title: HEK_adGFP_B


title: HEK_adGFP_A

status: Public on Aug 07 2018

type: SRA

city: Bethesda

first: Maria

middle: Irene

last: Morasso

state: Maryland

address: Bldg 50

country: USA

institute: NIAMS NIH

library_source: transcriptomic

data_processing:
Demultiplex and Convert to FastQ: CASAVA 1.8.2
Map to hg19 transcriptome: tophat 2.1.0
Calculate RPKM: Partek GS 6.6
Genome_build: hg19
Supplementary_files_format_and_content: Excel format, containing gene level RPKM values

molecule: polyA RNA

organism: Homo sapiens

source_name: HEKdGFP

extract_protocol:
RNA was harvested 48hs after siRNA transfection or viral transduction and sequencing was performed using Illumina.
cDNA library preparation for RNA-seq analysis was performed on samples using the Mondrian SP kit (Illumina, San Diego, CA). Sequencing was performed using the Illumina HiSeq 2000.

treatment_protocol: All cells were cultured at 37°C in the presence of 5% CO2. NOK culture was performed as described. HEK were from LONZA. NOK cells were maintained in defined keratinocyte serum free media (KSFM) (GIBCO) supplemented with antibiotics. HEK cells where cultured in KGM-Gold™ Keratinocyte Growth Medium (LONZA). For siRNA experiments, primary cells were transfected with the corresponding siRNAs next day after plating and imaged/harvested as indicated. siRNA was transfected at a concentration of 8 pmol cm-2 using HiPerfect transfection reagent (QIAGEN) according to manufacturer’s instructions. siRNAs were from GE Dharmacon siGENOME SMARTpool for human PAX9 M-012242-01-0005, PITX1 M-017246-01-0005, PITX2 M-017315-02-0005, SOX2 M-011778-00-0005 and non-targeting control siRNA D-001206-13. For adenoviral transduction, cells where incubated with MOI 10 adeno-GFP (control), adeno-h-SOX2 (NM_003106) and adeno-h-PITX1 (Genbank RefSeq: BC009412.1) for 24 hs. Adenoviruses were from Vector Biolabs.

tag: cell line

value: HEK

tag: cell type

value: Human epidermal keratinocytes

tag: transfected with

value: adGFP


title: run1289_lane12_read2_indexN706-S507=Nov18_Cell_47

status: Public on Aug 08 2018

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: Single cell RNA-seq

data_processing:
Raw fastq data was quality trimmed to a minimum Phred score of 20 using trimmomatic.
Reads were then filtered against mouse ribosomal sequences using bowtie2, followed by full genome and transcriptome alignment to mouse reference mm10 using STAR.
Apparent PCR duplicates and unassignable reads were removed using Picard Mark Duplicates.
SNPs for CAST/EiJ mice were obtained from release-1505-GRCm38 from Sanger Institute’s ftp site (ftp://ftp-mouse.sanger.ac.uk/). SNPs with quality score of at least 100, reported by Sanger, were retained for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Allele distributions (*subset.txt files): Only Sanger SNPs with a coverage of at least 30 in at least one sample were included for further analysis. The allele counts are summarized in the allele distribution files (*_subset.txt): each position in the Ig kappan (top section) and lambda (bottom section) loci is listed with its coordinates and V or J segment name, the overall sequencing depth at that position (ACGT bases only), and the percent of B6, CAST, or unassigned alleles. Allele counting was performed using samtools mpileup. When cells do not express these loci, the processed data files will contain no data beyond the header.
Supplementary_files_format_and_content: Summary statistics (*summary.txt files): Summary files for each cell over each V and J segment in the Ig kappa (top section) and lamda (bottom section) loci were compiled giving the sequencing depth, number of heptamer/nonamer motifs found, allelic specificity of the expression, and any splicing observed between that segment and other segments in the same locus. Read counts and splicing instances were obtained using bedtools; motif instances were found by string matches to the motif sequence with wildcards for spacer sequences (regex); allelic expression was determined from all SNPs with coverage of at least 10 on a segment from the allele distribution files.
Supplementary_files_format_and_content: Raw expression count table (bulk D3 null samples): Raw read counts per gene were obtained for all regular RNA-seq (non-single-cell) data using htseq-count. Gene annotations for mm10 from iGenomes were supplemented with the Ig kappa and lambda segments.

