title: 26P

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

institute: University of Illinois at Urbana

description: Peritoneal macrophages were obtained and RNA extracted using standards protocols (Nikodemova and Watters, 2012 Journal of Neuroinflammation; Gelsthorpe, Gelshorpe and Sokol, 1997, BioTechniques)

data_processing:
Quality-scores line in fastq files processed with Casava1.8 use an ASCII offset of 33
Sequences were trimmed for adaptor seuqences and masked for low-complexity and low-quality
100 nt paired-end reads were mapped to the C57Bl/6J mouse genome (version GRCm38) using TopHat v2.0.6 and default settings (Trapnell et al., 2012; Nature Protocols)
Reads were assembled into transcript isoforms using Cufflinks Version 2.1.1 (Trapnell et al., 2012)
Genome_build: C57Bl/6J mouse genome (version GRCm38)
Supplementary_files_format_and_content: csv format, comma-delimited file including RPKM values for each sample, one column per sample

source_name: Peripheral macrophages

extract_protocol:
Following cell storage in Trizol, RNA was extracted based upon the Tri-spin method (Reno et al., 1997 Biotechniques)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: BCG challenge

value: 22 weeks

tag: gender

value: male


title: SmartSeqA_C9

status: Public on Sep 09 2016

type: SRA

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

description: Library preparation was performed with the Fluidigm C1 platform as per manufacturers' protocol.

library_source: transcriptomic

data_processing:
base-calls were performed with Illumina bcl2fastq
all cDNA reads were aligned with Star v2.4.0
SCRB-seq and Drop-seq protocol reads were tagged with its mate-pair UMI and cell barcode; unique reads were obtained; more information see README file
Smart-seq and Smart-seq2 reads were assigned to genes using Rsubread
only cells were considered with at least 1,000,000 reads; doublets discarded and failed libraries filtered by low nearest-neighbor correlation coefficients
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with unique gene-wise counts of cells considered for final analysis: ziegenhain_complete_data.txt

molecule: total RNA

organism: Mus musculus

source_name: mouse embryonic cell line

growth_protocol: J1 mESC were cultured in ground pluripotency states by 2i/LIF culture as described previously.

extract_protocol: single-cell lysate

tag: library preparation

value: Smart-seq / C1

tag: cell line


title: SmartSeqA_C8


title: 24P

country: USA

tag: strain

tag: age


title: 18P


title: 22P


title: 19P


title: SmartSeqA_C5


title: SmartSeqA_D1


title: SmartSeqA_C6


title: 11P


title: 10P


title: 8P


title: SmartSeqA_C2


title: SmartSeqA_C10


title: SmartSeqA_C11


title: 4P


title: SmartSeqA_C1


title: SmartSeqA_B5


title: 6P


title: SmartSeqA_B4


title: 26B

description: Brain microglia were obtained and RNA extracted using standards protocols (Nikodemova and Watters, 2012 Journal of Neuroinflammation; Gelsthorpe, Gelshorpe and Sokol, 1997, BioTechniques)

source_name: Brain microglia


title: SmartSeqA_A9


title: 2P


title: RiboMin-TotalRNA-Ercc1-AL

city: Rotterdam

first: Akos

last: Gyenis

address: Wytemaweg 80

department: Genetics

country: Netherlands

institute: ERASMUS MC

description: Ribosomal RNA depleted

data_processing:
Basecalling is performed by using NARWAL
Raw FASTQ files
FPKM values from separated long reads were calculated using Cufflinks2
Genome_build: Mus musculus (mm10)
Supplementary_files_format_and_content: TXT files with FPKM values

source_name: Liver

extract_protocol:
Total RNA from flash frozen liver was extracted by using QIAzol lysis Reagent and miRNAeasy Mini Kits (QIAGEN). Ribosomal RNA species were removed by using RiboMinus kit (Ambion).
Illumina TruSeq v3 protocol

tag: tissue

value: Liver

tag: background strain

tag: genotype

value: Ercc1 delta/-

tag: diet

value: Ad libidum diet

value: 16 weeks


title: SmartSeqA_A7


title: 24B


title: SmartSeqA_C7


title: 12P


title: SmartSeqA_C4


title: SmartSeqA_A6


title: SmartSeqA_A3


title: 18B


title: SmartSeqA_A2


title: 10B


title: 22B


title: 11B


title: 12B


title: SCRBseqB_TTTACA

description: Library preparations were performed with the SCRB-seq protocol from FACS-sorted single cells as described in Soumillon et al. 2014

value: SCRB-seq


title: 8B


title: SmartSeqA_A12


title: 19B


title: 4B


title: SCRBseqB_TTTCTT


title: SCRBseqB_TCTTAA


title: 6B


title: SmartSeqA_A1


title: SCRBseqB_TATTGT


title: XR5_high

city: Chongqing

first: Ran

last: He

address: 30th Gaotanyan street

country: China

institute: Third Military Medical University

description:
20150328_41K_dataset.txt
RNA-seq0415.xlsx

data_processing:
The raw sequence reads were first aligned to mouse UniGene with bowtie (v1.0.0)
TopHat2 was used to align the reads to the reference mouse genome (GRCm38) with the aligning parameter –bowtie1 and Ensemble annotated transcripts (version 77) as guide reference.
The uniquely mapped reads were used for quantifying gene expression and differential gene expression evaluation by Cuffdiff, a subpackage of Cufflinks (v2.1.1) with Ensemble annotated genes (version 77).
Abundance of transcripts was calculated and normalized in RPKM as described above from the raw RNA-seq data and used for Gene Set Enrichment Analysis (GSEA, Broad Institute)
Genome_build: GRCm38
Supplementary_files_format_and_content: [20150328_41K_dataset.txt] represents RPKMs
Supplementary_files_format_and_content: [RNA-seq0415.xlsx] represents RPKMs and differential gene expression

source_name: Splenocytes

extract_protocol:
The total RNA samples are extracted by Trizol reagent (Life Technologies), and then purified with Dnase I (Qiagen) treatment.
The RNA-seq library construction for the RNA samples is according to the strand-specific RNA sequencing library preparation protocol. The initial amount of total RNA for library construction is tow micrograms, and mRNA transcripts are enriched by two rounds of poly (A+) selection with Dynabeads oligo(dT)25 (Invitrogen) before library construction. The prepared library is sequenced by the Illumina Hiseq 2000 sequencer.

tag: cell type

value: CD8 T cells

tag: cell subset

tag: virus infection


title: 2B


title: SCRBseqB_TGGCCG


title: XR5_low


title: Naïve


title: SmartSeqA_A10


title: SCRBseqB_TATGAA


title: SCRBseqB_TATAGA


title: Armstrong

value: LCMV-Armstrong


title: SCRBseqB_TAGTAA


title: Peripheral macrophages_55

description: Peripheral peritoneal macrophages were obtained and RNA extracted using standards protocols  (Nixon et al., 2015 J Bioinform Comput Biol. 2015 Apr;13(2):1550010. doi: 10.1142/S0219720015500109; Zhang et al., 2008 Current protocols in immunology / edited by John E.Coligan)

value: Peripheral macrophages

value: IDO knockout (IDO(-/-))

value: 22 weeks old


title: SCRBseqB_TAAGAT


title: Peripheral macrophages_51


title: Peripheral macrophages_53


title: SCRBseqB_TAATGA


title: Peripheral macrophages_50


title: SCRBseqB_GTTTAT


title: Peripheral macrophages_48


title: SCRBseqB_TAAAGT


title: Peripheral macrophages_47


title: Peripheral macrophages_45


title: SCRBseqB_GTAATA


title: Peripheral macrophages_44


title: Peripheral macrophages_42


title: Peripheral macrophages_38


title: SCRBseqB_GCTCGC


title: iPSC_D28_1

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: Nrlp-GFP+ flow sorted cells from day 28 iPSC replicate 1

data_processing:
Trimming Illumina adapters, defined in TrueSeq3-PE-2.fa file, by Trimmomatic (version 0.36) from paired end data.
Transcript level abundance was quantified against Ensemble release 84 cDNA FASTA file by Kallisto (version 0.42.5).
Gene level quantifications were summarized and then normalized using tximport with the option “countFromAbundance=lengthScaledTPM”. The gene level count values were converted to count per million (CPM) via edgeR.
Genome_build: GRCm38.p4/Ensembl 84
Supplementary_files_format_and_content: comma separated value files of raw count and transcripts per million (TPM) data and normalized counts per million (CPM) data

molecule: polyA RNA

source_name: Nrlp-GFP+ flow sorted cells

growth_protocol: ESC clones were isolated from the inner cell mass (ICM) of 3.5-day blastocysts of Nrl-GFP transgenic mice on feeders of mouse embryonic fibroblast (MEF) in the presence of leukemia inhibitory factor (LIF) and 3i and maintained under the same conditions at 37℃, 5% CO2. Clones of iPSCs were generated by infection of E14.5 MEFs from Nrl-GFP mice of Dox-inducible lentiviral vectors carrying Oct3/4, Sox2, Klf4 and c-Myc genes individually and then cultured on MEF feeder cells for three weeks. ES-like colonies were picked and transferred onto fresh feeder cells, followed by evaluation of quality by morphology, proliferation rate and Nanog expression. Nrl-GFP ESCs and iPSCs were maintained on feeder cells in Knockout DMEM supplemented with 1x MEM non-essential amino acids, 1x GlutaMAX, 1x Penicillin-Streptomycin, 1x 2-Mercaptoethanol, 2000 U/ml LIF, and 15% ES cell-qualified FBS . Cells were passaged using TrypLE Express.

extract_protocol:
RNA was extracted using TriPure reagent.
Illumina Stranded mRNA Library Prep Kit

treatment_protocol: ESCs and iPSCs (passage 15-25) were differentiated using SFEBq protocol, and also after modifications in culture conditions as follows: (i), hypoxic condition was applied from D0 to D10; (ii), 36 uncut retinal organoids were cultured in 100 mm poly-HEMA-coated dish after D14; (iii), β-mercaptoethanol was freshly added to media every time; (iv), retinoic acid (RA) was added to the culture from D14 to D26; (v), retinal organoids were supplied with DMEM/F12 with GlutaMAX supplemented by 2% FBS, 1x Penicillin-Streptomycin, 1x MEM non-essential amino acid, 1x N-2 supplemen and 1x B-27 supplement; and (vi) 1x β-mercaptoethanol were added to all media every time. Briefly, 72 retinal organoids were transferred at D7 to a 100 mm polyHEMA-coated petridish with 10 ml retinal maturation medium (DMEM/F12 with GlutaMAX with 1x POS). The maturation medium of retinal cultures was changed at D10 and 1 mM Taurine and 500 nM RA were added. At D14, half of the media was changed and the culture density reduced to 36 organoids per 100 mm dish. The cultures were maintained till D26 with half of the media changed every 3 days. At 26, full media was replaced with DMEM/F12 containing GlutaMAX that was supplemented by 2% FBS, 1x PS, 1x NEAA, 1x N-2 and 1x-B27. Half of the media was then changed every 2 days. The cultures were incubated at 5% O2 from D0 to D10 and with 20% O2 from D10 onwards.

tag: derived source

value: iPSC

tag: day post differentition initiation

value: Nrlp-GFP


title: iPSC_D35_1

description: Nrlp-GFP+ flow sorted cells from day 35 iPSC replicate 1


title: SCRBseqB_GCGGTC


title: SmartSeqA_A11


title: iPSC_D25_2

description: Nrlp-GFP+ flow sorted cells from day 25 iPSC replicate 2


title: Peripheral macrophages_37


title: Peripheral macrophages_35


title: SCRBseqB_GCGCTG


title: iPSC_D25_1

description: Nrlp-GFP+ flow sorted cells from day 25 iPSC replicate 1


title: SCRBseqB_GAGCGG


title: Peripheral macrophages_21


title: ESC_D35_1

description: Nrlp-GFP+ flow sorted cells from day 35 ESC replicate 1

value: ESC


title: iPSC_D18_2

description: Nrlp-GFP+ flow sorted cells from day 18 iPSC replicate 2


title: Peripheral macrophages_20


title: iPSC_D18_1

description: Nrlp-GFP+ flow sorted cells from day 18 iPSC replicate 1


title: SCRBseqB_GACCGC


title: SCRBseqB_GTGCGC


title: Peripheral macrophages_17


title: ESC_D25_1

description: Nrlp-GFP+ flow sorted cells from day 25 ESC replicate 1


title: SCRBseqB_GGTGGC


title: SCRBseqB_CTATAT


title: SCRBseqB_CTTTAA


title: Peripheral macrophages_16


title: ESC_D28_1

description: Nrlp-GFP+ flow sorted cells from day 28 ESC replicate 1


title: Peripheral macrophages_15


title: ESC_D21_3

description: Nrlp-GFP+ flow sorted cells from day 21 ESC replicate 3


title: SCRBseqB_CTAGGC


title: ESC_D21_2

description: Nrlp-GFP+ flow sorted cells from day 21 ESC replicate 2


title: Peripheral macrophages_14


title: SCRBseqB_CGGTGG


title: iPSC_D21_1

description: Nrlp-GFP+ flow sorted cells from day 21 iPSC replicate 1


title: SCRBseqB_CGGGCT


title: Peripheral macrophages_13


title: Peripheral macrophages_9


title: ESC_D21_1

description: Nrlp-GFP+ flow sorted cells from day 21 ESC replicate 1


title: SCRBseqB_CGGCCA


title: ESC_D18_2

description: Nrlp-GFP+ flow sorted cells from day 18 ESC replicate 2


title: Peripheral macrophages_7


title: ESC_D18_1

description: Nrlp-GFP+ flow sorted cells from day 18 ESC replicate 1


title: SCRBseqB_CGCTGC

description: Library preparations were performed with the SCRB-seq protocol from FACS-sorted single cells as described in Soumillon et al. 2014


