title: Vgat Input 2

first: Alexander

middle: R

last: Nectow

state: New York

address: 630 W 168th St., Physicians and Surgeons

department: Medicine

institute: Columbia University

description: Immunoprecipitated RNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
The reads were then aligned to mouse reference genome (mm9) and Ensembl gene model (NCBIM37) using Tophat (tophat-2.0.8b) aligner with the following paramers[-p 4 --bowtie1 --no-coverage-search -a 10 -g 20 --no-novel-juncs]
Cuffdiff (cufflinks-2.0.0 ) was used to determine differentially expressed genes between IP and input and between Vgat IP and Vglut IP with the following parameters (cuffdiff -N -p 3 --max-bundle-frags 3000000)
Genome_build: mm9
Supplementary_files_format_and_content: cuffdiff output between IP/INPUT with FPKM columns

source_name: Brain

extract_protocol:
Agilent Absolutely RNA Nanoprep Kit
Clontech SMARTer Kit for Illumina sequencing (Low Input), Illumina Nextera XT DNA Sample Preparation Kit

value: Brain

value: Dorsal Raphe Nucleus Neurons

tag: cell subtype

value: GABAergic Neurons

tag: rip antibody


title: Vgat IP1

status: Public on Jun 09 2017

type: SRA

city: New York

country: USA

description: Immunoprecipitated RNA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: tissue region

value: Dorsal Raphe Nucleus

tag: cell type

tag: rip antibodies

value: Htz-GFP-19C8 and Htz-GFP-19F7 (two GFP mouse monoclonal antibodies, Memorial-Sloan Kettering Monoclonal Antibody Facility)


title: VGLUT IP3

description: Immunoprecipitated RNA

value: Glutamatergic Neurons


title: CreNegative_MHCPositive3

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

country: United Kingdom

institute: University of Glasgow

description:
CreNegative_MHCPositive3_ID68722
CreNeg-MHCPos_vs_CrePos-MHCNeg.CuffDiff.gene_exp.diff
CreNeg-MHCPos_vs_Control.CuffDiff.gene_exp.diff
FPKM_Matrix.csv

data_processing:
Basecalls performed in phred64 (solexa1.3-quals).
Sequenced reads were mapped to mm10 whole genome using Tophat with default settings
FPKM matrix was derived using Cufflinks suite using default settings
Differential expression quantified using CuffDiff at p-FDR < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: Summary files describe the results of CuffDiff differential expression analysis for core comparisons as well as FPKM matrix for all replicate created using Cufflinks suite.

source_name: Nevus Melanocytes

growth_protocol: Animals were kept in conventional animal facilities and monitored frequently. All experiments were carried out in compliance with UK Home Office guidelines at the Beatson Institute for Cancer Research mouse facility (Home Office PCD 60/2607) under project license 60/4079. Mice were genotyped by PCR analysis.

extract_protocol:
Qiagen RNA extraction kit.
Samples were sequenced in house on a single flow cell on the Illumina Genome Analyzer IIx

treatment_protocol: Mice carrying a tyrosinase promoter driven NrasQ61K gene (Tyr-NrasQ61K) have been described (Ackermann et al., 2005). Mice conditionally expressing the mutant BrafV600E gene under control of tyrosinase driven CRE-ER (Delmas et al., 2003) (Tyr-CRE-ER : LSL-BrafV600E) have also been described (Dhomen et al., 2009). Albino mice carrying the Tyr-NrasQ61K allele were generated by cross-breeding with the albino FVB/NJ (Taketo et al., 1991) strain. Control wild type mice were littermate albino mice lacking the Tyr-NRasQ61K transgene.

tag: mhcii status

value: wtMHCII

tag: nras status

tag: strain

value: FVB/NJ (Cross)


title: CreNegative_MHCPositive2

description:
CreNegative_MHCPositive2_ID68718
CreNeg-MHCPos_vs_CrePos-MHCNeg.CuffDiff.gene_exp.diff
CreNeg-MHCPos_vs_Control.CuffDiff.gene_exp.diff
FPKM_Matrix.csv


title: 2d GFP infected pancreatic organoids_1_2

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

description: processed data header: CTRL_GFP_1_2

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts(.txt)

source_name: Dissociated pancreatic organoid cells

extract_protocol:
Three-dimensional cultures of pancreatic ductal cells (organoids, Huch et al 2013) were infected with GFP vectors (GFP only controls, GFP-WT-Ngn3 and GFP-6SA-Ngn3). Organoids were dissociated to single cells and GFP+ cells were separated by FACS Influx (BD Biosciences). Pool of 50 cells were sorted by FACS directly into individual wells of a 96-well plate containing lysis buffer. RNA-Seq analysis was performed as described previously (Picelli et al., 2014). Pooled libraries were then run on the Illumina Hi-Seq 2500.
RNA libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit

tag: days of transgene induction

value: 2 days

tag: passage


title: VGLUT IP1

description: Immunoprecipitated RNA


title: VGLUT Input3

description: Immunoprecipitated RNA


title: VGLUT Input1

description: Immunoprecipitated RNA


title: VGLUT Input2

description: Immunoprecipitated RNA


title: Control2

description:
Control2_ID71309
CrePos-MHCNeg_vs_Control.CuffDiff.gene_exp.diff
CreNeg-MHCPos_vs_Control.CuffDiff.gene_exp.diff
FPKM_Matrix.csv

value: wtNRAS

value: FVB/NJ


title: Vgat IP2

description: Immunoprecipitated RNA


title: Control1

description:
Control1_ID46419
CrePos-MHCNeg_vs_Control.CuffDiff.gene_exp.diff
CreNeg-MHCPos_vs_Control.CuffDiff.gene_exp.diff
FPKM_Matrix.csv


title: CrePositive_MHCNegative3

description:
CrePositive_MHCNegative3_ID68717
CreNeg-MHCPos_vs_CrePos-MHCNeg.CuffDiff.gene_exp.diff
CrePos-MHCNeg_vs_Control.CuffDiff.gene_exp.diff
FPKM_Matrix.csv

value: MHCII-KO


title: Vgat Input 1

description: Immunoprecipitated RNA


title: CrePositive_MHCNegative2

description:
CrePositive_MHCNegative2_ID61602
CreNeg-MHCPos_vs_CrePos-MHCNeg.CuffDiff.gene_exp.diff
CrePos-MHCNeg_vs_Control.CuffDiff.gene_exp.diff
FPKM_Matrix.csv


title: CreNegative_MHCPositive1

description:
CreNegative_MHCPositive1_ID61600
CreNeg-MHCPos_vs_CrePos-MHCNeg.CuffDiff.gene_exp.diff
CreNeg-MHCPos_vs_Control.CuffDiff.gene_exp.diff
FPKM_Matrix.csv


title: T96s1_H12

city: Boston

first: Ignacio S.

last: Caballero

state: MA

address: 620 Albany St., NEIDL 401V

department: NEIDL/Microbiology

institute: Boston University School of Medicine

data_processing:
Reads were aligned using BWA Aln version 0.7.10.
Raw counts were calculated using a custom algorithm from the Broad Institute
Genome_build: UCSC Refseq Human 19

organism: Homo sapiens

growth_protocol: Differentiation of control and mutant iPSC lines into intestinal tissue was performed as described[15] with the following modifications. First, iPSC lines were cultured in feeder-free conditions for at least 3 passages. iPSC colonies were then triturated into 1-2 mm fragments, transferred onto Matrigel-coated 24-well dishes, and cultured in mTeSR™1 medium for three to four days. Once cells reached 80% confluence, intestinal differentiation was begun by aspirating mTeSR™1 media and adding endoderm differentiation media containing Activin A on days 1, 2, and 3, as described [15]. Fresh mid/hindgut differentiation media was changed daily from day 3 to day 8, as indicated in the text, and consisted in RPMI-1640 media supplemented with human recombinant FGF4 (500 ng/ml) and the GSK3β inhibitor CHIR99021 (3 μM), instead of Wnt3a protein. Starting as early as two days after exposure of cells to mid/hindgut differentiation media, intestinal spheroids were collected and embedded into ice-cold intestinal Matrigel (Matrigel® Matrix. Corning: supplemented as the intestinal growth media below). Intestinal matrigel drops containing the Spheroids were placed onto 24-well plates and allowed to solidify by incubating them at 37 °C for 10 min. Fresh DMEM/F12 based intestinal growth media containing Rspondin1 (500ng/mL), Noggin (100ng/mL), and EGF (100 ng/mL) was added and replaced every 4 days. iPSC-derived “intestinal organoids” (Passage 1) were split approximately every other week or used for experiments.

extract_protocol:
Poly(A)+ mRNA from isolated single cells were converted to cDNA decorated with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) using a template-switching reverse transcriptase. Decorated cDNA from multiple cells were then pooled, amplified and prepared for multiplexed sequencing using a modified transposon-based fragmentation approach that enriches for 3’ ends and preserves strand information. Frozen cells were thawed for 5 minutes at room temperature and cell lysis was enhanced by a treatment with proteinase K (200μg/mL;Ambion) followed by RNA desiccation to inactivate the proteinase K and simultaneously reduce the reaction volume (50 °C for 15 in sealed plate, then 95 °C for 10 min with seal removed ). Diluted ERCC RNA Spike-In Mix (1μl of 1:107 ; Life Technologies) was added to each well. Template switching reverse transcription reaction was carried out using Maxima H Minus Reverse Transcriptase (Thermo Scientific). Following the template switching reaction, cDNA from 384 wells were pooled together, and then purified and concentrated using a single DNA Clean & Concentrator-5 column (Zymo Research). Pooled cDNAs were treated with Exonuclease I (New England Biolabs) and then amplified by single primer PCR using the Advantage 2 Polymerase Mix (Clontech). Full length cDNAs were purified with Agencourt AMPure XP magnetic beads (0.6x, Beckman Coulter) and quantified on the Qubit 2.0 Flurometer using the dsDNA HS Assay (Life Technologies).
Full-length cDNA was then used as input to the Nextera XT library preparation kit (Illumina) according to the manufacturer’s protocol, with the exception that the i5 primer was replaced by our P5NEXTPT5 primer (Integrated DNA Technologies). The resulting sequencing library was purified with Agencourt AMPure XP magnetic beads (0.6x, Beckman Coulter), size selected (300-800bp) on a E-Gel EX Gel, 2% (Life Technologies), purified using the QIAquick Gel Extraction Kit (Qiagen) and quantified on the Qubit 2.0 Flurometer using the dsDNA HS Assay (Life Technologies). Libraries were sequenced on Illumina Hiseq paired-end flow cells with 17 cycles on the first read to decode the well barcode and UMI, a 9 cycle index read to decode the i7 Nextera barcode that serves as a plate / pool barcode, and finally a 46 cycle second read to sequence the cDNA.