molecule: total RNA

organism: Mus musculus

source_name: Small Pre-B cells

extract_protocol:
B6 X CAST small pre-B cells were FACs sorted for CD19+B220+IgM-CD43low, and used for bulk or single cell sorting and sequencing.
Bulk sorted CD19+B220+IgM-CD43low small pre-B cells were single cell sorted on pre-primed C1 Fluidic Chips. Cells were lysed, RT performed (Clontech SMARTer) and cDNAs transferred to 96 well plates. Libraries were prepared using Nextera XT (Illumina) then tagmented. Pooled libraries were purified with AMPure magnetic separation assayed for quality with Qubit® dsDNA HS (Life Tecnologies) and sequenced (75bp paired).

value: Small Pre-B cells

tag: strain

value: B6 x CAST F1 hybrid

tag: genotype

value: wildtype


title: igfbp3_tss_ko

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute on Aging

library_source: genomic

data_processing:
Library strategy: 4C-Seq
For 4C-Seq analyses, the publicly available w4CSeq analysis pipeline was used (https://github.com/WGLab/w4CSeq) using default settings.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bedgraph: Bedgraph files were generated as part of the w4CSeq analysis pipeline.

molecule: genomic DNA

growth_protocol: MCF7 cells were cultured in DMEM (+GlutaMAX, Thermo Scientific) supplemented with 10% FBS (Sigma) and 1% penicillin-streptomycin (Sigma).

extract_protocol:
3 million MCF7 and TRPS1 KO cells were cross-linked with 1% (v/v) formaldehyde (Sigma) in culture medium for 10 min at room temperature. Cells were lysed in lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl) containing 0.5% (v/v) NP-40. Nuclei were digested with 800 U EcoRI (NEB) in Cutsmart buffer (NEB) supplemented with 0.3% SDS and 2% Triton X-100, overnight at 37°C while shaking. The first ligation was carried out with 100 U T4 DNA ligase (Thermo Scientific) at 16°C overnight. After decross-linking and phenol/chloroform extraction, 25 mg of the 3C library was digested with 100 U DpnII in DpnII buffer (NEB) overnight at 37°C while shaking. After a second ligation carried out with 200 U T4 ligase at 16°C overnight, DNA was extracted with phenol/chloroform and purified with the ChIP DNA clean and concentratorTM kit (Zymo Research).
Per PCR (50 µl reaction), 100 ng DNA were used as template to amplify libraries of the IGFBP3 TSS using specific primer (Fw: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGAGAAATAAAGTTCCTGCCTTGC ; Rev: CAAGCAGAAGACGGCATACGACTTCCTTGGTCCAAATCCGC) and Phusion hot start II polymerase (Thermo Scientific) as recommended by the manufacturer. PCR reactions were pooled and purified with Agencourt AMPure XP Beads (Beckman Coulter). In total, 1 µg of genomic DNA was amplified in 10 reactions. Equal amounts of specific libraries were combined and sequenced on an Illumina Hiseq 2500 with 75 cycles.

treatment_protocol: To generate TRPS1 KO cells by CRISPR, MCF7 cells were transfected with a pX461 vector (carrying WT Cas9 and not the nickase version) carrying a sgRNA sequence that targets human TRPS1. Transfection was performed using Lipofectamine 3000. Transfected (GFP+) cells were sorted by flow cytometry into a 96-well plate as single cells. The Knockout of TRPS1 was verified by Western Blot and Sanger Sequencing.

value: breast cancer cell line

tag: genotype/variation

value: TRPS1 KO


title: t47d_input

data_processing:
FASTQ files were processed (adapter removal, length filter, quality filter) using cutadapt (version 1.12) with the following options: --discard-trimmed -m 25 -q 10
FASTQ files were aligned to hg19 using bowtie2 (version 2.2.9) using the --local option
Peak calling was performed using MACS2 (version 2.1.1) using the following settings: B --nomodel --SPMR -g hs --extsize 147. The resulting normalized (per million reads) bedgraph files were converted to bigWig files using bdg2bw.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bw: The MACS2-derived normalized (per million reads) bedgraph files were converted to bigWig files using bdg2bw.

growth_protocol: MCF7 and T47D cells were cultured in DMEM (+GlutaMAX, Thermo Scientific) supplemented with 10% FBS (Sigma) and 1% penicillin-streptomycin (Sigma). T47D culture medium was additionally supplemented with 1 µl/ml human insulin solution (Sigma).