title: Peripheral macrophages_5

description: Peripheral peritoneal macrophages were obtained and RNA extracted using standards protocols  (Nixon et al., 2015 J Bioinform Comput Biol. 2015 Apr;13(2):1550010. doi: 10.1142/S0219720015500109; Zhang et al., 2008 Current protocols in immunology / edited by John E.Coligan)


title: SCRBseqB_CTCTGC


title: SCRBseqB_CGCGCA


title: SCRBseqB_CGAGGC


title: 18.5-6

city: Dallas

first: Galvin

last: Swift

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: U TX Southwestern Medical Center

description: total RNA RIN 9.3

data_processing:
Illumina HiSeq Control Software version 2.0.10.0 used for basecalling
Sequences were mapped to mm9 mouse genome using TopHat v2.0.4 (by use of Bowtie v0.12.7.0) with parameters --no-novel-juncs --segment -length 25 --segment-mismatches 3
Sequences per gene were counted using Samtools ( v0.1.18.0) /HTSeq (v0.6.0)
Counts-per-million (CPM) were calculated using TMM normalization according to Robinson et al., Bioinformatics, 2010. Data set was filtered for minimal expression by "keep <- rowSums(cpm(d)) >= 3"
Differential gene expression analysis was performed with edgeR v3.0.8 (FDR < 0.05)
Genome_build: mm9
Supplementary_files_format_and_content: Normalized counts-per-million (CPM) for each sample in tab-delimited text file
Supplementary_files_format_and_content: EdgeR results as .xlxs spreadsheets, comparison with Adult induced knockout samples GSM2299179  6d_cKO1, GSM2299180  6d_cKO2, GSM2299181  6d_cKO3  and control animals from this study GSM2299174  6d_CT1, GSM2299175  6d_CT2, GSM2299176  6d_CT3, GSM2299177  6d_CT4, GSM2299178  6d_CT5  and fdr < 0.05.

source_name: pancreas

growth_protocol: timed matings.  noon of day that sperm plug was detected was considered E0.5.  Embryos were collected at noon on E18.5.

extract_protocol:
RNA preparation:  pancreas was homogenized in 4 M Guanidine Thiocyanate, 0.1 M Tris HCl pH 7.5, 1% 2-mercaptoethanol with a Tekmar Tissuemizer.  RNA was isolated from an aliquot of the homogenate by addition of N-Lauroylsarcosine sodium salt to 0.5%, Potassium Acetate pH 5.5 to 0.1 M, and Acetic Acid to 0.08 M, followed by addition of 0.75 volume ethanol while vortexing.  RNA was allowed to precipitate from the solution at -20 C for at least 1 hour, collected by centrifugation at 12,000 g for 5', and the RNA pellet resuspended in Trizol (equal volume to starting homogenate).  Subsequent steps were as per manufacturer's protocol (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina True-seq protocols

value: pancreas

tag: embryonic day


title: 18.5-4

description: total RNA RIN 9.2


title: Peripheral macrophages_1


title: 18.5-3

description: total RNA RIN 9.0


title: SCRBseqB_CCTGGC


title: Brain microglia_55

description: Brain microglia were obtained and RNA extracted using standards protocols  (Nikodemova and Watters, 2012 Journal of Neuroinflammation; Gelsthorpe, Gelshorpe and Sokol, 1997, BioTechniques)

value: Brain microglia


title: 18.5-1

description: total RNA RIN 8.8


title: SCRBseqB_CCGTCG


title: SmartSeq2A_H9

description: Library preparations were performed using the Smart-seq2 protocol, as described in Picelli et al., Nature Methods 2013


title: Brain microglia_51

value: male


title: SCRBseqB_CCACAT


title: SCRBseqB_CCCACG


title: SCRBseqB_CATTAT


title: Peripheral macrophages_3


title: SmartSeq2A_H8


title: Brain microglia_50


title: SCRBseqB_CAAATA


title: Brain microglia_45


title: ESC_D18_3

description: Nrlp-GFP+ flow sorted cells from day 18 ESC replicate 3


title: SmartSeq2A_H7


title: SCRBseqB_ATGAAT


title: SmartSeq2A_H4


title: Brain microglia_47


title: SmartSeq2A_H2


title: Brain microglia_42


title: SmartSeq2A_H6


title: SCRBseqB_AGACCT


title: SCRBseqB_ACAATA


title: SmartSeq2A_G9


title: SmartSeq2A_H12


title: SCRBseqB_ATTCTA


title: Brain microglia_48


title: Brain microglia_37


title: SmartSeq2A_H5


title: Brain microglia_44


title: SCRBseqB_ATTACT


title: SCRBseqB_AGATTA


title: Brain microglia_38


title: SmartSeq2A_H10


title: SCRBseqA_TTTCTT


title: Brain microglia_35


title: SCRBseqB_AATACA


title: SmartSeq2A_G8


title: Brain microglia_21


title: SmartSeq2A_G4


title: SmartSeq2A_G3


title: SCRBseqA_TTATTG


title: SCRBseqB_AAATTG


title: SmartSeq2A_G7


title: SCRBseqA_TTAGTT


title: Brain microglia_13


title: SmartSeq2A_G1


title: Brain microglia_53


title: Brain microglia_20


title: SCRBseqA_TTAATC


title: Brain microglia_9


title: Brain microglia_17


title: SCRBseqA_TTTTGA


title: Brain microglia_15


title: SmartSeq2A_G5


title: SCRBseqA_TTTACA


title: SCRBseqB_AAAGTT


title: SmartSeq2A_G6


title: Brain microglia_14


title: SmartSeq2A_G10


title: SCRBseqA_TGGCCG


title: Brain microglia_3


title: SmartSeq2A_G2


title: SCRBseqA_TATAGA


title: SmartSeq2A_F9


title: SCRBseqA_TACTAT


title: Brain microglia_7


title: Brain microglia_16


title: SCRBseqA_TGTTTA


title: Brain microglia_5


title: SmartSeq2A_F7


title: NOD-Control

city: Shanghai

first: Fei

last: Su

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Science and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using tophat with default parameters
Calling the differentially expressed gene with cuffdiff
Supplementary_files_format_and_content: abundance measurements

source_name: NOD-Control

growth_protocol: Wild-type (WT) female BALB/c or female NOD were mated with C57BL/6 male mice.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: On embryonic day 6.5, WT and NOD mice were injected IP with CpG ODN (ODN1826; InvivoGen) at a dose of 25 μg/dam in 200 μl PBS. Control mice were injected with control ODN (ODN 2138; InvivoGen) at the same dose on E6.5.

value: NOD

value: female

tag: developemental stage

value: embryonic day 6.5

tag: injected with

value: control ODN (ODN 2138; InvivoGen)

value: placentas with decidua basalis


title: Brain microglia_1

tag: gender


title: SmartSeq2A_F4

tag: library preparation


title: SmartSeq2A_F8

tag: cell line


title: SmartSeq2A_F6


title: SmartSeq2A_F5


title: SCRBseqA_TAATGA

value: SCRB-seq


title: SCRBseqA_TAGTAA


title: SCRBseqA_GTTCGA


title: WT-Control

source_name: WT-Control

tag: strain

value: BALB/c


title: SCRBseqA_GTGCGC


title: SCRBseqA_GTTTAT


title: SmartSeq2A_F3


title: SCRBseqA_TATGAA


title: NOD-CpG

source_name: NOD-CpG

value: CpG ODN (ODN1826; InvivoGen)


title: SCRBseqA_GTAATA


title: WT-CpG

source_name: WT-CpG


title: SmartSeq2A_E8


title: SmartSeq2A_F1


title: SCRBseqA_GCTCGC


title: SCRBseqA_GGGCAG


title: SmartSeq2A_E9


title: SmartSeq2A_E7


title: SmartSeq2A_E5


title: SCRBseqA_GCACGG


title: SCRBseqA_CTGCGG


title: SmartSeq2A_E6


title: SCRBseqA_CTTTAA


title: SmartSeq2A_E2


title: SmartSeq2A_E12


title: SCRBseqA_CGGCCA


title: SmartSeq2A_E4


title: SCRBseqA_CGGTGG


title: SmartSeq2A_F2


title: SCRBseqA_CGCGCA


title: SmartSeq2A_E11


title: SCRBseqA_CCGGAC


title: SmartSeq2A_D9


title: SmartSeq2A_E10


title: SCRBseqA_CGCCCT


title: SmartSeq2A_F10


title: SCRBseqA_CCCCGT


title: SCRBseqA_CCCACG


title: SmartSeq2A_D8


title: SCRBseqA_CATTAT


title: SmartSeq2A_D5


title: SmartSeq2A_D7


title: SCRBseqA_ATTTCA


title: SCRBseqA_CACCAA


title: SCRBseqA_ATTCTA


title: SmartSeq2A_D3


title: SCRBseqA_ATGAAT


title: SCRBseqA_ATATAG


title: SmartSeq2A_D2


title: SmartSeq2A_D11


title: SmartSeq2A_D1


title: SmartSeq2A_D4


title: SCRBseqA_ACTTAT


title: SCRBseqA_AAATTG


title: SmartSeq2A_C9


title: SCRBseqA_AAAGTT


title: SmartSeq2A_C8


title: DropSeqB_TTTAATATGC

description: Library preparations were performed with the Drop-seq protocol by emulsion of single-cells with primer-microbreads, as described in Macosko et al. 2015

value: Drop-seq


title: DropSeqB_TTGAAGGTGT


title: SmartSeq2A_C4


title: DropSeqB_TGCCGTAACG


title: SmartSeq2A_D6


title: DropSeqB_TGATAGGCCA


title: SmartSeq2A_C3


title: DropSeqB_TCTTGTCCAA


title: DropSeqB_TCCATGTCTG


title: SmartSeq2A_C11


title: SCRBseqA_ATCAAA


title: SmartSeq2A_C10


title: SmartSeq2A_D10


title: DropSeqB_GGCCTGAAAA


title: DropSeqB_GTCGGCCCGT


title: DropSeqB_GTCACCATTA


title: SmartSeq2A_B8


title: DropSeqB_GAGCAGCCCA


title: SmartSeq2A_C7


title: DropSeqB_GCTCCATTGC


title: SmartSeq2A_B7


title: SmartSeq2A_C6


title: SmartSeq2A_B5


title: DropSeqB_CTGAAAACTA


title: SmartSeq2A_C2


title: SmartSeq2A_B2


title: DropSeqB_CTCGGAGTGA


title: SmartSeq2A_C1


title: DropSeqB_CTCAACACTT


title: DropSeqB_CTCACACTTT


title: SmartSeq2A_B12


title: SmartSeq2A_B9


title: SmartSeq2A_B11


title: SmartSeq2A_B1


title: DropSeqB_TCGACTTCTA


title: DropSeqB_CGAAACAGCG


title: DropSeqB_CCGTAGAGCC


title: SmartSeq2A_A7


title: SmartSeq2A_A9


title: DropSeqB_CTTGTATGTG


title: DropSeqB_CAATTAACAC


title: DropSeqB_CAATTAACAA


title: SmartSeq2A_B6


title: SmartSeq2A_A5


title: DropSeqB_ATTCGACTGA


title: DropSeqB_CTGGGGCCTA


title: SmartSeq2A_A6


title: SmartSeq2A_A4


title: SmartSeq2A_B4


title: SmartSeq2A_A8


title: SmartSeq2A_A3


title: DropSeqB_ATCGACTGAC


title: SmartSeq2A_A11


title: SmartSeq2A_A1


title: DropSeqB_AGCTGATTTG


title: DropSeqB_ACGGGAAGTG


title: DropSeqB_ATCTGGCCTC


title: DropSeqB_ACGGACTTCC


title: DropSeqB_CCTTACTTTT


title: DropSeqB_ACGCAAAAGT


title: DropSeqB_ACCACGTGTA


title: Cse4 log-1 INPUT

city: Vienna

first: Stefan

last: Westermann

address: Dr. Bohr-gasse 7

country: Austria

institute: Institute of Molecular Pathology

library_source: genomic

data_processing:
instrument amd control software: HiSeq2500; SCS 2.2.58
basecalling: RTA 1.18.64.0
conversion of output to unaligned bam: illumina2Bam, V1.16-1-g590b59e-dirty
demultiplexing: BamIndexDecoder V1.16-1-g590b59e-dirty
alignment: bowtie 1.0.0
Genome_build: SacCer_Apr2011/sacCer3
Supplementary_files_format_and_content: bed file of aligned reads. Submitter states that no other processed data were produced. The aligned reads were plotted directly.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Cse4 log-1 INPUT

growth_protocol: yeast cell culture

extract_protocol:
Refer: Pekgoz Altunkaya et al., CCAN Assembly Configures Composite Binding Interfaces to Promote Cross-Linking of Ndc80 Complexes at the Kinetochore, Current Biology (2016)
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: epitope tags


title: DropSeqB_ACTCTGGCCT


title: DropSeqA_TTTTTGCTAA


title: DropSeqB_AAGCTGATTT


title: Cnn1 log-1 INPUT

source_name: Cnn1 log-1 INPUT

tag: other genetic traits


title: Cse4 log-1 IP

source_name: Cse4 log-1 IP


title: DropSeqA_TTTTGCTAAA


title: HUVEC non-treated cells (DMSO control) replicate 3

city: La Jolla

first: Helge

last: Weissig

state: CA

address: 11025 N. Torrey Pines Rd.