tag: genotype

value: APC+/-

value: hIOs

value: Mutant human iPSC-derived intestinal organoids (Passage 3)


title: VGLUT IP2

description: Immunoprecipitated RNA


title: Control3

description:
Control3_ID71310
CrePos-MHCNeg_vs_Control.CuffDiff.gene_exp.diff
CreNeg-MHCPos_vs_Control.CuffDiff.gene_exp.diff
FPKM_Matrix.csv


title: T96s1_H11


title: CrePositive_MHCNegative1

description:
CrePositive_MHCNegative1_ID61601
CreNeg-MHCPos_vs_CrePos-MHCNeg.CuffDiff.gene_exp.diff
CrePos-MHCNeg_vs_Control.CuffDiff.gene_exp.diff
FPKM_Matrix.csv


title: T96s1_H10


title: T96s1_G12


title: T96s1_G9

value: hiPSCs

value: Undifferentiated BU1 #18 APC +/1246 isogenic clone (mTesR)


title: T96s1_H7


title: T96s1_H8


title: T96s1_H9


title: T96s1_G11


title: T96s1_G8


title: T96s1_G7


title: T96s1_F10


title: T96s1_F12


title: 2d GFP-6SA-Ngn3 infected organoids_1_1

description: processed data header: SA_1_1


title: T96s1_F11


title: T96s1_F8


title: T96s1_F7


title: T96s1_E11


title: T96s1_E12


title: T96s1_F9


title: T96s1_D11

value: APC+/+

value: Wild-type human iPSC-derived intestinal organoids (Passage 3)


title: T96s1_E8


title: T96s1_E10


title: T96s1_D10


title: T96s1_G10


title: T96s1_D9

value: Undifferentiated BU1 clone (mTesR)


title: T96s1_E9


title: T96s1_D8


title: T96s1_D7


title: T96s1_C10


title: T96s1_C12


title: T96s1_C11


title: T96s1_C8


title: T96s1_C9


title: T96s1_C7


title: T96s1_B12


title: T96s1_B11


title: T96s1_B10


title: T96s1_B8


title: T96s1_D12


title: T96s1_A11


title: T96s1_A12


title: T96s1_A9


title: T96s1_A8


title: T96s1_A10


title: T96s1_A7


title: T96s1_E7


title: T96s1_B7


title: T96s1_B9


title: P-HAg-28

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

description: Hepatitis B

data_processing:
miRDeep2 default
DEseq2 normalization
Genome_build: miRBase v21
Supplementary_files_format_and_content: processed_data_file.txt reports miRNA profiles (normalized abundance)

source_name: HBV, serum

extract_protocol:
Qiagen miRNeasy Serum/Plasma Kit
TruSeq small RNA prep kit

tag: disease state

value: HBV

tag: sample type

value: serum


title: P-HAg-16

description: Hepatitis B


title: P-HAg-22

description: Hepatitis B


title: P-HAg-13

description: Hepatitis B


title: P-HAg-12

description: Hepatitis B


title: P-HAg-08

description: Hepatitis B


title: HE-PA-695

description: Healthy Control

source_name: HC, serum

value: HC


title: HE-PA-726

description: Healthy Control


title: P-HAg-05

description: Hepatitis B


title: HE-PA-692

description: Healthy Control


title: HE-PA-683

description: Healthy Control


title: HE-PA-687

description: Healthy Control


title: HE-PA-129

description: Healthy Control


title: HE-PA-601

description: Healthy Control


title: HE-PA-03

description: Healthy Control


title: GGTP-004

description: Liver Cirrhosis

source_name: LC, serum

value: LC


title: C-EtOH-57

description: Liver Cirrhosis


title: GGTP-023

description: Liver Cirrhosis


title: ACTMN-9

description: early APAP overdose

source_name: APAP, serum

value: APAP


title: C11

description: Healthy Control


title: C-EtOH-59

description: Liver Cirrhosis


title: C27

description: Healthy Control


title: C-EtOH-33

description: Liver Cirrhosis


title: C15

description: Healthy Control


title: C-EtOH-18

description: Liver Cirrhosis


title: C5

description: Healthy Control


title: C-EtOH-02

description: Liver Cirrhosis


title: C12

description: Healthy Control


title: C14

description: Healthy Control


title: ACTMN-4

description: early APAP overdose


title: ACTMN-131

description: late APAP overdose


title: GGTP-070

description: Liver Cirrhosis


title: C-EtOH-51

description: Liver Cirrhosis


title: C19

description: Healthy Control


title: ACTMN-17

description: late APAP overdose


title: ACTMN-130

description: late APAP overdose


title: ACTMN-22

description: late APAP overdose


title: A1C-177

description: Type 2 Diabetis Mellitus

source_name: T2DM, serum


title: ACTMN-128

description: early APAP overdose


title: ACTMN-129

description: late APAP overdose


title: C21

description: Healthy Control


title: ACTMN-3

description: late APAP overdose


title: A1C-188

description: Type 2 Diabetis Mellitus


title: 2d GFP-6SA-Ngn3 infected organoids_2_1

description: processed data header: SA_2_1

value: 2 days


title: A1C-053

description: Type 2 Diabetis Mellitus


title: 2d GFP-6SA-Ngn3 infected organoids_1_3

description: processed data header: SA_1_3


title: A1C-074

description: Type 2 Diabetis Mellitus


title: A1C-023

description: Type 2 Diabetis Mellitus


title: A1C-024

description: Type 2 Diabetis Mellitus


title: SN449-1_s_5_1

city: Luxembourg

first: Arnaud

last: Muller

address: 84 Val Fleuri

department: DONC

country: Luxembourg

institute: LIH

data_processing:
FASTQ files were submitted to TopHat (v2.0.6) {Trapnell, 2009 #28} using Bowtie (v2.0.2.0) as the core read-alignment engine {Langmead, 2009 #29}. The mapping has been made using default parameters with the reference human genome GRCh37.69 from Ensembl annotation. Corresponding BAM files were indexed and sorted with SAMtools (v0.1.18.0) for downstream convenience {Li, 2009 #30}. Counts for gene expression were obtained using HTSeq {Anders, 2015 #52}. Exon counting was made using featureCounts function of Rsubread R/Bioconductor package, which implement a flexible and powerful counting algorithm {Liao, 2014 #54}. Between-array normalization at gene level was performed by R/Bioconductor package edgeR {Robinson, 2010 #5}. Relative scaling factors for the libraries were calculated and normalized counts-per-million (CPM) values in edgeR were obtained.
Genome_build: GRCh37.69
Supplementary_files_format_and_content: Text files that contain the raw sequence counts for each gene (Ensembl gene identifier) produced by the program Ht-seq count.

source_name: adjacent-SCC

extract_protocol:
Total RNA was extracted from biological samples using miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA quantity was determined using the NanoDrop Spectrophotometer. RNA quality was checked using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Diegem, Belgium).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue type

value: Adjacent normal lung tissue


title: SN450-1_s_2_1


title: ST449-1_s_4_1

source_name: tumor-SCC

value: Lung squamous cell carcinoma

tag: Stage

value: I


title: ST450-1_s_8_1


title: ST354-1_s_8_1


title: SN667-1_s_4_1


title: ST349-1_s_6_1


title: SN354-1_s_1_1


title: SN679-1_s_1_1


title: ST328-1_s_2_1


title: SN405-1_s_3_1


title: SN328-1_s_3_1


title: A1C-062

description: Type 2 Diabetis Mellitus


title: ST679-1_s_6_1


title: SN349-1_s_7_1


title: ST667-1_s_8_1


title: SN327-1_s_6_1


title: Restricted 8 TP2

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

description: Experimental: day 55 with ad libitum diet following 125 days of restricted diet Period 2

data_processing:
Basecalls performed using CASAVA version 1.4
RNAseq reads were aligned to UMD3.1 genome using Bowtie (--very-senstive setting, --solexa1.3-quals), sorted and possible PCR duplicates were removed using Samtools.
Raw counts were enumerated using HTSEQ-count (settings: mode = union)
Raw read counts were normalized using scaling factors estimated by the Trimmed mean of M-Values (TMM) method implemented  the edgeR software package. The normalised values represent read counts per million mapped reads, adjusted for sample library size.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab delimited txt files. First row contains the ENSEMBL gene IDs and second row the raw number of reads that map to each gene

organism: Bos taurus

source_name: rumen epithelium

growth_protocol: Purebred Holstein Friesian bulls were assigned to one of two feeding treatments (i) restricted feed allowance for 125 days (n=9) followed by ad libitum access to feed for a further 55 days (n=10) or (ii) a control group with ad libitum access to feed through out the 180 days trial (n=19).  The first 125 days of the trial were denoted as Period 1, during which treatment groups were fed differentially. The subsequent 55 days, denoted as Period 2 during which all bulls were fed ad libitum. All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial, with the amount of feed provided different dependent on each treatment group. Restricted fed animals were fed to grow at 0.6 kg /day during Period 1, with ad libitum animals expected to gain in excess of 1.5 to 2 kg/day.

extract_protocol:
Total RNA was extracted from frozen muscle tissue by homogenization using the Qiagen Rneasy RNA isolation kit.
Single-end mRNA-seq libraries were constructed using the Illumina Truseq sample prep kit.

treatment_protocol: 19 bulls fed a restricted diet for 125 days to grow at 0.6kg/day, after which they were fed ad libitum for a further 55 days. The remaining 19 bulls in the control group were fed ad libitum throughout

tag: breed

value: Holstein Friesian

tag: gender

value: male

tag: diet

value: 70% concentrate, 30% grass silage diet

tag: feeding period

value: Period 2

tag: feeding treatment

value: Realimentation period

value: rumen epithelium

tag: biopsy day

value: day 55 of Period 2


title: Restricted 6 TP2

tag: tissue


title: Restricted 5 TP2


title: Restricted 7 TP2


title: Restricted 10 TP2


title: ST405-1_s_7_1


title: Restricted 3 TP2


title: Restricted 2 TP2


title: Restricted 1 TP2


title: Restricted 9 TP1

description: Experimental: day 125 with restricted diet Period 1

value: Period 1

value: Differential feeding

value: day 125 of Period 1


title: Restricted 8 TP1


title: Restricted 7 TP1


title: Control 6 TP2

description: Control: day 55 with ad libitum diet Period 2


title: Control 10 TP2


title: Restricted 3 TP1


title: Control 9 TP2


title: ST327-1_s_5_1


title: Restricted 6 TP1


title: Restricted 2 TP1


title: Restricted 9 TP2


title: Restricted 1 TP1


title: Restricted 4 TP1


title: Control 5 TP2


title: Control 7 TP2


title: Control 4 TP2


title: Control 8 TP2


title: Control 2 TP2


title: Control 3 TP2


title: Restricted 4 TP2


title: Control 1 TP1

description: Control: day 125 with ad libitum diet Period 1


title: Control 5 TP1


title: Restricted 5 TP1


title: Control 1 TP2


title: Control 8 TP1


title: Control 3 TP1


title: Control 9 TP1


title: Control 2 TP1


title: 6_CS_RT

city: Hangzhou

first: Diming

last: Wang

address: 866 yuhangtang RD

country: China

institute: Zhejiang University

data_processing:
Alignment to Genome with Tophat2
Alignment output piped to Ht-seq-count
Reads mapped were normlized into counts per million
Differential analysis was performed using edgeR
Functional anlaysis with Ingenuity Pathway Anlaysis, David and Panther
Genome_build: umd3.1
Supplementary_files_format_and_content: Content is normalized expressional abundance of each gene each animal

source_name: rumen epithelial tissue

extract_protocol:
After feeding trail, cows were slaughtered and rumen epithelial samples were collected from each animal and immediately flash frozen in liquid nitrogen within 10 min after death of the animal. Samples were stored at -80 °C until RNA was extracted. 100 mg of powdered rectal tissue was used for RNA extraction using a mirVana total RNA Isolation Kit
Illumina truseq_stranded_total_rna_sample_preparation kit

treatment_protocol: Cattle with three diet (Alfalfa hay, rice straw or corn stover)

value: rumen epithelial

value: corn stover


title: 4_CS_RT


title: 5_CS_RT


title: 3_CS_RT


title: 5_RS_RT

value: rice straw


title: 4_RS_RT


title: 1_CS_RT


title: 3_RS_RT


title: 6_AL_RT

value: alfalfa hay


title: 2_CS_RT


title: 2_RS_RT


title: 1_RS_RT


title: 4_AL_RT


title: 2_AL_RT


title: 5_AL_RT


title: 6_RS_RT


title: 3_AL_RT


title: Control 7 TP1


title: 1_AL_RT


title: Control 4 TP1


title: IgG_ChIPSeq

city: Nanchang

first: Yanyu

last: Dean

address: Lushanzhong888, Changbei district

institute: Jiangxi Agricultural University

library_source: genomic

data_processing:
ChIP-seq reads were mapped to the pig genome (Sscrofa 10.2) using BEDtools.
Only the alignments with fewer than two mismatches were considered for enriched-region (peak) identification (peak calling) using the Model-based Analysis of ChIP-seq (MACS) algorithm.
MEME 4.6.1 software was used to identify the PPARD binding motif.
PeakAnalyzer software was used for peak annotation and the analysis of the nearest downstream gene.
Genome_build: the pig genome (Sscrofa 10.2)
Supplementary_files_format_and_content: wig files were generated with MACS algorithm.

molecule: genomic DNA

organism: Sus scrofa

growth_protocol: Auricular-derived primary cartilage cells were cultured at 37 °C in a humid atmosphere of 5% CO2 in DMEM-F12 medium freshly supplemented with 20% fetal bovine serum and antibiotics.

