 29 nt) mapping to antisense transposon consensus normalized to total miRNA reads comparing CG9754 heterozygous and mutant in sheet "het_vs_mut_CG9754". In sheet "untethered_vs_tethered", read counts of small RNAs (24 nt to 29 nt) mapping to piRNA clusters are shown.

growth_protocol: Flies were raised at 25°C on standard cornmeal-molasses agar medium.

extract_protocol:
Total RNA from ovaries of 2-3 day old females of the indicated knockdowns was isolated using TRIzol (Invitrogen).
Small libraries were prepared as described (Czech et al., 2013 Mol Cell).
small RNA cloning (End cloning)

treatment_protocol: Flies were fed with yeast paste. Germline specific knockdowns were done as described (Czech et al., 2013 Mol Cell).

value: ovaries


title: Ute_P1_Neg_35

description: Single cell

value: TEC


title: Ute_P1_Neg_34

description: Single cell

value: SC (i)


title: Ute_P1_tdTom_48

description: Single cell


title: Ute_P1_tdTom_58

description: Single cell


title: Ute_P1_tdTom_46

description: Single cell


title: CG9754_het_rep1_smRNAseq

description: small RNA sequencing


title: Ute_P1_tdTom_45

description: Single cell


title: Ute_P1_Neg_30

description: Single cell


title: Ute_P1_Neg_31

description: Single cell


title: CG9754_mutant_rep1_smRNAseq

description: small RNA sequencing


title: Ute_P1_Neg_33

description: Single cell


title: Ute_P1_GFP_53

description: Single cell


title: Ute_P1_GFP_51

description: Single cell

value: SC (ii)


title: Ute_P1_GFP_52

description: Single cell

value: SC (ii), Striola


title: Ute_P1_GFP_48

description: Single cell


title: Ute_P1_GFP_50

description: Single cell


title: Ute_P1_GFP_47

description: Single cell


title: CG9754_mut_asterix_het_rep1_RNAseq

description: NSR RNAseq


title: Ute_P1_GFP_49

description: Single cell


title: CG9754_het_rep2_RNAseq

description: NSR RNAseq


title: CG9754_mutant_rep1_RNAseq

description: NSR RNAseq


title: Asterix_mutant_rep2_RNAseq

description: NSR RNAseq


title: Ute_P1_GFP_45

description: Single cell


title: CG9754_het_rep1_RNAseq

description: NSR RNAseq


title: Ute_P1_GFP_43

description: Single cell


title: Ute_P1_GFP_41

description: Single cell


title: Ute_P1_GFP_42

description: Single cell


title: CG9754_mutant_rep2_smRNAseq

description: small RNA sequencing


title: Ute_P1_Neg_29

description: Single cell

value: SINGuLAR Outlier


title: Ute_P1_GFP_40

description: Single cell


title: Ute_P1_GFP_46

description: Single cell


title: CG9754_mutant_rep2_RNAseq

description: NSR RNAseq


title: Ute_P1_GFP_38

description: Single cell


title: Asterix_het_rep1_RNAseq

description: NSR RNAseq


title: Ute_P1_GFP_37

description: Single cell


title: Co_P1_Ep_GFP_21

description: Single cell

value: IFC 6

value: NSC (i)


title: Asterix_mutant_rep1_RNAseq

description: NSR RNAseq


title: Ute_P1_GFP_36

description: Single cell

value: Enzymatic/mechanical

value: IFC 4


title: Ute_P1_GFP_34

description: Single cell


title: Ute_P1_GFP_35

description: Single cell


title: Ute_P1_tdTom_44

description: Single cell

value: IFC 3


title: Ute_P1_GFP_44

description: Single cell


title: λN-CG9754_Firefly_Tethered_rep1_GROseq

description: BrU labeled transcription run-on RNAs

data_processing:
The GRO-seq data were mapped first to the transposon database using the Bowtie2 software package (version 2.0.0-beta17) (57). Due to the repetitive nature of transposon sequences, reads were allowed to map to up to 10 different canonical transposons, with read counts distributed evenly among all potential matches. For all samples, the percentage of reads that mapped exactly one time to the canonical transposon database was always more than the percentage of reads that aligned to multiple transposon sequences. To obtain an accurate estimate of the ‘‘library size’’ for each sample, we used all reads that failed to align to the transposon database and mapped just those sequences to the genome using the same alignment criteria (two mismatches per read, 10 total alignments). We then added together the total number of sequenced reads that were mappable to either the transposon or genome database and used this number as a normalization factor for all subsequent analyses, reporting all feature abundances as reads per million (RPM) mapped. To obtain accurate estimates of genomic features that might overlap partial transposon sequences, we remapped all reads to the genome using more stringent criteria (one mismatch per read, 10 total alignments) but still retaining the normalization factor obtained above as the global normalization factor.
Feature abundances were obtained by annotating each alignment with a genomic feature using intersectBed from BedTools (version-2.10.1), dividing each alignment by the total number of matches as described above, summing the alignments with the BEDTools ‘‘groupBy,’’ and maintaining the strandedness of all reads.
For differential expression analysis, we integrated the gene count table and the transposon count table together and fed to the DESeq package with parameters advisable for data sets with few replicates (2 or 3) (fit, “local’’; method, “pooled’’; and sharing Mode, ‘‘fit-only’’), accepting only changes greater than twofold, with adjusted p-values < 0.05 and counts per feature >20.
Genome_build: dm3/2006
Supplementary_files_format_and_content: results of DESeq analysis for transposons or genes which are deferentially expressed under the indicated experimental conditions include fold change in raw counts normalized according to DESeq protocol (Anders and Huber 2010, Genome Biol 11:R106) and p-values.