department: Bioinformatics

institute: ActivX Biosciences, Inc.

data_processing:
Genome Analyzer Pipeline Software (bcl2fastq ver.2.15.0.4, Illumina, San Diego, CA) was used to perform image analysis, base calling, and demultiplexing
Adaptors and low scoring basepairs were removed using CutAdapt
Per-exon gene counts were generated using TopHat2 software (www.ccb.jhu.edu) and the HG19 release of the human genome.
Raw count data analysis was performed using the Bioconductor software framework (www.Bioconductor.org) and differential expression statistics were calculated using the DESeq2 package (www.bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genes differentially expressed in compound treated-samples vs. DMSO-treated samples were tabulated and results from both experiment sets were compared to each other using a cutoff of p-value levels less than 0.01.
Genome_build: hg19
Supplementary_files_format_and_content: The combined processed results are contained in the Excel workbook processed_results.xlsx, which includes spreadsheets for raw counts and per-gene DESeq2 statistics (log2 fold changes [log2FC] and adjusted p-value) for HUVEC and HeLa cells treated with AX15839 (839) or I-BET762 (iBET) as well as separately for AX15836 treated samples.

organism: Homo sapiens

source_name: HUVEC non-treated cells (DMSO control)

growth_protocol: Primary human umbilical vein endothelial cells (HUVECs) were grown in complete EGM-2 media (Lonza, Walkersville, MD) and used at passages 2-3. HeLa cells were maintained in Eagles Minimum Essential Media (EMEM) containing 10% (v/v) charcoal-dextran treated, heat-inactivated FBS (Omega Scientific, Tarzana, CA), and 1x Penicillin/Streptomycin/Amphotericin B (Lonza, Walkersville, MD).

extract_protocol: Cells were processed to total RNA using the RNeasy kit (Qiagen, Valencia, CA).

treatment_protocol: Cells were pre-incubated with 0.1% DMSO vehicle, 1 μM AX15836 (ERK5 inhibitor), 5 μM AX15839 (dual ERK5/BRD inhibitor), or 1 μM I-BET762 (BRD inhibitor) for 1 hr. HUVEC and HeLa cells were then stimulated with their respective agonists (10 μg/mL Pam3CSK4 or 50 ng/mL EGF) for 5 hrs at 37°C.

value: HUVEC cells

tag: compound

value: none (DMSO)

tag: concentration

tag: molecule subtype

value: ribo-depleted total RNA


title: Cnn1 HU-1 INPUT

source_name: Cnn1 HU-1 INPUT


title: HUVEC non-treated cells (DMSO control) replicate 1

tag: cell type


title: HUVEC non-treated cells (DMSO control) replicate 2


title: DropSeqA_TGCCACCGTG


title: HUVEC I-BET762 treated cells replicate 3

source_name: HUVEC I-BET762 treated cells

value: 1 uM


title: HUVEC I-BET762 treated cells replicate 1


title: DropSeqA_TGTCAAAGTC


title: HUVEC I-BET762 treated cells replicate 2


title: SmartSeq2A_B3


title: HUVEC AX15839 treated cells replicate 2

source_name: HUVEC AX15839 treated cells

value: 5 uM


title: Cnn1 Noc-1 IP

source_name: Cnn1 Noc-1 IP


title: DropSeqA_TGACCACCGT

source_name: mouse embryonic cell line


title: DropSeqB_ACGCAAAAAG


title: Cnn1 HU-1 IP

source_name: Cnn1 HU-1 IP


title: HUVEC AX15839 treated cells replicate 1


title: Cnn1 37oC-1 INPUT

source_name: Cnn1 37oC-1 INPUT


title: DropSeqA_TGACCACCTG


title: DropSeqA_TGAAACGAAG


title: Cnn1 37oC-1 IP

source_name: Cnn1 37oC-1 IP


title: Cnn1 Noc-1 INPUT

source_name: Cnn1 Noc-1 INPUT


title: DropSeqA_TGAAACGAGA


title: HUVEC AX15836 treated cells replicate 3

source_name: HUVEC AX15836 treated cells


title: Cnn1 log-1 IP

source_name: Cnn1 log-1 IP


title: HUVEC AX15836 treated cells replicate 2


title: Cnn1 ctf3∆ Noc-2 INPUT

source_name: Cnn1 ctf3∆ Noc-2 INPUT

value: cdc15-2::LEU2, ∆ctf3::URA3


title: DropSeqA_TCGTTGCATC


title: HUVEC AX15836 treated cells replicate 1


title: DropSeqA_TCTGGACAAT


title: Cnn1 ctf3∆ Noc-2 IP

source_name: Cnn1 ctf3∆ Noc-2 IP


title: DropSeqA_TCGTGGACAA


title: HeLa I-BET762 treated cells replicate 3

source_name: HeLa I-BET762 treated cells

value: HeLa cells


title: Cnn1 ctf3∆ Noc-1 INPUT

source_name: Cnn1 ctf3∆ Noc-1 INPUT


title: HeLa I-BET762 treated cells replicate 1


title: Cnn1 ctf3∆ Noc-1 IP

source_name: Cnn1 ctf3∆ Noc-1 IP


title: DropSeqA_TCGGACTCAA


title: HUVEC AX15839 treated cells replicate 3


title: Cnn1 ctf3∆ log-2 INPUT

source_name: Cnn1 ctf3∆ log-2 INPUT


title: HeLa non-treated cells (DMSO control) replicate 2

source_name: HeLa non-treated cells (DMSO control)


title: HeLa non-treated cells (DMSO control) replicate 3


title: DropSeqA_TCCTATTACT


title: HeLa non-treated cells (DMSO control) replicate 1


title: DropSeqA_TCGATTGCAT


title: HeLa AX15839 treated cells replicate 3

source_name: HeLa AX15839 treated cells


title: DropSeqA_TCCACGGCAG


title: Cnn1 ctf3∆ log-1 IP

source_name: Cnn1 ctf3∆ log-1 IP


title: HeLa AX15839 treated cells replicate 2


title: Cnn1 37oC-2 INPUT

source_name: Cnn1 37oC-2 INPUT


title: DropSeqA_GGGCTCCCAG

source_name: mouse embryonic cell line


title: Cnn1 ctf3∆ log-1 INPUT

source_name: Cnn1 ctf3∆ log-1 INPUT


title: DropSeqA_TCCTATTAAC


title: Cnn1 ctf3∆ log-2 IP

source_name: Cnn1 ctf3∆ log-2 IP


title: DropSeqA_GGCAGAAGGA


title: HeLa I-BET762 treated cells replicate 2


title: Cnn1 37oC-2 IP

source_name: Cnn1 37oC-2 IP


title: DropSeqA_TCCACGGCGT


title: Cnn1 Noc-2 IP

source_name: Cnn1 Noc-2 IP


title: HeLa AX15839 treated cells replicate 1


title: DropSeqA_GGAGATGCTA


title: Cnn1 HU-2 INPUT

source_name: Cnn1 HU-2 INPUT


title: HeLa AX15836 treated cells replicate 3

source_name: HeLa AX15836 treated cells


title: Cnn1 Noc-2 INPUT

source_name: Cnn1 Noc-2 INPUT


title: DropSeqA_GCTCCCAGGT


title: HeLa AX15836 treated cells replicate 2


title: DropSeqA_GCTCCCAGGG


title: HeLa AX15836 treated cells replicate 1


title: Cnn1 log-2 INPUT

source_name: Cnn1 log-2 INPUT


title: DropSeqA_GCTTCCTCCG


title: Cnn1 HU-2 IP

source_name: Cnn1 HU-2 IP


title: DropSeqA_GCTCCCAGGC


title: Cnn1 log-2 IP

source_name: Cnn1 log-2 IP


title: DropSeqA_GCAGAAGGAG


title: DropSeqA_GAGCCATATA


title: DropSeqA_CACTCGACGA


title: Cse4 log-2 INPUT

source_name: Cse4 log-2 INPUT


title: DropSeqA_GCTCCCAGGA


title: DropSeqA_ATCTAAGGTT


title: Cse4 log-2 IP

source_name: Cse4 log-2 IP


title: DropSeqA_ACCACCTCAC


title: DropSeqA_CAGTGAAAAT


title: DropSeqA_GAGGACCGAC


title: DropSeqA_CAACCGGTAC


title: DropSeqA_CTATGTGTAT


title: DropSeqA_AGCTAAGGTT


title: DropSeqA_ACCACCTACA


title: SUPT4H1 siRNA rep.2 (Line 2)

city: Boston

first: Nicholas

last: Kramer

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description: Population Control Fibroblast

data_processing:
Alignment to reference genome UCSC hg19 using TopHat2.1
Transcript assembly and expression evaluatd using Cufflink2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file containing gene abundance measurements in FPKM per sample

source_name: Fibroblast

growth_protocol: Standard Cell Culture (DMEM + 10%FBS with PenStrep)

extract_protocol:
Ambion PureLink RNA Mini
Standard Illumina polyA library preparation protocols

treatment_protocol: siRNA transfection using Lipofectamine RNAiMax

value: fibroblast cell line

value: Coriell Line ND38530

tag: sirna


title: DropSeqA_GCGACTTCCA


title: DropSeqA_AATTCGTAGA


title: DropSeqA_AATTGTGGTT


title: DropSeqA_AATTGTGTTC


title: Control siRNA rep.2 (Line 2)

description: Population Control Fibroblast

value: control


title: HBEC1MBT_DAC

first: Adam

middle: C

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

data_processing:
Multiplexing performed with CASAVA version 1.4
Adapter trimming performed with fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit)
miRNA reads aligned to human genome build using Bowtie v0.12.7 with parameters (Bowtie -a --best --strata -v 3  -m 10 -q -t)
Counts per mature miRNA from aligned reads computed using Bedtools and list of genomic features from miRBase v17
Counts were normalized to rpm (total # reads aligned per sample) and log2 transformed.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file including separate tabs for raw counts and RPM values

source_name: Lung

growth_protocol: cultured using ATCC method and suggested media

extract_protocol:
total RNA was isolated with TRIzol following manual instructions
Small molecular weight fraction (<200 bp) RNA was size fractioned using the Ambion (Life Technologies) flashPAGE fractionator to obtain small RNAs of 10-40nts. Small RNA sequencing libraries were created using SOLiD Small RNA Expression Kit (Ambion) starting with 200 ng of the size-fractionated material following the manufacturer’s instructions.  Libraries were sequenced on an Applied Biosystems (Life Technologies) SOLiD System to obtain 36bp reads.

treatment_protocol: DAC treated cell lines were treated daily with vehicle or 5-aza-2’deoxycytidine (500 nM) for four days

tag: treatment


title: SUPT4H1 siRNA rep.1 (Line 2)

description: Population Control Fibroblast


title: SW900_DAC


title: HBEC1MBT

value: vehicle


title: H23


title: H2170


title: Control siRNA rep.2 (Line 1)

description: Population Control Fibroblast

value: Coriell Line ND29510


title: H23_DAC


title: H2085_DAC


title: Control siRNA rep.1 (Line 1)

description: Population Control Fibroblast


title: H2023


title: Control siRNA rep.1 (Line 2)

description: Population Control Fibroblast


title: SUPT4H1 siRNA rep.2 (Line 1)

description: Population Control Fibroblast


title: H2085


title: H1993_DAC


title: H1993


title: DropSeqA_ATCCACGGCA


title: H2023_DAC


title: DropSeqA_ATGCTAAGGT


title: SC-1-15

city: Woods Hole

first: Sibel

last: Karchner

address: 45 Water St

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing:
Data was assembled using Newbler 2.5 (Roche, Indianapolis, IN).
Supplementary_files_format_and_content: MWG-454AllContigs.fna: fasta, assembly of samples 1 through 4.
Supplementary_files_format_and_content: R1-R2-454AllContigs.fna: fasta, assembly of samples 5 and 6.
Supplementary_files_format_and_content: 454_Counts.xlsx: spreadsheet of mapped counts

organism: Fundulus heteroclitus

source_name: untreated embryos

extract_protocol:
shotgun cDNA library - ESTs sequenced
Total RNA was isolated using STAT60 method.