extract_protocol:
ChIP samples were prepared from auricular-derived primary cartilage cells using the SimpleChIP Enzymatic Chromatin IP kit (CST) according to the manufacturer’s instructions. The cells were harvested and chemically cross-linked with 1% formaldehyde for 10 minutes at 16-20°C. The cell nuclei were released via sonication using an Ultrasonic Processor (SONXI). The collected nuclei were digested with micrococcal nuclease (CST) for 20 minutes at 37 °C. Sheared chromatin was incubated with Anti-FLAG M2 Affinity Gel (Sigma) for 4 hours. Immunoprecipitated DNA was treated with RNase A (CST) and purified with the SimpleChIP kit (CST).
A sequencing library was constructed from enriched DNA fragments using the TruSeq ChIP Library Prep kit (Illumina). Final DNA libraries were validated and sequenced at 50 bp per sequence read using a HiSeq 2000 sequencer (Illumina) at a depth of approximately 20 million sequences.

treatment_protocol: When the confluence reached 70%, the third-generation of auricular-derived primary cartilage cells were collected for subsequent ChIP-seq analyses.

value: Duroc x (Landrace x Large White)

tag: cell type

tag: passagers

value: 3 passage

tag: chip antibody

value: IgG


title: Control 6 TP1

value: Holstein Friesian


title: Exp 1 Treated rep 2

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

description: processed data file: Exp1_PE_count_matrix.txt, Exp1_SE_count_matrix.txt,

data_processing:
The reads for Experiment 1 were mapped to the Ensembl Mus musculus genome (GRCm38). Mapping was performed with Tophat2 (v 2.0.12) [14] calling Bowtie2 (v 2.1.0)
The featureCounts function of Subread  was used to generate counts of reads uniquely mapped to annotated genes using the GRCm38 annotation gtf file.
Comparison of controls in the PE, and SE  datasets was performed using edgeR (v3.14.0). Comparison of the controls versus treated samples in each of the four experiments was performed using functions in the edgeR (v 3.14.0) [23] and limma (v 3.28.17) [17] Bioconductor packages
genome build: Ensembl Mus musculus genome (GRCm38)
processed data files format and content: Tab-delimited text file with read count for each sample.

source_name: Lip tissue

extract_protocol:
RNA was extracted from the dissected mouse tissues using TRI-reagent (Sigma), following the manufacturer’s instructions, which included a chloroform phase separation and ethanol precipitation. RNA was resuspended in 70 μL of RNase-free water. RNA samples were assessed for quantity and quality using a NanoDrop UV spectrophotometer (Thermo Fisher Scientific Inc), conventional RNA electrophoresis and using a Bioanalyser (Agilent Technology Inc). All RNA integrity numbers (RIN) for the analysed samples ranged from 9 to 9.5
mRNA libraries were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia). The Illumina TruSeq RNA Prep Kit was used for Experiment 1. TThe six RNA-Seq libraries in Experiment 1 were sequenced on the Illumina HiSeq2000 platform at the Ramaciotti Centre for Genomics UNSW. R1.fastq and R2.fastq files were produced for each sample.

tag: batch

tag: condition

value: lip


title: Exp 1 Treated rep 3


title: ADE-24

city: Kunming

first: Qiangming

last: Sun

state: Yunnan

address: 935 Jiaoling Road

institute: Chinese Academy of Medicine Science and Peking Union Medical College

description: microRNA sequencing after 24h in PBMCs with DENV-3  source strain ADE infection

data_processing:
illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Human genome using bowtie-0.12.9 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Afterward, the mapped clean reads were mapped to known miRNA precursors, and the mature miRNAs were deposited in miRBase 19.0 (available online: http://www.mirbase.org/).Unmappable sequences were used to predict potentially novel candidate miRNAs with miREvo_v1.1 with parameters -i -r -M -m  -k -p 10 -g 50000 and mirdeep2_0_0_5 with parameters -p -m  -r -y -g 0 -T 10  .
The samples were normalized by calculating tags per million of total RNA reads (TPM) and used to compare the relative abundances of specific miRNAs within each data set.
processed data files format and content: xlsx files are comprised of two sheets, one for knonw miRNAs, the other for novel miRNAs, and each a sheet include gene_id,reacount and tpm values for each Sample.

source_name: PBMCs

growth_protocol: PBMCs plated onto T25 flask at 4.2 × 105 cells per ml were cultivated in RPMI 1640 medium (BI, China) supplemented with 10% foetal bovine serum (FBS, SJQ, China) plus penicillin and streptomycin and incubated 2 hours at 37 ◦C in 5% CO2 in a humidiﬁed incubator.

extract_protocol: 8 h and 24 h after infection, total RNA was extracted from the DENV-infected cells and the corresponding mock-infected cells using TRIzol reagent (Invitrogen China Ltd., Shanghai, China) according to manufacturer's instructions.  Subsequently, the isolated RNA was treated with DNase I (TaKaRa, Dalian, China) to remove DNA contaminants. Total RNA was electrophoresed by 15% denaturing polyacrylamide gel electrophoresis (PAGE) with 8 M urea, and small RNAs, of 15～30 nt, were excised out of the gel and purified. Subsequently, 5' RNA adaptors and 3' RNA adapters were ligated to the sRNA ends. The sRNAs with adapters were amplified by RT-PCR using the Small RNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions, and the generated cDNA libraries were sequenced using Illumina HiSeqTM 2500 sequencing technology(Shanghai biotechnology corporatio Ltd, Shanghai,China).

treatment_protocol: The DENV-3 virus strain that originated from an epidemic in Guangdong, China in 2014 and DENV-2 anti-prM monoclonal antibody (abcam, AB41473), were propagated in PBMCs at multiplicity of infection (MOI) of 5 the 2 hours later. Cells were infected in triplicate and collected at 0, 8 and 24 h post infection (hpi). Cells infected with DENV-3 and DENV-3 ADE for 0 hpi were  used as controls. We defined the different experimental groups as DENV-3–0 h, DENV-3–8 h, DENV-3–24 h, DENV-3 ADE–0 h, DENV-3 ADE–8 h and DENV-3 ADE–24 h. Additionally, a subset of the DENV-3-0 h and DENV-3 ADE–0 h groups were subjected to normalization (the  normalization value was set to 1), and these two groups were then designated Con.

tag: time point

value: Peripheral Blood Mononuclear Cell

tag: infection

value: DENV-3  source strain ADE infection


title: Exp 1 Treated rep 1


title: Exp 1 Control rep 3

value: Control


title: ADE-8

description: microRNA sequencing after 8h in PBMCs with DENV-3  source strain ADE infection


title: 3--24

description: microRNA sequencing after 24h in PBMCs with DENV-3  source strain infection

value: DENV-3 source strain infection


title: Exp 1 Control rep 2


title: 3--8

description: microRNA sequencing after 8h in PBMCs with DENV-3  source strain infection


title: 0

description: microRNA sequencing after 0h in PBMCs with DENV-3-none infection

value: DENV-3-none infection


title: Exp 1 Control rep 1


title: SPRIGHTLY_Input RNA

city: St. Petersburg

first: Bongyong

last: Lee

state: Florida

address: 501 6th Ave S

institute: The Johns Hopkins University

data_processing:
Library strategy: dChIRP-seq
Reads were mapped to hg19 via Bowtie2
The peakes were called by MACS2/Homer using all the Bowtie alignments
MACS2 results were reported
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files

source_name: A375 cells

growth_protocol: A375 cells (ATCC CRL-1619) were grown in Complete Tu Medium containing a 4:1 mixture of MCDB-153 medium with 1.5 g/L sodium bicarbonate and Leibovitz's L-15 medium with two mM L-glutamine, 2% FBS, and 1.68 mM CaCl2 (42). The cells were grown in a humidified incubator at 37°C, 5% CO2.

extract_protocol:
Lysates were clarified from sonicated cells and used for pull down SPRIGHTLY with biotin labeled probes.
dChIRPed RNAs were subjected to double strand cDNA synthesis using an Ovation RNA-Seq System V2 (NuGen Technologies, Inc., San Carlos, CA). High-throughput sequencing libraries were constructed using the TruSeq ChIP Sample preparation kit (Illumina, San Diego, CA) and sequenced on a HiSeq 2500 (Illumina) with 50 bp read lengths.

treatment_protocol: Cells were treated with 0.3% formaldehyde for 10 min at room temperature.

value: melanoma cell line

tag: cell line


title: SPRIGHTLY_D1 dChIRP-Seq


title: SPRIGHTLY_D2 dChIRP-Seq


title: SPRIGHTLY_D3 dChIRP-Seq


title: HT1080_H3K4me3_ChIP-seq

city: Hefei

first: Ping

last: Gao

state: Anhui

address: Huangshan Road 443

department: Innovation Center for Cell Biology

institute: School of Life Science, University of Science and Technology of China

data_processing:
As to RNA-seq data, raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reads were alligned to the human genome hg19 with BOWTIE v2.2.3 and clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
As to ChIP-seq data, raw data (raw reads) of fastq format were firstly processed through BGI programs.
Data filtering parameters：Clean Parameter: SOAPnuke1.5.0 filter -l 5 -q 0.5 -n 0.1 -i -c 25 -Q 2 --seqType 1
Sequenced reads were mapped to the UCSC human genome hg19 using software Bowtie2 (version 2.2.6). Aligned reads were used for subsequent generation of bindingprofiles, peak callings, motif analyses and traveling ratio analyses. MACS (version 1.4.2) was used for peak callings from the aligned reads
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements and peak files

source_name: Human fibrosarcoma HT1080 cells

growth_protocol: Human fibrosarcoma HT1080 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% FBS. Cells were maintained in a water-jacketed incubator with 5% CO2 in 37 °C.

extract_protocol:
As to RNA-seq, total RNA was extracted using TRIZOL Reagent (Life technologies) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100.Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
The ChIP was performed with an EZ-ChIP kit (Millipuro) following the manufacture’s instruction. In this experiment, the DNA fragments were sonicated between 100bp to 500bp. For H3K4me3 ChIP, 2 X 107 cells were used. For MYC, Menin, RNA Pol II, 8X 107 cells were used.
RNA-sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
ChIP-sequencing libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: shRNAs were purchased form Sigma. HT1080 cells were harvested after infecting with viruses containing shRNAs 48 hours.

value: Human fibrosarcoma cells

value: H3K4me3 antibody (Millipore, 07-473)


title: HT1080_NTC_Pol_II_ChIP-seq

tag: transfected with

value: non-targeting control shRNA

value: RNA Pol II antibody (Santa Cruz Biotechnology, sc-899)


title: MC37

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Base calls were made using HiSeq Control Software v.2.0.10.0
Spliced mapping was run with TopHat2 (Bowtie2) to the hg19 genome using the RefSeq gene models from UCSC.
Expression levels were then computed using HTSeq.
Raw expression levels were normalized using Bioconductor package DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: contains HTSeq counts that have been scaled(normalized) using Bioconductor package DESeq

source_name: peritoneal metastasis

extract_protocol:
RNA was extracted from fresh frozen tissue using the Roche High Pure FFPE kit (Roche Diagnostics). After Ribogreen quantification and quality control via Agilent BioAnalyzer, 0.5 to 1 ug of total RNA underwent stranded TruSeq library preparation according to the manufacturer's instructions (Illumina), with 6 cycles of PCR.
Samples were barcoded and run on a HiSeq 2000 in a 50bp/50bp paired-end run, using the TruSeq SBS Kit v3 (Illumina). An average of 69 million paired reads were generated per sample. Ribosomal reads represented at most 0.83% of total reads, while mRNA bases accounted for an average of 61% of reads.

