title: F1r DRN Rep#4

description:
Dorsal Raphe/Flowcell5_s5/110722_SN343_0177_BC001DABXX,IlluminaIndex6,GCCAAT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAAT,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt


title: F1r DRN Rep#5

status: Public on Aug 01 2015

type: SRA

city: Salt Lake City

first: Christopher

last: Gregg

state: Utah

address: 323 Wintrobe Bldg 530, 20 North 1900 East

department: Neurobiology & Anatomy

country: USA

institute: University of Utah

description:
Dorsal_Raphe/Flowcell10_s8/110822_SN343_0193_BC05GBACXX,59,IlluminaIndex12,CTTGTA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTA,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt

library_source: transcriptomic

data_processing: Supplementary_files_format_and_content: Allele expression counts are derived by summing reads from SNPs in the same gene and presented as Cast (CastEiJ) and C57 (C57BL/6J) allele read counts for each replicate. Column titles indicate the cross direction (F1i: Cast mother X C57 father; F1r: C57 mother X Cast father), the allele (Cast or C57) and the replicate (1-9)

molecule: total RNA

organism: Mus musculus

source_name: Adult female dorsal raphe nucleus

extract_protocol:
RNA was extracted using Trizol reagent and Dnase Treated and purified using Qiagen Rneasy Kit
Libraries were prepared according to the Illumina TrueSeq sample prep kit manual
Illumina TrueSeq mRNA Sample Prep with poly(A) selection

tag: strain

value: F1R Hybrid (CastEiJ father X C57BL/6J mother)

tag: gender

value: female

tag: age

value: 8 weeks

tag: tissue

value: dorsal raphe nucleus


title: F1r DRN Rep#2

description:
Dorsal Raphe/Flowcell4_s6/110719_SN343_0176_BB0AVFABXX,59,IlluminaIndex7,CAGATC,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATC,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt


title: F1i ARN Rep#2

description:
Arcuate/Flowcell1_s6/110617_SN343_0146_AC01YBABXX,59,IlluminaIndex4,TGACCA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt

source_name: Adult female arcuate nucleus

value: F1i Hybrid (CastEiJ mother X C57BL/6J father)

value: arcuate nucleus


title: F1r ARN Rep#8

description:
Arcuate/Flowcell3_s2/110625_SN343_0150_AB0B4TABXX,59,IlluminaIndex12,CTTGTA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTA,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt


title: F1r ARN Rep#6

description:
Arcuate/Flowcell2_s3/110607_SN343_0140_BC03LUABXX,59,IlluminaIndex4,TGACCA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt


title: F1i ARN Rep#9

description:
Arcuate/Flowcell3_s7/110625_SN343_0150_AB0B4TABXX,59, IlluminaIndex6,GCCAAT, GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAAT,ATCTCGTATGCCGTCTTCTGCTTG,CGATGT
ARN_AlleleCountData.txt


title: F1r DRN Rep#1

description:
Dorsal Raphe/Flowcell4_s5/110719_SN343_0176_BB0AVFABXX,IlluminaIndex6,GCCAAT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAAT,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt


title: F1i ARN Rep#8

description:
Arcuate/Flowcell3_s6/110625_SN343_0150_AB0B4TABXX,IlluminaIndex5,ACAGTG,GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTG,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt


title: F1i DRN Rep#1

description:
Dorsal Raphe/Flowcell4_s1/110719_SN343_0176_BB0AVFABXX,59,IlluminaIndex2,CGATGT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGT,ATCTCGTATGCCGTCTTCTGCTTG,CGATGT
DRN_AlleleCountData.txt


title: F1r ARN Rep#3

description:
Arcuate/Flowcell1_s3/110617_SN343_0146_AC01YBABXX,59,IlluminaIndex2,CGATGT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGT,ATCTCGTATGCCGTCTTCTGCTTG,CGATGT
ARN_AlleleCountData.txt


title: F1r ARN Rep#2

description:
Arcuate/Flowcell1_s2/110617_SN343_0146_AC01YBABXX,59,IlluminaIndex6,GCCAAT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAAT,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt


title: F1r ARN Rep#4

description:
Arcuate/Flowcell2_s1/110607_SN343_0140_BC03LUABXX,IlluminaIndex5,ACAGTG,GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTG,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt


title: F1r DRN Rep#3

description:
Dorsal Raphe/Flowcell4_s7/110719_SN343_0176_BB0AVFABXX,59,IlluminaIndex12,CTTGTA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTA,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt


title: F1i ARN Rep#4

description:
Arcuate/Flowcell2_s5/110607_SN343_0140_BC03LUABXX,59,IlluminaIndex6,GCCAAT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAAT,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt


title: F1r ARN Rep#1

description:
Arcuate/Flowcell1_s1/110617_SN343_0146_AC01YBABXX,59,IlluminaIndex4,TGACCA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt


title: F1i ARN Rep#7

description:
Arcuate/Flowcell3_s5/110625_SN343_0150_AB0B4TABXX,59,IlluminaIndex4,TGACCA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt


title: F1i ARN Rep#6

description:
Arcuate/Flowcell2_s7/110607_SN343_0140_BC03LUABXX,59,IlluminaIndex12,CTTGTA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTA,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt


title: KARPAS-299 Crizotinib

city: toulouse

first: Coralie

last: Hoareau-Aveilla

address: 2 avenue Hubert Curien

department: CRCT

country: France

institute: INSERM

library_source: genomic

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Reads were mapped to the human chr19 (hg19) using bismark software and bowtie options: -q -n 2 -l 75 -k 2 --best --chunkmbs 512.
Methylation percentages for each CpG site were obtained by processing the bismark BAM files further using the scripts "bismark_methylation_extractor" and "genome_methylation_bismark2bedGraph_v4.pl".
Genome_build: hg19

molecule: genomic DNA

organism: Homo sapiens

source_name: Anaplastic large-cell lymphoma

growth_protocol: Cells were cultured in Iscove Modified Dulbecco’s medium (IMDM, Gibco-BRL) supplemented with 15% Foetal Calf Serum (FCS) and were maintained in exponential growth phase.

extract_protocol:
Genomic DNA was extracted using Zymo's Quick-gDNA™ MiniPrep kit (D3025). DNA was bisulfite converted using Zymo's kit D5005 with a proteinase K pretreatment. Target regions were amplified using primers designed with the methprimer software (http://www.urogene.org/cgi-bin/methprimer/methprimer.cgi).
PCR products were multimerized using T4 DNA ligase before sonication to an average length of ~200 bp. Sonicated DNA was then used to generate standard Illumina libraries using the Apollo 324 NGS Library Prep System and barcoded amplification primers.

treatment_protocol: 500 nM of crizotinib or 5 µM of 5-Aza-2′-deoxycytidine or decitabine (Sigma-Aldrich, St Louis, MO, USA) for 96h

tag: cell line

tag: treatment

value: 500 nM of crizotinib

tag: chromosomal translocation


title: F1i ARN Rep#1

description:
Arcuate/Flowcell1_s5/110617_SN343_0146_AC01YBABXX,59,IlluminaIndex2,CGATGT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGT,ATCTCGTATGCCGTCTTCTGCTTG,CGATGT
ARN_AlleleCountData.txt


title: F1r ARN Rep#9

description:
Arcuate/Flowcell3_s3/110625_SN343_0150_AB0B4TABXX,59,IlluminaIndex5,ACAGTG,GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTG,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt


title: KARPAS-299 PBS

value: PBS


title: RPL_human_noligase

city: San Francisco

first: Vijay

last: Ramani

state: California

department: Biochemistry & Biophysics

institute: UCSF

data_processing:
Adapter trimming and read fusion of mate-pairs by SeqPrep
Alignment via STAR/2.4.0 (following parameters:
Processing of STAR intron calls using custom bash/python scripts provided with manuscript
Genome_build: hg19 / SacCer3
Supplementary_files_format_and_content: "Pairs" files that document coordinates of ligation junctions between/within molecular species

source_name: GM12878 lymphoblastoid cell line

growth_protocol: GM12878 were grown at 37 in RPMI-1640 containing 15% FBS, 1X Anti-Anti, and 1X Plasmocin; FY were struck out on YPD plates and grown at 30

extract_protocol:
RNA was extracted using TRIZol and Zymo DirectZOL columns
Illumina TruSeq

treatment_protocol: Cells were treated in situ using the RPL protocol as described in the associated manuscript

tag: cell type

value: B-lymphocyte


title: F1i ARN Rep#3

description:
Arcuate/Flowcell1_s7/110617_SN343_0146_AC01YBABXX,59,IlluminaIndex12,CTTGTA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTA,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt


title: F1r ARN Rep#7

description:
Arcuate/Flowcell3_s1/110625_SN343_0150_AB0B4TABXX,IlluminaIndex2,CGATGT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGT,ATCTCGTATGCCGTCTTCTGCTTG,CGATGT
ARN_AlleleCountData.txt


title: KARPAS-299 Decitabine

value: 5 µM of 5-Aza-2?-deoxycytidine or decitabine


title: F1r ARN Rep#5

description:
Arcuate/Flowcell2_s2/110607_SN343_0140_BC03LUABXX,59,IlluminaIndex7,CAGATC,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATC,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt


title: KARPAS-299 DMSO

value: DMSO


title: F1i ARN Rep#5

description:
Arcuate/Flowcell2_s6/110607_SN343_0140_BC03LUABXX,59,IlluminaIndex7,CAGATC,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATC,ATCTCGTATGCCGTCTTCTGCTTG
ARN_AlleleCountData.txt


title: 4h-post-CIP_IP

city: London

middle: L

last: Pin

state: Ontario

address: 800 Commissioners Rd. E

department: Physiology and Pharmacology/Peadiatrics

country: Canada

institute: The University of Western Ontario/CHRI

description: Input DNA

data_processing:
PCR duplicates were removed from aligned reads using Samtools (http://samtools.sourceforge.net ) and converted to bed format with Bedtools 2 (https://github.com/arq5x/bedtools2) for peak calling.
bigwig flies were generated from aligned reads using Peakranger 1.17 (http://ranger.sourceforge.net/).

source_name: pancreatic tissue

growth_protocol: Mice were grown on normal Chow diet.

extract_protocol:
Chromatin samples were prepared using pancreatic tissue obtained from 2-4 months old mice injected with cerulein. Chromatin Immunoprecipitation was carried out using Anti-ATF3 (sc-188; Santa Cruz). After reverse cross-linking and treatment with Proteinase K, the samples were treated with Phenol Chloroform twice. The DNA was Ethanol precipitated, washed with 70% Ethanol. Samples were eluted and pooled in 40ul of H2O. This eluted DNA was sent for sequencing.
Library was constructed by the Beijing Genomics Institute (Hong Kong), following their established protocol (http://www.genomics.cn/en/).

treatment_protocol: Male mice 2-4 months old were given intraparitoneal injections of cerulein (50 μg/kg body weight) for 4 hours.

value: male

value: 4 hours after the initiation of CIP

tag: antibody


title: 4h-post-CIP_ATF3

description: Anti-ATF3 (cat#sc-188 Santa Cruz)

value: Anti-ATF3 (cat#sc-188 Santa Cruz)


title: RPL_human_ligase


title: Cost siCTL

value: Cost

value: siCTL


title: Dnmt3l-KO-Rep2 (T10)

city: Taipei City

first: Shau-Ping

last: Lin

state: select a state

address: 4F, No. 81, Chang-Xing St.,

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

data_processing:
The adaptor trimmed reads were aligned against the mm10 mouse reference genome using TopHat2 (v2.0.12) with sequence-specific parameter
and were used for transcript fragment assembly using Cufflinks (v2.2.1)  (Trapnell et al. 2012, Kim et al. 2013).
After the assembly, transcript expressions were calculated based on eXpress (v1.4.1) (Roberts & Pachter 2013) against mm10 refseq database to identify differentially expressed genes and transcripts.
For cross-sample comparison, expressions were normalized and analyzed using DESeq2 (v1.8.0) (Love et al. 2014).
Genome_build: mm10
Supplementary_files_format_and_content: text file include counts and FPKM values for each Sample.