extract_protocol:
Adult ovaries were dissected in cold PBS. Nuclei preparation and in vitro transcription run-on were done as described (Rozhkov et al., Genes and Dev., 2013)
Libraries were prepared for sequencing using iCLIP protocols (Huppertz et al., 2014, Methods)
GRO-Seq

value: 3-5 old

tag: antibody/beads

value: BrdU Antibody (IIB5) Agarose (santa cruz, sc-32323 AC)


title: Ute_P1_tdTom_43

description: Single cell


title: Ute_P1_tdTom_42

description: Single cell


title: λN-CG9754 _Firefly_Tethered_rep2_GROseq

description: BrU labeled transcription run-on RNAs

value: Ovary


title: Firefly_untethered_rep1_GROseq

description: BrU labeled transcription run-on RNAs


title: Asterix_het_rep2_RNAseq

description: NSR RNAseq


title: Firefly_untethered_rep2_GROseq

description: BrU labeled transcription run-on RNAs


title: nanosGAL4_CG9754_rep2_GROseq

description: BrU labeled transcription run-on RNAs


title: Ute_P1_tdTom_41

description: Single cell

value: HC (iii-iv), Striola


title: Ute_P1_tdTom_39

description: Single cell

value: HC (iii-iv), Extrastriola


title: nanosGAL4_dsPiwi_rep2_GROseq

description: BrU labeled transcription run-on RNAs


title: Ute_P1_tdTom_40

description: Single cell


title: Ute_P1_tdTom_37

description: Single cell

value: HC (i)


title: Ute_P1_tdTom_36

description: Single cell


title: nanosGAL4_dsWhite_rep2_GROseq

description: BrU labeled transcription run-on RNAs


title: Ute_P1_tdTom_34

description: Single cell


title: Ute_P1_GFP_39

description: Single cell


title: Ute_P1_tdTom_32

description: Single cell

value: HC (ii)


title: Ute_P1_tdTom_35

description: Single cell


title: Firefly_untethered_Input

data_processing:
Any identifiable sequencing barcodes (at the 5' end of reads) and adaptors (Illumina TruSeq adaptors, present at the 3' end of the reads) were clipped using the fastx toolkit version 0.0.13.2. For ChIP-seq data, sequences <20 nt in length after clipping were discarded. A set of canonical transposon sequences for D. melanogaster (version 9.42) was obtained from FlyBase (http://flybase.org). The dm3 release of the D. melanogaster genome was obtained from the University of California at Santa Cruz genome database. To this genome database, we also added the X-TAS heterochromatic sequences, which represent GenBank entry L03284 and comprise X-telomeric TAS repeats from the OregonR strain. For genomic annotations, we used the D. melanogaster release 5.57 gene annotation file in gff format from FlyBase (http://flybase.org). The H3K9me3 ChIP-seq data were mapped first to the transposon database using the Bowtie2 software package (version 2.3.0). Due to the repetitive nature of transposon sequences, reads were allowed to map to up to 10 different canonical transposons, with read counts distributed evenly among all potential matches. All reads that failed to align to the transposon database were then mapped to the genome using the same criteria. The sum of the number of reads mapped to the genome and transposon database is used as the actual “library size”, and used later for normalization. To obtain the genome-wide enrichment of H3K9me3, we re-mapped all reads to the genome with one mismatch and allowing uniquely mapped reads only, and removed presumptive PCR duplicates with the same mapped coordinates.
We used the SICER software package (version 1.1) to call significantly enriched peaks at a false discovery rate (FDR) of 0.05 relative to the input samples. For the SICER peak-calling program, we additionally set the parameters such that reads were binned in windows of 500 bp, aggregating all peaks within a distance of 500 bp.
For differential enrichment analysis, we combined genomic peaks identified above and transposons with 2 fold changes against the input and counts >100, and used the DESeq package, with parameters advisable for data sets with few replicates (2) (fit, “local’’; method, “pooled’’; and sharing Mode, ‘‘fit-only’’), accepting only changes greater than twofold, with adjusted p-values < 0.05.
Genome_build: dm3/2006
Supplementary_files_format_and_content: In sheet "HetA_RPM", "TART_RPM", and "Firefly_transgene_locus_RPM", normalized read counts of H3K9me3 ChIP mapping to each position of the indicated genes or transposon consensus. In sheet "Untethered_vs_tethered_RPM", normalized read counts of H3K9me3 ChIP mapping to the indicated genes. In sheet "het_vs_mut_fold" and "nanosGAL4_control_vs_gene_fold", fold changes (log2) for each transposon consensus were shown deviding H3K9me3 ChIP reads from control by that from the indicated experiments (Klenov et al., NAR, 2013).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody against H3K9me3 (ab8898).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, Taq DNA polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Taq DNA polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15-18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Flies were fed with yeast paste. Germline specific knockdowns were done as described (Czech et al., 2013 Mol Cell). Dissected ovaries were crosslinked with 2% formaldhyde for 10min at room temperature and quenched with Glycine for 10min before lysis.

value: 3-5 days old

value: adult fly ovaries


title: Ute_P1_tdTom_38

description: Single cell


title: λN-CG9754_Firefly_tetehred_Input


title: Ute_P1_tdTom_31

description: Single cell


title: Ute_P1_tdTom_29

description: Single cell


title: Ute_P1_tdTom_28

description: Single cell


title: Ute_P1_tdTom_33

description: Single cell


title: Ute_P1_tdTom_27

description: Single cell


title: 388_002_glu

city: Pasadena

first: Yihan

last: Lin

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: California Institute of Technology/HHMI

data_processing:
Illumina RTA 1.17.21.3 and RTA 1.18.61 for steady-state and transient experiments, respectively.
Standard Galaxy workflow was used for processing the data. Tophat for Illumina was used to map the trimmed reads to yeast genome.
DeSeq2 was used to compare expression between treated (NaCl or ethanol) and untreated (ctrl) samples (using two biological replicates) for transient experiments. Cufflinks was used to calculate the FPKM values for steady state experiments.
Genome_build: sacCer3
Supplementary_files_format_and_content: csv files contain results of differential expression from DeSeq2 (data generated using two replicates). text files contain FPKM reads from Cufflinks.