tag: patient id

tag: patient age at resection

tag: patient sex

value: M


title: HT1080_MYC_ChIP-seq

value: Myc antibody (Cell Signaling Technology, 9402S)


title: MC19

source_name: normal liver


title: MC20

source_name: liver tumor


title: HT1080_shM_Pol_II_ChIP-seq

value: MYC shRNAs


title: MC3

source_name: mediastinal metastasis


title: MC8

source_name: recurrent liver tumor


title: MC9

source_name: lymph node metastasis


title: MC34

value: F


title: PPARD_ChIPSeq

source_name: Auricular-derived primary cartilage cells

tag: breed

value: Duroc x (Landrace x Large White)

value: 3 passage

value: PPAR-beta Antibody (H-74) X (Santa Cruz)


title: MC32


title: MC33


title: MC27


title: MC41


title: MC42


title: MC30


title: MC22


title: MC11


title: MC25


title: HT1080_Input

value: none (input)


title: MC10


title: HT1080_Menin_ChIP-seq

value: Menin antibody (Bethyl lab, A300-105A)


title: MC6

source_name: omental metastasis


title: MC24


title: MC7


title: MC14


title: MC35


title: MC36


title: MC39


title: MC18


title: MC21


title: MC16


title: MC17


title: MC38


title: MC40


title: MC5


title: MC4


title: MC28


title: alg-5(ram2) mutant

city: FORT COLLINS

first: Taiowa

last: Montgomery

state: CO

address: 1878 Campus Delivery

institute: Colorado State University

description: small RNA

data_processing:
Reads were parsed from adapter sequeces and filtered for low-quality (Q<30) sequences using CASHX v2.3.
Reads were aligned to the C. elegans genome (WS230) using CASHX v.2.3.
Data processing, quality assessment, and analysis were done using custom scripts in Python and R. miRNA annotations were based on miRBase release 20. Mutator class siRNA annotation was based on (Phillips et al 2012) . CSR-1 class siRNA annotation was based on (Claycomb et al 2009). piRNA annotation was based on WormBase release WS230. New miRNAs were identified using miRDeep2.
Excel spreadsheet containing library-size normalized reads (RPM) as determined by CASHX 2.3.
Base calling and fastq files were generated using Illumina software.
Other data processing steps added to SAMPLES section.
Genome_build: WS230
Supplementary_files_format_and_content: Spreadsheet of CuffDiff estimated abundances (FPKM) for each gene (mRNA_counts.xlsx) or CASHx abundances (RPM) for each small RNA (smRNA_counts.xlsx)

organism: Caenorhabditis elegans

source_name: Whole worm cell lysate, Late L4

growth_protocol: Animals were grown on NGM plates seeded with E. coli strain OP50 at 20˚C for 68h (gravid adult) or 49h (L4) post L1 synchronization. alg-1(gk214) reps 1-3 were stage matched by collecting worms at 53 hours for mRNA sequencing.

extract_protocol: Total RNA was extracted from whole worm lysates using Trizol followed by two chloroform extractions and isopropanol precipitation.

treatment_protocol: Animals were flash frozen in liquid nitrogen and lysed in 50 mM Tris-Cl, pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igepal CA-630, 0.5 mM PMSF, and 1X Proteinase Inhibitor (Life Technologies, 88266). Cell debris was removed by centrifugation and cell lysates were either collected for RNA extraction (input fraction) or incubated with anti-HA affinity matrix (Roche, 11815016001) or anti-GFP mAb-agarose (MBL, D153-8) for 1 hr (immunoprecipitate) and washed 4x with lysis buffer prior to RNA isolation.

tag: genotype

value: alg-5(ram-2) I

tag: barcode

value: TTAGGC

value: Small RNAs (18-28-nt) were purified from total RNA by size selection using 17% polyacrylamide gels and treated with RNA polyphosphatase or Tobacco Alkaline Phosphatase to facilitate capture of 22G-RNAs, followed by ligation of preadenylated 3’ adapters and non-adenylated 5’ adapters. Adapter-ligated small RNAs were size selected at each ligation step from 12-15% polyacrylamide gels. Adapter-bound small RNAs were reverse transcribed and then amplified using PCR. PCR products (~136-146 bp) were size selected from 10% polyacrylamide gels


title: Wild type exp 4

description: small RNA

value: ATCACG


title: Wild type exp 3

description: small RNA

source_name: Whole worm cell lysate, Gravid Adult

value: ACAGTG


title: alg-5(tm1163) mutant

description: small RNA

value: CAGATC


title: GFP::ALG-5 input fraction

description: small RNA

value: alg-5(ram-1[GFP::3xFLAG::alg-5 + loxP]) I

value: CGATGT


title: HA::ALG-5 input fraction

description: small RNA


title: Wild type exp 2

description: small RNA


title: ALG-1::HA::ALG-2 immunoprecipitate

description: small RNA

value: alg-1::HA::alg-2 IV; alg-1(gk214) X

value: TGACCA


title: alg-1(gk214) mutant

description: small RNA

value: TAGCTT


title: HA::ALG-2 immunoprecipitate

description: small RNA

value: alg-2(ok304) II; alg-2::HA::alg-2 IV


title: alg-2(ok304) mutant

description: small RNA

value: alg-2(ok304) II

value: GGCTAC


title: MC26

value: M


title: dnBrd4_f9_rep5

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description:
raw_feature_counts.txt
f9-5

data_processing:
Adapters were trimmed from sequencing reads using cutadapt.
Reads were mapped to the human reference genome GRCh38 as well as rRNA sequences using ContextMap 2.
Read counts per gene were determined using featureCounts on the Ensembl gene annotation (release 84). Reads were assigned to a gene if they overlapped with an exon of the gene by at least 25 nt and mapped uniquely to that gene.
Genes were included in downstream analyses if the average read count across all samples was ≥25.
Differential expression analysis for each condition against the control was performed with limma, edgeR and DESeq2. Multiple testing correction was performed using the Benjamini–Hochberg method.Genes were selected for further analysis if they were identified as differentially expressed by at least two of the three methods (multiple testing corrected p-value ≤0.05).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-separated text-file containing raw read counts for each gene (rows) in each sample (columns)

molecule: polyA RNA

source_name: Bukitt lymphoma

growth_protocol: Raji cells were routinely cultured at a cell densitiy of 4*105 to 1*106 cells per mL in T75 flasks using RPMI1640 medium (Gibco, Life Technologies) supplemented with 10 % fetal calf serum, 2 mM L-glutamine (Gibco, Life Technologies), and 1% penicillin streptomycin (Gibco, Life Technologies) at 37°C, 5 % CO2.

extract_protocol:
24 hours after induction/JQ1 treatment, 3*106 cells were washed twice in DPBS (Gibco, Life Technologies), resuspended in 1.5 mL TRIzol reagent (Ambient, Life Technologies) and short-term stored at -80 °C until library preparation. Total RNA was isolated using the Direct-zol kit (Zymo research)
1 µg of total RNA was used for preparation of Illumina-compatible strand-specific cDNA (RNA-seq) libraries using the mRNA-SENSE kit from Lexogen (Vienna). Briefly, polyA RNA was bound to oligo dT beads, starter and stopper heterodimer oligos were annealed to captured mRNA. Starter oligos served as primer for cDNA Synthesis which continued until stopper. Stopped cDNA and stopper were ligated to yield a cDNA fragment that is flanked by Illumina P5 and P7 sequences. This was followed by PCR amplification, which introduced barcodes and adaptor sequences to the libraries. PCR products were purified with Apure XP beads (Beckman-Coulter), followed by quantification and quality control with Agilent BioAnalyzer 2100 using a DNA 1500 chip.

treatment_protocol: pRTS-1 vector-driven expression was induced with 25 ng/ml doxycycline for 24 h.

value: RAJI

tag: expression vector

tag: treatment


title: dnBrd4_f9_rep3

description:
raw_feature_counts.txt
f9-3


title: dnBrd4_f9_rep4

description:
raw_feature_counts.txt
f9-4


title: Wild type exp 1

description: small RNA


title: HA::ALG-1 input fraction

description: small RNA

value: alg-1::HA::alg-1 IV; alg-1(gk214) X

value: ACTTGA


title: dnBrd4_f9_rep1

description:
raw_feature_counts.txt
f9-1


title: HA::ALG-5 immunoprecipitate

description: small RNA


title: N7103 rep 4 Caswell

city: Raleigh

first: Earl

middle: William

last: Taliercio

state: NC

address: 3127 Ligon St

institute: USDA/ARS

description: Sample 60

data_processing:
bcl2fastq2 for base calling
trimmed primers with fastQ quality trimmer
removed low quality sequences with phred score less than 34 with fastQ quality trimmer
validated trimmed sequences with FastQC
Used tophat to align to reference soybean genome
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: text files with Cufflinks output.

organism: Glycine max

source_name: leaf

growth_protocol: Field grown in NC in 2015

extract_protocol:
qiagen RNA extraction with on column DNAse digestion
New England Biolabs rna kits

value: recurrent  G. max parent

tag: tissue

value: leaf

tag: location

value: Caswell


title: dnBrd4_f9_rep2

description:
raw_feature_counts.txt
f9-2


title: GFP::ALG-5 immunoprecipitate

description: small RNA

value: Small RNAs (18-28-nt) were purified from total RNA by size selection using 17% polyacrylamide gels and treated with RNA polyphosphatase or Tobacco Alkaline Phosphatase to facilitate capture of 22G-RNAs, followed by ligation of preadenylated 3’ adapters and non-adenylated 5’ adapters. Adapter-ligated small RNAs were size selected at each ligation step from 12-15% polyacrylamide gels. Adapter-bound small RNAs were reverse transcribed and then amplified using PCR. PCR products (~136-146 bp) were size selected from 10% polyacrylamide gels


title: dnBrd4_f3_rep5

description:
raw_feature_counts.txt
f3-5


title: alg-5(ram2) mutant Rep 3

description: rRNA-depleted mRNA

data_processing:
Adapter sequences and low quality bases (4-base average Q of <30) were trimmed from mRNA sequences using Trimmomatic 0.35
Trimmed sequences were aligned to the C. elegans WS230 genome using TopHat2
Data processing and quality assessment were done using custom scripts in Python and R. Differentially regulated protein-coding genes were identified using CuffDiff2 and HTSeq-count followed by DESeq2. rRNA, tRNA, and mtRNA were masked from the analysis.
Excel spreadsheet containing normalized reads (FPKM) as determined by CuffDiff2
Base calling and fastq files were generated using Illumina software.
Other data processing steps added to SAMPLES section.
Genome_build: WS230
Supplementary_files_format_and_content: Spreadsheet of CuffDiff estimated abundances (FPKM) for each gene (mRNA_counts.xlsx) or CASHx abundances (RPM) for each small RNA (smRNA_counts.xlsx)

treatment_protocol: Whole worms were flash frozen in liquid nitrogen prior to extraction

value: alg-5(ram2) I

value: ATGTCA

value: RNA was depleted of rRNA using RiboZero and enriched for >200nt sizes with Zymo RNA clean and concentrator-5. RNA was then fragmented into 200-350 bp segments. Fragments were reverse transcribed using dUTP during second strand synthesis to preserve strand information. cDNA was dA-tailed, end repaired, and ligated to adapters, followed by PCR amplification. Size selection and library purification was done using AMPure XP beads.


title: alg-5(ram2) mutant Rep 1

description: rRNA-depleted mRNA

value: AGTCAA


title: N7103 rep 3 Caswell

description:
omitted from data analyses
Sample 59


title: dnBrd4_f3_rep4

description:
raw_feature_counts.txt
f3-4


title: HA::ALG-1 immunoprecipitate

description: small RNA

value: CGATGT


title: N7103 rep 2 Caswell

description: Sample 58


title: N7103 rep 1 Caswell

description: Sample 56


title: ALG-1::HA::ALG-2 input fraction

description: small RNA

value: alg-1::HA::alg-2 IV; alg-1(gk214) X

value: TAGCTT


title: alg-2(ok304) mutant Rep 2

description: rRNA-depleted mRNA

value: alg-2(ok304) II


title: dnBrd4_f3_rep1

description:
raw_feature_counts.txt
f3-1


title: dnBrd4_f3_rep3

description:
raw_feature_counts.txt
f3-3


title: HA::ALG-2 input fraction

description: small RNA

value: alg-2(ok304) II; alg-2::HA::alg-2 IV

value: GATCAG


title: NMS4-44-329 rep 4 Caswell

description: Sample 55

value: Parent with G soja in pedigree


title: dnBrd4_f3_rep2

description:
raw_feature_counts.txt
f3-2

value: RAJI


title: alg-1(gk214) mutant Rep 3

description: rRNA-depleted mRNA


title: alg-2(ok304) mutant Rep 1

description: rRNA-depleted mRNA


title: alg-5(ram2) mutant Rep 2

description: rRNA-depleted mRNA

value: AGTTCC


title: NMS4-44-329 rep 3 Caswell

description: Sample 54


title: NMS4-44-329 rep 2 Caswell

description: Sample 53


title: alg-1(gk214) mutant Rep 2

description: rRNA-depleted mRNA

value: ACTTGA


title: luc_JQ1_rep4

description:
raw_feature_counts.txt
JQ1-4

value: 500 nM JQ1


title: NMS4-44-329 rep 1 Caswell

description: Sample 52

value: leaf

value: Caswell


title: luc_JQ1_rep3

description:
raw_feature_counts.txt
JQ1-3


title: F1 hybrid rep 4 Caswell

description: Sample 50

value: F1 hybrid


title: alg-2(ok304) mutant Rep 3

description: rRNA-depleted mRNA

value: CTTGTA


title: luc_JQ1_rep2

description:
raw_feature_counts.txt
JQ1-2


title: alg-5(tm1163) mutant Rep 2

description: rRNA-depleted mRNA

value: ACAGTG

value: RNA was depleted of rRNA using RiboZero and enriched for >200nt sizes with Zymo RNA clean and concentrator-5. RNA was then fragmented into 200-350 bp segments. Fragments were reverse transcribed using dUTP during second strand synthesis to preserve strand information. cDNA was dA-tailed, end repaired, and ligated to adapters, followed by PCR amplification. Size selection and library purification was done using AMPure XP beads.