source_name: Mouse E13.5/14.5 MEF

growth_protocol: MEFs were cultured with 10% FBS in DMEM

extract_protocol:
the C57BL/6 (B6) wild-type and Dnmt3l-KO MEF cell lines were derived from day 13.5-14.5 embryos via Dnmt3l heterozygote (Dnmt3l+/-) intercrosses
rRNA-free RNAs were fragmented into small pieces, copied into first-strand cDNA using random primers, followed by second-strand cDNA synthesis, a single A base addition and adapter ligation using a TruSeq RNA library preparation kit (Illumina, San Diego, CA). The products were then enriched through 12 cycles PCR amplification to create the final cDNA library.

tag: genotype

value: MEFs

tag: passages


title: newborn lens_FAIRE-seq

city: Bronx

first: Shira

last: Rockowitz

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
library strategy: FAIRE-seq
The FAIRE-seq reads were aligned to the mouse genome (GRCm37/mm9)
Peak detection was performed with the MACS2 program without controls.
Genome_build: mm9
Supplementary_files_format_and_content: A bed file of the peaks from MACS2.

source_name: newborn lens

extract_protocol:
FAIRE-seq: The newborn (P1) lenses of CD-1 mice (Charles River Laboratories) were dissected, tissue was freshly crosslinked and homogenized. Sonicated lysates were subjected to the pheno/chloroform extraction to purify the nucleosome free regions of chromatin
Libraries were prepared according to Illumina's instructions.

tag: strain background

tag: developmental stage

value: newborn (P1)

value: lenses


title: Dnmt3l-KO-Rep1 (T8)


title: WT-Rep1 (T7)

value: wild type


title: WT-Rep2 (T9)


title: 808_7_miRNA_Endo

city: Dunsany

first: Kieran

middle: Gerard

last: Meade

state: Co. Meath

address: Grange

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

description: Non-coding RNA

data_processing:
Adapter sequences were trimmed with Cutadapt (version 1.1). Reads shorter than 18bp were discarded, and the fastq quality filter (version 0.0.13) removed reads where less than 50% of bases with a Phred score of 20. Reads passing all the filters were also trimmed at their ends to remove low-quality bases (Phred score < 20).
High quality reads were aligned to the bovine genome (UMD 3.1) with Novoalign (version 2.07.11) implementing the “-m” miRNA mode. Reads that aligned to more than one position in the genome were discarded.
HTSeq-count, (version 0.5.3p9) utilising default parameters, with the exception of specifying non strand-specific data (-s no), assigned uniquely aligned reads to the Ensembl (version 66) annotation of the bovine genome.
Bioconductor package edgeR (edgeR_3.2.4) (Robinson et al. 2010) was applied in R (R version 3.0.1) to identify statistically significant differentially expressed genes.
To account for biological and technical variation, data was modeled as a negative binomial distribution using a generalisation of the Poisson distribution model. A low read count filter was applied to remove lowly expressed genes. Genes with greater than 1 read count per million reads (cpm), in n-1 animals, were retained.
The data was normalised across library sizes, between samples using the trimmed mean of M-values (TMM) normalization method (Robinson & Oshlack 2010). Tagwise dispersions were estimated for the normalised dataset. Statistical tests were corrected for multiple testing using the Benjamini-Hochberg (Benjamini & Hochberg 1995) method. Genes that were differentially expressed (DE) with a false discovery rate (FDR) adjusted p-value < 0.1 were retained.
Genome_build: UMD3.1.69
Supplementary_files_format_and_content: text file with read counts for each sample.

organism: Bos taurus

source_name: At each time-point, an endometrial biopsy was taken from the same post-gravid horn as previously described (Chapwanya et al., 2010)

extract_protocol:
Homogenization: A Pro Scientific homogeniser model PRO200 (PRO Scientific Inc., Oxford, CT, USA) was used to homogenise the biopsy in TRIzol® (Life Technologies™, Paisley, UK) with 3 sec pulses 10 times.
Clean-up: Total RNA was then cleaned up using the Qiagen RNeasy® MinElute® Cleanup Kit (Qigen Ltd)
he Illumina® TruSeq™ Small RNA sample preparation kit was used to prepare 20 cDNA sequencing libraries according to the manufacturer’s instructions.

value: Endometrium

tag: timepoint

value: 7 Days Post Partum

tag: breed

value: Holstein-Friesian


title: 809_7_miRNA_Endo

description: Non-coding RNA


title: 812_7_miRNA_Endo

description: Non-coding RNA


title: 809_21_miRNA_Endo

description: Non-coding RNA

value: 21 Days Post Partum


title: 812_21_miRNA_Endo

description: Non-coding RNA


title: 802_7_miRNA_Endo

description: Non-coding RNA


title: 803_7_1_miRNA_Endo

description: Non-coding RNA


title: 685_7_miRNA_Endo

description: Non-coding RNA


title: 808_21_miRNA_Endo

description: Non-coding RNA


title: 728_21_miRNA_Endo

description: Non-coding RNA


title: 728_7_miRNA_Endo

description: Non-coding RNA


title: 803_21_miRNA_Endo

description: Non-coding RNA


title: 673_7_miRNA_Endo

description: Non-coding RNA


title: Cost siALK

value: siALK


title: 685_21_miRNA_Endo

description: Non-coding RNA


title: 340_7_1_miRNA_Endo

description: Non-coding RNA


title: 340_21_miRNA_Endo

description: Non-coding RNA


title: 812_21

data_processing:
Tophat version 2.0.6 was used to align reads in each library to the bovine genome, including the --mate-inner-dist option (UMD3.1.69). Only reads that mapped uniquely to the bovine genome were kept (-g 1). The default value of two mismatches per read was allowed. Sensitivity of Bowtie2 was set for the best alignment of each read (--b2-very-sensitive). Only concordantly mapped reads were allowed (--no-disconcordant), and paired reads that don’t map concordantly were not aligned separately (--no-mixed). The segment length was set to 24bp (--segment-length 24).
HTSeq-count, (version 0.5.3p9) utilising default parameters, with the exception of specifying non strand-specific data (-s no), assigned uniquely aligned reads to the Ensembl (version 69) annotation of the bovine genome.
Bioconductor package edgeR (edgeR_3.2.4) (Robinson et al. 2010) was applied in R (R version 3.0.1) to identify statistically significant differentially expressed genes.
To account for biological and technical variation, data was modeled as a negative binomial distribution using a generalisation of the Poisson distribution model. A low read count filter was applied to remove lowly expressed genes. Genes with greater than 1 read count per million reads (cpm), in n-1 animals, were retained.
The data was normalised across library sizes, between samples using the trimmed mean of M-values (TMM) normalization method (Robinson & Oshlack 2010). Tagwise dispersions were estimated for the normalised dataset. Statistical tests were corrected for multiple testing using the Benjamini-Hochberg (Benjamini & Hochberg 1995) method. Genes that were differentially expressed (DE) with a false discovery rate (FDR) adjusted p-value < 0.1 were retained.
Genome_build: UMD3.1.69
Supplementary_files_format_and_content: text file with read counts per sample.

molecule: polyA RNA

extract_protocol:
Homogenization: A Pro Scientific homogeniser model PRO200 (PRO Scientific Inc., Oxford, CT, USA) was used to homogenise the biopsy in TRIzol® (Life Technologies™, Paisley, UK) with 3 sec pulses 10 times.
Clean-up: Total RNA was then cleaned up using the Qiagen RNeasy® Plus Mini kit (Qiagen Ltd)
Input total RNA was uniformly 4 µg in a volume of 50 µl nuclease-free H2O for each sample. Indexes from Illumina® TruSeq® v2 A and B kits were allocated to specific samples prior to library construction so that at least two unique and compatible bar codes were in each pool which made provision for a pooling strategy following the Illumina® TruSeq® pooling guidelines. After adapter ligation the ds cDNA fragments were enriched by PCR which created the final sequencing cDNA library. In the PCR enrichment stage of the protocol 10 PCR cycles were used altered from 15 PCR cycles stated in the manufacture’s protocol. Seven equimolar pools of 5 multiplexed cDNA sample libraries were constructed. Indexes from Illumina® TruSeq® v2 kits A and B were allocated to specific samples following the Illumina® TruSeq® pooling guidelines.


title: 462_7_miRNA_Endo

description: Non-coding RNA


title: 462_21_miRNA_Endo

description: Non-coding RNA


title: 812_7


title: 803_21


title: 809_21


title: 802_7


title: 803_7


title: 808_21


title: 802_21_miRNA_Endo

description: Non-coding RNA


title: 808_7


title: 802_21


title: 783_21


title: 728_7


title: 727_7


title: 759_21


title: 673_21_miRNA_Endo

description: Non-coding RNA


title: 759_7


title: 720_21


title: 720_7


title: 727_21


title: 728_21


title: 685_7


title: 685_21_TRP1


title: 673_7


title: 809_7


title: 783_7


title: 673_21


title: 462_7


title: 340_21_TRP2


title: 462_21


title: 670_21


title: outer medulla

city: Shanghai

first: Feng

last: Wang

address: 600 Yishan Road

department: Nephrology

country: China

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

data_processing:
bcl2fastq 2.15.0 is used for base-calling
Genome_build: rn5
Supplementary_files_format_and_content: RPKM

organism: Rattus norvegicus

source_name: outer medulla

extract_protocol:
TRIzol
TruSeq Stranded RNA LT kit (Illumina)

value: BN

value: 6 weeks old


title: 340_7_TRP1


title: left ventricle

source_name: left ventricle


title: 670_7


title: adrenal glandin

source_name: adrenal glandin


title: hypothalamus

source_name: hypothalamus


title: KO SA1 KO E17.5 cortex Pcdha-R1_4C

city: Madrid

first: Ana

last: Losada

state: Madrid

address: C/ Melchor Fernández Almagro, 3.

department: Molecular Oncology Programme

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

description:
6cutter 4C sequencing
processed data file: HPancreas_KOEbrain_l5.txt.zip

data_processing:
Library strategy: 4C-seq
Read files were quality-checked with FastQC.
Convert BAM files to FASTQ using bedtools v2.20.1 where needed
Transform to Illumina FASTQ using NGSQCToolkit v2.3
Convert and process (map, calculate cis interactions) FASTQ files using 4cseqpipe
Genome_build: GRCm37/mm9
Supplementary_files_format_and_content: Processed data files are 4cseqpipe mapped files for each original FASTQ/BAM file. They allow to generate figures for interactions around the viewpoints with 4cseqpipe

source_name: whole brain

extract_protocol:
Preparation of 4C samples was performed as described (van de Werken, 2012) with some modifications. Freshly collected tissues were incubated with collagenase (0.0065% collagenase I in 10% FBS/PBS for cortex, and 1.33 mg/ml collagenase P in HBSS for pancreas) for 40 min at 37ºC in a shaker. The resulting cell suspension was filtered through a 40-μm cell strainer in order to get a single cell preparation. Cells were centrifuged at 1,100 rpm for 5 min at RT and the cell pellet was resuspended in 10 ml of fixing solution containing 2% formaldehyde in 10% FBS/PBS. After 10 min, 0.125 M glycine was added to stop fixation and the mixture was incubated for 5 min at RT. Cells were pelleted and nuclei isolated upon incubation in cold lysis buffer in the following conditions: For the brain, 10 min in 50 mM Tris pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100 + protease inhibitors cocktail; for the pancreas, 40 min in 50 mM Tris pH 7.5, 50 mM NaCl, 5 mM EDTA, 1% NP40, 2% TX-100 + protease inhibitors cocktail. Proper lysis was determined by methyl green-pyronin staining.
4C-seq libraries were amplified using long primers with 18-21 bp homology to the bait sequence and Illumina paired-end adapter flanks. HindIII and CvIQ (NEB) were used as as first and second cutters, respectively for preparation of the 6-cutter libraries. DpnII and CvIQ (NEB) were used as first and second cutters, respectively for preparation of the 4-cutter libraries.  Pairs of samples were sequenced together thus the raw and processed data files are shared among samples. The 4cseqpipe software identifies the viewpoints and the possible cut points out of the raw data files and flags them in the processed files.