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at RT. Nuclei were extracted using hypotonic buffer (20 mM Tris, pH 7.4, 2 mM MgCl2, 5% glycerol) and lysed with ChIP lysis buffer (20 mM Tris pH 7.4, 150 mM NaCl, 1% NP40, 0.5% DOC, 0.1% SDS, 1 mM EDTA). Chromatin was sonicated to obtain fragments of 200 bp. Equilibration of beads (Dynabeads, Thermo Scientific) with antibodies (2 μg for ChIP, 10 μg for ChIP-Seq) was performed overnight, following immunoprecipitation of chromatin for 6h. After extensive washing, bound chromatin was eluted using ChIP elution buffer (50 M Tris, pH 8.0, 1 mM EDTA, 1% SDS, 50 mM NaHCO3) and de-crosslinked and RNase A/Proteinase K (Roth) digested over night. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
ChIP-Seq libraries were generated according to the manufacturer’s protocol (NEBNext Ultra II DNA Library Prep Kit for Illumina, NEB) using Dual Index Primers (NEBNext Multiplex Oligos for Illumina, NEB). The number of PCR cycles varied between 9-12 PCR cycles. The optimal PCR cycle number was determined beforehand using a qPCR machine with 10% of the material used for the final amplification.

treatment_protocol: For YAP ChIP, an MCF7 cell line carrying a doxycycline-inducible YAP 5SA allele was used. YAP 5SA was induced by adding 1 µg/ml doxycycline for 18 hours and subsequently subjected to formaldehyde crosslinking. For generating TRPS1 KO cells by CRISPR, MCF7 cells were transfected with a pX461 vector (carrying WT Cas9 and not the nickase version) carrying a sgRNA sequence that targets human TRPS1. Transfection was performed using Lipofectamine 3000. Transfected (GFP+) cells were sorted by flow cytometry into a 96-well plate as single cells. The Knockout of TRPS1 was verified by Western Blot and Sanger Sequencing.

value: WT

tag: yap 5sa induced

value: No

tag: chip antibody


title: O12

description: H3878_oral mucosa_day 6

source_name: oral mucosa_day 6

extract_protocol:
RNA from frozen skin and oral biopsies or cells was extracted using RNeasy kit (Qiagen) according to the manufacturer’s instructions. For biopsies, four samples of each day were processed for RNA extraction, with matching skin and oral wounds from the same subject for that day.
cDNA library preparation for RNA-seq analysis was performed on samples collected from skin and oral sampels Day 1, Day 3 and Day 6,  (n=4 for each day) using the Mondrian SP kit (Illumina, San Diego, CA). Sequencing was performed using the Illumina HiSeq 2000.

treatment_protocol: Sample isolation and treatment as specified in Clinicaltrials.gov #NCT01078467

tag: subject id

tag: subject status

value: healthy volunteer

tag: tissue

value: oral mucosa

tag: day sample/biopsy

value: day 6


title: t47d_tead1

value: TEAD1 (BD Bioscience, Cat# 610923)


title: mtHTT-RIP3

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

description: Striatal tissue collected 3 weeks after unilateral injection of AAV-mtHTT

data_processing:
Adaptor sequences were removed using cutadapt
Reads obtained from mouse tissue were mapped to the mouse genome using STAR_2.4.0j (for microRNAs 1 mismatches per 20nt were allowed)
Reads were quantified using the Rsubread package for R using miRbase annotation (miRNAs)
Genome_build: mm10 for mouse tissue
Supplementary_files_format_and_content: txt files containing abundance measurements of miRNA features from miRBase, repeats annotation from repeatMasker. Whitespace separated. Columns: [Geneid- Chr- Start- End- Strand- Length - #reads mapping to feature]

source_name: freshly dissected tissue

growth_protocol: All stereotactic injections into the striatum were performed as described before with minor changes (Malmevik, J. et al. Identification of the miRNA targetome in hippocampal neurons using RIP-seq. Scientific reports 5, 12609 (2015)). All mice were adult C57BL/6 females aged 9 to 10 weeks old at the time of surgery. Injections were unilateral, always on the right side of the brain with a total of 1 µl injected. The injection coordinates were: AP: +0,9 mm; ML: +/-1.8 mm; DV (from dura): -2.7 mm.