title: F1 hybrid rep 3 Caswell

description: Sample 49


title: luc_JQ1_rep1

description:
raw_feature_counts.txt
JQ1-1


title: F1 hybrid rep 2 Caswell

description: Sample 48


title: alg-5(tm1163) mutant Rep 1

description: rRNA-depleted mRNA

value: TGACCA


title: F1 hybrid rep 1 Caswell

description: Sample 46


title: Wild type Rep 2

description: rRNA-depleted mRNA

value: CGATGT


title: luc_DMSO_rep3

description:
raw_feature_counts.txt
Luc3

value: DMSO


title: N7103 rep 4 Clayton

description: Sample 45

value: recurrent  G. max parent

value: Clayton


title: luc_DMSO_rep4

description:
raw_feature_counts.txt
Luc4


title: Wild type Rep 1

description: rRNA-depleted mRNA

value: ATCACG


title: N7103 rep 3 Clayton

description: Sample 43


title: N7103 rep 2 Clayton

description: Sample 42


title: luc_DMSO_rep1

description:
raw_feature_counts.txt
Luc1


title: luc_DMSO_rep2

description:
raw_feature_counts.txt
Luc2


title: alg-1(gk214) mutant Rep 1

description: rRNA-depleted mRNA

value: CAGATC


title: luc_JQ1_rep5

description:
raw_feature_counts.txt
JQ1-5

value: RAJI


title: N7103 rep 1 Clayton

description: Sample 41


title: Bfl-1 C55S library resort round 5 (FL 5')

first: Amy

middle: E

last: Keating

state: Massachusetts

department: Biology and Biological Engineering

institute: Massachusetts Institute of Technology

description: DNA encoding BH3 peptide

data_processing:
The data was filtered for sequences with barcodes that had high Phred Scores (> 20).
Sequences were reconstructed by aligning pair end reads.
Sequences observed fewer than 20 times were removed from the data set.
Supplementary_files_format_and_content: .csv file with the peptide sequence (seq), BH3 background sequence (bg: P=PUMA, B=BIM), and read count (count)

molecule: other

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae EBY100

growth_protocol: The libraries were grown from glycerol stocks in selective media containing glucose (SD+CAA) at 30 °C to passage. To induce expression, cultured were diluted (40 mL inoculate/L) into selective media containing galactose (SG+CAA) for 16-24h at 30 °C.

extract_protocol:
The plasmid DNA from yeast was extracted using the Zymoprep Yeast Plasmid Miniprep II (Zymo Research) reagents and Qiagen miniprep columns.
The BH3 library was amplified with PCR using primers that encoded an MmeI restriction enzyme binding site at 5′ end and a universal Illumina sequencing region on the 3′ end. After purification with the Qiagen PCR purification kit, the PCR products were digested with MmeI for 1 h at 37 °C before being heat inactivated. Each digestion product was then ligated to double-stranded DNA fragments containing Illumina adapters, with the adapter containing a unique barcode.

tag: strain

tag: yeast display vector

value: pCT


title: Bfl-1 C55S library resort round 6 (FL 6')

description: DNA encoding BH3 peptide


title: alg-5(tm1163) mutant Rep 3

description: rRNA-depleted mRNA

value: GCCAAT


title: NMS4-44-329 rep 4 Clayton

description: Sample 40

value: Parent with G soja in pedigree


title: Bfl-1 library round 6 (FL 6)

description: DNA encoding BH3 peptide


title: Bfl-1 library round 5 (FL 5)

description: DNA encoding BH3 peptide


title: NMS4-44-329 rep 3 Clayton

description: Sample 39

value: leaf


title: Bfl-1 library round 4 (FL 4)

description: DNA encoding BH3 peptide


title: luc_DMSO_rep5

description:
raw_feature_counts.txt
Luc5


title: Isolation 1 (I1)

city: santiago

first: Romilio

middle: T

last: Espejo

state: REGIÓN METROPOLITANA

address: C Antunez 2243, providencia

country: Chile

institute: University of Chile

description: Grown 37ºC

data_processing:
Random selection to 19 million reads in each sample using ShortRead Bioconductor package (v1.32)
Filtration by removing adaptors and quality control of reads using BBDuk (v36.28)
Aligned using Burrows-Wheeler Aligner (BWA)(v0.7.15) and algorithm BWA-BackTrack.
Alignments were ordered by position in the reference genome using SAMtools (Li et al., 2009). Annotation of the V. parahaemolyticus RIMD2210633 genome was done using information in RefSeq (Pruitt et al., 2007) for ORF, tRNA, and rRNA, and BSRD (Li et al., 2013) for sRNA with a custom script.
Reads counting for each feature were determined using HTSeq-count (v0.6.0)
The differential expression analysis was performed using the DESeq2 package of Bioconductor (v1.14.1) (>3-fold, Padj <1 × 10−5)
Genome_build: NC_004603.1, NC_004605.1
Supplementary_files_format_and_content: read counts are contained in the files: E1_reads.count, E2_reads.count, E3_reads.count,I1_reads.count, I2_reads.count,I3_reads.count

organism: Vibrio parahaemolyticus

source_name: Vibrio parahaemolyticus_Isolation 1 (I1)

growth_protocol: The strain was grown in two conditions: A) LB, NaCl 3%, 12ºC and B) LB, NaCl 0.9%, bile salt 0.04%, 37ºC.

extract_protocol:
Total RNA was isolated from the pellet with Trizol Max Bacterial (ThermoFisher) according to the manufacturer’s protocol. The quantity of total RNA was determined by Nanodrop (Thermo Scientific) and Ribogreen (QuantiFluor), and quality and  integrity of the RNA was determined by electrophoresis in the Bioanalyzer (Agilent  Technologies). Yield of RNA per optical density was 0.6-times lower in condition A than  condition B. RNA integrity (RIN) was higher than 7.8 in all RNA samples. No differences  in the electrophoretic patterns of the RNA in the two conditions were evident.
Libraries prepared following the TruSeq Stranded mRNA Sample Preparation Guide (Part no. 15031047, Rev. E October 2013), following the low sample protocol (LS) but bypassing the mRNA purification. protocol (LS) but bypassing the mRNA purification. The following barcodes were used: sample I1, AR013 - AGTCAA(C); sample I2, AR014 - AGTTCC(G); sample I3, AR015- ATGTCA(G); sample E1, AR016 - CCGTCC(C); sample E2, AR018 - GTCCGC(A);sample E3, AR019 - GTGAAA(C)

treatment_protocol: Bacteria were collected by centrifugation from three parallel independent cultures for both conditions. Cultures were harvested in exponential phase at an OD600 of1.0 and rinsed once with PBS.

value: VpKx

tag: country source

value: Japan

tag: growth phase

value: Exponential phase

tag: growth temperature


title: Wild type Rep 3

description: rRNA-depleted mRNA

value: TTAGGC


title: NMS4-44-329 rep 2 Clayton

description: Sample 38


title: Isolation 2 (I2)

description: Grown 37ºC

source_name: Vibrio parahaemolyticus_Isolation 2 (I2)


title: Bfl-1 library round 3 (FL 3)

description: DNA encoding BH3 peptide


title: Isolation 3 (I3)

description: Grown 37ºC

source_name: Vibrio parahaemolyticus_Isolation 3 (I3)


title: Environmental 2 (E2)

description: Grown 12ºC

source_name: Vibrio parahaemolyticus_Environmental 2 (E2)


title: NMS4-44-329 rep 1 Clayton

description:
omitted from data analyses
Sample 36


title: naïve library pool

description: DNA encoding BH3 peptide


title: HT1080_shMEN1_RNA-seq

source_name: Human fibrosarcoma HT1080 cells

tag: cell line

tag: cell type

value: Human fibrosarcoma cells

value: MEN1 shRNAs


title: F1 hybrid rep 3 Clayton

description: Sample 33

value: F1 hybrid


title: F1 hybrid rep 1 Clayton

description: Sample 31


title: HT1080_NTC_RNA-seq

tag: transfected with

value: non-targeting control shRNA


title: HT1080_shMYC_RNA-seq

value: MYC shRNAs


title: F1 hybrid rep 2 Clayton

description: Sample 32

value: Clayton


title: 2_8__C

status: Public on Jun 08 2017

city: New York

first: Rohit

last: Bose

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The output data (FASTQ files) were mapped to the target genome using the rnaStar aligner
The 2 pass mapping method47 was used in which the reads were mapped twice
The first mapping pass used a list of known annotated junctions from Ensemble. Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was done (on the second pass the RemoveNoncanonical flag is used)
post-processed the output SAM files using the PICARD tools to: add read groups, AddOrReplaceReadGroups which sorts the file and converts it to the compressed BAM format.
computed the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq)
The raw count matrix generated by HTSeq was then processed using the R/Bioconductor package DESeq48 (www-huber.embl.de/users/anders/DESeq), which was used to both normalize the full dataset
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited text files include DESeq values for each Sample

extract_protocol:
Cell RNA extraction via RNAeasy Qiagen kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: lentivirus

value: shNT

tag: dht


title: 2_7__C


title: 2_10_D

value: shERF


title: 2_6__B


title: 2_4__B


title: 2_2__A


title: 2_3__A


title: 2_9__C


title: INPUT for AR and ERG

data_processing:
The reads were aligned to the human genome (hg19) using the program BWA (default parameters) within the PEMapper
analysed by the software MACS2 (-q 0.1) for peak identification with data from ChIP input DNAs as controls
Genome_build: HG19
Supplementary_files_format_and_content: BED files

source_name: VCaP

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols by MSKCC Integrated Genomics Operation core

value: VCaP

tag: doxycycline

tag: chip antibody

value: none (input)


title: Environmental 3 (E3)

description: Grown 12ºC

source_name: Vibrio parahaemolyticus_Environmental 3 (E3)


title: 2_12_D


title: F1 hybrid rep 4 Clayton

description: Sample 35

tag: genotype


title: 2_5__B


title: MC15

tag: patient id

tag: patient age at resection

tag: patient sex

value: M


title: Environmental 1 (E1)

description: Grown 12ºC

source_name: Vibrio parahaemolyticus_Environmental 1 (E1)


title: INPUT green replicate one


title: VCaP red replicate two


title: AR ChIP-seq


title: VCaP red replicate one


title: INPUT red replicate two


title: VCaP green replicate two


title: VCaP green replicate one


title: WT-AST

city: 上海

first: Bo

last: Jing

state: 上海

address: 同济大学医学院713

institute: 同济大学医学院

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: ftp://www.icugi.org/pub/genome/cucumber/Chinese_long/v2/cucumber_ChineseLong_v2_genome.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Astrocytes

growth_protocol: Astrocytes were cultured with DMEM plus 10%FBS, and identified by GFAP immunofluorescence staining；NSC were cultured as neurospheres with DMEM/F12 plus N2 supplements, and identified by sox2/nestin immunofluorescence staining.

extract_protocol:
Cultured medium was removed, cells were washed twice with PBS, and RNA was harvested using Trizol reagent. RNA library prep kit for Illumina (NEB.Cat#E7530S) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Cortex

tag: age

value: 10 weeks

tag: genotype/variation

value: wild type


title: GFPplus3_ATAC-seq

city: Worcester

first: Nathan

middle: D.