value: E17.5 embryo


title: KO SA1 KO E17.5 cortex Pcdha-R2_4C

description:
6cutter 4C sequencing
processed data file: Pancreas_KOEBrain_l4.txt.zip


title: Adult pancreas Pcdha-R2_4C

description:
6cutter 4C sequencing
processed data file: 2nd_Pancreas,txt.zip

source_name: pancreas

value: 8-10 week old


title: Wt E17.5 cortex Pcdha-R1_4C

description:
6cutter 4C sequencing
processed data file: Hpancreas_Ebrain_l4.txt.zip


title: Adult pancreas Pcdha-R1_4C

description:
6cutter 4C sequencing
processed data file: Pancreas,txt.zip


title: Adult cortex Pcdha-R1_4C

description:
6cutter 4C sequencing
processed data file: Brain.txt.zip

source_name: cortex


title: CantonS

city: matsugasakihashigami tyo

first: Kohei

last: Shimaji

department: Applied biology

country: Japan

institute: Kyoto Institute of Technology

data_processing:
The sequence reads with low quality bases were trimmed using the FASTQ Quality Trimmer program in FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) (version 0.0.13) with the Phred quality score of 20 as a cutoff, and the reads shorter than 38 bp after the trimming were discarded.
RNA-seq reads were aligned to the reference Drosophila melanogaster genome sequence (UCSC dm3) using the TopHat (Kim D et al., 2013) program version 2.0.6 with the default parameters.
Cufflinks (Trapnell C et al., 2013) (version 2.0.2) was then used with the default parameters to assemble transcripts and to calculate fragments per kilobase of transcript per million mapped fragments (FPKM).
Genome_build: UCSC dm3

organism: Drosophila melanogaster

source_name: about 0-2h-old embryos

growth_protocol: Embryos were laid on standard food for 2 h at 25℃ and collected.

extract_protocol:
After dechorionation with 10% paraformaldehyde, total RNAs were isolated using Trizol reagent. Total RNAs were isolated from two collections of eggs and mixed into one sample in each strains.These isolated RNAs were prepared for Illumina mRNA-seq libraries using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) according to the manufacture’s instruction.
The libraries were subjected for sequencing on a Genome Analyzer GAIIx instrument (Illumina) for 41 cycles.

treatment_protocol: Embryos were laid on standard food for 2 h at 25℃. Laid eggs were collected twice.

value: Canton S

value: around 0-2h


title: liver

source_name: liver

value: male


title: cortex


title: S5-GODL

city: Los Angeles

first: Sanaz

last: Memarzadeh

state: CA

address: 610 Charles E Young Dr East

department: Obstetrics and Gynecology

institute: UCLA

data_processing:
Illumina RTA software used for basecalling.
Demultiplex data without allowing mismatches
Align to genome with Tophat with hg19 and Ensembl 75 gene annotation, allowing 2 mismatches and unique alignments only
Run alignment file (BAM format) through HTSeq-package script along with Ensembl 75 human gene annotation gtf file to create gene counts matrix, then run gene matrix though DESeq to normalize and test for differential expression
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include  raw gene counts values for each Sample ...

source_name: high grade serous ovarian cancer

extract_protocol:
RNA was isolated from bulk primary human high grade serous ovarian cancers or matched low passage cell lines using the Qiagen allprep micro kit.
Isolated total RNAs (500 ng) were converted to indexed cDNA libraries using the Illumina TruSeq RNA sample preparation kit (# RS-930-2001)

tag: tumor subpopulation

value: tumor cell line passage 4

tag: tumor state

value: tumor derived cell line

tag: cell storage

value: freshly derived cell line


title: S3-GODL


title: Adult cortex Pcdha-R2_4C

description:
6cutter 4C sequencing
processed data file: 2nd_Brain.txt.zip

tag: strain


title: JD001 parental tumor

value: Bulk tumor

value: ascites

value: cryopreserved tumor


title: PA040 parental tumor

value: solid tumor


title: BY071 parental tumor


title: S1-GODL


title: dG9a null

value: w dG9aRG5

tag: age


title: Wt E17.5 cortex Pcdha-R2_4C

description:
6cutter 4C sequencing
processed data file: Brain_Ebrain_l3.txt.zip


title: Pt.J.CA125+

description: LM005 plus

extract_protocol:
Primary human high grade serous ovarian cancers, dissociated to single cells and either used fresh or cryopreserved, were FACS isolated based on expression of CA125. RNA was isolated using the Qiagen allprep micro kit.
Isolated total RNAs (50 ng) were amplified to cDNA using the Clontech SMARTer kit (# 634820 ), then converted to indexed cDNA libraries using the Nextera  DNA Library preparation kit (#FC-121-1030)

value: CA125 positive

value: cryopreserved primary cells


title: Pt.J.CA125-

description: LM005 minus

value: CA125 negative


title: Pt.I.CA125-

description: PA040 minus


title: Pt.F.CA125-

description: fq_1122 minus

value: freshly isolated primary cells


title: Pt.G.CA125+

description: JK006 plus

value: freshly isolatedprimary cells


title: Pt.D.CA125-

description: JD001 minus


title: Pt.G.CA125-

description: JK006 minus


title: Pt.E.CA125-

description: fq_1028 minus


title: Pt.H.CA125+

description: MS053 plus


title: Pt.B.CA125-

description: AS100 minus


title: Pt.C.CA125+

description: BY071 plus


title: Pt.E.CA125+

description: fq_1028 plus


title: Pt.A.CA125+

description: AS022 plus


title: Pt.B.CA125+

description: AS100 plus


title: Pt.C.CA125-

description: BY071 minus


title: Pt.A.CA125-

description: AS022 minus


title: Pt.F.CA125+

description: fq_1122 plus


title: Sample12125 Cushing's

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
cDNA libraries from polyA mRNA were prepared using TruSeq cDNA synthesis kit and sequenced using a HiSeq 2000 (Illumina)
Samples were run on 2 lanes of a HiSeq 2000 (Illumina) generating  8 612 682 to 16 469 501 single-ended 50 bp reads per sample.
These were aligned to the human genome (Enembl GRCh37.74, Genbank Assembly ID GCA_000001405.14) using TopHat version 2.0.10 (4), Bowtie 2 version 2.1.0 (5) and Samtools version 0.1.18
Reads were mapped to known genes using HTseq.  Gene expression was analyzed using DESeq2 version 1.2.10
Genome_build: GRCh37.74
Supplementary_files_format_and_content: comma seperated text files include RPKM values for each Sample

source_name: Adipose

extract_protocol:
During the course of pituitary surgery a routine subcutaneous fat graft is utilized to seal the surgical field upon completion of the procedure. 500 mg of this fat graft was used for the study.  ~100 mg were utilized for ex vivo lipolysis assay, ~200 mg was snap frozen in liquid nitrogen and stored at -80 degrees for RNA preparation. 25 mg pieces of adipose tissue were pre-incubated for 15 minutes in KRBH buffer (sigma) at 37°C and then incubated for 1 hour at 37°C in 300 μl KRBH in the presence or absence of isoproterenol 30nM in duplicate. Glycerol was assayed in supernatants using a glycerol assay kit (sigma) as instructed by manufacturer.
cDNA libraries from polyA mRNA were prepared using TruSeq cDNA synthesis kit and sequenced using a HiSeq 2000 (Illumina)
At the University of Michigan DNA Sequencing Core, cDNA libraries from polyA mRNA were prepared using TruSeq cDNA synthesis kit and sequenced using a HiSeq 2000 (Illumina).

tag: phenotype

value: Cushing's

tag: tissue

value: Adipose

tag: patient #


title: Control shRNA trophoblast cells rep 2

first: Stephen

middle: J

last: Renaud

address: 1151 Richmond St, MSB428

institute: University of Western Ontario

data_processing:
Following generation of sequencing images, the pixel-level raw darta collection, image analysis, and base-calling were performed by Rea Time Analysis software (Illumina)
Base call files were converted to qseq files by BCL converter (Illumina), and qseq files were converted to fastq files for downstream analysis.
Reads from fastq files were mapped to the human reference genome (hg19) using CLC Bio Genomics Workbench 7.0 (CLC Bio, Aarhus, Denmark)
Genome_build: hg19
Supplementary_files_format_and_content: excel file containing reads per kilobase per million reads (RPKM).

source_name: BeWo trophoblast cells

growth_protocol: Cells were grown in DMEM/F12 media supplemented with 10% fetal bovine serum, pennicillin/streptomycin in standard tissue culture conditions (5% CO2, 37 C).

extract_protocol:
RNA was extracted using Trizol according to the manufacturer's recommendations.
Libraries were prepared from poly-A containing RNAs according to protocols provided by the TruSeq RNA sample preparation kits (Illumina). 500 ng of RNA from cells expressing control shRNA (3 replicates) or OVO-like 1 shRNA (3 replicates) was used as input.

treatment_protocol: Cells were transduced via lentivirus with control shRNA or an shRNA targeting OVO-like 1. After puromycin selection, all cells received 250 uM 8-Bromo cyclic adenosine monophosphate to stimulate trophoblast differentiation.

value: Choriocarcinoma trophoblast

tag: status

value: exposed to 8-bromo-cAMP

tag: treatment

value: control

tag: barcode

value: CGATGT


title: Pt.D.CA125+

description: JD001 plus


title: Control shRNA trophoblast cells rep 1

tag: cell type

value: AGTTCC


title: Sample12118 Cushing's


title: OVOL1 shRNA trophoblast cells rep 3

value: OVOL1 shRNA

value: GCCAAT


title: OVOL1 shRNA trophoblast cells rep 2

value: TGACCA


title: Control shRNA trophoblast cells rep 3

value: ACAGTG


title: Sample12114 Cushing's


title: Sample12117 Cushing's


title: Sample12106 Cushing's


title: Pt.I.CA125+

description: PA040 plus

value: solid tumor


title: Sample12127 Control

value: Control


title: Sample12112 Control


title: OVOL1 shRNA trophoblast cells rep 1

value: ATGTCA


title: Fat4-/- mutant embryo 2

city: Toronto

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

description: processed data header: MAZ6_CAGATC_R1_001

data_processing:
Gene expression analysis for 6 RNA-Seq samples (3 wildtype and 3 Fat4 mutant samples, ~100 millions of reads per sample in paired ends, 101-mer) was performed essentially as previously described (Labbé et al., 2012) using vast-tools (Irimia et al., 2014).  Basically, reads were mapped to the transcriptome using bowtie (Langmead et al., 2009). Correction for multiple mapping was done as follows: each position in each transcript using 50-basepair windows was mapped back against the whole transcriptome using bowtie with the same parameters. If this sequence mapped somewhere else in addition to itself, it was discarded and discounted from the transcript effective length (length-49). This “effective length” was then used to divide the raw read counts per million mapped reads for each gene to obtain corrected-RPKM values (cRPKM).
Genome_build: mm9
Supplementary_files_format_and_content: text

source_name: E13.5 kidneys (includes both kidney, and most of the ureter is  removed) including the dividing ureteric bud, condensing mesenchyme and surrounding stroma.

growth_protocol: Mice were housed at the Toronto Centre for Phenogenomics (Toronto, Canada), given access to water and food ad libitum. A single pregnant female was dissected, and the embryos were quickly dissected out and placed on ice. Both kidneys were dissected out of each embryo, quicky flash frozen with liquid nitrogen and placed in a -80˚C freezer.

extract_protocol:
Total RNA was subsequently extracted using TRIzol and according to the manufacturer's protocol.
Illumina protocol.