extract_protocol:
smallRNA was extracted using the miRNeasy Mini kit from Qiagen
NEBNext Multiplex Small RNA Library Prep Set for Illumina

treatment_protocol: Strital tissue was harvested 3 weeks after virus injection and immediately lysed for AGO2-RIPseq

tag: lentiviral mediated overexpression

value: mHTT


title: mtHTT-RIP1

treatment_protocol: Striatal tissue was harvested 3 weeks after virus injection and immediately lysed for AGO2-RIPseq.


title: O11

description: H3879_oral mucosa_day 6


title: mtHTT-IN3

treatment_protocol: Striatal tissue was harvested 3 weeks after virus injection and immediately lysed for RNA extraction and smallRNA sequencing.


title: trps1_ko_hdac3

value: HDAC3 (Cell Signaling, Cat# 85057)


title: mtHTT-IN2


title: O10

description: H3892_oral mucosa_day 6


title: trps1_ko_h3k27ac

value: H3K27ac (Abcam, Cat# ab4729)


title: trps1_ko_ctbp2

value: CtBP2 (BD Bioscience, Cat# 612044)


title: P2216_121

description:
Striatal tissue collected 10 days after unilateral injection of AAV-wtHTT
featC.polyAinvivorefseq.txt

data_processing:
Adaptor sequences were removed using cutadapt
Reads from samples obtained from 293T cells were aligned to the human genome, reads obtained from mouse tissue were mapped to the mouse genome using STAR_2.4.0j (default settings for mRNA, for microRNAs 2 mismatches per 20nt were allowed)
Reads were quantified using the Rsubread package for R using miRbase annotation (miRNAs), refseq annotations (for mRNA) and Ensembl (for snoRNA and snRNA)
Genome_build: hg19 for 293T cells; mm10 for mouse tissue
Supplementary_files_format_and_content: txt files containing abundance measurements of miRNA features from miRBase / snoRNA, snRNA features from Ensembl/ refseq features for mRNA. Whitespace separated. Columns: [Geneid- Chr- Start- End- Strand- Length - #reads mapping to feature]

source_name: freshly frozen striatal tissue

extract_protocol:
RNA was extracted using the miRNAeasy Mini Kit from Qiagen
Illumina Strand-specific TruSeq RNA library kit using poly-A selection

treatment_protocol: The striatum was quickly dissected from decapitated vector-injected mice (10 days or 3 weeks after injection), frozen on dry ice and homogenised in Tissue LyserLT (50 Hz, 2 x 2 min).

value: wtHtt

tag: time after virus injection

value: 10 days


title: P2216_120


title: P2216_122

description:
Striatal tissue collected 10 days after unilateral injection of AAV-mtHTT
featC.polyAinvivorefseq.txt

value: mHtt


title: O9

description: H3885_oral mucosa_day 6


title: P2216_119


title: O8

description: H3891_oral mucosa_day 3

source_name: oral mucosa_day 3

value: day 3


title: O6

description: H3875_oral mucosa_day 3


title: O7

description: H3882_oral mucosa_day 3


title: mcf7_hdac3


title: P2216_118

description:
Striatal tissue collected 3 weeks after unilateral injection of AAV-mtHTT
featC.polyAinvivorefseq.txt


title: mcf7_h3k27ac


title: P2216_116


title: P2216_117


title: P2216_124


title: mcf7_trps1_ko_input

value: WT & TRPS1 KO


title: mcf7_ctbp2

value: breast cancer cell line


title: mcf7_yap

value: Yes

value: YAP (Abcam, Cat# ab52771)


title: P2216_115

description:
Striatal tissue collected 3 weeks after unilateral injection of AAV-wtHTT
featC.polyAinvivorefseq.txt