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Synthetic minimal media was used for all experiments. Specifically, overnight cultures were diluted to OD600 = 0.075 with 20mL of 0.2% glucose in 250mL flask and allowed to grow until the OD600 reached above 0.2 (about 3-4hrs). For transient stress experiments, cultures were then diluted back to OD600 = 0.2 with 20mL of 0.05% glucose in 250mL flask and allowed to grow for another 2hrs. For steady-state experiments, cells were diluted to OD600 = 0.1 with 4mL fresh media of designated glucose condition in 50mL falcon tube. Cultures were allowed to grow for another 2hrs.

extract_protocol:
Cultures were mixed quickly with cold methanol. After >1hr in cold methanol, cells were collected by centrifuging at 4 degree C and washed with ice cold water. Prior to performing standard RNA extraction protocols (with on-column DNase digestion) with RNeasy min kits (Qiagen), cells were enzymatically treated with 100uL  2U/uL lyticase solution (Sigma #L2524) for 10min at 30 degree C.
RNA libraries were prepared according to standard Illumina protocols

treatment_protocol: For transient stress experiments, cultures were split into 14mL polypropylene tubes (4mL each). Stresses were applied by mixing highly concentrated stock solutions (such as 5M NaCl, 100% ethanol) with the culture. Precisely after 10min of stress application, each culture was mixed with 6mL pre-chilled methanol (with dry ice/ethanol bath) in a 50mL falcon tube to rapidly fix the cells.

tag: Stage

value: steady state

value: 0.02% glucose


title: 390_02_glu

value: 0.2% glucose


title: Ute_P1_tdTom_25

description: Single cell

tag: purification


title: 388_00125_glu

value: 0.0125% glucose


title: Ute_P1_tdTom_26

description: Single cell

tag: c1 ifc #


title: 388_005_glu

value: 0.05% glucose


title: Ute_P1_tdTom_23

description: Single cell

value: Enzymatic/mechanical

tag: gfp (i)


title: Ute_P1_tdTom_20

description: Single cell

tag: tdtomato (i)


title: Ute_P1_tdTom_21

description: Single cell

tag: classifications


title: 388_0025_glu

value: 0.025% glucose


title: 388_0075_glu

value: 0.075% glucose


title: Ute_P1_tdTom_22

description: Single cell

value: IFC 3


title: Ute_P1_Neg_28

description: Single cell

value: TEC


title: Ute_P1_tdTom_30

description: Single cell


title: 388_015_glu

value: 0.15% glucose


title: Ute_P1_tdTom_19

description: Single cell


title: 388_01_glu

value: 0.1% glucose


title: Control

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
Sample name: 20121015_21
Control
SOLiD5500, Life Technology. Sequencing of 35b. with 10b. barcoding sequences.
Small-RNA seq
Processed data file: norm1Msignal_human.txt

data_processing:
Lifescope v2.5 smallRNA pipeline. Mapping with mapreads, default parameters.
Bam files were then merged per samples with keeping read group per lane.
Bam files were then processed with a java home made class, based on picard java classes to perform identification and produce raw data count of microRNAs (mirbase release 18), tRNAs from  UCSC web server (UCSC tables), yRNAs and ncRNAs from ensembl ncRNAs release 69 and piRNAs from fRNAdb.
Genome_build: hg19
Supplementary_files_format_and_content: [norm1Msignal_human.txt] Tabulated text file of raw data counts normalized to 1000000 count in each sample.

source_name: Control

extract_protocol:
RNA extraction with Trizol
1.5 µg of total RNA were ligated, reverse transcribed and amplified (11 cycles) with the reagents from the NEBNext Small RNA Library Prep Set for SOLiD. Amplified libraries were size-selected from 110 nt to 150 nt on a 8% acrylamide gel. Libraries were then quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent).

treatment_protocol: 1 mM Staurosporine (STS) treatment samples for 4h and 6h

tag: cell type

value: macrophage

tag: treatment

value: Control

tag: time

tag: concentration sample (ng/ul)

tag: rin number


title: Ute_P1_Neg_24

description: Single cell


title: Ute_P1_Neg_26

description: Single cell

value: HC (i)


title: Ute_P1_Neg_27

description: Single cell


title: Ute_P1_Neg_22

description: Single cell


title: 388_02_glu

tag: strain

tag: condition


title: Ute_P1_Neg_25

description: Single cell


title: Ute_P1_GFP_32

description: Single cell

value: SC (ii), Extrastriola


title: 388_04_glu

value: 0.4% glucose


title: 390_EtOH_rep2

description: processed data file: YL390_ctrlvsEtOH_deseq2.csv

value: transient

value: 10min after 2.5% ethanol


title: Ute_P1_GFP_33

description: Single cell


title: STS 4h

description:
Sample name: 20121015_22
STS 4h
SOLiD5500, Life Technology. Sequencing of 35b. with 10b. barcoding sequences.
Small-RNA seq
Processed data file: norm1Msignal_human.txt

source_name: STS 4h

value: Staurosporine


title: Ute_P1_tdTom_24

description: Single cell

value: HC (iii-iv), Extrastriola


title: Ute_P1_GFP_31

description: Single cell

value: SC (ii)


title: STS 6h

description:
Sample name: 20121015_23
STS 6h
SOLiD5500, Life Technology. Sequencing of 35b. with 10b. barcoding sequences.
Small-RNA seq
Processed data file: norm1Msignal_human.txt

source_name: STS 6h


title: 390_ctrl_rep2

description: processed data file: YL390_ctrlvsEtOH_deseq2.csv, YL390_ctrlvsNaCl_deseq2.csv

value: no stress


title: 390_NaCl_rep2

description: processed data file: YL390_ctrlvsNaCl_deseq2.csv

value: 10min after 200mM NaCl


title: stalk_rep2

city: Shanghai

first: Renyi

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the Cucumber genome sequence (v2i; genome sequence and annotation data downloaded from http://cucumber.genomics.org.cn/page/cucumber/download.jsp (click link FTP2) ) using TopHat. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 10 TPTM (transcripts per ten million) in at least two samples were kept for further analysis.
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file includes abundance measurements (TPTM values) for six Samples

organism: Cucumis sativus

source_name: stalk

growth_protocol: Cucumber (Cucumis sativus L.) inbred line 9930 was used in this study. Seeds were grown in pots in a growth chamber under 16h/8h with 28 ºC/18 ºC in day/night. Upon the two true-leaf stage, cucumber seedlings were transferred to a greenhouse in the experimental field of the China Agricultural University in Beijing. Pest control and water management were carried out according to standard protocols.