tag: age

tag: population

value: Scorton Creek

tag: tissue

value: embryos


title: H1975_DAC


title: SUPT4H1 siRNA rep.1 (Line 1)

description: Population Control Fibroblast


title: SW900


title: H2170_DAC


title: NBH-1-15

value: New Bedford Harbor


title: H1975


title: H1568


title: DMSO-SC-10

source_name: 10 dpf embryos were treated with DMSO for 6 hours before sampling for RNA.

extract_protocol:
3'-anchored non-normalized cDNA library - single read per transcript
Total RNA was isolated using STAT60 method.

value: 10 dpf


title: PCB126-SC-10

source_name: 10 dpf embryos were treated with PCB-126 for 6 hours before sampling for RNA.


title: CALU6_DAC


title: CALU6


title: FB4-R2

status: Public on Sep 08 2016

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 31

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stipped of trailing poly(A) sequence.
Reads are aligned using bowtie2 (v2.2.5 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Multi-mapping reads are assigned to one location at random.
Reads aligning to the locations expected based on primer sequences are counted.
Genome_build: hg38
Supplementary_files_format_and_content: count.csv contains counts of reads aligning to each primer location in each sample.  regions.gff contains the locations of amplified regions in the genome, and associated primer sequence.

source_name: HEK293T: NDUFB4 KO

extract_protocol:
Total RNA was extracted from snap frozen cell pellets byTrizol extraction and Direct-zol (zymo) column purification. 1 microgram of this was input into the library preperation.
Library construction was by the mPAT approach. Breifly this involves a modified the TVN-PAT approach to cDNA synthesis and the multiplexed amplification of the 3'UTRs of 50 target transcripts. Two rounds of amplification in a nested configuration allow incorporation of the illumina platform specific adapters.
Cluster Generation: 5pM of libraries were sequecing with 500cSBS v2 300base sequencing.The libraries were mixed with 20% similarly treated PhiX174 Genomic DNA  Control Library V3 (Illumina Inc., San Diego CA, USA). Manuacturer's instruction Cat. #SY-410-9001DOC part #15027617
Sequencing chemistry: MiSeq : 500c SBS V2

treatment_protocol: Gene edited and control HEK293T cells were cultured in DMEM (ThermoFisher) supplemented with 10% (v/v) FBS and 50 µg/mL uridine.


title: No_antibiotic

city: Nashville

first: James

last: Marks

state: Tennessee

address: 638A Robinson Research Building

institute: NIAMS/NIH

description: Ribosomal Footprint

data_processing:
Wig files were generated using the Galaxy pipeline described in Kannan et al., Proceedings of the National Academy of Sciences, 2014
Ribosome P-site were assigned as 15 nt from the 3' end of the sequencing read
Genome_build: U00093.3
Supplementary_files_format_and_content: WIG file

organism: Escherichia coli

source_name: Exponential E. coli cells

extract_protocol:
Ribosome profiling was carried out using the antibiotic hypersusceptible E. coli strain BWDK, a derivative of the strain BW25113 with inactivated tolC gene. The overnight culture grown in LB medium was diluted 100 fold into three conical baffled 1 L flasks with 100 ml of LB supplemented with 0.2% glucose and grown with vigorous shaking at 37°C. When the culture density reached OD600 ~ 0.5, CHL or LZD were added to a final concentration of 100 µg/ml or 800 µg/ml (100 x fold MIC) and incubation continued for 2.5 min. The control culture did not receive a drug treatment. Cells were harvested by rapid filtration, frozen in liquid nitrogen and processed for ribosome profiling as described. The library for Illumina sequencing was prepared using RNA fragments ranging in size between 28 and 42 nt. Analysis of ribosome profiling was carried out using the GALAXY pipeline. The first position of the P site codon was assigned at 15 nt away from the 3’ end of the read.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BWDK (-tolC)


title: PCB126-NBH-10


title: FB7-R2

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 35

source_name: HEK293T: NDUFB7 KO


title: H1568_DAC


title: FB11-R1

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 22

source_name: HEK293T: NDUFB11 KO


title: Chl_treated

description: Ribosomal Footprint

value: 100 µg/mL CHL


title: DMSO-NBH-10


title: Lzd_treated

description: Ribosomal Footprint

value: 400 µg/mL LZD


title: FC1-R2

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 39

source_name: HEK293T: NDUFC1 KO


title: FB7-R1

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 7


title: FB4-R1

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 23


title: FB10-R2

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 19

source_name: HEK293T: NDUFB10 KO


title: FB10-R1

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 40


title: FA1-R1

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 1

source_name: HEK293T: NDUFA1 KO


title: FS5-R1

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 2

source_name: HEK293T: NDUFS5 KO


title: FA1-R2

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 26


title: FC1-R1

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 16


title: FA8-R2

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 29

source_name: HEK293T: NDUFA8 KO


title: FA8-R1

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 15


title: FA2-R1

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 13

source_name: HEK293T: NDUFA2 KO


title: FS6-R2

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 30

source_name: HEK293T: NDUFS6 KO


title: FS6-R1

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 20


title: FV3-R2

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 28

source_name: HEK293T: NDUFV3 KO


title: FV3-R1

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 14


title: FB11-R2

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 33


title: HEK293T-R2

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 34


title: FA2-R2

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 37


title: IP_H3K27me3_LNCaP-Ctrl

city: New York

first: Etienne

last: Dardenne

state: NY

address: 1300 York Avenue

department: Pathology

institute: Weill Cornell Medecine

data_processing:
Sequencing reads were aligned using STAR (Dobin et al., 2013) to hg19
HTSeq (Anders et al., 2015) and Cufflinks (Trapnell et al., 2012) were then used to generate read counts and FPKM respectively
For the LNCaP samples, the gene counts were used with DESeq2 (Love et al., 2014) to identify differentially expressed genes, defined to be those with adjusted p < 0.10 and absolute log2 fold change > 1
For the mouse samples, Cuffdiff (Trapnell et al., 2012) was then used to identify differentially expressed genes, defined to be those with p < 0.05.
For the H3K27me3 ChIP-seq: Sequencing reads were aligned to hg19 using the Burrows-Wheeler Alignment (bwa) Tool (Li and Durbin, 2009). Genes were considered direct targets if there was more read coverage by H3K27me3 than input at promoter regions, which were defined to be 2kb upstream of the transcription start site of RefSeq transcripts. Coverage plots were generated using the Integrative Genomics Viewer (IGV) (Robinson et al., 2011). H3K27me3 levels were normalized by input and differences in log2 fold change at N-Myc signature genes were statistically tested using the Mann–Whitney U test. Promoters with more than 2-fold increase relative levels of H3K27me3 were considered to be differentially expressed and were tested for enriched signatures using the hypergeometric test and the MSigDB database (Liberzon et al., 2011).
Genome_build: hg19/mm9

source_name: LNCaP cells

growth_protocol: LNCaP and 22RV1 cell lines were culture in RPMI supplemented with 10% of FBS (Life technology) and a cocktail of penicillin/streptomycin (Life technology).

extract_protocol:
For mouse tissues frozen embedded prostate H&E were assessed for pathology and normal, HGPIN or prostate cancer lesions were core from the frozen blocks and the RNA extracted using RNA simply Kit (Promega). For cell line, RNA extraction was performed using Trizol (Life technology) following manufacturer recommendation.
For the ChIp-Seq: Fifty million LNCaP-N-Myc or LNCaP control cells were washed in PBS twice and then fixed using 1% formaldehyde for 8 minutes at room temperature and quenched 5 min using 125 mM glycine. The cells were centrifuged and the cell pellet was resuspended in 2 milliliters of dilution buffer (10mM Tris HCL pH8.0, 0.1% SDS, 1.0mM EDTA with protease and phosphatase inhibitors). Protein-bound chromatin was fragmented by sonication for 15 minutes (Covaris series E220). H3K27me3 antibody was purchase from Diagenode (A1811-001P).
Libraries were prepared according to Illumina's instructions

treatment_protocol:
cell lines were culture in RPMI supplemented with 10% of FBS (Life technology) and a cocktail of penicillin/streptomycin (Life technology).
EZH2 siRNAs were purchase from Dharmacon as On-target plus siRNA and transfected as a final concentration of 60nM with lipofectamine RNAimax (Life technology). Cells were treated with GSK343 (Sigma Aldrich SML0766) at 5uM for 6 days

tag: antibody

value: LNCaP cells


title: LNCaP_N-Myc_vehicule

value: Vehicule


title: LNCaP_N-Myc_siEzh2

value: EZH2 siRNAs were purchase from Dharmacon as On-target plus siRNA


title: LNCaP_N-Myc_GSK343#2

value: GSK343 (Sigma Aldrich SML0766) at 5uM for 6 days


title: LNCaP_N-Myc_siCtrl

value: Control


title: LNCaP_N-Myc_GSK343#1


title: Input_LNCaP_N-Myc

value: Input


title: Input_LNCaP_Ctrl


title: 22RV1_N-Myc_1

description: processed data file: 22Rv1_RPKM (nMYC_c5)

source_name: 22RV1 cells

value: 22RV1 cells


title: 22RV1_N-Myc_2

description: processed data file: 22Rv1_RPKM (nMYC_c5_s3)


title: 22RV1_Ctrl_2

description: processed data file: 22Rv1_RPKM (EV-b)


title: 22RV1_Ctrl_3

description: processed data file: 22Rv1_RPKM (EV)


title: Neurog2 ChIP

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Fastq reads have been filtered for a mean quality score > 10 and aligned against the mm9 reference genome With Bowtie v0.12.3
Peak calling has been performed with MACS v1.4 with the following settings: Bandwidth=200; P-Value <=1.0E-5; Fold Enrichment to BG <30 >10; FDR<0.1
Region mapping to genes and the summary statistics for DNA-protein binding sites have been performed with GeneProf v1.1411131
Genome_build: mm9
Supplementary_files_format_and_content: Neurog2.bed contains Neurog2 peaks called with MACS; Tbr2.bed contains Tbr2 peaks called with MACS; Neurog2.bigwig contains Neurog2 ChIP-seq tracks; Tbr2.bigwig contains Tbr2 ChIP-seq tracks

source_name: E14.5 cerebral cortices

extract_protocol:
Brain tissue were fixed 45' in PBS containing 2mM Di-succinimidyl-glutarate (DSG). After washing with PBS, protein-DNA-interactions were fixed by 10min incubation in 1% formaldehyde at room temperature; chromatin was fragmented to the desidered lenght with Diagenode's Bioruptor, according to manufacturer's instructions.
Library construction have been performed with ChIP-Seq DNA Sample Prep Kit, according to manufacturer's instructions.

tag: developmental stage

value: brain

tag: brain region

value: cerebral cortex

value: anti-Neurog2, non-commercial:a gift of Prof. Yongchao Ma, Chicago


title: FS5-R2

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 27


title: 22RV1_Ctrl_1

description: processed data file: 22Rv1_RPKM (EV-a)


title: Tbr2 ChIP

value: anti-Tbr2, Chemicon cat.no AB9618


title: HEK293T-R1

description:
Tissue Culture
Purified Cells
multiplexed PCR Amplicons
Illumina index 25


title: LnCaP N-Myc 4

description: processed data file: LNCaP_RPKM.txt


title: LnCaP N-Myc 3

description: processed data file: LNCaP_RPKM.txt


title: LnCaP N-Myc 2

description: processed data file: LNCaP_RPKM.txt


title: LnCaP N-Myc 1

description: processed data file: LNCaP_RPKM.txt


title: LNCaP Ctrl 3

description: processed data file: LNCaP_RPKM.txt


title: input DNA DAC + EPZ6438 IMR5-75

city: Heidelberg

first: Chunxuan

last: Shao

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

data_processing:
ChIP-seq single-end reads were aligned to the hg19 genome using Bowtie and only uniquely aligned reads were kept.
BAM-Files of aligned reads were further processed using the deepTools suite2. Input files were subtracted from the treatment files using the bamCompare tool, applying the SES method for normalization of signal to noise.
Resulting signals were normalized to an average 1X coverage to produce signal (bigWig) files.
Genome_build: hg19

growth_protocol: Cells were grown in RPMI medium (10%FCS) under standard conditions.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies. Antibodies against H3K27ac (ab4729), H3K4me3 (ab8580, Abcam) and H3K27me3 (ab6002, Abcam) were used for precipitation.
Library preparation was performed using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, US) according to the manufacturer’s protocol.  Libraries were sequenced (50 bases single-end) on the Illumina sequencing platform (German Cancer Research Center Core facility).

treatment_protocol: The neuroblastoma cell lines Be(2)-C and IMR5-75 were treated with a combination of DAC (1µM, 72h) and EPZ-6438 (1µM 96h) . Controls were treated with solvent (DMSO).

value: neuroblastoma cell line

tag: chip antibody


title: Input chromatin

value: none (input)


title: IP_H3K27me3_LNCaP-N-Myc

value: H3K27me3 antibody was purchase from Diagenode (A1811-001P).