tag: Stage

value: embryo

tag: genotype/variation

value: kidney

value: C57BL6/6 (Backcrossed 6 times:N6)


title: Fat4-/- mutant embryo 3

description: processed data header: MAZ8_AGTCAA_R1_001


title: Sample12109 Control


title: Fat4-/- mutant embryo 1

description: processed data header: MAZ2_ACAGTG_R1_001


title: Sample12119 Control


title: Wildtype control embryo 3

description: processed data header: MAZ7_CTTGTA_R1_001


title: Wildtype control embryo 1

description: processed data header: MAZ1_TGACCA_R1_001


title: Sample12110 Control


title: Wildtype control embryo 2

description: processed data header: MAZ5_GCCAAT_R1_001


title: Sample12101 Control


title: Sample12104 Control


title: Sample12120 Control


title: Sample12105 Control


title: Ctrl.iPS1BC4_D14

city: ny

first: mingyan

last: lin

address: 1925 morris park ave

institute: aecom

data_processing:
First, 3’ adaptor sequences (TGGAATTCTCGGGTGCCAAGG) were removed from the raw miRNA-seq reads using a java script “AdRec.jar” from seqbuster. Out of the total, ~7% of reads were without adaptors. 92% of processed reads after adaptor trimming were 15-35bp in length. The trimmed reads were then mapped to known pre-miRNA sequences deposited in miRBase (hsa database from miRBASE20) (http://www.mirbase.org/), allowing for one mismatch at most using bowtie. For any read to be considered as from a known mature miRNA, its 5’ and 3’ ends needed to be within 1-3 bp from the 5’ and 3’ ends of the mature miRNAs annotated in miRBase, respectively. To avoid mis-mapping, all trimmed reads were also mapped to the human genome reference sequences (hg19). Any read with superior hits in non-microRNA genomic regions was discarded. We considered -5p and -3p derivatives of the same miRNA name as two separated miRNAs.
To determine differentially expressed (DE) miRNAs, we applied DESeq2 to analyze the read counts of all microRNAs. Specifically, DESeq2 models the variance in miRNA read counts across replicates using the negative binomial distribution and tests whether, for a given miRNA, the change in counts between the control and SZ/22q11.2 samples is significantly larger as compared to the variation within each replicate group. A nominally significant p-value of < 0.01 and fold change >1.5-fold were chosen as the cutoffs for identifying differentially expressed miRNAs between SZ and controls, but a multiple comparison correction was also applied to adjust the p-values for genome-wide significance.
Genome_build: miRBASE20
Supplementary_files_format_and_content: excel files for raw counts of all samples

source_name: control_neuron derived from iPSC

extract_protocol:
total cellular RNA was isolated using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols. (1) Dilute Oligos and MgCl2 (2) Ligate the Small RNA 3' Adapter and 5' Adapter (3) Isolate Ligated Small RNA by Denaturing PAGE Gel (4) Recover the Isolated RNA (5) Reverse Transcribe and Amplify the Small RNA Ligated with Adapters (6) Purify the Amplified cDNA Construct

tag: subject group

tag: tissue/cell type

value: Day 14 neuron derived from iPSC

tag: molecule subtype

value: small RNA


title: Ctrl.iPS2C4_d14


title: Ctrl.iPS6C4_D14


title: RPL_yeast_imidazole_noligase_rep2

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae strain FY

value: FY


title: Ctrl.iPS2C1_D14


title: Ctrl.iPS1BC23_d14


title: RPL_yeast_imidazole_noligase


title: Ctrl.iPS5C4_D14


title: Sample12121 Control

value: Adipose


title: Ctrl.iPS1BC10_d14


title: Ctrl.690C5_d14


title: Sample12115 Control


title: Ctrl.553C2_d14


title: SZ.iPS15BC6_D14

source_name: SZ patient_neuron derived from iPSC

value: schizophrenia-22q11.2 deletion


title: RPL_yeast_noligase


title: SZ.22q11.60C2_d14


title: SZ.22q11.30C9_d14


title: RPL_yeast_imidazole_ligase_rep2


title: SZ.22q11.10C5_d14


title: RPL_yeast_imidazole_ligase


title: SZ.1220C2_d14


title: AR LNCaP Input

city: Chicago

first: Yuwen

last: Liu

state: IL

address: 900 East 57th Street. KCDB building. Room 10250

department: Human Genetics

institute: University of Chicago

description: 2 biological replicates

data_processing:
Illumina Casava1.7 software used for basecalling.
bowtie-0.12.7 was used for aligning reads onto hg18 human genome, and only uniquely mapped reads were used for downstream analyses
MACS-2.0.7 was used for calling binding sites for each biological replicate
IDR was used to call consistent peaks across two biological replicates
Genome_build: hg18

source_name: LNCaP cells

growth_protocol: LNCaP cells were grown in charcoal-stripped RPMI medium before treatment

extract_protocol:
LNCaP cells were starved in phenol-free RPMI medium supplemented with 10% charcoal-stripped FBS for 3 days followed by treatment with 10nM DHT or 100nM calcitriol for 1hr. Cells were fixed in 1% formaldehyde for 15min and quenched with 0.125M glycine. Chromatin was isolated with lysis buffer and glass homogenization, then sonicated by Bioruptor (Diagenode). For each ChIP, An aliquot of 50 ug chromatin was pre-cleared with BSA-blocked magnetic protein G beads at 4°C  overnight (Millipore). 5ug antibody was added to pre-cleared chromatin and incubated at 4°C for 6 hrs. BSA-blocked beads were then added and incubated at 4°C overnight. Samples were then washed 4 times with washing buffer and 2 times with TE, followed by Rnase A treatment for 2hr and proteinase K treatment for 2hr. Crosslinks were reversed by incubation overnight at 65 C. Finally, ChIPped DNA was extracted by MinElute PCR Purification kit (Qiagen).
DNA samples after ChIP were made into libraries with TrueSeq DNA Sample Prep Kit (Illumina) and run on Illumina Hiseq 2000 to generate single end 50bp reads.

treatment_protocol: 10nM DHT for AR ChIP, 100nM calcitriol for VDR and FOXA1 ChIPs

value: LNCaP

tag: antibody

value: none (input)


title: VDR LNCaP ChIP-Seq

description: 2 biological replicates

value: homemade


title: FOXA1 LNCaP Input

description: 2 biological replicates


title: FOXA1 LNCaP ChIP-Seq

description: 2 biological replicates

value: Abcam, ab5090


title: VDR LNCaP Input

description: 2 biological replicates


title: AR LNCaP ChIP-Seq

description: 2 biological replicates

value: Santa cruz N21


title: RPL_human_yeast_mix_noligase_rep2

organism:
Saccharomyces cerevisiae
Homo sapiens

source_name: GM12878 lymphoblastoid cell line and S. cerevisiae strain FY

value: mixture of human B-lymphocyte and yeast (FY) cells


title: RPL_human_yeast_mix_ligase


title: RPL_human_yeast_mix_noligase


title: At_rosette_R1

city: Olomouc - Holice

first: Ales

last: Pecinka

address: Slechtitelu 31

department: Centre of Plant Structural and Functional Genomics

country: Czech Republic

institute: Institute of Experimental Botany

description: Sample 1

data_processing:
read quality control (FastQC)
low quality read trimming (FASTX tools)
mapping to Arabidopsis TAIR10; and Alyrata_107 genome assembly (TopHat)
retrieving number of reads per gene coordinates (qualimap)
Genome_build: TAIR10 for samples 1-2; Alyrata_107 genome assembly for samples 3-7 and gene annotation v2 (Rawat et al. 2015)
Supplementary_files_format_and_content: EXCEL file, readcounts per gene for each of the libraries and RPKM values

organism: Arabidopsis thaliana

source_name: vegetative rosette

growth_protocol: plants were grown in soil under 16 h light : 8 h dark at 21°C.

extract_protocol:
Dissected shoot apices (hypocotyl and roots, cotyledons and true leaves were cut away with a razor blade) and entire rosettes were harvested at five-leaves stage (at approximately three weeks old plants). Entire inflorescences were collected from the main stem. The tissues were flash frozen with liquid nitrogen and RNA was extracted using the RNeasy Mini Kit (Qiagen) with additional on column DNAse I (Roche) digest.
mRNA libraries were prepared for sequencing using RNA TruSeq kit (Illumina) using manufacturer's instructions

treatment_protocol: nos special treatment; growth under long day conditions

tag: cultivar

value: entire vegetative rosette


title: Al_inflorescence_R2

description: Sample 7

organism: Arabidopsis lyrata subsp. lyrata

source_name: inflorescence

value: entire inflorescence


title: At_H6R48_R2

description: Sample 6

data_processing:
read quality control (FastQC)
low quality read trimming (FASTX tools)
mapping to Arabidopsis TAIR10; and Alyrata_107 genome assembly (TopHat)
retrieving number of reads per gene coordinates (qualimap)
Genome_build: TAIR10 for samples 1-6; Alyrata_107 genome assembly for samples 7-12 and gene annotation v2 (Rawat et al. 2015)
Supplementary_files_format_and_content: EXCEL file, readcounts per gene for each of the libraries and RPKM values

source_name: rosette leaves

growth_protocol: Plants were grown for 3 weeks on soil in a growth chamber under long day (16 h light: 8 h dark) regime at 21°C (mock treatment).

extract_protocol:
Leaves were dissected with a razor blade, flash frozen in liquid nitrogen and total RNA was extracted using the RNeasy Mini Kit (Qiagen) with additional on column DNAse I (Roche) digest
RNA libraries were prepared using RNA TruSeq kit (Illumina) using standard protocol

treatment_protocol: Plants were transferred to 37°C for 6 hours (heat stress). For recovery, heat stressed plants were placed back to mock conditions for 48 hours.

value: rosettes - 5 leaves stage

tag: exposure time

value: heat stress (37°C 6 h) + recovery (21°C 48 h)


title: At_H6R48_R1

description: Sample 5


title: At_H6_R2

description: Sample 4

value: heat stress 6 h 37°C


title: RPL_human_yeast_mix_ligase_rep2

data_processing:
Adapter trimming and read fusion of mate-pairs by SeqPrep
Alignment via STAR/2.4.0 (following parameters:
Processing of STAR intron calls using custom bash/python scripts provided with manuscript
Genome_build: hg19 / SacCer3
Supplementary_files_format_and_content: "Pairs" files that document coordinates of ligation junctions between/within molecular species

extract_protocol:
RNA was extracted using TRIZol and Zymo DirectZOL columns
Illumina TruSeq


title: SZ.iPS15BC4_d14


title: Al_SAM_R1

description: Sample 5

source_name: apical meristem

value: dissected shoot apical meristem


title: SZ.1804C6_D14

value: Day 14 neuron derived from iPSC


title: Al_rosette_R2

description: Sample 4


title: Al_inflorescence_R1

description: Sample 6


title: Al_rosette_R1

description: Sample 3


title: RNA-seq, si ESRP2 OS-RC-2

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

institute: University of Tokyo

description:
ESRP2 siRNA transfected
genes.fpkm_tracking.txt
isoforms.fpkm_tracking.txt

data_processing:
RNA-seq reads were trimmed down to 150 bases and processed by Tophat2 (version 2.0.10) and Bowtie2 (version 2.1.0) using hg19 version of index files. Parameters used are as follows: -a 6 --segment-length 25 --no-coverage-search --read-realign-edit-dist 0 -G.
FPKM calculation was performed by using Cuffdiff (cufflinks version 2.1.1, with options -m 200 -u).
Genome_build: hg19
Supplementary_files_format_and_content: Expression data of the three samples were summarized into single processed file by Cuffdiff. Gene-level expressions are in genes.fpkm_tracking.txt and isoform-level expressions are in isoforms.fpkm_tracking.txt.

growth_protocol: OS-RC-2 cells were obtained from RIKEN Cell Bank (Tsukuba, Japan) and maintained in RPMI 1640 (#11875; Life Technologies) supplemented with 10% fetal bovine serum. Cells were grown in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNAs were extracted as described previously (Mizutani et al., 2011, J Biol Chem).
Libraries were prepared using  Dynabeads mRNA DIRECT Purification Kit (Life Technologies) and Ion Total RNA-seq kit v2 (Thermo Scientific). Sequencing was performed using Ion PI Chip Kit v2 BC and ion PI IC200 kit (Thermo Scientific).

treatment_protocol: siRNAs were introduced into cells using Lipofectamine RNAiMAX reagent (Invitrogen) with a reverse method. Cells were harvested 48 h after seeding.

tag: sirna

tag: tgf-beta treatment

value: no

tag: histology

value: clear-cell renal cell carcinoma

value: ESRP2 siRNA transfected

tag: cell line


title: Al_H6R48_R2

description: Sample 12

tag: tissue


title: RNA-seq, si Arkadia OS-RC-2

description:
Arkadia siRNA transfected
genes.fpkm_tracking.txt
isoforms.fpkm_tracking.txt

value: Arkadia

value: Arkadia siRNA transfected


title: At_mock_R1

description: Sample 1

value: heat stress 0 h


title: Al_H6R48_R1

description: Sample 11


title: At_rosette_R2

description: Sample 2


title: Al_H6_R1

description: Sample 9


title: RNA-seq, si Negative control OS-RC-2

description:
control siRNA transfected
genes.fpkm_tracking.txt
isoforms.fpkm_tracking.txt

value: Negative control

value: control siRNA transfected


title: At_H6_R1

description: Sample 3


title: RNA-seq, si Arkadia

description: Arkadia siRNA transfected

growth_protocol: HEK293T cells were maintained in Dulbecco's modified Eagle's medium (#11965; Life Technologies) supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNAs were extracted as described previously (Mizutani et al., 2011, J Biol Chem).
Libraries were prepared using  Dynabeads mRNA DIRECT Purification Kit (Life Technologies) and Ion Total RNA-seq kit v2 (Thermo Scientific). Sequencing was performed using Ion PI Chip Kit v2, PI Template OT2 200 Kit v3 and Ion PI Sequencing 200 Kit v3 (Thermo Scientific).