extract_protocol:
Samples were fixed in Farmer’s Fixative, dehydrated through an ethanol/xylene series followed by a xylene/paraplast series, and embedded in paraplast as described previously17. Embedded samples were sectioned at 10-um-thick using a rotary microtome (YD-355AT Yidi Microsystems, China). The sections from pedicle, stalk and fruit were expanded in the Biological tissue spreading machine (KEDEE KD-P, China) with diethylpyrocarbonate-treated deionized water, and then mounted on RNAse free Leica FrameSlides. The slides with the sectioned samples were dried overnight at 42ºC and stored at 4ºC until used for laser microdissection. Laser microdissection was performed using Leica LMD 6500 (Leica Microsystems, Germany). Two biological replicates were performed for each tissue.Total RNA was extracted from the collected phloem tissues using the Arcturus PicoPure RNA isolation Kit (Applied Biosystems). DNaseI treatment was performed to remove potential DNA contamination using Qiagen DNaseI. TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (Epicentre Biotechnologies) was used for RNA amplification according to the manufacture’s protocol.
Approximately 3ug RNA per sample was used as input material for RNA-seq. The RNA-Seq libraries were constructed using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, Ispawich, USA) following manufacturer’s instructions, and four index codes were added to attribute sequences to each sample42. In brief, mRNA was purified using magnetic beads with Oligo (dT) (Life technologies, CA, USA), and fragmentation was carried out using divalent cations under elevated temperature in NEB proprietary fragmentation buffer. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. After adenylation of 3’ ends of DNA fragments, NEBNext adaptor oligonucleotides were ligated to cDNA fragments, and AMPure XP beads system (Beckman Coulter, Beverly, USA) were used to select cDNA fragments of approximately 150~200 bp in length. DNA fragments with ligated adaptor molecules on both ends were selectively enriched using NEB Universal PCR Primer and Index primer in a 10 cycles PCR reaction. Products were purified (AMPure XP beads system) and quantified using the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) following the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq 2000 platform and 100 bp paired-end reads were generated.

treatment_protocol: Cucumber young fruits at 3 DPA (days post anthesis) were harvested together with the respective pedicles. Pedicle, stalk and fruit were separated and cut into 3-mm cylinder, and proceeded for fixation.

tag: inbred line

tag: organ

value: stalk

tag: tissue

value: phloem


title: stalk_rep1

tag: age

value: young fruits at 3 DPA (days post anthesis)


title: Ute_P1_GFP_28

description: Single cell

value: Enzymatic/mechanical

value: IFC 3


title: Ute_P1_GFP_29

description: Single cell


title: Ute_P1_GFP_25

description: Single cell


title: pedicle_rep2

source_name: pedicle

value: pedicle


title: Ute_P1_GFP_26

description: Single cell

value: SC (i)


title: Ute_P1_GFP_27

description: Single cell

value: SC (ii), Striola


title: 389_EtOH_rep2

description: processed data file: YL389_ctrlvsEtOH_deseq2.csv

tag: Stage


title: Ute_P1_Neg_23

description: Single cell

tag: purification

value: TEC


title: Ute_P1_GFP_24

description: Single cell

tag: c1 ifc #

value: SC (ii), Extrastriola


title: 389_NaCl_rep2

description: processed data file: YL389_ctrlvsNaCl_deseq2.csv

value: transient


title: pedicle_rep1


title: Ute_P1_GFP_30

description: Single cell

tag: gfp (i)


title: Ute_P1_GFP_22

description: Single cell

tag: tdtomato (i)


title: 388_EtOH_rep2

description: processed data file: YL388_ctrlvsEtOH_deseq2.csv

value: 10min after 2.5% ethanol


title: Ute_P1_tdTom_18

description: Single cell

value: IFC 2

tag: classifications


title: Ute_P1_tdTom_17

description: Single cell

value: HC (iii-iv), Extrastriola


title: Ute_P1_tdTom_16

description: Single cell


title: 388_NaCl_rep2

description: processed data file: YL388_ctrlvsNaCl_deseq2.csv


title: Ute_P1_tdTom_15

description: Single cell

value: HC (ii)


title: Ute_P1_tdTom_14

description: Single cell


title: 388_ctrl_rep2

description: processed data file: YL388_ctrlvsEtOH_deseq2.csv, YL388_ctrlvsNaCl_deseq2.csv

value: no stress


title: fruit_rep1

source_name: fruit

value: fruit


title: Ute_P1_Neg_21

description: Single cell


title: STS_6h_2

description:
Sample name: STS6H_2.010
Staurosporine 6h replicate 2
Instrument model: Ion Proton (P1 chip)
Small-RNA seq
Processed data file: hg19_tableCount.txt

data_processing:
Adaptor trimming with cutadapt-1.2.1, then bowtie2 v2.2.4 mapping versus hg19 build with " --local --very-sensitive-local -k 10" parameters.
Bam files were then processed with a java home made class, based on picard java classes to perform identification and produce raw data count of microRNAs (mirbase release 20), tRNAs from UCSC web server (UCSC tables), yRNAs and ncRNAs from Ensembl ncRNAs release 75 and piRNAs from fRNAdb.
Genome_build: hg19
Supplementary_files_format_and_content: [hg19_tableCount.txt] Tabulated text file containing raw data of small RNAs, including miRNA from miRBase v20, tRNAs for tRFs identification from UCSC table browser and Ensembl non-coding RNAs r75, no normalisation.

extract_protocol:
RNA extraction with Trizol
50 ng of RNA were treated with the trilink library kit (TriLink Biotechnologies). 17 cycles of PCR were performed. Libraries were size-selected for the 130 to 155 nt fraction on a caliper 300 XT chip. Libraries were sequenced on the Ion Proton, 10 libraries were loaded on one P1 Chip.

tag: cell type

value: macrophage

value: Staurosporine


title: 390_EtOH_rep1


title: Ute_P1_Neg_20

description: Single cell


title: STS_6h_1

description:
Sample name: STS6H_1.007
Staurosporine 6h replicate 1
Instrument model: Ion Proton (P1 chip)
Small-RNA seq
Processed data file: hg19_tableCount.txt

tag: treatment


title: STS_4h_1

description:
Sample name: STS4H_1.006
Staurosporine 4h replicate 1
Instrument model: Ion Proton (P1 chip)
Small-RNA seq
Processed data file: hg19_tableCount.txt

tag: time


title: STS_4h_2

description:
Sample name: STS4H_2.009
Staurosporine 4h replicate 2
Instrument model: Ion Proton (P1 chip)
Small-RNA seq
Processed data file: hg19_tableCount.txt

tag: concentration sample (ng/ul)


title: Ute_P1_Neg_18

description: Single cell


title: 390_NaCl_rep1

value: 10min after 200mM NaCl


title: Ute_P1_GFP_23

description: Single cell

value: Enzymatic/mechanical


title: 389_ctrl_rep2

description: processed data file: YL389_ctrlvsEtOH_deseq2.csv, YL389_ctrlvsNaCl_deseq2.csv


title: Ute_P1_Neg_19

description: Single cell


title: 390_ctrl_rep1


title: CTRL_2

description:
Sample name: CTRL_2.008
Control replicate 2
Instrument model: Ion Proton (P1 chip)
Small-RNA seq
Processed data file: hg19_tableCount.txt