title: input DNA DMSO IMR5-75


title: H3K27me3 DAC + EPZ6438 IMR5-75

value: ab6002 (Abcam, Cambridge, UK)


title: LNCaP Ctrl 1

description: processed data file: LNCaP_RPKM.txt


title: H3K4me3 DMSO IMR5-75

value: ab8580 (Abcam, Cambridge, UK)


title: H3K27ac DMSO IMR5-75

value: ab4729 (Abcam, Cambridge, UK)


title: H3K27me3 DAC + EPZ6438 Be(2)-C


title: input DNA DAC + EPZ6438 Be(2)-C


title: H3K4me3 DMSO Be(2)-C


title: H3K27me3 DMSO Be(2)-C


title: IMR5-75 MYCN-low 24h replicate B

description: neuroblastoma cell line with stable tet-inducible MYCN knockdown (shRNA), plus tet

data_processing:
mRNA-seq raw data were mapped to hg19 by Tophat (2.0.5)
Number of reads per gene was calculated using HTSeq (0.5.3p9)
Normalization was done using DESeq2 (R / Bioconductor).
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts by Htseq

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit  according to the manufacturer's protocol. Total RNA was depleted from ribosomal RNAs using the Ribo-Zero rRNA Removal Kit (epicentre) according to the manufacturer's protocol.
RNA libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer's protocol with the following changes: RNA was fragmented for 20 min at 94°C followed by first strand cDNA synthesis for 10 min at 25°C, 50 min at 42°C and 15 min at 70°C. Size selection of adapter-ligated DNA was done with a bead:DNA ratio of 0.4 (AMPure XP beads, Beckman Coulter) removing index primer and short fragments. Quality, quantity and sizing (approximately 320 bp) of the RNA Library were analyzed using a DNA High Sensitivity DNA chip run on a 2100 Bioanalyzer (Agilent Technologies). Libraries were sequenced (50 bases single-end) on the Illumina sequencing platform (German Cancer Research Center Core facility).

treatment_protocol: MYCN was downregulated by addition of 1µg/ml tetracycline to IMR5-75-shMYCN cells. Control IMR5-75-shMYCN cells were treated with solvent (ethanol). RNA was isolated at indicated time points

tag: cell line

tag: genotype/variation

value: 1µg/ml tetracycline

tag: time point


title: H3K27ac DMSO Be(2)-C


title: Erα Knockout 3

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat 1.3.3 with parameters -a 8 -m 0 -i 70 -I 500000 -g 20 --library-type fr-unstranded --max-insertion-length 3 --max-deletion-length 3 --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2 --segment-length 25 --min-segment-intron 50 --max-segment-intron 500000
Differential expression analysis was performed on the mapped reads using the edgeR package in R.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw counts values for each gene in each sample

source_name: quadriceps

extract_protocol:
Quadriceps were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: quadriceps

value: 20 weeks

tag: genotype

value: muscle-specific estrogen receptor alpha -/-


title: IMR5-75 MYCN-high 24h replicate A

description: neuroblastoma cell line with stable tet-inducible MYCN knockdown (shRNA), minus tet

value: ethanol


title: IMR5-75 MYCN-high 24h replicate B

value: stable tet-inducible MYCN knockdown (shRNA)


title: IMR5-75 MYCN-low 12h replicate A


title: IMR5-75 MYCN-low 12h replicate B


title: Erα Knockout 2


title: IMR5-75 MYCN-high 12h replicate A


title: WT Control 3

value: wild type


title: IMR5-75 MYCN-high 12h replicate B


title: IMR5-75 MYCN-low 6h replicate A


title: WT Control 2


title: LNCaP Ctrl 2

description: processed data file: LNCaP_RPKM.txt

value: LNCaP cells


title: IMR5-75 MYCN-high 6h replicate B


title: IMR5-75 MYCN-high 6h replicate A


title: WT Control 1


title: H3K27me3 DMSO IMR5-75


title: input DNA DMSO Be(2)-C


title: IMR5-75-shMYCN-MYCN low input DNA

data_processing:
ChIP-seq single-end reads were aligned to the hg19 genome using Bowtie and only uniquely aligned reads were kept.
The HOMER tool suite (version 4.6) was used for H3K27me3 bedgraph file generation.
H3K4me1, H3K27ac and H3K4me3 peaks were called using the MACS 1.4 tool using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files are generated by HOMER.

source_name: IMR5-75-shMYCN-MYCN low

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies. Antibodies against H3K4me1 (ab8895, Abcam, Cambridge, UK), H3K27ac (ab4729), H3K4me3 (ab8580, Abcam) and H3K27me3 (ab6002, Abcam) were used for precipitation.
Library preparation was performed using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, US) according to the manufacturer’s protocol.  Libraries were sequenced (50 bases single-end) on the Illumina sequencing platform (German Cancer Research Center Core facility).

treatment_protocol: For modulation of MYCN levels, stable neuroblastoma cell models were used where MYCN can be either up- or downregulated upon addition of 1µg/ml tetracycline (SH-SY5Y-MYCN and IMR5-75-shMYCN, respectively)

value: neuroblastoma cell line with stable tet-inducible MYCN knockdown (shRNA), plus tet

tag: chip antibody catalog/vender


title: IMR5-75-shMYCN-MYCN low H3K27me3_ChIP_seq


title: IMR5-75-shMYCN-MYCN high input DNA

source_name: IMR5-75-shMYCN-MYCN high

value: neuroblastoma cell line with stable tet-inducible MYCN knockdown (shRNA), minus tet


title: IMR5-75-shMYCN-MYCN high H3K27me3_ChIP_seq


title: HEK293_Input_control_63

city: Basel

first: Christian

last: Beisel

address: Mattenstrasse 26

department: Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

description:
Sample 5
Starting material for the library preparation was DNA purified from chromatin preparation #63. This input control sample matches to ChIP samples HEK293_ChIP_ASXL1 and HEK293_ChIP_O-GlcNAc.

data_processing:
Short mreads alignment was performed with Bowtie2 v2.0.0, with parameters -N 1 -L 32 -M 100 -t
Peak calling was performed using MACS 1.4 and standard parameters
Genome_build: hg19
Supplementary_files_format_and_content: The peaks are in BED format. BED files contain the genomic coordinates of peaks genome-wide and are suitable for UCSC browser visualization.

source_name: Flp-In HEK293 T-REx cell line

growth_protocol: Flp-In HEK293 T-REx cells (Invitrogen)  were cultured in DMEM (4.5 g/l glucose, 10% FCS, 2 mM L-glutamine) at 37°C.

extract_protocol:
Chromatin fixation and immunoprecipitation were performed essentially as described in Orlando et al. (1997; PMID:8993033). Cells (3-4x108) were fixed in 200 mL of medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 150–400 bp. Soluble chromatin was separated from insoluble material by centrifugation. The supernatant containing chromatin of 1-2x107 cells was used for immunoprecipitation.
Sequencing libraries were prepared with the NEB Genomic DNA Sample Preparation Kit according to NEB’s instructions. After adapter ligation, library fragments of 250-350 bp were isolated from an agarose gel. The DNA was PCR amplified with Illumina primers with 18 cycles, purified, and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx (TrueSeq cBot-GA v2 and TruSeq v5 SBS kit) and HiSeq 2000 (HiSeq Flow Cell v3 and TruSeq SBS Kit v3) following the manufacturer’s protocols.

value: Flp-In HEK293 T-REx

value: none (chromatin Input control sample)


title: HEK293_ChIP_O-GlcNAc

description:
Sample 3
Chromatin preparation #63 was used as starting material of this ChIP. HEK293_Input_control_63 matches to this sample and was used as control.

value: Anti-GlcNAc (HGAC85), Novus Biologicals


title: Erα Knockout 1


title: IMR5-75 MYCN-low 24h replicate A


title: IMR5-75-shMYCN-MYCN high H3K27ac_ChIP_seq


title: HEK293_ChIP_ASXL1

description:
Sample 1
Chromatin preparation #63 was used as starting material of this ChIP. HEK293_Input_control_63 matches to this sample and was used as control.

value: Anti-ASXL1 (sc85283),  Santa Cruz Biotechnology


title: SH-SY5Y-MYCN-OFF H3K27me3_ChIP_seq

value: neuroblastoma cell line with stable tet-inducible MYCN, minus tet

value: ab6002 (Abcam, Cambridge, UK)


title: SH-SY5Y-MYCN-ON input DNA

value: neuroblastoma cell line with stable tet-inducible MYCN, plus tet


title: SH-SY5Y-MYCN-OFF H3K27ac_ChIP_seq

value: ab4729 (Abcam, Cambridge, UK)


title: SH-SY5Y-MYCN-OFF input DNA


title: IMR5-75-shMYCN-MYCN high H3K4me3_ChIP_seq

value: ab8580 (Abcam, Cambridge, UK)


title: IMR5-75 MYCN-low 6h replicate B

value: 1µg/ml tetracycline


title: Be(2)-C input DNA

value: neuroblastoma cell line


title: IMR5-75-shMYCN-MYCN high H3K4me1_ChIP_seq

value: ab8895 (Abcam, Cambridge, UK)


title: SH-SY5Y-MYCN-ON H3K27me3_ChIP_seq


title: SH-SY5Y-MYCN-OFF H3K4me1_ChIP_seq


title: Be(2)-C H3K27me3_ChIP_seq


title: SH-SY5Y-MYCN-OFF H3K4me3_ChIP_seq


title: Be(2)-C H3K4me3_ChIP_seq


title: Be(2)-C H3K27ac_ChIP_seq


title: IMR5-75_DAC + EPZ6438 replicate 2

data_processing:
mRNA-seq raw data were mapped to hg19 by Tophat (2.0.5)
Number of reads per gene was calculated using HTSeq (0.5.3p9)
Normalization was done using DESeq2 (R / Bioconductor).
Genome_build: hg19
Supplementary_files_format_and_content: csv file with raw read counts

source_name: IMR5-75 neuroblastoma cell line_DAC and EPZ6438

treatment_protocol: The neuroblastoma cell lines Be(2)-C and IMR5-75 were treated with DAC (1µM, 72h) and EPZ-6438 (1µM 96h) in combination or alone. Controls were treated with solvent (DMSO).

value: neuroblastoma


title: IMR5-75_EPZ6438 replicate 2

source_name: IMR5-75 neuroblastoma cell line_EPZ6438


title: IMR5-75_DMSO replicate 2

source_name: IMR5-75 neuroblastoma cell line_DMSO


title: IMR5-75_DAC replicate 1

source_name: IMR5-75 neuroblastoma cell line_DAC


title: IMR5-75_DAC replicate 2


title: IMR5-75_DAC + EPZ6438 replicate 1


title: IMR5-75_EPZ6438 replicate 1


title: IMR5-75_DMSO replicate 1


title: Be(2)-C_EPZ6438 replicate 2

source_name: Be(2)-C neuroblastoma cell line_EPZ6438


title: Be(2)-C H3K4me1_ChIP_seq


title: Be(2)-C_DAC + EPZ6438 replicate 1

source_name: Be(2)-C neuroblastoma cell line_DAC and EPZ6438


title: Be(2)-C_DAC + EPZ6438 replicate 2


title: Be(2)-C_DAC replicate 2

source_name: Be(2)-C neuroblastoma cell line_DAC


title: Be(2)-C_DAC replicate 1


title: MDA27ad

city: Houston

first: Jian

last: Chen

address: 1515 Holcombe Boulevard - Unit 1466

institute: The University of Texas M. D. Anderson Cancer Center

description:
MDA27ad
MDA27N-27P_RPKM

data_processing:
Whole-transcriptome RNA sequencing of 7 matched human colon adenoma samples and normal mucosa.  The sequencing was carried out on an Illumina HiSeq2000 sequencer.
The raw data quality was assessed using a FastQC software.
Adaptor presence was tested using Trimmomatic.
The readings were then aligned to the NCBI Human  chromosome genome build 37.2 using  the splice-aware aligner Tophat2 v2.0.10.
Transcript quantification was carried using HTSeq
A gene model gtf file corresponding to the NCBI human reference genome build 37.2 was used in the quantification.
DESeq2 was used to identify significant differences in gene expression profiles between the noemal mucosa and colon adenomas.
Genome_build: hg19
Supplementary_files_format_and_content: PRKM with fold change comparison and p-value calculation

source_name: Human colon adenoma from patient

extract_protocol:
Total RNA was extracted using TRIZOL reagent (Invitrogen) according to the manufacturer’s instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human colon adenoma


title: MDA33ad

description:
MDA33ad
MDA33N-33P_RPKM


title: MDA34N

description:
MDA34N
MDA34N-34P_RPKM

source_name: Human normal mucosa from patient

value: Human normal mucosa


title: MDA31ad

description:
MDA31ad
MDA31N-31P_RPKM


title: MDA33N

description:
MDA33N
MDA33N-33P_RPKM


title: MDA27N

description:
MDA27N
MDA27N-27P_RPKM


title: MDA3ad

description:
MDA3ad
MDA3N-3P_RPKM


title: MDA2ad

description:
MDA2ad
MDA2N-2P_RPKM


title: MDA3N

description:
MDA3N
MDA3N-3P_RPKM


title: MDA2N

description:
MDA2N
MDA2N-2P_RPKM


title: MDA34ad

description:
MDA34ad
MDA34N-34P_RPKM


title: HEK293_Input_control_62

description:
Sample 4
Starting material for the library preparation was DNA purified from chromatin preparation #62. This input control sample matches to ChIP sample  HEK293_ChIP_FOXK1.