value: wt Htt


title: P2216_123


title: P2216_113


title: mtHTT-IN1


title: mcf7_tead1

value: WT

value: No


title: O5

description: H3886_oral mucosa_day 3

value: healthy volunteer

value: oral mucosa


title: O1

description: H4632_oral mucosa_day 1

source_name: oral mucosa_day 1

value: day 1


title: O4

description: H3888_oral mucosa_day 1


title: O3

description: H4631_oral mucosa_day 1


title: O2

description: H3880_oral mucosa_day 1


title: S12

description: H3878_skin_day 6

source_name: skin_day 6

value: skin

value: day 6


title: mcf7_trps1

value: TRPS1 (self-made affinity-purified antibody raised against aa 920-1281)


title: siTRPS1_rep3

description:
mRNA
Processed data file: t47d_sitrps1_rpkm_table.txt

data_processing:
FASTQ files were processed (adapter removal, length filter, quality filter) using cutadapt (version 1.12) with the following options: --discard-trimmed -m 25 -q 10
FASTQ files were aligned to hg19 using bowtie2 (version 2.2.9) using default parameters.
Differentially expressed genes (DGEs) were determined using edgeR (version 3.12.1).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_rpkm_table.txt: Tab-delimited text files; RPKM values were determined using custom scripts.

extract_protocol:
Total RNA was extracted using RNeasy® Mini Kit (Qiagen) with on-column DNaseI (Qiagen) digestion. RNA integrity was verified with the Agilent 2100 Bioanalyzer automated electrophoresis system (Agilent Technologies).
mRNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB) and library preparation was conducted with the NEBNext® Ultra RNA Library Prep Kit for Illumina (NEB) with Dual Index Primers (NEBNext® Multiplex Oligos for Illumina, NEB). Size selection of the libraries for 270 bp was performed with Agencourt AMPure XP Beads (Beckman Coulter). Cycles for amplification of the cDNA were determined and conducted using qRT-PCR. Libraries were quantified with the Agilent 2100 Bioanalyzer automated electrophoresis system (Agilent Technologies) and subjected to Illumina Sequencing (HiSeq 2500).

treatment_protocol: To determine YAP-dependent gene expression changes in MCF7 cells, an MCF7 cell line carrying a doxycycline-inducible YAP 5SA allele (pInducer21-Strep-YAP 5SA) was used. YAP 5SA was induced by adding 1 µg/ml doxycycline for 18 hours and subsequently subjected to RNA-Sequencing. TRPS1 was depleted in MCF7 cells using three independent shRNAs targeting TRPS1 (shTRPS1 Seq1-3) or a non-targeting control (shNTC). TRPS1 was depleted in T47D cells using 20 nM siRNAs (Dharmacon, SmartPool) or a non-targeting control from the same company.

tag: construct/sirna

tag: induction

tag: replicate


title: S8

description: H3891_skin_day 3

source_name: skin_day 3


title: mcf7_input

tag: cell line


title: siTRPS1_rep2

tag: cell type


title: S10

description: H3892_skin_day 6


title: siTRPS1_rep1


title: siCtrl_rep1

value: siCtrl


title: NPA1-HTP

city: PARIS

first: Simon

last: Lebaron

address: 4 avenue de l'observatoire

country: France

institute: Université Paris Descartes

description: cDNA librairies obtained after reverse transcription and PCR amplification of associated RNAs after digestion (Rnace it)

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, using Flexbar with a barcode and an adaptor file using --adapter-trim-end RIGHT option.
Alignement was performed using Novoalign and -r Random option.
Aligned reads were analyzed using pyCRAC software.
Genome_build: R64 (S.cerevisiae)
Supplementary_files_format_and_content: One of the sequence analysis corresponds to the numbert of hits in each genes per 1000000 reads.

organism: Saccharomyces cerevisiae

source_name: Total extract

growth_protocol: Yeast were gorwn in YMM, -trp + glucose, until final OD=0.6

extract_protocol:
Cell lysis was perfomed using Zirconium beads (5x 1minutes, with 1 minutes intervals on ice). Complex was isolated by two succesive Ips.
Library was constructed by linking to digested RNA illumina compatible 5' Adaptaters and 3' linkers. Then, those modified RNA were extracted and a Reverse Transcription was performed using Superscript III followed by a final moderate PCR enrichement (16 cycles). This was then analyzed on HiSeq plateform from illumina.
CRAC

treatment_protocol: Protein were corss-linked to RNA using Megatron

tag: tag

value: HTP (His-Tev-ProtA)