value: Control

tag: rin number


title: 389_EtOH_rep1

tag: strain


title: 389_NaCl_rep1

tag: condition


title: fruit_rep2

tag: inbred line

value: phloem

value: young fruits at 3 DPA (days post anthesis)


title: CTRL_1

description:
Sample name: CTRL_1.005
Control replicate 1
Instrument model: Ion Proton (P1 chip)
Small-RNA seq
Processed data file: hg19_tableCount.txt


title: Ute_P1_Neg_16

description: Single cell


title: Ute_P1_Neg_17

description: Single cell

value: Downsample Outlier


title: 389_ctrl_rep1


title: Ute_P1_Neg_15

description: Single cell

value: SC (i)


title: mature berry sequencing sample

city: Nanjing

first: Chen

state: Jiangshu

address: Weigang 1#

department: Horticulture College

institute: Nanjing Agriculture University

description: Sample 6

data_processing:
HCS1.5 + RTA1.13.48 + BclConverter-1.9.0-11-03-08 HCS为HiSeq Sequencing Control Software，RTA is Real-time analysis software，the sequencing profiles were performed basecalling，and turned into binary file bcl，then the bcl file was tranferred into the readable sequence file by the BclConverter-1.9.0-11-03-08 software,  the quality value of the fasta produced by this version is phred+64.
We use software developed by BGI (unpublished)to deal with the data from HiSeq sequencing  adaptor sequence,  or low-quality sequence
Map the small RNA tags to genome by SOAP to analyze their expression and distribution on the genome with paremeter -v 0 -r 2 -M 0 -a clean.fa -D ref_genome.fa.index -o match_genome.soap
If there is miRNA information of the species in miRBase , we use NCBI BLAST softare analysis the known miRNA, the main paremeter is -p blastn -F F -e 0.01, the other parameter is deault.  If there is no miRNA information of the species in miRBase ,We use software developed by BGI tag2miRNA with deault paremeter
Map to GeneBank databse, Rfam database to identify all small RNA contain rRNA、sRNA、snRNA、tRNA with Blast software with paremeter -p blastn -F F -e 0.01
We use software OVERLAP developed by BGI (unpublished) to Align small RNA tags to exons and introns of mRNA to find the degraded fragments of mRNA in the small RNA tags
Genome_build: We developed a prediction software Mireap to predict novel miRNA by exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the unannotated small RNA tags which could be mapped to genome. Mireap can be accessed from the following link: http://sourceforge.net/projects/mireap/
We use plant targets prediction pipeline for indentify target prediction are based on those suggested by Allen et al. (microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 2005, 121:207-221) - Supplemental document S1 and by Schwab et al. (Specific effects of microRNAs on the plant transcriptome. Dev. Cell, 2005, 8: 517 - 527)
GO enrichment analysis is used on predicted target gene candidates of novel miRNAs . It will provide all GO terms significantly enriched in the predicted target gene candidates of novel miRNAs compared to the reference gene background, as well as the genes corresponding to certain biological function. The result could reveal the functions significantly related with predicted target gene candidates of novel miRNAs. This method firstly maps all target gene candidates to GO terms in the database (http://www.geneontology.org/), calculating gene numbers for each term, then using hypergeometric test to find significantly enriched GO terms in target gene candidates comparing to the reference gene background.We use the Bonferroni Correction for the p-value to obtain a corrected p-value. GO terms with corrected p-value <= 0.05 are defined as significantly enriched in target gene candidates.
KEGG pathway analysis is also used for the target gene candidates. In organisms, genes usually interact with each other to play different roles in certain biological function. The analysis based on pathways could facilitate the understanding of biological functions of genes. KEGG is the major public pathway-related database[8]. KEGG pathway analysis identifies significantly enriched metabolic pathways or signal transduction pathways in target gene candidates comparing with the whole reference gene background. The calculating formula is the same as that in GO analysis. Here N is the number of all genes with KEGG annotation, n is the number of target gene candidates in N, M is the number of all genes annotated to a certain pathway, and m is the number of target gene candidates in M. Genes with FDR<=0.05 are considered as significantly enriched in target gene candidates
Supplementary_files_format_and_content: counts

organism: Vitis vinifera

source_name: mature berry

extract_protocol:
The modified CTAB method
RNA libraries were prepared for sequencing using standard Illumina protocols
small RNA Solexa sequencing and mRNA Degradome sequencing

value: berry with 15 days after veraison


title: young berry sequencing sample

description: Sample 5

source_name: young berry

value: berry with 20 days


title: 388_EtOH_rep1

value: transient

value: 10min after 2.5% ethanol


title: 388_NaCl_rep1


title: 388_ctrl_rep1


title: flower sequencing sample

description: Sample 4

source_name: flower

value: full flowering


title: Ute_P1_Neg_14

description: Single cell

source_name: Vestibular epithelium

value: IFC 2

value: TEC


title: Ute_P1_GFP_21

description: Single cell

value: HC (ii)


title: Ute_P1_GFP_19

description: Single cell

value: SC (ii)


title: inflorescence sequencing sample

description: Sample 3

source_name: inflorescence

value: inflorescence with 20 days


title: mature leaf sequencing sample

description: Sample 2

source_name: mature leaf

value: leaf with 45 days


title: young leaf sequencing sample

description: Sample 1

source_name: young leaf

value: leaf with 15 days


title: Ute_P1_GFP_20

description: Single cell

value: Enzymatic/mechanical


title: Ute_P1_GFP_17

description: Single cell


title: Ute_P1_GFP_18

description: Single cell


title: Ute_P1_GFP_12

description: Single cell


title: Ute_P1_GFP_15

description: Single cell


title: Ute_P1_GFP_16

description: Single cell


title: Ute_P1_GFP_11

description: Single cell


title: Ute_P1_GFP_13

description: Single cell


title: Ute_P1_tdTom_9

description: Single cell

value: IFC 1

value: HC (i)


title: Ute_P1_tdTom_4

description: Single cell

value: HC (iii-iv), Striola


title: Ute_P1_tdTom_8

description: Single cell

value: HC (iii-iv), Extrastriola


title: Ute_P1_tdTom_5

description: Single cell


title: Ute_P1_GFP_10

description: Single cell

value: SC (i)