title: Be(2)-C_EPZ6438 replicate 1


title: MDA1N

description:
MDA1N
MDA1N-1P_RPKM


title: MDA1ad

description:
MDA1ad
MDA1N-1P_RPKM


title: Be(2)-C_DMSO replicate 2

source_name: Be(2)-C neuroblastoma cell line_DMSO


title: HEK293_ChIP_FOXK1

description:
Sample 2
Chromatin preparation #62 was used as starting material of this ChIP. HEK293_Input_control_62 matches to this sample and was used as control.

value: Anti-FOXK1 (ab18196),  Abcam


title: control biological replicate 1

city: São Paulo

first: Sergio

last: Verjovski-Almeida

state: São Paulo

address: Av. Vital Brasil 1500

country: Brazil

institute: Instituto Butantan

data_processing:
Basecalling software: Reads were processed using CASAVA 1.8 and demultiplexed based on index sequences.
RNA-seq data were processed as aggregates of the two biological replicates to increase resulting transcriptome coverage. Aggregated sequenced reads were trimmed with Trimmomatic v.0.30 with parameters -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15. Trimmed reads were then mapped with TopHat v.2.0.12 and Bowtie v.2.2.3, and a custom GTF file to guide transcriptome assembly. This custom GTF file was built by using the human transcriptome annotation GTF file downloaded from Ensembl Project web-site (http://www.ensembl.org/) and modified to include all lncRNAs reported in Cabili et al, Genes & Development 2011. The following parameters for TopHat were used: --no-coverage-search --b2-sensitive --library-type fr-secondstrand.
TopHat alignment output files were first sorted by read names using sort command from SAMtools package v. 0.1.19-44428cd, and then RNA-seq reads were counted using htseq-count v.0.6.1p1.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes read counts for an aggregate of the two biological replicates

source_name: LNCaP cell line_absence of androgen

growth_protocol: LNCaP cell line (ATCC) was cultured in RPMI-1640 medium (Gibco) supplemented with 1x Pen-Strep (Vitrocell Embriolife), 10 mM HEPES (Gibco), and 10 % FBS (Vitrocell Embriolife); the latter was substituted with 10 % charcoal stripped FBS (Sigma) 48 h prior to RNA extraction.

extract_protocol:
LNCaP poly(A)+ RNA was extracted with FastTrack MAG Maxi mRNA Isolation Kit (Invitrogen), as per manufacturer’s protocol, treated with 25 U of DNase I, Amplification Grade (Invitrogen) for 1 h at room temperature, quantified using Quant-iT RiboGreen RNA Reagent (Invitrogen) and assessed for integrity on 2100 Bioanalyzer (Agilent).
RNA samples from two biological replicates were processed and sequenced on Illumina HiSeq 2000.  Approximately 1 µg of this RNA was prepared for Next Generation Sequencing using a modified version of the Illumina protocol, Directional_mRNA-Seq_SamplePrep_Guide_15018460_A.pdf, in which 12 cycles of PCR were performed instead of 15 and standard Truseq adapters and Truseq barcoded primers were used instead of the v1.5 adapters and primers described in the guide.  A final size selection was performed using agarose gel to capture library with insert sizes ranging from 150 – 250 bases in length suitable for 2 x 75 base paired end sequencing. Library product was purified from agarose using standard oligo purification columns. The prepared library was then loaded onto an Illumina HiSeq v2 single-read flowcell, standard cluster generation was performed on a Cbot followed by paired-end sequenced of 2 x 75 bases of the insert and 7 bases of the index read using standard HiSeq sequencing reagents except for the use of an alternative read-2 sequencing primer which was designed as the reverse complement of the indexing read sequencing primer. Strand-oriented paired-end RNA-seq protocol.

value: LNCaP


title: E14 cells Akap95 shRNA rep2

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA version 1.8.4
RNA-Seq: reads were mapped using TopHat2 and Calculating insert size and standard deviation for paired-end RNA-Seq data were performed using Picard v.1.126
RNA-Seq: read counting performed using HTSeq v0.6.0 (--mode=union --stranded=no --minaqual=30 --idattr=gene_name Ã¢â‚¬â€œtype=exon)
RNA-Seq: Normalization and Deferential expression analysis performed using DEseq v3.0
RNA-Seq: BAM to bedgraph performed using bedtools v2.17.0 and were normalized based on Read Per Million (RPM) and then bedgraph to bigwig was performed using bedGraphToBigWig v4
RIP-Seq: reads were mapped using TopHat2
RIP-Seq: peak calling was performed using MACS v1.4.2 and read count tables for peaks were created using bedtools
RIP-Seq: differential binding analysis was performed using DESeq
RIP-Seq: ChIPseeker v1.8.0 and HOMER v4.8 were used for peak annotations and motif discovery was performed using HOMER
RIP-Seq: NGSplot v2.47 and and ChIPseeker were used for binding site visualizations
RIP-Seq: MACS generated wig files were normalized based on Read Per Million (RPM) and were converted to BigWig files using bedGraphToBigWig v4
RIP-Seq: All the downstream statistical analysis and data visualizations were performed in R environment
Genome_build: mm10, hg19
Supplementary_files_format_and_content: BigWig (coverage for mapped reads)

source_name: E14 cells Akap95 shRNA rep2

growth_protocol: Indicated stable cell lines were cultured under appropriate conditions and harvested (after doxycycline induction when applicable)

extract_protocol:
For samples 1-8, Cells (~50 millions) were harvested and lysed in 2ml RIPA buffer (50mM Tris-HCl pH 7.4, 1% NP-40, 0.5% sodium dexoycholate, 0.1% SDS, 1mM EDTA, 150mM NaCl, 1mM DTT, 50 units/ml RNase Out). The cell lysates were sonicated at Bioruptor (Diagenode) at â€˜high modeâ€™ for 60 cycles to shear to 400-800bp. After centrifuge, the clear lysate were immunoprecipitated at 4Â°C overnight. Beads were washed by low salt (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl pH 8.1, 150mM NaCl), high salt (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl PH8.1, 500mM NaCl),  LiCl immune (0.25M LiCl, 1% NP-40, 1% deoxycholic acid, 1mM EDTA, 10mM Tris-HCl PH8.1), and TE buffer (1mM EDTA, 10mM Tris-HCl pH8.0). After proteinase K digestion and turbo DNase I (4U/sample) treatment, the RNA was recovered by acidic phenol/chloroform extraction and ethanol precipitation. For samples 9-10, total RNAs were extracted using the RNeasy kit (Qiagen).
For mRNA-seq, 2 rounds of polyA+ selection was performed. For RIP-seq including the Input RNA-seq, no polyA+ or other selection was performed, followed by conversion to cDNAs. We used the stranded mRNA library generation kits per manufacturerâ€™s instructions (Agilent, Santa Clara, CA). Library construction consists of random fragmentation of the RNA, followed by cDNA production using random primers with inclusion of Actinomycin D in the first strand reaction. The ends of the cDNA are repaired, A-tailed and adaptors ligated for indexing (4 different barcodes per lane) during the sequencing runs. The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation. Clusters were generated to yield approximately 725 K to 825 K clusters/mm2. Cluster density and quality were determined during the run after the first base addition parameters were assessed. We ran paired end 2x50bp sequencing runs to align the cDNA sequences to the reference genome.

treatment_protocol: For samples 1-8, Cells were cross-linked with 1.2% formaldehyde 15 minutes or irradiated with UV light at 254nm, 400mJ/cm2. For samples 9-10, cells were harvested without prior treatment.

value: mouse ES cells

tag: culture protocols

value: complete ES growth medium (knockout DMEM [Invitrogen] supplemented with 15% ES-certified fetal bovine serum, 2 mM L-glutamine, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol, and recombinant LIF)

tag: harvest time

value: stable cell line, harvest anytime in culture


title: E14 cells control shRNA rep2

source_name: E14 cells control shRNA rep2

tag: cell type


title: E14 cells control shRNA rep1

source_name: E14 cells control shRNA rep1


title: control biological replicate 2


title: Be(2)-C_DMSO replicate 1


title: MDA31N

description:
MDA31N
MDA31N-31P_RPKM


title: KO H3K27me3

description: Sample 14

data_processing:
Basecalls performed using CASAVA version 1.8.4
RNA-Seq: reads were mapped using TopHat2 and Calculating insert size and standard deviation for paired-end RNA-Seq data were performed using Picard v.1.126
RNA-Seq: read counting performed using HTSeq v0.6.0 (--mode=union --stranded=no --minaqual=30 --idattr=gene_name –type=exon)
RNA-Seq: Normalization and Differential expression analysis performed using DEseq v3.0
RNA-Seq: BAM to bedgraph performed using bedtools v2.17.0 and were normalized based on Read Per Million (RPM) and then bedgraph to bigwig was performed using bedGraphToBigWig v4
ChIP-Seq: reads were mapped using Bowtie2 (local alignment)
ChIP-Seq: peak calling was performed using MACS v1.4.2 and read count tables for peaks were created using bedtools
ChIP-Seq: differential binding analysis was performed using DESeq
ChIP-Seq: ChIPseeker v1.8.0 and HOMER v4.8 were used for peak annotations and motif discovery was performed using HOMER
ChIP-Seq: NGSplot v2.47 and and ChIPseeker were used for TSS binding visualizations
ChIP-Seq: MACS generated wig files were normalized based on Read Per Million (RPM) and were converted to BigWig files using bedGraphToBigWig v4
ChIP-Seq: All the downstream statistical analysis and data visualizations were performed in R environment
Genome_build: mm10
Supplementary_files_format_and_content: [.bw] BigWig files representing coverage for mapped reads; [.txt] count tables representing read counts for genomic features.

source_name: H3K27me3 ChIP DNA fromMx1-Cre; Dpy30F/- Lineage negative bone marrow cells

extract_protocol:
For samples 1-8, total RNAs were isolated using RNeasy Plus Mini (for non-HSCs) or Micro (for HSCs) Kit (Qiagen). For samples 9-14, standard ChIP assays was performed.
For samples 1-8, Two rounds of polyA+ selection was performed, followed by conversion to cDNAs. Due to the very low amounts, RNAs from the donor-derived LT-HSCs were amplified using Ovation RNA-seq System V2 (Nugen) before library preparation. No amplification was performed for RNAs from non-HSCs. We used the mRNA library generation kits per manufacturer’s instructions (Agilent, Santa Clara, CA). The indexed cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation. For samples 9-14, input and ChIP DNAs were used to construct libraries for sequencing following Illumina’s standard protocol.

treatment_protocol: For samples 1-8, which are all from mixed BM chimera assays, 1.25 × 106 donors bone marrow cells (CD45.2+) and 2.5 × 105 competitor cells (C57Bl/6J, CD45.1+) were transplanted into irradiated recipient mice (CD45.1+). Recipients were then injected with pIpC (InvivoGen, 7.5µg/g) 4 times over 10 days starting at 7 weeks post transplantation. The first two injections were 2 days apart and last injections were 4 days apart. Chimera mice at 2 weeks after the last pIpC injection were used for harvesting bone marrow cells and lin- BMs were enriched with magnetic Lineage depletion beads (Miltenyi Biotec) following manufacturer's instructions. Cells were further sorted to indicated populations and used for RNA extraction. For samples 9-14, Mx1-Cre; Dpy30F/+ and Mx1-Cre; Dpy30F/- littermates at 6-8 weeks of age were injected with pIpC (InvivoGen, HMW, 7.5µg/g) once every other day for a total of 4 times. Bone marrow cells were harvest at 10 days after the initial pIpC injection. Following lineage depletion, cells were used for standard ChIP assays.