value: embryonic kidney cells


title: Al_mock_R2

description: Sample 8


title: RNA-seq, si ESRP2

description: ESRP2 siRNA transfected


title: Al_mock_R1

description: Sample 7


title: serum miRNA from non-drinking control subject replicate 8 [miRNA-Seq]

status: Public on Jul 31 2015

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description:
miRNA expression data from the peripheral blood serum
14-374

data_processing:
After phasing, prephasing, normalization and cross talk correction are taken into account, base calling was performed by Illumina Real Time Analysis (RTA) software (version 1.17.28) on the MiSeq instrument
Sequenced reads were trimmed for adaptor sequence, FASTQ files were subsequently imported into Partek Flow and Strand NGS suites for alignment and analysis. Base calls below a phred score of 20 were trimmed. Reads were aligned to the human hg19 reference genome using the Bowtie algorithm. These were then quantified against both miRBase (version 20) and RefSeq transcript miRNA annotations (4-29-14). Any miRNAs that were detected in fewer than 5 human subjects were discarded from further analysis. Raw miRNA counts were then normalized to the total number of miRNA reads per sample and expressed as a percentage of that total.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include percent of total read values for each sample

source_name: Peripheral blood serum

extract_protocol:
Qiagen total RNA
RNA libraries were prepared for sequencing using Illumina TruSeq small RNA protocol

tag: broad diagnosis

value: non-drinking control

tag: narrow diagnosis

tag: age (years)

tag: Sex

value: Male


title: serum miRNA from non-drinking control subject replicate 10 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-405


title: serum miRNA from non-drinking control subject replicate 9 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-404

value: Female


title: serum miRNA from non-drinking control subject replicate 7 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-132


title: serum miRNA from non-drinking control subject replicate 6 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-051


title: At_mock_R2

description: Sample 2

value: rosettes - 5 leaves stage


title: serum miRNA from non-drinking control subject replicate 4 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-039


title: serum miRNA from non-drinking control subject replicate 5 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-040


title: serum miRNA from non-drinking control subject replicate 3 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-038


title: serum miRNA from non-drinking control subject replicate 1 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-030


title: serum miRNA from alcohol use disorder subject replicate 17 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-351

value: alcohol use disorder

value: alcohol dependence


title: serum miRNA from non-drinking control subject replicate 2 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-035


title: serum miRNA from alcohol use disorder subject replicate 16 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-331


title: serum miRNA from alcohol use disorder subject replicate 14 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-172


title: Al_H6_R2

description: Sample 10

value: heat stress 6 h 37°C


title: serum miRNA from alcohol use disorder subject replicate 12 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-118


title: serum miRNA from alcohol use disorder subject replicate 10 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-101


title: serum miRNA from alcohol use disorder subject replicate 13 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-126


title: serum miRNA from alcohol use disorder subject replicate 9 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-087


title: RNA-seq, si Negative control

description: control siRNA transfected

tag: treatment


title: serum miRNA from alcohol use disorder subject replicate 8 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-043


title: serum miRNA from alcohol use disorder subject replicate 3 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-125

value: alcohol abuse


title: serum miRNA from alcohol use disorder subject replicate 6 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-016


title: serum miRNA from alcohol use disorder subject replicate 7 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-020


title: serum miRNA from alcohol use disorder subject replicate 2 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-120


title: serum miRNA from alcohol use disorder subject replicate 4 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-343


title: serum miRNA from alcohol use disorder subject replicate 5 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-013


title: Pt.H.CA125-

description: MS053 minus

tag: tumor subpopulation

value: CA125 negative

tag: tumor state

value: solid tumor

tag: cell storage

value: cryopreserved primary cells


title: serum miRNA from alcohol use disorder subject replicate 1 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-034


title: serum miRNA from alcohol use disorder subject replicate 15 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-322


title: Subject 2 Amygdala

city: Bethesda

first: Clifton

middle: Lee

last: Dalgard

state: Maryland

address: 4301 Jones Bridge Road B2038

department: Anatomy Physiology & Genetics

institute: Uniformed Services University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the Macaca mulatta reference genome using TopHat version 2.0.10 with Bowtie2 version 2.1.0
Cufflinks was utilized to quantify the expression level in FPKM
Non-default parameters upper quartile normalization (-N), bias detection and correction (-b), and rRNA/tRNA mask (-M) were utilized.
Genome_build: Mmul_1
Supplementary_files_format_and_content: fpkm_tracking files were generated from Cufflink version 2.1.1

organism: Macaca mulatta

source_name: Brain

extract_protocol:
Forty brain region specific micropunches are collected from each brain region directly into 350 μL of Qiazol Lysis Reagent before total RNA isolation using the miRNeasy Mini Kit.
Sequencing libraries were prepared using the standard Illumina TruSeq RNA v2 protocol

tag: brain region

value: amygdala

tag: age

value: 5 years

tag: gender

value: male


title: Subject 1 Anterior Cingulate Cortex

value: anterior cingular cortex

value: 4 years


title: Subject 2 Brodmann Area 25

value: Brodmann Area 25


title: Subject 1 Amygdala


title: Subject 1 Brodmann Area 25


title: Subject 1 Hippocampus

value: hippocampus


title: Pancreas CTCF_ChIP-seq

description:
Processed data file: Pancreas_CTCF_Losada.bed
Chromatin immunoprecipitation

data_processing:
Read files were quality-checked with FastQC.
Reads where aligned to mm9 with Illumina's Eland
Same sample replicas where merged
Peaks were called with MACS 1.4 - All samples where compared to Input - Only peaks with FDR <=5% were retained
Genome_build: GRCm37/mm9
Supplementary_files_format_and_content: BED files with mm9 coordinates of peaks with FDR <= 5%

source_name: pancreas

extract_protocol:
ChIP was performed in tissues (cerebral cortex and pancreas, in the case of 8-10 week old C57Bl/6 mice, and whole brain in the case of E17.5 embryos) from wildtype, SA1 heterozygous and SA1-null mice with custom made rabbit polyclonal antibodies against SA1 and SMC1 and RNApolIISer2P (AB5095, Abcam) as described (Cuadrado et al. 2010). Mice were housed in a pathogen-free animal facility following the animal care standards of the institution. Fresh tissues collected in 6 MW plates containing cold PBS with 1 mM PMSF and protease inhibitor cocktail (Roche) were immediately minced to get small fragments of about 1 mm diameter. Tissue pieces (pooled from three individuals) were centrifuged at 2000 rpm for 2 minutes at 4ºC, resuspended in 1 ml of fixing solution (1% formaldehyde, 50 mM HEPES-KOH, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and incubated 20 min at room temperature in a rotating wheel. Cross-linking was stopped by adding 1/20 volume of 2.5M Glycine for 5 minutes at RT. Tissue pieces were washed twice with cold PBS, recovered by centrifugation at 3000 rpm for 7 minutes at 4ºC, resuspended in 2 ml lysis buffer (1% SDS, 10mM EDTA, 50 mM Tris-HCl pH 8.1; 2x107 cells per ml) and sonicated in Covaris system (shearing time 30 min, 20% duty cycle, intensity 10, 200 cycles per burst and 30 seconds per cycle).
DNA samples were provided by the user. 15 ng of ChIP DNA as quantitated by fluorometry was used. Electrophoretic fraction of 100-200bp was processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (11 cycles). The resulting purified DNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

value: pancreas

tag: strain

value: 8-10 week old


title: serum miRNA from alcohol use disorder subject replicate 11 [miRNA-Seq]

description:
miRNA expression data from the peripheral blood serum
14-115

value: Female


title: Pancreas Igg_ChIP-seq

description:
Processed data file: Pandreas_Igg_Losada.bed
Chromatin immunoprecipitation


title: YAMC Cdk8 KO - clone 19_2

city: South San Francisco

first: Florian

last: Gnad

address: 1 DNA Way

institute: Genentech

description:
YAMC Cdk8 KO - clone 19
SAM17864065

data_processing:
Alignment with GSNAP version ‘2012-01-11' -M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap
Differential gene expression analysis using DEseq
FASTQ to BAM
Genome_build: NCBIM37
Supplementary_files_format_and_content: RPKM

source_name: mouse intestinal cells (YAMC)_Cdk8_ko_clone19

growth_protocol: YAMC cells were grown at 32 degrees Celsius and harvested for RNA extraction during logarithmic growth phase

extract_protocol:
RNA was extracted using RNA-easy kit
TruSeq RNA Sample Preparation kit

value: small intestine

tag: genotype


title: YAMC Cdk8 KO - clone 19_1

description:
YAMC Cdk8 KO - clone 19
SAM17864064


title: YAMC parental_2

description:
YAMC parental
SAM17864058

source_name: mouse intestinal cells (YAMC)_parental

value: wildtype


title: YAMC Cdk8 KO - clone 1_2

description:
YAMC Cdk8 KO - clone 1
SAM17864061

source_name: mouse intestinal cells (YAMC)_Cdk8_ko_clone1


title: YAMC parental_3

description:
YAMC parental
SAM17864060


title: YAMC Cdk8 KO - clone 1_3

description:
YAMC Cdk8 KO - clone 1
SAM17864062


title: YAMC Cdk8 KO - clone 19_3

description:
YAMC Cdk8 KO - clone 19
SAM17864066


title: YAMC parental_1

description:
YAMC parental
SAM17864059


title: YAMC Cdk8 KO - clone 1_1

description:
YAMC Cdk8 KO - clone 1
SAM17864063


title: Subject 2 Hippocampus


title: Subject 2 Anterior Cingulate Cortex


title: Single_cell_RNASeq [ctx11]

city: Heidelberg

last: Martin-Villalba

state: Deutschland

address: Im Neuenheimer Feld 280

department: Molekulare Neurobiologie (A290)

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing:
Basecalls performed using RTA 1.18.64
Before alignment, adapter sequences in raw reads were trimmed by Btrim64 (http://graphics.med.yale.edu/trim)
Trimmed reads were mapped to mouse genome (ENSEMBL Release 78) using STAR_2.4.0g.
Expression level of each gene was quantified in unites by transcript per million (TPM) and fragments per kilobase of transcript per million fragments mapped (FPKM) using RSEM 1.2.18 with default parameters.To compare expression levels of different genes across samples, we performed an additional TMM (trimmed mean of M-values) normalization on FPKM using Trinity (http://trinityRNA-seq.github.io/) based on edgeR  (abbreviated TMM-FPKM). The purpose of this normalization is to account for differences in total cellular RNA production across all cells.
We developed custom R scripts based on FactoMineR library (http://factominer.free.fr/) performing PCA analysis on gene expression matrices.PCA analysis was performed on cells passed quality control using all genes expressed in more than two cells and with a variance in log2 (TMM-FPKM) across all single cells greater than 0.5. Subsequently, genes with the highest correlation coefficient with one of the first three or four principal components were identified using dimdesc function in FactoMineR. Hierarchical clustering was performed on cells and on the genes identified by PCA using Euclidean distance or correlation metric.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrices (TMM-FPKM value) of each gene in each cells in CSV format

growth_protocol: C57BL/6 male mice between 8-12 weeks of age were used for all experiments. Mice were purchased from Charles River or bred in house at the DKFZ Center for Preclinical Research facility. Animals were housed under standard conditions and fed ad libitum. All procedures were in accordance to the DKFZ guidelines and approved by the Regierungpräsidium Karlsruhe. Global ischemia was performed using the bilateral common carotid artery occlusion method essentially. Briefly, mice were deeply anesthetized and a laser Doppler probe (Perimed) was fixed at the skull for continuous measurements of regional cerebral blood flow (rCBF). Next, both common carotid arteries were exposed and clamped with surgical microclamps (Stoelting) for a period of 22 minutes prior to reperfusion. Only animals with an ischemic rCBF smaller than 13% of the pre-ischemic value were used.