title: Ute_P1_tdTom_7

description: Single cell


title: Ute_P1_tdTom_13

description: Single cell


title: Ute_P1_GFP_8

description: Single cell


title: Ute_P1_tdTom_6

description: Single cell


title: Ute_P1_tdTom_2

description: Single cell


title: Ute_P1_GFP_9

description: Single cell


title: Ute_P1_GFP_14

description: Single cell


title: Ute_P1_tdTom_0

description: Single cell


title: Ute_P1_tdTom_12

description: Single cell


title: Ute_P1_Neg_7

description: Single cell


title: Ute_P1_tdTom_10

description: Single cell


title: Ute_P1_tdTom_1

description: Single cell


title: Ute_P1_Neg_6

description: Single cell


title: Ute_P1_tdTom_3

description: Single cell


title: Ute_P1_Neg_5

description: Single cell


title: Ute_P1_Neg_4

description: Single cell

value: SC (ii), Striola


title: Ute_P1_Neg_3

description: Single cell


title: Ute_P1_Neg_2

description: Single cell


title: Ute_P1_Neg_13

description: Single cell


title: Ute_P1_Neg_12

description: Single cell


title: EM

city: Seoul

first: Hideyo

last: Yasuda

address: 1 Hwayang-dong, Kwangjin-gu

department: Animal Biotechnology

country: South Korea

institute: Konkuk University

description: purified with oligo dT resin

data_processing:
The tags were mapped to mouse genome (mm9) by Illumina analysis pipeline (Eland).
For tags that couldn't be mapped, they were then mapped to junction sequences by bowtie.
Junction sequences were (-32bp, +32bp) of all the splice junction sites from refseq genes.
Then the number of tags mapped to each gene was counted.
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

source_name: rib chondrocytes treated with Adeno-CMV-Null

growth_protocol: primary cultrue of rib chondrocyte using DMEM supplemented with 10%FBS

extract_protocol:
total RNA was extracted with Trizol and then polyA RNA was purified by use of oligodT resin
Adaptors were ligated to cDNA

treatment_protocol: 48hr with 200 moi Adeno-CMV-Cre or Adeno-CMV-Null

value: postnatal day4

tag: genotype

value: SOX9 floxed

value: primary culture of rib chondrocyte

tag: infection

value: Adeno-CMV-Null


title: Ute_P1_Neg_11

description: Single cell

value: TEC


title: Ade-Cre

description: purified with  oligo dT resin

source_name: rib chondrocytes treated with Adeno-CMV-Cre

tag: age

value: Adeno-CMV-Cre


title: Ute_P1_Neg_32

description: Single cell

value: IFC 4


title: control_RNAseq_4

city: Philadelphia

first: Edward

last: Lee

state: PA

address: 605B Stellar Chance Laboratories, 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

description: NLS_norm_counts_all.txt, NLS_deseq2_all_alluniq_vs_mmu9htdp43nls.txt

data_processing:
3' Illumina adaptors trimmed with cutadapt
Mapped to mm9 genome build with Bowtie, version 0.12.7 with options --time -k 100 --best --strata -v 2 -p 3, and filtered to a mismatch rate of 6%
Mapped reads were counted for each exon using bedtools multicov and merged into raw gene counts with bedtoools groupBy
DESeq2 was used to normalize read counts. Genes were filtered to have a minimum of 10 reads per million in at least one sample, and those counts were used to test for differential expression
Genome_build: mm9
Supplementary_files_format_and_content: NLS_deseq2_all_alluniq_vs_mmu9htdp43nls.txt is the differential expression output of DESeq2. NLS_norm_counts_all.txt is the file of normalized read counts per gene as computed by DESeq2. The counts are in matrix format, one file for the whole experiment.

source_name: Cortex

extract_protocol:
Hippocampi and right cortex were removed from all mice after sacrifice and immediately solubilized in QIAzol (QIAGEN)..
Samples were homogenized by passing through a series of 3 increasingly higher-gauge needles. After homogenization, total RNA was isolated from the samples by following the protocol for the miRNeasy kit (QIAGEN). RNA was run on an Agilent 2100 Bioanalyzer to assess quality; only samples with excellent RNA quality (RNA Integrity Number [RIN] > 7) were used. Samples were depleted of DNA using Turbo DNase (Ambion). Poly-A- containing mRNA was selected from 20 µg of RNA using the Dynabeads mRNA direct kit (Invitrogen). The mRNA was fragmented, a 5’ phosphate was added using T4 polynucleotide kinase (Invitrogen), and the library was size- selected (60-200 nucleotides) on a 15% TBE-urea gel. Illumina v1.5 RNA adapters were ligated to ends of the fragmented products using T4 RNA ligase 2 (New England Biolabs). A cDNA library was generated using Superscript II (Invitrogen) and PCR-amplified using Phusion HiFi DNA polymerase (New England Biolabs). The library was purified on a 6% TBE gel (Invitrogen). The quality of the library was verified prior to Illumina sequencing by cloning into Zero Blunt TOPO (Invitrogen) and analyzing 6-10 clones by standard sequencing to determine a) the presence of adapters, b) appropriate size selection, c) the abundance of ribosomal RNA, and d) the diversity of the library products. The verified size-selected poly- A stranded cDNA library was submitted to the Penn Genome Frontiers Institute (PGFI, University of Pennsylvania, Philadelphia, PA) for sequencing. The Illumina Solexa GAII platform was used to obtain 50-bp single-end sequencing reads,

value: nontransgenic

tag: tissue

value: brain cortex


title: control_RNAseq_2


title: Ute_P1_Neg_10

description: Single cell

tag: purification


title: Ute_P1_Neg_9

description: Single cell

tag: c1 ifc #


title: control_RNAseq_1


title: Ute_P1_tdTom_11

description: Single cell

tag: gfp (i)


title: Ute_P1_GFP_7

description: Single cell

tag: tdtomato (i)

value: SC (ii), Extrastriola


title: Ute_P1_Neg_8

description: Single cell

value: Enzymatic/mechanical

tag: classifications


title: Ute_P1_Neg_1

description: Single cell

value: IFC 1


title: bigenic_RNAseq_4

value: bigenic Camk2a-tTa / deltaNLS-hTDP-43


title: Ute_P1_GFP_6

description: Single cell

value: SC (ii)