value: pooled bone marrow from 2 mice and lineage depleted

value: Lineage negative bone marrow cells

value: Mx1-Cre; Dpy30F/-


title: Control H3K4me3

description: Sample 11

source_name: H3K4me3 ChIP DNA from Mx1-Cre; Dpy30F/+ Lineage negative bone marrow cells

value: Mx1-Cre; Dpy30F/+

value: 10 days after the initial pIpC injection


title: Control H3K27me3

description: Sample 13

source_name: H3K27me3 ChIP DNA fromMx1-Cre; Dpy30F/+ Lineage negative bone marrow cells


title: KO H3K4me3

description: Sample 12

source_name: H3K4me3 ChIP DNA from Mx1-Cre; Dpy30F/- Lineage negative bone marrow cells


title: KO LSK

description: Sample 4

source_name: Mx1-Cre; Dpy30F/- LSK cells

value: pooled bone marrow from 2-3 chimera mice and FACS sorted

value: LSK cells

value: 2 weeks after the last pIpC injection into the chimeras


title: TP1-control HSC

description: Sample 5

source_name: Transplant 1, Mx1-Cre; Dpy30F/+ LT-HSCs

value: pooled bone marrow from 7-9 chimera mice and FACS sorted

value: LT-HSCs


title: Control input

description: Sample 9

source_name: Input DNA from Mx1-Cre; Dpy30F/+ Lineage negative bone marrow cells


title: organoids_pbCre+/+_Ptenf/f_LSL-MYCN-/-_3

description: processed data file: NMYC_Pb-Cre_mouse_RPKM.txt (PB-3)

source_name: pbCre Mouse Prostate organoids

value: pbCre Mouse Prostate organoids


title: TP2-KO HSC

description: Sample 8

source_name: Transplant 2, Mx1-Cre; Dpy30F/- LT-HSCs


title: TP1-KO HSC

description: Sample 7

source_name: Transplant 1, Mx1-Cre; Dpy30F/- LT-HSCs


title: TP2-control HSC

description: Sample 6

source_name: Transplant 2, Mx1-Cre; Dpy30F/+ LT-HSCs


title: KO MyePro

description: Sample 2

source_name: Mx1-Cre; Dpy30F/- MyePro cells

value: MyePro cells


title: E14 cells Akap95 shRNA rep1

source_name: E14 cells Akap95 shRNA rep1


title: organoids_pbCre+/+_Ptenf/f_LSL-MYCN-/-_2

description: processed data file: NMYC_Pb-Cre_mouse_RPKM.txt (PB-2)


title: organoids_pbCre+/+_Ptenf/f_LSL-MYCN+/+_3

description: processed data file: NMYC_Pb-Cre_mouse_RPKM.txt (PB_plus_3)


title: WGBS_P15.rep6

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
fastq:  Illumina's HiSeq Control Software
We aligned paired-end μChIP-seq reads to the mm10 reference genome by using BWA-mem. Unmapped, non-uniquely mapped, and low quality reads were removed. We also removed PCR duplicate reads with Picard.
RNA-seq reads were aligned to mm10 reference genome using BWA-mem. Unmapped and non-uniquely mapped reads were removed. Gene expression values were obtained based on GENCODE annotation v3 and normalized to FPKM values using Cufflinks.
MethylC-seq reads were trimmed by Trimmomatic with default parameters to remove the reads containing adapters and showing low quality. Trimmed reads were aligned by using Bismark (V12.5) Bisulfite Mapper against to mouse reference mm10. Duplicate reads were removed with Picard after split aligned reads into Waston and Crick strands. CpG methylation level was extracted with Samtools mpileup . Strands were merged to calculate the CpG methylation level per dinucleotide CpG site. Methylation level was calculated for each site spanned by at least 4 reads.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files and txt file for gene expression FPKM values

source_name: P15 oocyte

growth_protocol: See additional columns of the SAMPLES section for growth protocol

extract_protocol:
ChIP chromatin was preapred from whole cell lysates of cross-linked cells. Lysates were sonicated and chromatin complexes were isolated with antibodies coupled to magnetic beads. RNAs were extracted from whole cell lysates by following QIAGEN RNeasy Micro handbook. Genomic DNA for WGBS was obtained from lysates from 100-500 P12 or P15 oocytes.
ChIP-seq libraries were prepared according to Rubicon Genomics THRUPlex kit with minor modifications. RNA-seq library preparation was carried out according to TruSeq library preparation. MethylC-Seq libraris were prepared with modified library protocol from Wang, L., et al., 2014 Cell.

treatment_protocol: Isolated zygotes were injected at 0.5dpc with either fluorescein tagged morpholino oligonucleotides (Gene-tools) targeted to Kdm5a (TGACGGCCACCAAAGCCCTCTCA) and Kdm5b (AGCACAGGGCAGGCTCCGCAACC) or five base mismatch control morpholinos for Kdm5a (TGAaGGaCACaAAAcCCCTaTCA) and Kdm5b (AcCAaAGGGaAGGaTCCGaAACC).

value: P15 oocyte


title: organoids_pbCre+/+_Ptenf/f_LSL-MYCN+/+_2

description: processed data file: NMYC_Pb-Cre_mouse_RPKM.txt (PB_plus_2)


title: organoids_pbCre+/+_Ptenf/f_LSL-MYCN-/-_1

description: processed data file: NMYC_Pb-Cre_mouse_RPKM.txt (PB-1)


title: KO input

description: Sample 10

source_name: Input DNA from Mx1-Cre; Dpy30F/- Lineage negative bone marrow cells


title: organoids_pbCre+/+_Ptenf/f_LSL-MYCN+/+_1

description: processed data file: NMYC_Pb-Cre_mouse_RPKM.txt (PB_plus_1)


title: pbCre - Sample_PTENf/f_LSLMYCN+/+_2

description: processed data file: NMYC_Pb-Cre_mouse_RPKM.txt (791)

source_name: pbCre Mouse Prostate

value: pbCre Mouse Prostate


title: pbCre - Sample_PTENf/f_LSLMYCN+/+_1

description: processed data file: NMYC_Pb-Cre_mouse_RPKM.txt (791-L)


title: WGBS_P15.rep1


title: WGBS_P12.rep4

source_name: P12 oocyte

value: P12 oocyte


title: Control LSK

description: Sample 3

source_name: Mx1-Cre; Dpy30F/+ LSK cells


title: WGBS_P12_rep3


title: pbCre - Sample_PTEN+/+_LSLMYCN+/+_1

description: processed data file: NMYC_Pb-Cre_mouse_RPKM.txt (653)


title: WGBS_P15.rep2


title: WGBS_P12.rep2


title: 2-cell_embryo_RNA-seq_40cells

source_name: 2-cell embryos

growth_protocol:
Embryos were cultured in G1 plus media (Vitrolife) until late 2-cell stage.
See additional columns of the SAMPLES section for growth protocol

value: 2-cell embryos


title: Control MyePro

description: Sample 1

source_name: Mx1-Cre; Dpy30F/+ MyePro cells


title: pbCre - Sample_PTEN+/+_LSLMYCN-/-_2

description: processed data file: NMYC_Pb-Cre_mouse_RPKM.txt (760)


title: 2-cell_embryo_RNA-seq_20cells.rep2


title: 2-cell_embryo_RNA-seq_10cells


title: WGBS_P15.rep4


title: T2-Cre - Sample_PTENf/f_LSLMYCN+/+_1

description: processed data file: NMYC_T2-Cre_mouse_RPKM.txt (202)

source_name: Prostate

value: Prostate


title: 2-cell_embryo_RNA-seq_20cells.rep1


title: WGBS_P15.rep5


title: T2-Cre - Sample_PTENf/f_LSLMYCN-/-_1

description: processed data file: NMYC_T2-Cre_mouse_RPKM.txt (155)


title: WGBS_P15.rep3


title: T2-Cre - Sample_PTENf/f_LSLMYCN-/-_2

description: processed data file: NMYC_T2-Cre_mouse_RPKM.txt (165)


title: pbCre - Sample_PTEN+/+_LSLMYCN-/-_3

description: processed data file: NMYC_Pb-Cre_mouse_RPKM.txt (761)


title: WGBS_P12.rep1


title: Alpha-amanitin_treatment_RNA-seq_2-cell.rep1

source_name: Alpha-amanitin treated 2-cell embryos

value: Alpha-amanitin treated 2-cell embryos


title: AKAP95 KD (miR#12) 293 cell

source_name: AKAP95 KD (miR#12) 293 cell

value: 293 cell line

value: DMEM+10%fetal bovine serum

value: 48 h after doxycycline induction


title: Control_MO_injection_RNA-seq_2-cell.rep2

source_name: Control Kdm5a+b injected 2-cell embryos

value: Control Kdm5a+b injected 2-cell embryos


title: Alpha_amanitin_treatment_RNA-seq_2-cell.rep2


title: pbCre - Sample_PTEN+/+_LSLMYCN-/-_1

description: processed data file: NMYC_Pb-Cre_mouse_RPKM.txt (601)


title: AKAP95 KD (miR#8) 293 cell

source_name: AKAP95 KD (miR#8) 293 cell


title: Control 293 cell

source_name: Control 293 cell


title: pbCre - Sample_PTEN+/+_LSLMYCN+/+_2

description: processed data file: NMYC_Pb-Cre_mouse_RPKM.txt (655)


title: Control_MO_injection_RNA-seq_2-cell.rep1


title: AKAP95 KD 293 cell RNA Input

source_name: AKAP95 KD 293 cell

tag: fraction

value: total input RNA


title: T2-Cre - Sample_PTENf/f_LSLMYCN+/+_2

description: processed data file: NMYC_T2-Cre_mouse_RPKM.txt (145A)


title: Kdm5a+b_MO_injection_RNA-seq_2-cell.rep2

source_name: Kdm5a+b injected 2-cell embryos

value: Kdm5a+b injected 2-cell embryos


title: Control 293 cell RNA Input


title: Wild-type_RNA-seq_2-cell.rep3

source_name: WT 2-cell embryo

value: WT 2-cell embryo


title: Wild-type_RNA-seq_2-cell.rep2


title: Input_P15.rep2


title: Kdm5+b_MO_injection_RNA-seq_2-cell.rep1


title: Control 293 cell AKAP95 RIP

value: RIP RNA


title: FH-ZFc-s 293 cell FLAG RIP

source_name: FH-ZFc-s 293 cell


title: H3K4me3_ChIPSeq_P15.rep2

source_name: P15 oocyte

value: H3K4me3 (Merck Millipore, catalogue number 04-745)


title: Input_P15.rep1


title: H3K4me3_ChIPSeq_P15.rep1


title: Input_P12.rep1


title: Control 293 cell FLAG RIP


title: H3K4me3_ChIPSeq_P12.rep2


title: Input_P12.rep2


title: Input_NCCIT

data_processing:
fastq:  Illumina's HiSeq Control Software
We aligned single- and paired-end μChIP-seq reads from H3K27ac and H3K4me3 experiments to the mm10 reference genome by using BWA-mem.
For human ChIP-seq samples performed with human NCCIT cells, we aligned reads to the hg19 reference genome using BWA-mem.
Unmapped, non-uniquely mapped, and low quality reads were removed.
We also removed PCR duplicate reads with Picard.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Bigwig files

source_name: NCCIT (ATCC® CRL-2073)

growth_protocol: The base medium for this cell line is ATCC-formulated RPMI-1640 Medium. Remove spent medium, add fresh 0.25% trypsin, 0.03% EDTA solution, rinse and remove trypsin. Let the culture sit at room temperature (or at 37°C) for 2 to 5 minutes. Add fresh medium, aspirate and dispense into new flasks. Subculture two times weekly. A subcultivation ratio of 1:4 to 1:8 is recommended

extract_protocol:
Chromatin was preapred from whole cell lysates of cross-linked cells. Lysates were sonicated and chromatin complexes were isolated with antibodies coupled to magnetic beads.
Libraries were prepared according to Rubicon Genomics THRUPlex kit with minor modifications.

value: NCCIT (ATCC CRL-2073)


title: H3K4me3_ChIPSeq_NCCIT_5k


title: FH-(101-692) 293 cell FLAG RIP


title: H3K4me3_ChIPSeq_NCCIT_100k


title: H3K4me3_ChIPSeq_NCCIT_1k


title: H3K4me3_ChIPSeq_P12.rep1


title: Input_8cell.rep2

source_name: 8-cell embryos


title: H3K4me3_ChIPSeq_NCCIT_1million


title: Input_8cell.rep1


title: H3K27ac_ChIPSeq_8cell.rep1

value: H3K27ac antibody (Active Motif, catalogue number AM39133)


title: Wild-type_RNA-seq_2-cell.rep1


title: AKAP95 KD 293 cell AKAP95 RIP


title: H3K27ac_ChIPSeq_8cell.rep2


title: H3K4me3_ChIPSeq_8cell.rep1


title: H3K27ac_ChIPSeq_2cell.rep1


title: FH-AKAP95 293 cell FLAG RIP

source_name: FH-AKAP95 293 cell


title: H3K27ac_ChIPSeq_2cell.rep2


title: H3K4me3_ChIPSeq_2cell.rep1


title: Input_2cell.rep2


title: H3K4me3_ChIPSeq_2cell.rep2


title: Input_oocytes.rep1

source_name: oocytes


title: H3K4me3_ChIPSeq_NCCIT_10k


title: H3K4me3_ChIPSeq_oocytes.rep1


title: H3K4me3_ChIPSeq_8cell.rep2


title: H3K27ac_ChIPSeq_oocytes.rep1


title: Input_oocytes.rep2


title: H3K27ac_ChIPSeq_oocytes.rep2


title: Input_E14

growth_protocol: The base medium for this cell line is ATCC-formulated Dulbecco's Modified Eagle's Medium. Remove medium, add fresh 0.25% trypsin, 0.53mM EDTA solution. Allow the trypsin to loosen the cells, add fresh medium, aspirate and dispense into new flasks containing pre-plated mitomycin-C treated feeder cells (ATCC 56-X.2). A subcultivation ratio of 1:5 is recommended. Every 2 to 3 days


title: H3K4me3_ChIPSeq_oocytes.rep2


title: H3K27ac_ChIPSeq_E14_100k


title: H3K27ac_ChIPSeq_E14_500


title: H3K4me3_ChIPSeq_E14_500


title: H3K27ac_ChIPSeq_E14_1k


title: H3K27ac_ChIPSeq_E14_10k


title: H3K4me3_ChIPSeq_E14_1k


title: H3K4me3_ChIPSeq_E14_100k


title: H3K4me3_ChIPSeq_E14_10k


title: GC Tfh_Notstimulated_2

status: Public on Sep 07 2016

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina Casava1.8.2 software used for basecalling and demultiplexing.
Reads were mapped to Macaca_mulatta UNMC_v7.6 genome assembly with the STAR (v2.3.0e) aligner args: --outFileterMultimapNmax 1 --outFilterType BySJout --outSJfilterReads Unique --sjdbGTFfile UNMC_rhesus_annotation_v7.6 --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Per sample annotated transcript models were quantitated with Cufflinks (v2.1.1) args: -G UNMC_rhesus_annotation_v7.6.gtf
Sample transcript models were merged with Cuffmerge (v2.1.1)
FPKM (Fragments per kilobase of exon per million reads mapped) abundance estimates and differential expression was caluclated with Cuffdiff (v2.1.1)
Genome_build: UNMC_v7.6 is a presubmission version of the MacaM GCA_000772875.1 assembly. (MaSuRCA_Rhesus_Genome_v7_20130927.fasta, UNMC_rhesus_annotation_v7.6.gtf)
Supplementary_files_format_and_content: tab delimited text file containing FPKM for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: lymph node cells

growth_protocol: Standard incubator conditions, 37 C, 5% CO2

extract_protocol:
Total RNA was purified using RNAeasy Micro Kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent 2100 Bioanalyzer (RNA integrity number (RIN) >8.5; Eukaryote Total RNA Pico Kit, Agilent, USA)
Libraries were prepared on cDNA generated using Clontech SmartER kits. Illumina adapters were ligated using the NexteraXT DNA kit for Illumina sequencing.  Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell.  Clustered flowcell was sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.