extract_protocol:
Animals were sacrificed by cervical dislocation and their brains immediately placed on ice. The lateral SVZ was microdissected as a whole mount as previously described 2. Pooled SVZ tissue (1-5 mice) was digested with trypsin and DNAse according to the Neural Tissue Dissociation kit in a Gentle MACS dissociatior (Miltenyi) to maximize cell viability and recovery. Cells were stained for 20 minutes on ice in DPBS (without Ca and Mg) supplemented with 10% fetal calf serum. Combinations of the following antibodies were used: APC and PE anti-GLAST (ACSA-1, Miltenyi, 1/40), APC anti O4 (Miltenyi, 1:40), PE-Vio770 anti PSA-NCAM (Miltenyi, 1/50), APC and PerCP-eFluor710 anti-Prominin-1 (eBioscience, 1/75), Alexa488::EGF (Life Technologies, 1/100), APC-Cy7 anti-CD45 (BD, 1/200). Sytox Blue (Life Technologies, 1/1000) was added to the cell suspension prior to sorting. Stained cell suspensions were sorted in a FACSAriaII (BD) using a 100um nozzle at 20psi. Cells were collected in ice-cold Neurobasal medium supplemented with L-Glutamine, B27 and Penicillin/Streptomycin at a density of approx. 1cell/ul. TAP cells were isolated from the SVZ based on EGFpos GLAST/CD45/PSA-NCAM/O4neg. Str refers to GLASTpos CD45/O4neg cells from the striatum (SVZ was excluded). Str refers to GLASTpos CD45/O4neg from the somatosensory cortex. Immediately after sorting cells were manually picked with a thin gel-loading micropipette under continuous visual inspection in a Zeiss microscope. To ensure that only one cell was picked, we transferred sequentially 1ul of the cell suspension to the picking plate where a single cell was immediately picked in 0.3ul with another pipette before the addition of a new cell to the plate. Cells were directly transferred to ice-cold lysis buffer (0.2%Triton X-100 containing RNAse inhibitors, Clontech) and frozen at -80ºC until library preparation. Cells labeled as PSA, were sorted according to CD45negPSA-NCAMposGLASTneg; all the other cells were CD45negPSA-NCAMnegGLASTposPROM1pos.
RNA-seq libraries were prepared using Smart-seq2 technology as previously described. Briefly, lysed cells were thawed and subject to reverse transcription using an oligo(dT) primer and a locked nucleic acid (LNA)-containing template-switching oligonucleotide (Exiqon). In a randomly selected set of samples we included ERCC Spike-Ins (Ambion) at a 1:1000000 dilution. Full-length cDNAs were amplified by 20 cycles of PCR using KAPA HiFi DNA polymerase (KAPA biosystems). Amplified cDNAs for every single cell were quantified and run on a High Sensitivity Bioanalyzer chip (Agilent). Samples containing no material or in which the cDNA appeared degraded were excluded (approx. 5-10%) from further processing. cDNAs were then converted into libraries for Illumina sequencing according to the Nextera XT Sample Preparation (Illumina) protocol with minor modifications. Specifically, we extended the tagmentation step to 8 minutes and performed a double cleanup with 0.8X AMPure XP SPRI beads (Agencourt) after PCR amplification for 9 cycles. To control for technical variability we performed two replicate DNA libraries with cDNA from the same cell. For population studies, approx. 1ng of total RNA from 1000 cells was subject to SMARTer Ultra Low RNA kit (Clontech) according to the manufacturer?s instructions. cDNA products were quantified, run in a Bioanalyzer and subject to Illumina library preparation according to NEBNext  Ultra DNA Library Preparation Kit (NEB). Libraries were quantified, pooled at equal concentrations and the multiplex was cleaned up again with 1X AMPure beads and measured in a Bioanalyzer prior to 101bp paired-end sequencing in an Illumina HiSeq 2000.

value: 8 weeks

value: Cortex

tag: cell type

value: Astrocytes

tag: sample group

value: homeostasis samples


title: Single_cell_RNASeq [ctx12]


title: Single_cell_RNASeq [ctx1]


title: Single_cell_RNASeq [ctx18]


title: Single_cell_RNASeq [ctx16]


title: Single_cell_RNASeq [ctx17]


title: Single_cell_RNASeq [ctx2]


title: Single_cell_RNASeq [ctx20]


title: Single_cell_RNASeq [ctx5]


title: Single_cell_RNASeq [ctx3]


title: Single_cell_RNASeq [ctx7]


title: Single_cell_RNASeq [ctx21]


title: Single_cell_RNASeq [ctx23]


title: Single_cell_RNASeq [ctx6]


title: Single_cell_RNASeq [ctx8]


title: Single_cell_RNASeq [str33]

value: Striatum


title: Single_cell_RNASeq [str35]


title: Single_cell_RNASeq [str27]


title: Single_cell_RNASeq [str40]


title: Single_cell_RNASeq [str42]


title: Single_cell_RNASeq [tap54]

value: Subventricular zone

value: Neural progenitors


title: Single_cell_RNASeq [tap50]

value: male


title: Single_cell_RNASeq [ctx19]


title: Single_cell_RNASeq [tap55]


title: Single_cell_RNASeq [tap56]


title: Single_cell_RNASeq [tap58]


title: Single_cell_RNASeq [tap59]


title: Single_cell_RNASeq [tap62]


title: Single_cell_RNASeq [tap60]


title: Single_cell_RNASeq [tap61]


title: Single_cell_RNASeq [tap66]


title: Single_cell_RNASeq [tap68]


title: Single_cell_RNASeq [tap64]


title: Single_cell_RNASeq [tap65]


title: Single_cell_RNASeq [tap69]


title: Trp53 R172H/R172H mouse PolyA+ RNAseq

city: Philadelphia

first: Morgan

last: Sammons

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: PolyA+ RNAseq in primary p53 R172H knock-in MEFs

data_processing:
Raw fastq files were aligned to mm9 using Bowtie2, allowing for only uniquely aligned reads to be reported.
bowtie2 -N1 -k1 mm9
Uniquely mapped reads were processed into HOMER TagDirectories (makeTagDirectory <file> <TagDir_file>)
Bedgraphs were then generated using the command 'makeUCSCfile <ChIP_TagDirectory> -o auto'
Expression values (FPKM) for RNAseq experiments were derived using HOMER (analyzeRepeats.pl mm9 -condenseGene)
genome build:mm9
processed data files format and content: Text file (of FPKM expression values from RNAseq)
processed data files format and content: BedGraph files (from HOMER, for visualization in UCSC)

source_name: Trp53 R172H/R172H mouse

growth_protocol: All cells were grown in DMEM with 10% FBS, at 3% oxygen.

extract_protocol:
For ChIP-seq, cells were crosslinked with formaldehyde (1% final) for 10min at room temperature, and harvested for sonication.  Nuclei were extracted and chromatin was sheared to an average size of 200bp using a Covaris S220 sonicator
For RNA-seq, polyA+ RNA was isolated by two rounds of polyA selection using the Life Technologies mRNADirect kit per manufacturer's recommendations.
Sequencing libraries for ChIP-seq were constructed using the NEBNext Ultra kit as per manufacturer's recommended instructions.  Sequencing libraries for polyA+, stranded-RNA-seq were constructed using the NEBnext Ultra Directional RNAseq kit as per manufacturer's recommended instructions.

treatment_protocol: As indicated in the SAMPLES section

tag: p53 mutation status

value: Untreated

tag: antibody


title: Single_cell_RNASeq [tap72]

tag: tissue


title: WT mouse PolyA+ RNAseq

description: PolyA+ RNAseq in primary WT MEFs

source_name: WT mouse

value: WT


title: Single_cell_RNASeq [tap73]


title: Single_cell_RNASeq [tap49]


title: Trp53 R172H/R172H mouse Histone H3

description: ChIPseq for H3 in primary p53 R172H Knock-in MEFs

value: Histone H3 Abcam (ab1791)


title: Single_cell_RNASeq [tap74]


title: Single_cell_RNASeq [tap76]


title: Single_cell_RNASeq [tap75]


title: WT mouse Histone H3

description: ChIPseq for H3 in primary WT MEFs


title: Single_cell_RNASeq [tap63]


title: WT mouse H3K4me3

description: ChIPseq for H3K4me3 in primary WT MEFs

value: H3K4me3 Abcam (ab8580)


title: Single_cell_RNASeq [tap77]


title: Trp53 R172H/R172H mouse H3K4me3

description: ChIPseq for H3K4me3 in primary p53 R172H Knock-in MEFs


title: H3K4me3 ChIP_MDA-MB-468_p53 shRNA

description: H3K4me3 ChIP in MDA-MB-468 with p53 shRNA

data_processing:
Raw fastq files were aligned to hg18/ncbi36 using Bowtie, allowing for only uniquely aligned reads to be reported.
bowtie --chunkmbs 512 -m 1 --best <hg18_index> -q <file.fastq>  <file.map>
Significant p53 Peaks were called using HOMER,  First, HOMER-specifc TagDirectories were generated from bowtie output files (file.map) using the command 'makeTagDirectory <ChIP_TagDirectory> <ChIP_Bowtie_output.map> '
Peaks were then called using command 'findPeaks <tag directory> -style <factor|histone|groseq> -o auto -i <control tag directory>'
p53 Bedgraphs were then generated using the command 'makeUCSCfile <ChIP_TagDirectory> -o auto'
For H3K4me3-H3, track views were generated by binning all chIP-seq tags by the position of the tag head into non-contiguous, overlapping 10bp bins for both H3K4me3 and H3. Bin scores were then normalized by the number of millions of reads aligned and H3 scores were subtracted from H3K4me3 scores to normalize for sonication efficiency artifacts
Genome_build: ncbi36/hg18
Supplementary_files_format_and_content: BedGraph files (from HOMER, for visualization in UCSC)
Supplementary_files_format_and_content: BigWig files (for visualization in UCSC)

growth_protocol: All cells were grown in DMEM with 10% FBS, at 20% oxygen.

extract_protocol:
For ChIP-seq, cells were crosslinked with formaldehyde (1% final) for 10min at room temperature, and harvested for sonication.  Nuclei were extracted and chromatin was sheared to an average size of 200bp using a Diagenode Bioruptor.
Sequencing libraries for ChIP-seq were constructd using the NEBNext Ultra kit as per manufacturer's recommended instructions

tag: cell line

value: breast cancer cell line

tag: transfected with

value: p53 shRNA

tag: chip antibody

value: Anti-Histone H3 (tri methyl K4)

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: H3K4me3 ChIP_MDA-MB-468_control shRNA

description: H3K4me3 ChIP in MDA-MB-468 with control shRNA

value: control shRNA


title: Single_cell_RNASeq [tap70]

value: 8 weeks


title: H3 ChIP_MDA-MB-468_p53 shRNA

description: H3 ChIP in MDA-MB-468 with p53 shRNA

value: Anti-Histone H3


title: H3 ChIP_MDA-MB-468_control shRNA

description: H3 ChIP in MDA-MB-468 with control shRNA


title: Single_cell_RNASeq [tap87]


title: N_PSA_8

source_name: Single cell in Subventricular zone

treatment_protocol: Global ischemia was performed using the bilateral common carotid artery occlusion method essentially as previously described 1. Briefly, mice were deeply anesthetized and a laser Doppler probe (Perimed) was fixed at the skull for continuous measurements of regional cerebral blood flow (rCBF). Next, both common carotid arteries were exposed and clamped with surgical microclamps (Stoelting) for a period of 22 minutes prior to reperfusion. Only animals with an ischemic rCBF smaller than 13% of the pre-ischemic value were used.