title: Ute_P1_GFP_5

description: Single cell

value: HC (iii-iv), Extrastriola


title: bigenic_RNAseq_3


title: bigenic_RNAseq_2


title: bigenic_RNAseq_1


title: Ute_P1_GFP_4

description: Single cell


title: Ute_P1_Neg_36

description: Single cell


title: Ute_P1_GFP_2

description: Single cell

value: SC (i)


title: Ute_P1_GFP_3

description: Single cell


title: H3K9Me1 MC3T3

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Reads have been aligned against Mouse reference genome mm9 using Bowtie aligner with default parameters. Aligned reads for ab1 and ab2 have been used for peak-calling procedures using MACS software (version 1.3.7.1). A lower enrichment cutoff of 5 (mfold=5) has been set.
in order to find regions for significant coverage enrichment. Aligned reads for H3K4Me3, H3K9Me3 and PolII have been used for peaks calling procedures using SICER software. Window size and gap size have been set to 200 for H3K4Me3 and to 600 for H3K9Me3 and PolII. IgG signal has been used to model the background noise.
Genome_build: mm9
Supplementary_files_format_and_content: bed file containing the genomic positions of the significant peaks output by MACS and SICER

source_name: MC3T3 mouse cell line

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 min and cross-linking was quenched by addition of 0.125 M glycine. Cells were then harvested in ChIP buffer and sonicated with a Bioruptor UCD-300 to obtain fragments around 250 bp in size. Plolyclonal custom-made PRDM5 antibodies were used for Immunoprecipitation. Precipitated DNA was recovered by purification with a QIAquick PCR purification kit (Qiagen)
Libraries for sequencing were obtained using a ChIP-Seq DNA sample prep kit (Illumina) according to the manufacturer's reccomendations

tag: chip antibody

tag: cell strain


title: PolII MC3T3

value: PolII


title: Ute_P1_GFP_1

description: Single cell

data_processing:
Basecalling and sample demultiplexing by Illumina HAS 0.9
We prepared a Bowtie2_2.2.3 index from the NCBI whole genome mm10 reference transcriptome using default rsem1.2.19 parameters
Paired-end reads were aligned to transcriptome using rsem1.2.19 command rsem-calculate-expression -p 16 --calc-pme --calc-ci --ci-memory 20000 --bowtie2 --bowtie-chunkmbs 512 --no-bam-output --time --paired-end --forward-prob 0.5 --estimate-rspd *R1_001.fastq *R2_001.fastq /ReferenceLocation ./OutputLocation 2>./*.Log.txt 1>./*.Console.txt
Genome_build: NCBI GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file with the estimated expression (TPM) for each gene for each Sample as calculated by RSEM1.2.19. Tab-delmited text file with the estimated count for each gene for each Sample as calculated by RSEM1.2.19.

extract_protocol:
Following dissociation of tissue into a single-cell suspension, target cells were enriched by purification as described, cells were lysed, polyA RNA reverse-transcribed, and cDNA amplified using SMARTer ultra-low input cDNA synthesis (Clontech) on the C1 microfluidics platform (Fluidigm).
cDNA libraries were prepared for sequencing using Nextera XT tagmentation and 96-barcode indexing (Illumina). Barcoded samples were pooled, cleaned with Agencourt AMPure XP magnetic bead isolation (Beckman Coulter).


title: Prdm5 MC3T3 IgG


title: control_RNAseq_3


title: Ute_P1_Neg_0

description: Single cell


title: H3K4Me3 MC3T3


title: Ute_P1_GFP_0

description: Single cell


title: Prdm5 MC3T3 ab2


title: Co_PCP_2k_FACS_3

description: 2000 cell bulk population

source_name: Cochlear epithelium

value: FACS

value: Cochlear SC bulk population


title: Prdm5 MC3T3 ab1


title: Co_PCP_100_Epit

description: 100-200 cell bulk population

value: IFC 5

value: Cochlear epithelium bulk population


title: Ute_PCP4

description: 100-200 cell bulk population

value: IFC 2 Tube Control

value: Utricular epithelium bulk population


title: MRC5

city: Guangzhou

first: Yong

last: Zhao

state: Guangdong

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

description: stable cell line

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were filtered those adaptor comtiminated, unpaired, contains N , and  then mapped to hg19 whole genome using tophat 2.0.2 with default parameters
Reads count were calculated by htseq-count(Htseq Frame work v 0.6.0) with parameters  -s no
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C, Nat. Biotechnol. 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample, each column represents it's expression across all genes while each row shows gene abundence in al samples.

source_name: human fetal lung fibroblast (MRC5) cells_control

extract_protocol:
Total RNA was extracted using the Trizol reagent (Takara). A total of 3 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using a NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s recommendations.

tag: cell line

tag: treatment

value: control


title: Co_PCP_2k_FACS_1

description: 2000 cell bulk population


title: Ute_PCP1

description: 100-200 cell bulk population

value: IFC 1 Tube Control


title: MRC5+Tetra-Pt(bpy)-treated

description: stable cell line

source_name: human fetal lung fibroblast (MRC5) cells_Tetra-Pt(bpy)-treated

value: Tetra-Pt(bpy)-treated


title: Ute_PCP2

description: 100-200 cell bulk population


title: Ute_PCP3

description: 100-200 cell bulk population


title: Co_PCP_200_Epit

description: 100-200 cell bulk population


title: A549_glu_pos_rep3

first: Maxim

middle: N.

last: Artyomov

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

description: 3'end DGE

data_processing:
Data were sequenced on HiSeq 2500 instrument (Illumina, San Diego, CA) using 41bpX18bp paired-end sequencing. Second mate was used for sample demultiplexing, at which point individual single-end fastqs were aligned to hg19 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All. Gene expression was obtained using in-house scripts based on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file that includes raw count data for each sample with NCBI Gene ID numbers in the first column.

source_name: A549 cell line_with_glucose

extract_protocol:
not provided
For cDNA synthesis, custom oligo-dT primers were used with a barcode and adapter-linker sequence (CCTACACGACGCTCTTCCGATCT—XXXXXXXX-T15). After first strand synthesis, samples were pooled together based on Actb qPCR values, and RNA-DNA hybrids degraded using consecutive acid-alkali treatment. A second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated using T4 ligase (NEB) followed by SPRI clean-up. The mixture was then PCR enriched for 12 cycles and SPRI purified to yield final strand specific RNA-seq libraries as previously described (Jha et al., 2015)

treatment_protocol: A549 cells were cultured in the presence (25 mM) or absence of glucose for 48 hours prior to RNA extraction.