treatment_protocol: Total lymph node cells were either stimulated with 1 ug/ml SEB or left unstimulated for 6 hours at 37 degrees C. GC Tfh cells were then sorted using a BD FACSAria sorter.

value: Lymph node

value: GC Tfh

tag: stimulation

value: 6 hrs

tag: subjectid


title: GC Tfh_Stimulated_2

tag: tissue

value: SEB


title: GC Tfh_Stimulated_1


title: GC Tfh_Notstimulated_1


title: GC Tfh_Notstimulated_3


title: Input_2cell.rep1

source_name: 2-cell embryos


title: Pre-miR-17 RA Patient 2

city: Spokane

first: Salahuddin

last: Ahmed

state: WA

address: 412 E Spokane Falls Blvd, PBS411

department: Pharmaceutical Sciences

institute: Washington State University

description: RASFs were grown in 10% RPMI  and transfected for 48 h with pre-miR-17 (Life Technologies) in 150 mm dishes using Lipofectamine® RNAiMAX transfection reagent (Life Technologies) and Opti-MEM®I (1X)+ GlutaMAXTM-I and then media was changed back to 10% RPMI after 8 hours.

data_processing:
Basecalling, filtering, and trimming performed using Torrent Suite software version 4.4.3
Mapping and expression values calculated using ampliseqRNA plugin V4.4.0.4
Genome_build: hg19_AmpliSeq_Transcriptome_21K_v1.gc.bed
Supplementary_files_format_and_content: normalized counts

source_name: Pre-miR-17 RA

growth_protocol: RASFs were grown in RPMI 1640 containing 2 mM L-glutamine with 10% fetal bovine serum (FBS), at 37 °C, in a humidified atmosphere with 5% CO2.

extract_protocol:
total RNA was prepared using miRNeasy kit (Qiagen).Total RNA integrity was checked using an Agilent Technologies 2100 Bio analyzer
10 ng of high quality RNA was used to make cDNA for amplification with the Ion AmpliSeq Transcriptome Human Gene Expression kit (ThermoFisher Scientific).  The cDNA was subjected to 12 cycles of amplification with panel primers and barcoded with adapters as recommended.
Resulting sequencing libraries were quantified by qPCR using SYBR FAST master mix from KapaBiosystems (Wilmington, MA).  Sets of eight libraries were balanced, pooled and sequencing beads produced on an Ion Chef.  Sequencing was performed on an Ion P1 semi-conductor sequencing chip using an Ion Proton™ System (ThermoFisher Scientific, Grand Island, NY).

treatment_protocol: Transfection with pre-miR-17 or NC-pre-miR

value: RASF


title: NC-Pre-miR RA Patient 1

description: RASFs were grown in 10% RPMI  and transfected for 48 h with NC-pre-miR (Life Technologies) in 150 mm dishes using Lipofectamine® RNAiMAX transfection reagent (Life Technologies) and Opti-MEM®I (1X)+ GlutaMAXTM-I and then media was changed back to 10% RPMI after 6 hours.

source_name: NC-Pre-miR RA


title: NC-Pre-miR RA Patient 2

description: RASFs were grown in 10% RPMI  and transfected for 48 h with NC-pre-miR (Life Technologies) in 150 mm dishes using Lipofectamine® RNAiMAX transfection reagent (Life Technologies) and Opti-MEM®I (1X)+ GlutaMAXTM-I and then media was changed back to 10% RPMI after 8 hours .


title: Pre-miR-17 RA Patient 1


title: mtko2_sp_batch2

city: CAMBRIDGE

first: Meromit

last: Singer

state: MASSACHUSETTS

address: 415 main st, ROOM 6031

institute: Broad Institute of MIT and Harvard

description: population RNA-Seq data

data_processing:
Reads were aligned to a reference genome (mm9 Ensembl) using Bowtie
Expression levels were quantified using RSEM (inferred counts and tpm values), and log2(TPM+1) values generated.
samples of low technical quality and/or extreme outliers were excluded (see manuscript)
data was batch-normalized using COMBAT and then quantile normalized
Genome_build: mm9
Supplementary_files_format_and_content: text file with tab delimiters

source_name: Mus musculus CD8 TILs

extract_protocol:
TILs were isolated by dissociating tumor tissue in the presence of collagenase D (2.5 mg/ml) for 20 min prior to centrifugation on a discontinuous Percoll gradient (GE Healthcare).
Smart-seq2 (Picelli et al., Nature Methods, 2014)

tag: subpopulation

value: mtko2 sp


title: mtko3_dn_batch2

description: population RNA-Seq data

value: mtko3 dn


title: mtko3_sp_batch2

description: population RNA-Seq data

value: mtko3 sp


title: mtko2_dp_batch2

description: population RNA-Seq data

value: mtko2 dp


title: mtko2_dp_batch1

description: population RNA-Seq data


title: mtko1_dp_batch2

description: population RNA-Seq data

value: mtko1 dp


title: mtko1_sp_batch2

description: population RNA-Seq data

value: mtko1 sp


title: mtko2_sp_batch1

description: population RNA-Seq data


title: mtko2_dn_batch1

description: population RNA-Seq data

value: mtko2 dn


title: mtko1_dn_batch2

description: population RNA-Seq data

value: mtko1 dn


title: mtko2_dn_batch2

description: population RNA-Seq data


title: mtko1_dn_batch1

description: population RNA-Seq data


title: mtko1_sp_batch1

description: population RNA-Seq data


title: mtko1_dp_batch1

description: population RNA-Seq data


title: wt2_dn_batch2

description: population RNA-Seq data

value: wt2 dn


title: wt2_dp_batch2

description: population RNA-Seq data

value: wt2 dp


title: wt2_sp_batch2

description: population RNA-Seq data

value: wt2 sp


title: wt1_dp_batch2

description: population RNA-Seq data

value: wt1 dp


title: wt2_sp_batch1

description: population RNA-Seq data


title: wt1_dn_batch2

description: population RNA-Seq data

value: wt1 dn


title: wt2_dp_batch1

description: population RNA-Seq data


title: wt1_sp_batch2

description: population RNA-Seq data

value: wt1 sp


title: wt2_dn_batch1

description: population RNA-Seq data


title: wt1_sp_batch1

description: population RNA-Seq data


title: wt1_dn_batch1

description: population RNA-Seq data


title: wt1_dp_batch1

description: population RNA-Seq data


title: cd8t_act2

description: population RNA-Seq data

data_processing:
Reads were aligned to a reference genome (mm9 Ensembl) using Bowtie
Expression levels were quantified using RSEM (inferred counts and tpm values), and log2(TPM+1) values generated.
Genome_build: mm9
Supplementary_files_format_and_content: text file with tab delimiters

source_name: Mus musculus CD8

extract_protocol:
we isolated naïve CD8+ cells from non tumor bearing C57BL/6 mice and activated them with anti-CD3 and anti-CD28 in vitro.
Smart-seq2 (Picelli et al., Nature Methods, 2014)

value: CD8 T


title: cd8t_act3

description: population RNA-Seq data


title: mtko3_dp_batch2

description: population RNA-Seq data

value: mtko3 dp


title: naive_bl6_4

description: population RNA-Seq data


title: naive_bl6_3

description: population RNA-Seq data


title: H57VWBGXY_H8_S92

description: single-cell RNA-Seq data

data_processing:
Reads were aligned to a reference genome (mm10 Ensembl) using Bowtie
Expression levels were quantified using RSEM (inferred counts and tpm values), and log2(TPM+1) values generated.
cells were selected for subsequent analysis based on genecount and mapping rates to transcriptome (see manuscript)
Genome_build: mm10
Supplementary_files_format_and_content: text file with tab delimiters

value: CD8 TILs


title: H57VWBGXY_H9_S381

description: single-cell RNA-Seq data


title: H57VWBGXY_H9_S93

description: single-cell RNA-Seq data


title: H57VWBGXY_H8_S284

description: single-cell RNA-Seq data


title: cd8t_act1

description: population RNA-Seq data


title: H57VWBGXY_H8_S188

description: single-cell RNA-Seq data


title: H57VWBGXY_H7_S187

description: single-cell RNA-Seq data


title: H57VWBGXY_H6_S90

description: single-cell RNA-Seq data


title: H57VWBGXY_H5_S89

description: single-cell RNA-Seq data


title: H57VWBGXY_H6_S378

description: single-cell RNA-Seq data


title: H57VWBGXY_H7_S379

description: single-cell RNA-Seq data


title: H57VWBGXY_H8_S380

description: single-cell RNA-Seq data


title: H57VWBGXY_H5_S377

description: single-cell RNA-Seq data


title: H57VWBGXY_H6_S186

description: single-cell RNA-Seq data


title: H57VWBGXY_H7_S283

description: single-cell RNA-Seq data


title: H57VWBGXY_H6_S282

description: single-cell RNA-Seq data


title: naive_bl6_1

description: population RNA-Seq data


title: H57VWBGXY_H7_S91

description: single-cell RNA-Seq data


title: H57VWBGXY_H5_S281

description: single-cell RNA-Seq data


title: H57VWBGXY_H5_S185

description: single-cell RNA-Seq data


title: H57VWBGXY_H4_S88

description: single-cell RNA-Seq data


title: H57VWBGXY_H4_S376

description: single-cell RNA-Seq data


title: H57VWBGXY_H9_S189

description: single-cell RNA-Seq data


title: naive_bl6_2

description: population RNA-Seq data


title: H57VWBGXY_H9_S285

description: single-cell RNA-Seq data


title: H57VWBGXY_H4_S280

description: single-cell RNA-Seq data


title: H57VWBGXY_H4_S184

description: single-cell RNA-Seq data


title: H57VWBGXY_H3_S87

description: single-cell RNA-Seq data


title: H57VWBGXY_H3_S183

description: single-cell RNA-Seq data


title: H57VWBGXY_H2_S278

description: single-cell RNA-Seq data


title: H57VWBGXY_H2_S86

description: single-cell RNA-Seq data


title: H57VWBGXY_H3_S279

description: single-cell RNA-Seq data


title: H57VWBGXY_H3_S375

description: single-cell RNA-Seq data


title: H57VWBGXY_H1_S85

description: single-cell RNA-Seq data


title: H57VWBGXY_H1_S373

description: single-cell RNA-Seq data


title: H57VWBGXY_H2_S374

description: single-cell RNA-Seq data


title: H57VWBGXY_H12_S192

description: single-cell RNA-Seq data


title: H57VWBGXY_H12_S384

description: single-cell RNA-Seq data


title: H57VWBGXY_H1_S277

description: single-cell RNA-Seq data


title: H57VWBGXY_H11_S95

description: single-cell RNA-Seq data


title: H57VWBGXY_H1_S181

description: single-cell RNA-Seq data


title: H57VWBGXY_H12_S288

description: single-cell RNA-Seq data


title: H57VWBGXY_H10_S94

description: single-cell RNA-Seq data


title: H57VWBGXY_H11_S287

description: single-cell RNA-Seq data


title: H57VWBGXY_H11_S191

description: single-cell RNA-Seq data


title: H57VWBGXY_H10_S382

description: single-cell RNA-Seq data


title: H57VWBGXY_H11_S383

description: single-cell RNA-Seq data