last: Lawson

address: 364 Plantation Street

department: Molecular, Cell, and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
basecalls were made with standard Illumina HiSeq 1000 pipeline to generate fastq files
for mapping adapters were removed using cutadapt (v1.3) and bowtie2 (v2.1.0) was used for read alignment to Zv9 with default settings except -X 2000
bigwig files were generated from bowtie2 output (BAM files) using the bamcoverage command in deeptools
Peaks were called using MACS2.1.0 callpeak  -g 1.35e9 --qvalue 0.05 --bw 250 --mfold 10 30
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: bigwig files contain density plots of sequence reads across the genome for each sample.  narrowPeak files are output from MACS2 and contain areas of enrichment for ATAC-Seq reads for each sample; these files are in BED format and can be directly uploaded to UCSC for visualization.

organism: Danio rerio

source_name: endothelial cells

growth_protocol: Tg(fli1a:egfp) embryos were grown to 24 hours post fertiilization

extract_protocol:
Nuclei were isolated by gentle douncing of deyolked embryos.  Nuclei were washed and filtered to remove debris, followed by separation by fluorescence activated cell sorting.  Both GFP-plus and GFP-minus nuclei were collected for ATAC-Seq
20,000 nuclei for each sample were subjected to transposase treatment (Illumina) to insert adapters into open chromatin.  Libraries of insertions were amplified using bar-coded Nextera adapters (Illumina)

tag: strain

tag: developmental stage

value: 24 hours post fertilization

value: endothelial cells


title: S89G-AST


title: GFPminus2_ATAC-seq

source_name: non-endothelial cells

value: non-endothelial cells


title: GFPminus1_ATAC-seq


title: NC-Roy_RNA-seq

city: Athens

first: Scott

middle: A.

last: Jackson

state: Georgia

address: 111 Riverbend Rd.

department: Center for Applied Genetic Technologies

institute: University of Georgia

source_name: leaves

extract_protocol:
Tissue was flash frozen in liquid nitrogen and RNA was isolated using TRIzol (Thermo Scientific, Waltham, MA) following the manufacturer’s instructions.
RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.

value: leaves

value: V2 (18 days old)

tag: cultivar

value: NC-Roy


title: Gasoy 17_RNA-seq

value: Gasoy 17


title: Davis_RNA-seq

value: Davis


title: Pickett_RNA-seq

value: Pickett


title: GFPplus1_ATAC-seq


title: GFPplus2_ATAC-seq


title: NC-Raleigh_RNA-seq

value: NC-Raleigh


title: Holladay_RNA-seq

value: Holladay


title: GFPminus3_ATAC-seq


title: INPUT green replicate two

tag: cell line

value: VCaP


title: 5601T_RNA-seq


title: PI 88.788_RNA-seq


title: Centennial_RNA-seq

value: Centennial


title: Brim_RNA-seq

value: Brim


title: Ransom_RNA-seq

value: Ransom


title: Hill_RNA-seq

value: Hill


title: Hood_RNA-seq

value: Hood


title: Woodworth_RNA-seq

value: Woodworth


title: Dare_RNA-seq

value: Dare


title: Jackson_RNA-seq

value: Jackson


title: Zane_RNA-seq

value: leaves

value: Zane


title: Wayne_RNA-seq

value: V2 (18 days old)

value: Wayne


title: Tracy_RNA-seq

value: Tracy


title: Williams_RNA-seq

value: Williams


title: Perry_RNA-seq

value: Perry


title: Kent_RNA-seq

value: Kent


title: Shelby_RNA-seq

value: Shelby


title: Harosoy_RNA-seq

value: Harosoy


title: Harcor_RNA-seq

value: Harcor


title: Hawkeye_RNA-seq

value: Hawkeye


title: Ford_RNA-seq

value: Ford


title: Merit_RNA-seq

value: Merit


title: Corsoy_RNA-seq

value: Corsoy


title: Douglas_RNA-seq

value: Douglas


title: Clark_RNA-seq

value: Clark


title: Oakland_RNA-seq

value: leaves

value: Oakland


title: Cumberland_RNA-seq

value: V2 (18 days old)

value: Cumberland


title: Calland_RNA-seq

value: Calland


title: Pella_RNA-seq

value: Pella


title: Chippewa_RNA-seq

value: Chippewa


title: Century_RNA-seq

value: Century


title: Bonus_RNA-seq

value: Bonus


title: S-100_RNA-seq


title: Blackhawk_RNA-seq

value: Blackhawk


title: Roanoke_RNA-seq

value: Roanoke


title: Tokyo_RNA-seq

value: Tokyo


title: Beeson_RNA-seq

value: Beeson


title: Ogden_RNA-seq

value: Ogden


title: Amcor_RNA-seq

value: Amcor


title: Ralsoy_RNA-seq

value: Ralsoy


title: Mandarin_RNA-seq

value: Mandarin


title: Haberlandt_RNA-seq

value: leaves

value: Haberlandt


title: Richland_RNA-seq

value: V2 (18 days old)

value: Richland


title: Korean_RNA-seq

value: Korean


title: Mukden_RNA-seq

value: Mukden


title: Kanro_RNA-seq

value: Kanro


title: Illini_RNA-seq

value: Illini


title: Williams 82_RNA-seq

value: Williams 82


title: Anderson_RNA-seq

value: Anderson


title: Lawrence_RNA-seq

value: Lawrence


title: A.K. (Harrow)_RNA-seq

value: A.K. (Harrow)


title: Dunfield_RNA-seq

value: Dunfield


title: Capital_RNA-seq

value: Capital


title: PI 518.751_RNA-seq


title: PI 507.681B_RNA-seq


title: PI 561.370_RNA-seq


title: PI 574.486_RNA-seq


title: PI 398.881_RNA-seq


title: LG00-3377_RNA-seq


title: LG98-1605_RNA-seq


title: PI 437.169B_RNA-seq


title: LG04-6000_RNA-seq


title: 2_11_D

value: shERF


title: Lincoln_RNA-seq

value: Lincoln


title: 2_1__A

value: shNT


title: LG97-7012_RNA-seq

value: leaves


title: LG94-1906_RNA-seq


title: LG90-2550_RNA-seq


title: LG94-1128_RNA-seq


title: ERG ChIP-seq

value: VCaP

value: anti-ERG (ab92513)


title: LG05-4464_RNA-seq

value: V2 (18 days old)


title: LG05-4832_RNA-seq


title: PI 404.188A_RNA-seq


title: LG92-1255_RNA-seq


title: PI 427.136_RNA-seq


title: Young_RNA-seq

value: Young


title: WT-NSC-Trip2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm38.84 whole genome using HISAT2 with parameters -p 8 -dta
Genes expression level is quantified by a software package called Stringtie.
Reads aligned to genes were calculated using featurecounts.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Read count and TPM (Transcripts Per Kilobase Million) for each Sample

source_name: Neural stem cells

value: Sub-ventrical zone

value: 10 weeks

value: wild type


title: LG03-3191_RNA-seq


title: U03-100612_RNA-seq


title: Skylla_RNA-seq

value: Skylla


title: NE3001_RNA-seq


title: LG04-4717_RNA-seq


title: WT-NSC-Trip1


title: LG05-4292_RNA-seq


title: S89G-NSC-Trip3


title: LG03-2979_RNA-seq


title: WT-NSC-Trip3


title: S06-13640_RNA-seq


title: S89G-NSC-Trip1


title: S89G-NSC-Trip2

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm38.84 whole genome using HISAT2 with parameters -p 8 -dta
Genes expression level is quantified by a software package called Stringtie.
Reads aligned to genes were calculated using featurecounts.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Read count and TPM (Transcripts Per Kilobase Million) for each Sample


title: Maverick_RNA-seq

value: Maverick


title: Magellan_RNA-seq

value: Magellan


title: INPUT mouse red replicate 1

data_processing:
The reads were aligned to the mouse genome (mm10) using the program BWA (default parameters) within the PEMapper
analysed by the software MACS2 (-q 0.1) for peak identification with data from ChIP input DNAs as controls
Genome_build: mm10
Supplementary_files_format_and_content: BED files

source_name: normal murine prostate organoids

value: normal murine prostate organoids


title: INPUT mouse green replicate 2


title: LG05-4317_RNA-seq


title: LD02-9050_RNA-seq


title: LD00-3309_RNA-seq


title: mouse red replicate 2


title: LD02-4485_RNA-seq


title: mouse red replicate 1


title: LD01-5907_RNA-seq


title: mouse green replicate 2


title: HS6-3976_RNA-seq


title: Prohio_RNA-seq

value: Prohio


title: 5M20-2-5-2_RNA-seq


title: CL0J173-6-8_RNA-seq


title: INPUT mouse red replicate 2


title: CL0J095-4-6_RNA-seq


title: 18HPL_HBC_1

city: Boston

first: Brian

last: Lin

address: 136 Harrison Avenue

department: DMCB

institute: Tufts University

description: 18HPL injured HBCs

data_processing:
Demultiplexed reads are FASTQC trimmed
Mapped using Tophat for Illumina 1.5.0
Differential gene expression using Cuffdiff
Genome_build: MM9
Supplementary_files_format_and_content: csv

source_name: 18HPL Mouse Olfactory Epithelium

extract_protocol:
Cells were dissociated from donor animals anaesthetized with IP injection of a triple cocktail of ketamine (37.5 mg/kg), xylazine (7.5 mg/kg), and acepromazine (1.25 mg/kg) and perfused with cold Low Ca2+ Ringers solution (140mM NaCl, 5mM KCl, 10mM HEPES, 1mM EDTA, 10mM glucose, 1mM sodium pyruvate, pH7.2). The olfactory epithelium is isolated away from respiratory tissue, finely minced, and incubated in 0.05% Trypsin-EDTA for 10 minutes on an orbital shaker at 37°C where it forms a sticky ball. The supernatant was replaced with an enzyme cocktail containing (100 U/ml collagenase, 250 U/ml hyaluronidase, 75 U/ml DNase I, 0.1 mg/ml trypsin inhibitor, 2.5 U/ml Dispase II, 350 U/ml Collagenase Type I, 5U/ml papain; from Worthington Biochemical, Roche, and Sigma) in Regular Ringers solution (140mM NaCl, 5mM KCl, 10mM HEPES, 1mM EDTA, 10mM glucose, 1mM sodium pyruvate, 1mM CaCl2, 1mM MgCl2, pH7.2). The tissue was incubated in the enzyme cocktail on an orbital shaker at 37°C for 15 minutes, after which the supernatant was replaced with fresh enzyme cocktail and incubated once again for 15 minutes. The supernatant is stored on ice in the meantime. After the second incubation, the pooled supernatant is filtered through 30 µm filter and centrifuged at <500g on a swinging bucket rotor for 5 minutes. The pellet is resuspended in 1x HBSS containing 25 mM HEPES, 10 mM EDTA for FACS purification based on TdTomato positivity.
Libraries were generated using standard Illumina Nextera XT protocols

treatment_protocol: injured mice were exposed to 180 ppm MeBr gas for 8 hours, then tissue was harvested 18 hours later

value: Olfactory Epithelium

tag: cell type

value: Horizontal basal cell (HBC)

value: B6;KRT5-CreER;Ai9 fl(Stop)TdTomato

value: 12 wk


title: 4J105-3-4_RNA-seq

value: leaves


title: hPGC.D2.SB.2

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

description: Day 2 NANOS3-tdTomato+ve hPGC induced from hPSC with SOX17/BLIMP1 rep.2

data_processing:
Adapter-and quality-trimmed RNA-seq reads were mapped to the human reference genomes (UCSC GRCh37/hg19) using TopHat2 (http://ccb.jhu.edu/software/tophat, version: 2.0.13) guided by ENSEMBL 83 gene models. Raw counts per transcripts were obtained using featureCounts, only the longest transcript per gene was kept. Replicates were evaluated, raw counts were normalized, and the differential expression of transcripts was statistically evaluated by the R Bioconductor DESeq2 package (www.bioconductor.org). Expression-normalized transcript counts were further normalized by transcript length (per kB). Transcript annotations in all bioinformatics analyses were based on ENSEMBL (Release 83) considering protein coding, long-noncoding RNA and processed transcripts. Hierarchical clustering was performed with the R hclust function using the Ward’s method. Principal components were computed by singular value decomposition with the R princomp functioned on scaled DESeq-normalized expression levels. Only the 80% most highly expressed transcripts were used for clustering and principal component analysis.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Processed data files contain raw counts per ENSEMBL transcript obtained using 'featureCounts'

source_name: hPGC derived from hPSC

growth_protocol: Undifferentiated Comp-hPSC were maintained on irradiated mouse embryonic fibroblast (MEF) (purchased from MTI-GlobalStem or prepared in house) in knockout DMEM (Thermo Fisher Scientific) supplemented with 20% KSR, 0.1 mM NEAA, 0.1 mM 2-mercaptoethanol, 100 U/ml Penicillin- 0.1 mg/ml Streptomycin, 2 mM L-Glutamine, 20 ng/ml human LIF (Stem Cell Institute, university of Cambridge (SCI)), 8 ng/ml bFGF (SCI), 1 ng/ml TGF-b1 (Peprotech), 3 M GSK3i (CHIR99021,Miltenyi Biotec), 1 M ERKi (PD0325901,Miltenyi Biotec), 5 M p38i (SB203580,TOCRIS bioscience), and 5 M JNKi (SP600125, TOCRIS bioscience).  Cells were passed every 2-4 days using TrypLE express or 0.25% trypsin/EDTA (Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted from FACS sorted AP+ve hPSC or NANOS3-tdTomato+ve hPGC using PicoPure® RNA Isolation Kit (Thermo Fisher Scientific)
Total RNA (5 ng) was reverse transcribed and amplified into cDNA using Ovation RNA-Seq System V2 (Nugen). Amplified cDNA was sonicated into 250 bp by Covaris S220 Focused-ultrasonicators. Subsequently, RNASeq library was generated with 500 ng of fragmented cDNA using Ovation Rapid DR Multiplex System (Nugen). Library was quantified by qPCR using KAPA Library Quantification Kit (Kapa Biosystems).