value: lung carcinoma


title: λN-CG9754 _Firefly_tethered_rep2_smRNAseq

description: small RNA sequencing

source_name: adult fly ovaries

value: ovaries


title: A549_glu_neg_rep3

description: 3'end DGE

source_name: A549 cell line_without_glucose


title: A549_glu_neg_rep2

description: 3'end DGE


title: λN-CG9754_Firefly_tethered_rep1_smRNAseq

description: small RNA sequencing


title: A549_glu_pos_rep1

description: 3'end DGE


title: Firefly_untethered_rep1_smRNAseq

description: small RNA sequencing


title: A549_glu_neg_rep1

description: 3'end DGE


title: λN-CG9754 _Firefly_tethered_rep2_RNAseq

description: NSR RNAseq

value: 3-5 old

value: Ovary


title: λN-CG9754_Firefly_tethered_rep1_RNAseq

description: NSR RNAseq


title: Firefly_untethered_rep2_RNAseq

description: NSR RNAseq


title: CG9754_het_Input

value: 3-5 days old

value: adult fly ovaries


title: nanosGAL4_dsWhite_rep1_GROseq

description: BrU labeled transcription run-on RNAs

tag: antibody/beads

value: BrdU Antibody (IIB5) Agarose (santa cruz, sc-32323 AC)


title: nanosGAL4_dsPiwi_rep1_GROseq

description: BrU labeled transcription run-on RNAs


title: nanosGAL4_dsCG9754_rep1_RNAseq

description: NSR RNAseq


title: nanosGAL4_dsWhite_rep2_RNAseq

description: NSR RNAseq


title: nanosGAL4_dsPiwi_rep1_RNAseq

description: NSR RNAseq


title: nanosGAL4_dsPiwi_rep2_RNAseq

description: NSR RNAseq


title: CG9754_mutant_Input


title: BMDM_MCSF_W_B

description:
Sample name: BMDM_MCSF_B.004
M-CSF withdrawal replicate 2
Instrument model: Ion Proton (P1 chip)
Small-RNA seq
Processed data file: mm10_tableCount.txt

data_processing:
Adaptor trimming with cutadapt-1.2.1, then bowtie2 v2.2.4 mapping versus mm10 build with " --local --very-sensitive-local -k 10" parameters.
Bam files were then processed with a java home made class, based on picard java classes to perform identification and produce raw data count of microRNAs (mirbase release 21), tRNAs from UCSC web server (UCSC tables) and ncRNAs from ensembl ncRNAs release 73.
Genome_build: mm10
Supplementary_files_format_and_content: [mm10_tableCount.txt] Tabulated text file containing raw data of small RNAs, including miRNA from miRBase v21, tRNAs for tRFs identification from UCSC table browser and Ensembl non-coding RNAs r73, no normalisation.

source_name: M-CSF withdrawal_Small

extract_protocol:
RNA extraction with Trizol
50 ng of RNA were treated with the trilink library kit (TriLink Biotechnologies). 17 cycles of PCR were performed. Libraries were size-selected for the 130 to 155 nt fraction on a caliper 300 XT chip. Libraries were sequenced on the Ion proton, 10 libraries were loaded on one P1 Chip.

treatment_protocol: BMDM upon 36 hr with or without M-CSF withdrawal

tag: strain/background

tag: cell type

value: Bone Marrow Derived Macrophage

value: M-CSF withdrawal

tag: rna extract

value: small RNA

tag: concentration sample (ng/ul)

tag: rin number


title: BMDM_CTRL_A

description:
Sample name: BMDM_CTRL_A.001
Control replicate 1
Instrument model: Ion Proton (P1 chip)
Small-RNA seq
Processed data file: mm10_tableCount.txt


title: nanosGAL4_CG9754_rep1_GROseq

description: BrU labeled transcription run-on RNAs

tag: age


title: BMDM_MCSF_W_A

description:
Sample name: BMDM_MCSF_A.002
M-CSF withdrawal replicate 1
Instrument model: Ion Proton (P1 chip)
Small-RNA seq
Processed data file: mm10_tableCount.txt


title: BMDM_CTRL_B

description:
Sample name: BMDM_CTRL_B.003
Control replicate 2
Instrument model: Ion Proton (P1 chip)
Small-RNA seq
Processed data file: mm10_tableCount.txt


title: CG9754_mutant_rep1_H3K9me3ChIPseq

value: H3K9me3 (abcam, ab8898)

tag: tissue


title: Firefly_untethered_rep1_RNAseq

description: NSR RNAseq


title: CG9754_mutant_rep2_H3K9me3ChIPseq


title: nanosGAL4_dsWhite_rep1_RNAseq

description: NSR RNAseq


title: nanosGAL4_dsCG9754_rep2_RNAseq

description: NSR RNAseq


title: CG9754_het_rep2_H3K9me3ChIPseq


title: CG9754_het_rep1_H3K9me3ChIPseq


title: nanosGAL4_dsCG9754_rep2_H3K9me3ChIPseq


title: λN-CG9754_Firefly_tethered_H3K9me3ChIPseq


title: Firefly_untethered_rep2_smRNAseq

description: small RNA sequencing


title: Ovary

city: Madurai

first: Gopal

last: Pandi

state: Tamil Nadu

address: Department of Plant Biotechnology, School of Biotechnology

country: India

institute: Madurai Kamaraj University

description: Small RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn5 whole genome using bowtie v0.12.2
Mapped to the piRNA database using bowtie 2
Genome_build: rn5
Supplementary_files_format_and_content: Excel files with read count

organism: Rattus norvegicus

source_name: Ovary

growth_protocol: The animals are grown under normal conditions and provided feed and water ab libithum

extract_protocol:
Eight week old Wistar rats were sacrificed and the ovaries are harvested. RNA isolated by using trizol.
Small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Wistar

value: 8 weeks


title: nanosGAL4_dsWhite_Input


title: Firefly_untethered_H3K9me3ChIPseq


title: nanosGAL4_dsCG9754_rep1_H3K9me3ChIPseq


title: A549_glu_pos_rep2

description: 3'end DGE


title: nanosGAL4_dsPiwi_rep2_H3K9me3ChIPseq


title: nanosGAL4_dsPiwi_rep1_H3K9me3ChIPseq


title: nanosGAL4_dsWhite_rep1_H3K9me3ChIPseq


title: nanosGAL4_dsWhite_rep2_H3K9me3ChIPseq