value: WT; homeostasis sample

value: Male


title: Single_cell_RNASeq [tap86]

value: homeostasis samples


title: N_PSA_7

value: Subventricular zone


title: p53 ChIP_BT549

description: p53 ChIP in BT549

value: Anti-p53, clone DO-1

value: EMD Millipore


title: N_PSA_4


title: p53 ChIP_MDA-MB-468

description: p53 ChIP in MDA-MB-468


title: p53 ChIP_MCF7

description: p53 ChIP in MCF7

value: p53 WT


title: Single_cell_RNASeq [tap84]

value: male

value: Neural progenitors


title: N_PSA_31


title: N_PSA_30


title: N_PSA_32


title: p53 ChIP_MDA-MB-175VII

description: p53 ChIP in MDA-MB-175VII


title: Input

description: Chromatin immunoprecipitation

source_name: pancreas/brain

value: pancreas and brain

value: 8-10 week old


title: N_PSA_3


title: Single_cell_RNASeq [tap85]


title: N_PSA_29


title: Wt E17.5 brain SMC1-R2_ChIP-seq

description:
Processed data file: EBrain_SMC1_Losada.bed
Chromatin immunoprecipitation

source_name: whole brain

value: whole brain

value: E17.5 embryo


title: N_PSA_28


title: KO E17.5 brain SMC1-R1_ChIP-seq

description:
Processed data file: KO_SMC1_Losada.bed
Chromatin immunoprecipitation


title: N_PSA_27


title: N_PSA_25


title: Wt E17.5 brain SMC1-R1_ChIP-seq


title: Wt E17.5 brain SA1-R1_ChIP-seq

description:
Processed data file: EBrain_SA1_Losada.bed
Chromatin immunoprecipitation


title: N_PSA_26


title: p53 ChIP_HCC70

description: p53 ChIP in HCC70

value: breast cancer cell line


title: N_PSA_6


title: Pancreas RNAPolII-R2_ChIP-seq

description:
Processed data file: Pancreas_PolII_Losada.bed
Chromatin immunoprecipitation

value: pancreas


title: Wt E17.5 brain SA1-R2_ChIP-seq


title: Pancreas RNAPolII-R1_ChIP-seq


title: N_PSA_23


title: Adult cortex RNAPolII-R2_ChIP-seq

description:
Processed data file: Abrain_PolII_Losada.bed
Chromatin immunoprecipitation

source_name: cortex

value: cortex


title: N_PSA_24


title: N_PSA_19


title: Pancreas SMC1-R1_ChIP-seq

description:
Processed data file: Pancreas_SMC1_Losada.bed
Chromatin immunoprecipitation


title: N_PSA_20


title: N_PSA_18


title: Adult cortex RNAPolII-R1_ChIP-seq


title: N_PSA_21


title: KO E17.5 brain SMC1-R2_ChIP-seq


title: N_PSA_17


title: N_PSA_16


title: N_PSA_15


title: Adult cortex SMC1-R1_ChIP-seq

description:
Processed data file: ABrain_SMC1_Losada.bed
Chromatin immunoprecipitation


title: Pancreas SA1-R2_ChIP-seq

description:
Processed data file: Pancreas_SA1_Losada.bed
Chromatin immunoprecipitation


title: Pancreas SA1-R1_ChIP-seq


title: Adult cortex SMC1-R2_ChIP-seq


title: N_PSA_14


title: N_PSA_13


title: N_PSA_10


title: N_GP_9


title: N_GP_8B


title: Adult cortex SA1-R2_ChIP-seq

description:
Processed data file: ABrain_SA1_Losada.bed
Chromatin immunoprecipitation


title: Adult cortex SA1-R1_ChIP-seq


title: N_PSA_11


title: N_GP_7B


title: N_GP_7


title: N_GP_6


title: N_GP_5B


title: N_GP_55


title: N_GP_53


title: N_GP_50


title: N_GP_51


title: wt_62

tag: treatment

value: Ischemic injured


title: N_GP_5

value: WT; homeostasis sample


title: wt_60

value: Male


title: wt_59


title: N_GP_4B


title: N_GP_48


title: wt_58


title: N_GP_47


title: wt_54


title: wt_53


title: N_GP_6B


title: N_GP_46


title: N_GP_45


title: N_GP_44


title: wt_52


title: wt_64


title: N_GP_43


title: N_GP_42


title: wt_49


title: wt_50


title: N_GP_40S


title: wt_48


title: Pancreas SMC1-R2_ChIP-seq


title: wt_57


title: N_GP_39S


title: N_GP_38S


title: ik_8

value: Ischemic injured and Interferon gamma knockout


title: N_GP_35S

value: Subventricular zone


title: N_GP_33S


title: N_GP_34S


title: ik_6


title: N_GP_32B


title: wt_51


title: ik5


title: N_GP_32


title: ik_7


title: N_GP_31B


title: ik_41


title: N_GP_30


title: ik_44


title: N_GP_2B


title: N_GP_31


title: N_GP_29B


title: ik4


title: ik_43


title: ik_39


title: N_GP_30B


title: N_GP_3B


title: ik_36


title: ik_34


title: ik_42


title: N_GP_3


title: ik_9


title: N_GP_26B


title: N_GP_28B


title: N_GP_24


title: N_GP_28


title: ik_33


title: N_GP_27B


title: N_GP_23B


title: ik_31


title: N_GP_23


title: N_GP_27


title: ik_30


title: ik_28


title: Ik3


title: ik_27


title: ik_25


title: ik_26


title: N_GP_22


title: ik_29


title: N_GP_21B


title: ik_24


title: N_GP_2


title: ik_23


title: N_GP_20B


title: ik_21


title: N_GP_25


title: N_GP_20


title: ik_19


title: ik_20


title: N_GP_1B


title: N_GP_22B


title: N_GP_19B


title: Neg1240

city: Seattle

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

description: Neg

data_processing:
Basecalls were performed using CASAVA version 1.8.2.
Reads were aligned to the mm9 genome using BWA (0.7.5).
Peaks were called using in-house peak calling algorithm.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: ChIP-Seq peaks in bed format.

source_name: Negative control. ChIP-Seq with NeuroD2 antibody 1240 in mouse P19 cells

extract_protocol:
Cells were fixed in 1% formaldehyde for 11 minutes, quenched with glycine, lysed, and then sonicated to generate final DNA fragments of ~150-600 bp.
The soluble chromatin was diluted 1:10 and pre-cleared with a 1:1 Protein A:G slurry for 2 hours at 4oC. Chromatin was mixed with antibody overnight at 4oC, then Protein A:G beads for 2 hours. Beads were washed and de-crosslinked overnight for ~16 hours in 1% SDS, 0.1M NaHCO3 and 70 ug Proteinase K. The MyoD and NeuroD2 antibodies were raised in our lab.
Sequencing libraries were constructed using Nugen Ovation Ultralow Multiplex DR.

treatment_protocol: P19 cells were infected in MEMα media containing polybrene at a final concentration of 8 µg /ml. After 24 hours, media was replaced with fresh MEMα, and after 48 hours, cells were transitioned to Neurobasal media (GIBCO) containing B27 supplement and 5 mm glutamine(8). Neurobasal media was replaced every 24 hours until cells were harvested.

tag: transduction

value: NeuroD2 antibody 1240


title: ik_18


title: ND2M21240

description:
ND2
Processed data file: ND2.bed.gz

source_name: ChIP-Seq with NeuroD2 antibody 1240 in mouse P19 cells transduced with NeuroD2


title: N_GP_18B


title: N_GP_18


title: N_GP_17B


title: N_GP_19


title: ik_15


title: ND2M21165

description:
ND2
Processed data file: ND2.bed.gz

source_name: ChIP-Seq with NeuroD2 antibody 1165 in mouse P19 cells transduced with NeuroD2

value: NeuroD2 antibody 1165


title: MDND2WC6975

description:
MDND2WC
Processed data file: MDND2WC.bed.gz

source_name: ChIP-Seq with MyoD antibody 6975 in mouse P19 cells transduced with MD(ND2bHLH)WC mutant

value: MD(ND2bHLH)WC mutant

value: MyoD antibody 6975


title: ik_17


title: MDND2WCS6975

description:
MDND2WCS
Processed data file: MDND2WCS.bed.gz

source_name: ChIP-Seq with MyoD antibody 6975 in mouse P19 cells transduced with MD(ND2bHLH)WCS mutant

value: MD(ND2bHLH)WCS mutant


title: MDND2ChB

description:
P19MDND2
Processed data file: MDND2.bed.gz

source_name: ChIP-Seq with MyoD antibody 6975 in mouse P19 cells transduced with MD(ND2bHLH) chimera

value: MD(ND2bHLH) chimera


title: MDND2WC6196

source_name: ChIP-Seq with MyoD antibody 6196 in mouse P19 cells transduced with MD(ND2bHLH)WC mutant

value: MyoD antibody 6196


title: N_GP_17


title: ik_14


title: ik_40


title: ik_13


title: MDChB

description:
P19MD
Processed data file: MD.bed.gz

source_name: ChIP-Seq with MyoD antibody 6975 in mouse P19 cells transduced with MyoD

value: MyoD


title: Neg6975

description: Neg

source_name: Negative control. ChIP-Seq with MyoD antibody 6975 in mouse P19 cells


title: N_GP_16


title: N_GP_16B


title: ik_11


title: MDChA

description:
P19MD
Processed data file: MD.bed.gz

source_name: ChIP-Seq with MyoD antibody 6196 in mouse P19 cells transduced with MyoD


title: MDND2WCS6196

source_name: ChIP-Seq with MyoD antibody 6196 in mouse P19 cells transduced with MD(ND2bHLH)WCS mutant


title: MDND2WCS.100

data_processing:
Basecalls were performed using CASAVA version 1.8.2.
Reads were aligned to the mm9 genome using tophat 2.0.8.
Read counts for the genes were collected by Bioconductor Biostrings and IRanges packages.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Gene.counts.txt contains the raw read counts for each gene in all samples.

source_name: mouse P19 cells transduced with MD(ND2bHLH)WCS mutant, MOI 100

extract_protocol:
Using the Qiagen RNeasy kit or Trizol, total RNA was harvested from lentivirally transduced P19 cells that were neuronally differentiated as described in treatment protocol.
RNA libraries were prepared using oligo-dT selection and sequenced on the Illumina HiSeq 2500 according to the manufacturer's instructions.

value: MD(ND2bHLH)WCS mutant, MOI 100


title: N_GP_15B


title: N_GP_15


title: MDND2

source_name: mouse P19 cells transduced with MD(ND2bHLH) chimera


title: ND2

source_name: mouse P19 cells transduced with NeuroD2


title: MDND2.100

source_name: mouse P19 cells transduced with MD(ND2bHLH) chimera, MOI 100

value: MD(ND2bHLH) chimera, MOI 100


title: Ik1

source_name: Single cell in Subventricular zone


title: MDND2WCS

source_name: mouse P19 cells transduced with MD(ND2bHLH)WCS mutant


title: N_GP_14B


title: MD

source_name: mouse P19 cells transduced with MyoD


title: GFP

source_name: mouse P19 cells transduced with GFP

value: GFP


title: N_GP_14


title: MDND2ChA

source_name: ChIP-Seq with MyoD antibody 6196 in mouse P19 cells transduced with MD(ND2bHLH) chimera


title: N_GP_13B


title: N_GP_11


title: N_GP_13


title: Single_cell_RNASeq [ctx22]

value: male

value: 8 weeks

value: Cortex

value: Astrocytes

value: homeostasis samples


title: L4184_NULL_P1_S3

city: Dresden

first: Anthony

last: Gavalas

address: Fetscherstr. 105

institute: TU Dresden

data_processing:
Alignment of the short reads to the mm9 transcriptome was performed with pBWA, version 0.5.9-r32-MPI-patch2 (Peters et al., 2011).
Counts per gene were computed based on the Ensembl Genes v.67 annotation for mouse using BEDtools (v. 2.11).
Normalization of the raw readcounts based on the library size and testing for differential expression between the different cell types/treatments was performed with the DESeq R package (v.1.10.1)
Genome_build: mm9
Supplementary_files_format_and_content: p363_PROCESSED_RNA-SEQ.xlsx contains genes being differentially expressed and the complete counts table for all samples. For analysis raw data fastq files for individual samples were merged.

growth_protocol: Islets isolated from fresh pancreata

extract_protocol:
Total RNA was prepared using the RNeasy kit (Qiagen) with on-column genomic DNA digestion.
mRNA was isolated from 1ug total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturers instructions. Final elution was done in 15ul 2x first strand cDNA synthesis buffer (NEBnext, NEB). After chemical fragmentation by incubating for 15 min at 94°C the sample was directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB). For ligation custom adaptors were used  (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3'). After ligaton adapters were depleted by an XP bead purification (Beckman Coulter) adding bead in a ratio of 1:1. Indexing was done during the following PCR enrichment (15 cycles) using custom amplification primers carring the index sequence indicated with ‘NNNNNN’. (Primer1: Oligo_Seq AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, primer2: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, primer3: CAAGCAGAAGACGGCATACGAGAT NNNNNN GTGACTGGAGTT. After two more XP beads purifications (1:1) libraries were quantified using Qubit dsDNA HS Assay Kit (Invitrogen). For Illumina flowcell production, samples were equimolarly pooled and distributed on all lanes used for 75bp single read sequencing on Illumina HiSeq 2500.