value: hPGC like cell derived from human embryonic stem cell


title: hPGC.D2.SB.1

description: Day 2 NANOS3-tdTomato+ve hPGC induced from hPSC with SOX17/BLIMP1 rep.1


title: 18HPL_HBC_3

description: 18HPL injured HBCs


title: hPGC.D1.SB.2

description: Day 1 NANOS3-tdTomato+ve hPGC induced from hPSC with SOX17/BLIMP1 rep.2


title: hPGC.D1.SB.1

description: Day 1 NANOS3-tdTomato+ve hPGC induced from hPSC with SOX17/BLIMP1 rep.1


title: 18HPL_HBC_2

description: 18HPL injured HBCs


title: INPUT mouse green replicate 1


title: TN05-3027_RNA-seq


title: hPGC.D4.Cy.1

description: Day 4 NANOS3-tdTomato+ve hPGC induced from hPSC with cytokines rep.1


title: IA3023_RNA-seq


title: Nml_HBC_1

description: Uninjured HBCs

source_name: Nml Mouse Olfactory Epithelium


title: hPGC.D4.Cy.2

description: Day 4 NANOS3-tdTomato+ve hPGC induced from hPSC with cytokines rep.2


title: INPUT red replicate one

value: VCaP

value: none (input)


title: Nml_HBC_2

description: Uninjured HBCs


title: s_2m12_D

data_processing:
The output data (FASTQ files) were mapped to the target genome using the rnaStar aligner
The 2 pass mapping method47 was used in which the reads were mapped twice
The first mapping pass used a list of known annotated junctions from Ensemble. Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was done (on the second pass the RemoveNoncanonical flag is used)
post-processed the output SAM files using the PICARD tools to: add read groups, AddOrReplaceReadGroups which sorts the file and converts it to the compressed BAM format.
computed the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq)
The raw count matrix generated by HTSeq was then processed using the R/Bioconductor package DESeq48 (www-huber.embl.de/users/anders/DESeq), which was used to both normalize the full dataset
Genome_build: MM10
Supplementary_files_format_and_content: tab-delimited text files include DESeq values for each Sample

source_name: murine Pten+/+ prostate organoids

value: shERF


title: hPSC.SB.1

description: hPSC with inducible SOX17/BLIMP1 transgenes rep.1

source_name: hPSC

value: human embryonic stem cell

tag: culture condition

value: hPSC medium containing inhibitor(i)s (GSK3i, ERKi, p38i, JNKi)4 on MEF


title: hPSC.SB.2

description: hPSC with inducible SOX17/BLIMP1 transgenes rep.2


title: s_2m6_B

tag: lentivirus

value: shNT


title: 3225B3

city: Ottawa

first: Thien-Fah

last: Mah

state: ON

address: 451 Smyth Road

department: Biochemistry, Microbiology, and Immunology

country: Canada

institute: University of Ottawa

data_processing:
Base calls were made using the Illumina CASAVA pipeline.  Base quality is encoded in phred 33.
Read trimming and clipping was done with the Trimmomatic software (version 0.30) (reads trimmed from 3' end, Illumina sequencing adapters removed, and reads were required to have a length >32).
Reads were aligned to the Pseudomonas aeruginosa UCBPP-PA14 genome (http://pseudomonas.com/strain/show/109).  The alignment was performed with the combination of tophat (version 2.0.9) and bowtie (version 2.1.0) software.
Read counts were obtained using HTSeq.
Supplementary_files_format_and_content: Differential gene expression analysis was done using DESeq and edgeR R Bioconductor package with the HTSeq read counts as the input.

organism: Pseudomonas aeruginosa

source_name: Biofilm ΔPA3225

growth_protocol: Planktonic cells were grown 8hrs at 37oC and 250 rpm in 1x M63 supplemented with 0.4% arginine and 1 mM MgSO4 to an approximate OD600=0.65; Biofilms were grown by spotting overnight cultures on 1x M63 agar plates supplemented with 0.4% arginine and 1 mM MgSO4 at then incubating the plates at 37oC for 24 hours and then room temperature for 24 hours.

extract_protocol:
RNA from planktonic and biofilm cells was isolated using TriZOL reagent (Invitrogen) and the Purelink RNA Mini Kit (Invitrogen) as described by the manufacturer.  RNA preps were treated with Purelink DNaseI (Invitrogen) as required to remove DNA contamination.  RNA samples were submitted to the McGill University and Genome Quebec Innovation Centre for library construction.
The rRNA-depleted library was constructed for RNA-seq using the firststrand protocol.

value: UCBPP-PA14 deltaPA3225

tag: growth condition

value: biofilm


title: hPSC.2

description: NANOS3-tdTomato reporter hPSC rep.2


title: 3225B4


title: 3225B2


title: s_2m5_B


title: hPSC.1

description: NANOS3-tdTomato reporter hPSC rep.1


title: Nml_HBC_3

description: Uninjured HBCs


title: WTB6

source_name: Biofilm wild-type


title: RB24

tag: doxycycline

tag: lentivirus 2

tag: dht


title: Agarose purification [Custom_primer_N]

city: University Park

first: Zhao

last: SU

state: PA

address: 354 N. Frear

department: Biology

institute: The Penn State University

description:
Custom_primer_N
processed data file: All_info.xls

data_processing:
Library strategy: Structure-seq2
Trim 5' and 3' adapter using Cutadapt.
Bowtie2 mapping to rice genome and cDNA library.
Genome_build: ensemblgenomes_Oryza_sativa_release_31
Supplementary_files_format_and_content: All_info.xlsx: Raw read counts for each transcipt.

organism: Oryza sativa Japonica Group

source_name: Shoot

growth_protocol: Plants were germinated in a petri dish for 4-5 days, then transferred to potted soil for the remainder of 2 weeks.

extract_protocol:
Machery-Nagel NucleoSpin RNA Plant kit, and Thermo Fisher Scientific Poly(A) purist kit.
Standard Structure-seq2 protocol. Briefly, reverse transcription was performed with SuperScript III, followed by ligation and PCR. Specifics are included in the 'characteristics' field.

treatment_protocol: See the 'characteristics' field.

tag: subspecies

value: japonica

value: Nipponbare

value: shoot

value: 14 days

tag: treatment

value: -DMS

tag: rt denaturation

value: 90 °C with salt

tag: rt reaction

value: 55 °C

tag: biotin added

value: no

tag: rt purification

value: PAGE

tag: ligation method

value: T4 DNA ligase

tag: ligation purification

tag: pcr enzyme

tag: final purification

value: triple agarose

tag: sequencing primer

value: custom


title: WTB4

tag: strain


title: Low RT reactionTemp. [Custom_primer_M]

description:
Custom_primer_M
processed data file: All_info.xls

tag: cultivar

tag: tissue

tag: age

value: 50 °C


title: WTB3

tag: growth condition


title: 3225P6

description: planktonic_3225vsWT_Genes_DE_results.tsv

source_name: Planktonic ΔPA3225

value: planktonic


title: RB23

source_name: VCaP

tag: doxycycline

tag: lentivirus 2

value: shERF

tag: dht


title: RB21


title: Ex Taq DNA polymerase [Custom_primer_J]

description:
Custom_primer_J
processed data file: All_info.xls

tag: subspecies

tag: treatment

tag: rt denaturation

value: Ex Taq


title: 3225P5

value: UCBPP-PA14 deltaPA3225


title: RB20


title: Structure-seq2 Biotin variation (+DMS) Rep2 [Custom_primer_I]

description:
Custom_primer_I
processed data file: All_info.xls

value: japonica

value: +DMS

tag: rt reaction

tag: biotin added

value: yes

tag: rt purification

value: streptavidin


title: s_2m11_D

tag: lentivirus


title: 3225P4


title: RB19


title: WTP6

source_name: Planktonic wild-type


title: RB18

value: shNT


title: mouse green replicate 1

value: normal murine prostate organoids

tag: chip antibody


title: WTP5


title: Structure-seq2 Biotin variation (-DMS) Rep1 [Custom_primer_F]

description:
Custom_primer_F
processed data file: All_info.xls

value: Nipponbare

value: shoot

value: 14 days

value: -DMS

value: 90 °C with salt

value: 55 °C

tag: ligation method

tag: ligation purification

tag: pcr enzyme

tag: final purification

tag: sequencing primer


title: RB17


title: Structure-seq2 Biotin variation (-DMS) Rep2 [Custom_primer_G]

description:
Custom_primer_G
processed data file: All_info.xls

tag: cultivar

tag: tissue

tag: age

value: T4 DNA ligase

value: PAGE

value: custom


title: RB16

tag: doxycycline

tag: lentivirus 2

tag: dht


title: Biotin only [Custom_primer_E]

description:
Custom_primer_E
processed data file: All_info.xls

tag: subspecies

tag: treatment

tag: rt denaturation


title: RB15


title: Structure-seq2 (+DMS) Rep2 [Custom_primer_D]

description:
Custom_primer_D
processed data file: All_info.xls

tag: rt reaction

tag: biotin added

value: no

tag: rt purification


title: RB22

value: shERF


title: RB14


title: Structure-seq2 (+DMS) Rep1 [Custom_primer_C]

description:
Custom_primer_C
processed data file: All_info.xls

value: japonica

tag: ligation method


title: Low RT denaturationTemp. [Custom_primer_L]

description:
Custom_primer_L
processed data file: All_info.xls

value: 65 °C without salt

tag: ligation purification


title: RB13


title: RB12


title: RB11


title: Structure-seq2 (-DMS) Rep1 [Custom_primer_A]

description:
Custom_primer_A
processed data file: All_info.xls

tag: pcr enzyme


title: Structure-seq2 Biotin variation (+DMS) Rep1 [Custom_primer_H]

description:
Custom_primer_H
processed data file: All_info.xls

value: +DMS

value: yes

tag: final purification


title: Low RT reactionTemp. [Standard_primer_M]

description:
Standard_primer_M
processed data file: All_info.xls

value: 50 °C

tag: sequencing primer

value: standard


title: RB9


title: RB8


title: Low RT denaturationTemp. [Standard_primer_L]

description:
Standard_primer_L
processed data file: All_info.xls

tag: cultivar

value: Nipponbare


title: LW3

city: Beijing

first: Liyuan

last: Wang

state: China

address: No.2 of Yuanmingyuan West Road, Haidian District

department: Animal Sciencie and Technology

institute: China Agricultura University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using CLC Genomics Workbench(version:4.8)
Clean reads were aligned onto the whole reference genome (Sus scrofa 10.2)  using TopHat
The number of fragments per kilobase of exon length million mapped reads (FPKM) analyzed by Cufflink (version 2.1.2) was used as the value of the normalized gene expression.
Genome_build: Sus scrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for TP WJ LW