tag: cross-link

value: Megatron (100 secondes)

tag: sample type

value: cDNA


title: BY4741

value: no Tag


title: S9

description: H3885_skin_day 6


title: P2216_114

tag: strain


title: S5

description: H3886_skin_day 3

value: day 3


title: S3

description: H4631_skin_day 1

source_name: skin_day 1


title: siCtrl_rep3

value: breast cancer cell line


title: siCtrl_rep2


title: S7

description: H3882_skin_day 3


title: S4

description: H3888_skin_day 1


title: S6

description: H3875_skin_day 3


title: iYAP5SA_DOX_rep3

description:
mRNA
Processed data file: mcf7_yap_i5sa_rpkm_table.txt

value: pInducer21-Strep-YAP 5SA

value: DOX


title: iYAP5SA_EtOH_rep2

value: EtOH


title: iYAP5SA_DOX_rep2


title: iYAP5SA_DOX_rep1


title: shTRPS1_Seq3

description:
mRNA
Processed data file: mcf7_shtrps1_rpkm_table.txt

value: pGIPZ shTRPS1 Seq3


title: shTRPS1_Seq2

value: pGIPZ shTRPS1 Seq2


title: iYAP5SA_EtOH_rep1


title: Sample_KP-RNA-66Q-2

description:
non treated (NT), samples colleceted 3 days after LV transduction
featC.polyAinvitrorefseq.txt

source_name: 293T cells

growth_protocol: All cell culture work on 293T cells was performed as described before (Musiwaro, P., Smith, M., Manifava, M., Walker, S.A. & Ktistakis, N.T. Characteristics and requirements of basal autophagy in HEK 293 cells. Autophagy 9, 1407-1417 (2013)). Cells were grown to  ≈ 80 % confluence  in six well plates before harvesting.

extract_protocol:
RNA was extracted using the miRNeasy Mini kit from Qiagen
KAPA Stranded mRNA-Seq Kit from KAPAbiosystems

treatment_protocol: Cells were harvested 3 days after LV transduction.

value: mHTT

value: 293T cells


title: shTRPS1_Seq1

value: pGIPZ shTRPS1 Seq1


title: S2

description: H3880_skin_day 1

value: healthy volunteer

value: skin

value: day 1


title: Sample_KP-RNA-66Q-1


title: S1

description: H4632_skin_day 1


title: Sample_KP-RNA-18Q-3

value: wtHTT


title: Sample_KP-RNA-18Q-1


title: S11

description: H3879_skin_day 6

value: day 6


title: iYAP5SA_EtOH_rep3


title: Sample_KP-RNA-18Q-2


title: shNTC_rep3

value: pGIPZ shNTC


title: run1289_lane12_read2_indexN702-S517=Nov18_Cell_9

description: Single cell RNA-seq

value: Small Pre-B cells

value: B6 x CAST F1 hybrid

tag: genotype

value: wildtype


title: pig_muscle_MNase-seq

status: Public on Aug 06 2018

city: Irvine

first: Yumei

last: Li

state: CA

address: 825 Health Sciences Road

department: Department of Biological Chemistry

institute: University of California, Irvine

data_processing:
MNase-seq reads were filtered by inhouse scripts to get high quality reads.
High-quality reads were aligned to the corresponding genome using bwa (v0.7.13-r1126) with default parameters.
The PCR duplicates were removed by samtools (v1.3.1) rmdup command. The uniquely mapped reads with map quality greater than 30 were kept.
Nucleosome occupancy and position were called by DANPOS2 (v2.2.2) with parameters -jd 147 -m 1  --extend 74.
Genome_build: human: hg19, monkey: rheMac2, tree shrew: tupBel1, mouse: mm9, pig: susScr3
Supplementary_files_format_and_content: bigWig files were generated using DANPOS2; scores represented nucleosome occupancy.

organism: Sus scrofa

source_name: muscle

extract_protocol:
Pellets were washed with MNase digestion buffer (10mM Tris pH7.4, 15mM NaCl, 10mM KCl, 1.5mM CaCl2), after which were collected by 350g centrifugation for 5 min at 4°C. Pellets were further suspended with digestion buffer containing MNase (NEB, M0247S) and incubated at 37°C, then stopped by 2× stopping buffer (0.6% SDS, 40mM EDTA, 40mM EGTA).
E7370 kit was used for library construction. And the samples were indexed using Illumina Truseq indexes. The cycle number of the amplification was 4 or 5.