treatment_protocol: Maintained for two hours in RPMI-1640 supplemented with 10% FBS

value: postnatal day 1

tag: genotype/variation

value: Aldh1b1 null

value: islets


title: N_GP_11B

value: WT; homeostasis sample

tag: age

value: Subventricular zone

value: Male


title: L4183_NULL_P1_S2


title: ik_10

value: Ischemic injured and Interferon gamma knockout

tag: gender


title: N_GP_12B


title: N_GP_12


title: L4179_WT_P1_S1

value: wild type


title: L4182_NULL_P1_S1


title: N_GP_10B


title: MDND2WC

source_name: mouse P19 cells transduced with MD(ND2bHLH)WC mutant

value: MD(ND2bHLH)WC mutant


title: L4181_WT_P1_S3


title: L3524_MUT219_WK8

value: Aldh1b1tm1lacz; Aldh1b1 null


title: N_GP_1


title: L3522_MUT229_WK8


title: L3520_WT2_WK8


title: L3521_WT3_WK8


title: N7


title: N6


title: N48


title: N5


title: N46


title: L3519_WT1_WK8


title: N45


title: L4180_WT_P1_S2


title: N38


title: L3523_MUT218_WK8


title: N4


title: N42


title: N37


title: N35


title: N31


title: N36


title: N3


title: N33


title: N9


title: N30


title: N29


title: N24


title: N22


title: N34


title: N18


title: N27


title: N23


title: N2


title: N11


title: N26


title: I_GP_7

value: Ischemic injured


title: N1


title: I_GP_24


title: N13


title: I_GP_9


title: N28


title: I_GP_3


title: I_GP_4


title: I_GP_18


title: N17


title: I_GP_23


title: N25


title: I_GP_21


title: I_GP_8


title: I_GP_19


title: I_GP_20


title: I_GP_5


title: I_GP_16


title: I_GP_17


title: I_GP_10


title: I7


title: I_GP_15


title: I_GP_14


title: I_GP_11


title: I48


title: I_GP_6


title: I47


title: I46


title: I41


title: I40


title: I42


title: I38


title: I33


title: I37


title: I31


title: I_GP_13


title: I30


title: I27


title: I32


title: I24


title: I3


title: I9


title: I_GP_12


title: I23


title: IP8-wt

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

description:
total RNA - polyA-enrichment
RNA-interacting immunprecipitation for GFP-AGO2 fusion protein
Sample 20

data_processing:
Reads were mapped to the mouse genome using STAR [default settings]
Reads were quantitated using the Rsubread package for R using RefSeq and miRbase 3'UTR annotation
Differential expressed genes were found using EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing abundance measurements of mRNA features from refseq (gfp* and mir* samples) or ensembl (ip* samples). Whitespace separated. Columns: [GeneID – length - #reads mapping to feature]

source_name: Fresh hippocampal tissue

extract_protocol:
For IP samples: AGO2-RIP was conducted on fresh hippocampal tissue, followed by an incubation time of 24h. RNA was then extracted by using the miRNeasy micro kit from Qiagen.
Other samples: RNA was extracted from fresh hippocampal tissue using the RNeasy mini kit from Qiagen.
RNA libraries were prepared using NuGen (IP samples) and Illumina kits.

treatment_protocol: AAV5 injections into the hippocampus of adult C57BL/6 mice producing either of the following under a synapsin promoter: GFP only (Samples beginning with ‘GFP124…’ or ‘GFP125…’), GFP-miR124sp (Samples beginning with ‘miR124…’), GFP-miR125sp (Samples beginning with ‘miR125…’), GFP-AGO2-miR292sponge (samples ending with ‘…292’), GFP-AGO2-miR124sponge (samples ending with ‘…124’), GFP-AGO2-miR125sponge (samples ending with ‘…125’). All other samples were sham-injected.

tag: strain

value: sham control

tag: tissue type

value: fresh hippocampal tissue

value: hippocampal neurons

tag: ip antibody

value: GFP

tag: ip antibody vendor

value: abcam

tag: ip antibody cat. #

value: ab6556 and ab290


title: I19


title: I16


title: I44


title: I11


title: I1


title: IP1-125

description:
total RNA - polyA-enrichment
RNA-interacting immunprecipitation for GFP-AGO2 fusion protein
Sample 13

value: producing GFP-AGO2-miR125sponge under a synapsin promoter

tag: cell type


title: IP2-125

description:
total RNA - polyA-enrichment
RNA-interacting immunprecipitation for GFP-AGO2 fusion protein
Sample 14


title: IP4-124

description:
total RNA - polyA-enrichment
RNA-interacting immunprecipitation for GFP-AGO2 fusion protein
Sample 16

value: producing GFP-AGO2-miR124sponge under a synapsin promoter


title: IP5-292

description:
total RNA - polyA-enrichment
RNA-interacting immunprecipitation for GFP-AGO2 fusion protein
Sample 17

value: producing GFP-AGO2-miR292sponge under a synapsin promoter


title: miR125-9

description: Sample 12

source_name: Freshly frozen hippocampal tissue

value: producing GFP-miR125sp under a synapsin promoter

value: freshly frozen hippocampal tissue


title: miR125-6

description: Sample 11


title: miR125-24

description: Sample 10


title: miR124-2

description: Sample 8

value: producing GFP-miR124sp under a synapsin promoter


title: miR124-14

description: Sample 7


title: GFP125-4

description: Sample 6

value: producing GFP under a synapsin promoter


title: miR124-9

description: Sample 9


title: GFP125-14

description: Sample 4


title: GFP125-15

description: Sample 5


title: GFP124-15

description: Sample 1


title: GFP124-20

description: Sample 2


title: GFP124-8

description: Sample 3


title: IP6-292

description:
total RNA - polyA-enrichment
RNA-interacting immunprecipitation for GFP-AGO2 fusion protein
Sample 18


title: C57BL/6

city: Solna

first: Emma

last: Lundberg

address: Science for Life Laboratory, Tomtebodavägen 23A

institute: KTH Royal Institute of Technology

data_processing:
rsem_prepare_reference, prepared using a canonical reference genome fasta file (GRCm38_canon.fa) and canonical GTF gene model file (Mus_musculus.GRCm38.74.gtf).
rsem_calculate_abundance
Genome_build: GRCm38_canon.fa
Supplementary_files_format_and_content: Tabular files with transcript isoform abundances were generated for each sample.

source_name: pancreatic islets

extract_protocol:
Male C57BL/6J (B6) and CAST/EiJ (CAST) mice were purchased from The Jackson Laboratories (Bar Harbor, Maine) and housed in an environmentally controlled vivarium at the University of Wisconsin Biochemistry Department. Mice were provided standard rodent chow (Purina no. 5008) and water ad libitum, and maintained on a 12-hour light/dark cycle (6 AM – 6 PM). At 10 weeks of age, mice were sacrificed by CO2 asphyxiation. All animal procedures were preapproved by the University of Wisconsin Animal Care and Use Committee.
Intact pancreatic islets were isolated using a collagenase digestion procedure as previously described.[20] Briefly, 5 ml of collagenase type XI (Sigma), dissolved in Hanks’ balanced salt solution (Gibco), was injected into the pancreas via the common bile duct (0.45 mg/ml with 0.02% BSA). The pancreas was removed and incubated at 37°C for 16 min with intermittent agitation. A ficol gradient was used to partially purify islets from the digested pancreas, followed by further purification by manual picking under a stereomicroscope. During the purification procedure, islets were maintained in Krebs-Ringer bicarbonate buffer containing (mM): 118.41 NaCl, 4.69 KCl, 2.52 CaCl2, 1.18 MgSO4, 1.18 KH2PO4, 25 NaHCO3 and 5 HEPES supplemented with 0.2% BSA and 16.7 mM glucose. Islets from two B6 mice (and separately two CAST mice) were pooled and then apportioned for RNA-Seq (250 islets per sample) and protein analyses (remainder: 400 B6 islets, 470 CAST islets). For RNA profiling, whole islet RNA was purified as previously described yielding ~1 µg total RNA.[21] For protein analyses, islets were washed 3 times in ice-cold PBS, gently pelleted and snap frozen in liquid nitrogen.

tag: tissue

value: pancreatic islets


title: CAST

value: CAST


title: PDGFRαC Mu Colon

city: Reno

first: Seungil

last: Ro

state: NV

address: 1664 North Virginia St

department: Physiology and Cell Biology

institute: University of Nevada School of Medicine

description: Sample 10

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned against mouse genome (mm9) for junction identification using Tophat v1.4.1.
Abundance estimation and differential expression analysis are done using Cufflinks v2.0.2.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: isoforms_fpkm_tracking_04172013.xlsx: differential expression analysis using Cuffdiff

source_name: PDGFRα cells in colon mucosa

extract_protocol:
mirVana miRNA Isolation Kit
TruSeq RNA Sample Preparation

tag: background strain

value: PdgfraeGFP/+

tag: strain name (jackson lab)

value: 4 weeks

value: Colon mucosa

value: PDGFRalpha

tag: cell population

value: Sorted primary cells


title: Mu Colon

description: Sample 9

source_name: Colon mucosa

value: mucosal

value: Unsorted mixed cells


title: IP7-wt

description:
total RNA - polyA-enrichment
RNA-interacting immunprecipitation for GFP-AGO2 fusion protein
Sample 19

value: sham control

value: fresh hippocampal tissue

value: hippocampal neurons

value: GFP

value: abcam

value: ab6556 and ab290


title: IP3-124

description:
total RNA - polyA-enrichment
RNA-interacting immunprecipitation for GFP-AGO2 fusion protein
Sample 15

value: producing GFP-AGO2-miR124sponge under a synapsin promoter


title: SM Jejunum

description: Sample 7

source_name: Jejunum SM

value: KitcopGFP/+

value: Jejunum

value: SM


title: SM Colon

description: Sample 8

source_name: Colon SM

value: Colon


title: PDGFRαC Colon

description: Sample 6

source_name: PDGFRα cell in colon

value: PdgfraeGFP/+

value: 4 weeks


title: PDGFRαC Jejunum

description: Sample 5

source_name: PDGFRα cells in jejunum

value: PDGFRalpha


title: ICC Colon

description: Sample 4

source_name: ICC in colon

value: ICC

value: Sorted primary cells


title: N7_s_2_sequence_aligned.fastq

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Basecalling was done using Illumina CASAVA v1.4
Sequences were adaptor trimmed and aligned to hg18 genome using Novoalign V2.0.
Known piRNA sequences were downloaded from a publically available piRNA database (RNAdb: http://research.imb.uq.edu.au/rnadb/). The hg18 genome loci that matched perfectly to the piRNA sequences were identified and piRNA expression levels were counted using R scripts.
Genome_build: hg18
Supplementary_files_format_and_content: text format containing expression counts

source_name: Nomral renal tissue

extract_protocol:
Total RNA was isolated using the Recover All Total Nucleic Acid Isolation Kit (Ambion, Austin, TX, USA), following the manufacturers' protocols.
Libraries were prepared according to Illumina's instructions

tag: Stage

value: Normal


title: SMC Colon

description: Sample 2

source_name: SMC in colon

value: smMHCCre-eGFP/+

value: SMC


title: ICC Jejunum

description: Sample 3

source_name: ICC in jejunum


title: YP_Control-2_miRNA-seq

city: Beijing

first: Bo

last: Zhang

address: No. 2 Yuanmingyuan West Road, College Animal Science & Technology, China Agriculture University, Beijing

institute: China Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Sscrofa10.2.72 whole genome using bowtie v0.12.5 and  mirdeep2_0_0_2
All of the clean reads were initially searched against miRBase20.0 to identify known miRNAs and miRNA hairpins;unmappable reads subsequently were annotated and classified by reference to non-coding RNAs in the NONCODE database (version3.0), and Rfam (version11.0) database
We provided the known mature miRNA for pig, human, mouse, cow, sheep (326,257,1908,783,153, respectively) from miRBase 20.0 for use in software mirdeep2_0_0_2 to predict the pig novel  miRNA.
Transcripts per million (TPM) was calculated in the edgeR package using a protocol from Li et al., Bioinformatics, 2010. This is a two-step procedure of TPM normalization between compared libraries. First, the normalization factors were calculated by edgeR for each library. Second, the normalized read counts were calculated by the following formula: normalized read counts = mapped read count/Total reads × 106.
Genome_build: Sscrofa10.2.72
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample …

organism: Sus scrofa

extract_protocol:
Hearts were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Yorkshire pig

value: heart

value: 6 months

tag: Sex

value: male


title: SMC Jejunum

description: Sample 1

source_name: SMC in jejunum