source_name: Embryonic longissimus dorsi muscle of pig

extract_protocol:
Longissimus dorsi muscle were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TruSeq RNA Sample Preparation Guide (Part#15008136 Rev.A, Illumina)  was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Large White pig

tag: breed type

value: introduced pig breed

tag: developmental stage

value: embryonic

tag: tissue

value: Longissimus dorsi muscle


title: LW2


title: LW1


title: Circligase [Standard_primer_K]

description:
Standard_primer_K
processed data file: All_info.xls

value: shoot

tag: age

value: 14 days

value: -DMS

value: 90 °C with salt

value: 55 °C

value: Circligase


title: RB7

tag: doxycycline

tag: lentivirus 2

value: shERF

tag: dht


title: WTP4

tag: strain

tag: growth condition

value: planktonic


title: FD_female_3

city: Bonn

first: Kristin

middle: Simone

last: Henzel

address: Ludwig-Erhard-Allee 2

institute: German Center for Neurodegenerative Diseases (DZNE)

description: F1 offspring of dams fed a diet containing 40 mg folic acid/ kg diet before conception

data_processing:
Reads were adapter and quality trimmed (phred threshold of 5)
Trimmed reads were aligned with STAR
featureCounts was used with the ensembl annotation to generate counts
Genome_build: GRCm38
Supplementary_files_format_and_content: TSV, ensembl ids and counts

source_name: Hippocampus

extract_protocol:
Hippocampi were removed and flash-frozen in liquid nitrogen. RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: hippocampus

value: 129S6/SvEv x C57BL/6J

tag: genotype

value: wildtype

value: 14 weeks

tag: Sex

value: female


title: Ex Taq DNA polymerase [Standard_primer_J]

description:
Standard_primer_J
processed data file: All_info.xls

tag: subspecies

value: japonica

value: Nipponbare

tag: treatment

tag: rt denaturation

tag: rt reaction

tag: biotin added

value: no

tag: rt purification

value: PAGE

tag: ligation method

value: T4 DNA ligase

tag: ligation purification

value: Ex Taq

value: standard


title: FD_male_2

tag: tissue

value: male


title: RB6

value: shNT


title: Structure-seq2 Biotin variation (+DMS) Rep1 [Standard_primer_H]

description:
Standard_primer_H
processed data file: All_info.xls

tag: cultivar

value: shoot

tag: age

value: 14 days

value: +DMS

value: 90 °C with salt

value: 55 °C

value: yes

value: streptavidin

tag: pcr enzyme

tag: final purification

tag: sequencing primer


title: WJ1

tag: breed

value: Wujin pig

tag: breed type

value: indigenous Chinese pig breed

tag: developmental stage

value: embryonic

value: Longissimus dorsi muscle


title: Structure-seq2 Biotin variation (+DMS) Rep2 [Standard_primer_I]

description:
Standard_primer_I
processed data file: All_info.xls

tag: subspecies

value: japonica

value: Nipponbare

value: PAGE


title: Structure-seq2 (-DMS) Rep2 [Custom_primer_B]

description:
Custom_primer_B
processed data file: All_info.xls

tag: treatment

value: -DMS

value: no

value: T4 DNA ligase

value: custom


title: RB5

tag: doxycycline

tag: lentivirus 2

value: shNT

tag: dht


title: FD_male_1

value: hippocampus

tag: strain

value: 129S6/SvEv x C57BL/6J

tag: genotype

value: wildtype

value: 14 weeks

tag: Sex

value: male


title: RB10

value: shERF


title: Agarose purification [Standard_primer_N]

description:
Standard_primer_N
processed data file: All_info.xls

tag: tissue

value: shoot

value: 14 days

tag: rt denaturation

value: 90 °C with salt

tag: rt reaction

value: 55 °C

tag: biotin added

tag: rt purification

tag: ligation method

tag: ligation purification

value: triple agarose

value: standard


title: TP3

tag: breed

value: Tibetan pig

tag: breed type

value: indigenous Chinese pig breed

value: embryonic

value: Longissimus dorsi muscle


title: FD_female_1

tag: age

value: female


title: RB3

value: shNT


title: RB4


title: Structure-seq2 Biotin variation (-DMS) Rep2 [Standard_primer_G]

description:
Standard_primer_G
processed data file: All_info.xls

tag: subspecies

value: japonica

tag: cultivar

value: Nipponbare

tag: treatment

value: -DMS

value: yes

value: streptavidin

value: T4 DNA ligase

tag: pcr enzyme

tag: final purification

value: PAGE

tag: sequencing primer


title: TP2

tag: developmental stage


title: Structure-seq2 Biotin variation (-DMS) Rep1 [Standard_primer_F]

description:
Standard_primer_F
processed data file: All_info.xls

tag: tissue

value: shoot

value: 14 days

value: 90 °C with salt


title: RB2

tag: doxycycline

tag: lentivirus 2

tag: dht


title: Biotin only [Standard_primer_E]

description:
Standard_primer_E
processed data file: All_info.xls

tag: rt denaturation

tag: rt reaction

value: 55 °C

tag: biotin added

tag: rt purification

value: standard


title: CD_male_3

description: F1 offspring of dams fed a diet containing 2.3 mg folic acid/ kg diet before conception

value: hippocampus

tag: strain

value: 129S6/SvEv x C57BL/6J

tag: genotype

value: wildtype

value: 14 weeks

tag: Sex

value: male


title: CD_female_3

tag: age

value: female


title: TP1

tag: breed

value: Tibetan pig

tag: breed type

value: indigenous Chinese pig breed

value: embryonic

value: Longissimus dorsi muscle


title: WJ3

value: Wujin pig


title: RB1

value: shNT


title: WJ2


title: CD_female_2


title: FD_female_2


title: Testis_76

city: Dunedin

first: Sarah

middle: D

last: Diermeier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

data_processing:
Illumina Casava software used for basecalling.
The quality of the raw data was evaluated using FastQC.
NSR-Seq: reads were mapped using STAR and sorted using samtools.
Small RNA-Seq: reads were trimmed from 3′ linker and filtered for low-quality reads. Unique sequences 24 nt or longer in length were mapped using Bowtie.
Genome_build: anoCar2.0
Supplementary_files_format_and_content: bedgraph

organism: Anolis carolinensis

source_name: Testis

growth_protocol: RNA was isolated directly from adult brain or testis of Anolis carolinensis.

extract_protocol:
Total RNA and small RNA was extracted from homogenized testis and/or brain tissue using TRIzol .
For NSR-Seq libraries: First strand cDNA synthesis was performed using SuperScript III and the “not-so-random” forward primer set (5’ TCCGATCTCTNNNNNNN 3’), followed by second strand synthesis using exo- Klenow fragment and the “not-so-random” reverse primer set (5’ TCCGATCTGANNNNNNN 3’). In order to deplete ribosomal RNAs from the libraries, “not-so-random” primer sets were designed by pooling 749 unique hexamers with no perfect match to human cytoplasmic 18S and 28S rRNA and mitochondrial 12S and 16S rRNA transcripts.  Libraries were subsequently amplified by PCR using primers (5’ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTCT 3’ and 5’ CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGA 3’) and paired-end sequenced for 50x2 cycles on Illumina Genome Analyzer II according to manufacturers’ instructions. For small RNA libraries: RNA was ligated to 3′ and 5′ adaptors, gel purified after each ligation, reverse transcribed, and PCR amplified using Solexa sequencing primers. PCR product was gel purified, quantified, and sequenced for 36 cycles or 76 cycles on Illumina Genome Analyzer II according to manufacturers’ instructions.
"Not-So-Random" RNA-Seq, small RNA-Seq

tag: sequencing type

value: small RNA size of 52 to 68 nt


title: Structure-seq2 (+DMS) Rep2 [Standard_primer_D]

description:
Standard_primer_D
processed data file: All_info.xls

tag: subspecies

value: japonica

tag: cultivar

value: Nipponbare

value: shoot

value: 14 days

tag: treatment

value: +DMS

value: no

value: PAGE

tag: ligation method

value: T4 DNA ligase

tag: ligation purification

tag: pcr enzyme

tag: final purification

tag: sequencing primer


title: Testis_36

value: small RNA size of 19 to 33 nt


title: GFPplusRNA2

data_processing:
MiSeq Reporter was used for base calls and to generate fastq files
Reads from fastq files were mapped to Zv9 using Tophat2 (v2.0.9; Galaxy version 0.6) with default settings
Differentially expressed genes were identified by mapping reads onto a customized ENSEMBL transcript annotation of Zv9 using Cuffdiff (v2.1.1; Galaxy version 0.0.7) with the default settings
Genome_build: Zv9
Supplementary_files_format_and_content: Y1differentialGenes.tab is in tab-delimited format and contains differential gene output from Cuffdiff.  Includes FPKM, log2 fold change, and statistical values for each gene

source_name: GFPplusRNA

extract_protocol:
Tg(fli1a:egfp) were dissociated, fixed and subjected to fluorescence activated cell sorting, followed by RNA isolation according to the MARIS protcol
Total Script (Epicentre)

tag: developmental stage

value: 24 hours post fertilization

tag: cell type

value: endothelial cells


title: Structure-seq2 (+DMS) Rep1 [Standard_primer_C]

description:
Standard_primer_C
processed data file: All_info.xls

tag: tissue

tag: rt denaturation

value: 90 °C with salt

tag: rt reaction

value: 55 °C

tag: biotin added

tag: rt purification

value: standard


title: CD_male_2

value: hippocampus

tag: strain

value: 129S6/SvEv x C57BL/6J

tag: genotype

value: wildtype

tag: age

value: 14 weeks

tag: Sex

value: male


title: NSR_Testis

tag: sequencing type

value: NSR-Seq


title: GFPminusRNA2

source_name: GFPminusRNA

value: non-endothelial cells


title: Structure-seq2 (-DMS) Rep2 [Standard_primer_B]

description:
Standard_primer_B
processed data file: All_info.xls

tag: subspecies

value: japonica

tag: cultivar

value: Nipponbare

value: shoot

value: 14 days

tag: treatment

value: -DMS

tag: ligation method


title: CD_female_1

value: female


title: Structure-seq2 (-DMS) Rep1 [Standard_primer_A]

description:
Standard_primer_A
processed data file: All_info.xls

value: no

value: PAGE

value: T4 DNA ligase

tag: ligation purification

tag: pcr enzyme

tag: final purification

tag: sequencing primer


title: NSR_Brain

source_name: Brain


title: CD_male_1

tag: tissue


title: GFPminusRNA1

tag: developmental stage

value: 24 hours post fertilization

tag: cell type


title: RNA-Seq_atx-rep2

status: Public on Jun 07 2017

first: Yan

last: He

state: Beijing

address: 2 Yuanmingyuan West Road

department: Plant Genetics and Breeding

institute: China Agricultural University

description: processed data file: atxvsWT_gene_exp_diff.txt

data_processing:
Base calling  was performed following the standard Illumina protocol.
Sequenced ChIP-seq reads were trimmed for adaptor sequence and low-quality sequence,then aligned to the Arabidopsis genome TAIR10 using Bowtie version 1.0.1 with no more than 2 mismatches.
Peaks were called using MACS version 1.4.2 with the following setting: bandwidth(150nt), m-fold(5-50), p-value cutoff(1e-05).
Sequenced RNA-seq reads were trimmed for adaptor sequence and low-quality sequence ,then using Tophat version 2.0.10 and cufflinks version 2.2.1 to identify differentially expressed genes.
Wig files were normalized into the same level by dividing the total counts of tags.
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM values for mutant and wild-type.

organism: Arabidopsis thaliana

source_name: atx3/4/5 mutant_leaf_RNA-seq

growth_protocol: Plants were grown under normal condition with a photoperiod of 16 h light at 22°C and 8h dark at 20°C.

extract_protocol:
Nuclei was extracted using a rapid method as described in He et al., 2013. RNA was extracted using an RNeasy plant mini kit following manufacturer's recommendation (Qiagen, http://www.qiagen.com/).
RNA-seq library construction was performed with NEB Next® mRNA Library Prep Master Mix Set (NEB, Ipswich, MA, USA) following manufacturer’s instructions.

tag: ecotype

value: Columbia (Col-0)

tag: genotype/variation

value: atx3/4/5 mutant

value: four-week-old

value: rosette leaf


title: RNA-Seq_WT-rep2

value: wild type


title: RNA-Seq_WT-rep1