treatment_protocol: Tissues were obtained and immediately fixed in 1% V/V formaldehyde at room temperature for 10 min, followed by neutralization with 2.5M glycine (Sigma) and washed with PBS. Then the fixed tissues were homogenized with a T10 homogenizer (IKA) and collected by centrifugation. The collected samples were incubated in hypotonic buffer for 20 min and homogenized for 10-20 strokes.

value: muscle

tag: developmental stage

value: adult

tag: gender

value: male

value: wild type


title: pig_kidney_MNase-seq

source_name: kidney

value: kidney


title: pig_heart_MNase-seq

source_name: heart

value: heart


title: pig_liver_MNase-seq

source_name: liver

value: liver


title: pig_liver_RNA-seq

data_processing:
RNA-seq reads were filtered by inhouse scripts to get high quality reads.
High-quality reads were aligned to the corresponding genome using TopHat (v2.1.1).
Genome_build: human: hg19, monkey: rheMac2, tree shrew: tupBel1, mouse: mm9, pig: susScr3
Supplementary_files_format_and_content: bigWig files were generated using wiggles (v1.2.0); scores represented read coverage.

extract_protocol:
Total RNA of the tissues was extracted using the Trizol method and analyzed by an Agilent 2100 bio-analyzer (Agilent Technologies).
Strand-specific polyA+ RNA libraries were prepared for sequencing using standard Illumina protocols.


title: pig_brain_RNA-seq

source_name: brain

value: brain


title: Sample_KP-RNA-66Q-3

value: mHTT

value: 293T cells


title: pig_muscle_RNA-seq


title: emer_amoA

city: Bogotá

first: Sandra

middle: Milena

last: Gonzalez Sayer

state: Cundinamarca

address: 30th Avenue to 45th Street

department: Biotechnology Institute

country: Colombia

institute: National University of Colombia

data_processing:
Sequenced reads were trimmed for adaptor sequence, low-quality sequence using FASTX Toolkit v0.0.13.2, then processed with riboPicker to remove rRNA-like v.0.4.3 sequences from the dataset
The trimmed, high-quality reads were aligned using the BLAST and debugged reference database of amoA gene for Archaea and Bacteria domains, which was downloaded from the DDBJ-EMBL-GenBank database.
Supplementary_files_format_and_content: text files with read counts with phylum and order for identified amoA family genes.

organism: soil metagenome

source_name: rhizosphere soil, Edaphic Microbial Communities, emergence

extract_protocol:
RNA was extracted from 0.5mg of dry weight soil using a POWER SOIL® (Epicentre) commercial kit according to the manufacturer’s instructions. The lysis phase was performed with zirconia beads.
RNA libraries were prepared for sequencing using standard Illumina protocols. Libraries were prepared according to Illumina's instructions. Briefly, mRNA were separate of total RNA using (mRNA-prokaryotic mRNA isolation epicentre) kit. RNA transcripts were polyadenylated employing poly (A) polymerase Tailing kit epicenter and Later mRNA were amplified using T7 RNA polymerase and µMACSTM one step T7 template kit.

treatment_protocol: Soil attached to the root system was carefully separated by hand, placed in 2 ml Eppendorf tubes® and stored in liquid nitrogen. DNA and RNA were extracted within 36 h; RNA extraction was prioritized due to its rapid degradation.

tag: growth stage

value: emergence

tag: days after planting

tag: crop

value: Solanum phureja

tag: soil region

value: rhizosphere


title: pig_heart_RNA-seq

tag: tissue


title: pig_brain_MNase-seq


title: rSF+q1

city: Mannheim

first: Francesca

last: Tuorto

address: Ludolf-Krehl-Str. 13-17

department: Division of Biochemistry  Mannheim Institute for Innate Immunoscience (MI3)

institute: Deutsches Krebsforschungszentrum

description: combinedRNAseqCounts.txt

data_processing:
After quality and adapter trimming (AGATCGGAAGAGCACACGTCT), aligned to human tRNA (CCA-appended sequences from gtrnadb.ucsc.edu), rRNA (arb-silva, Ensembl ncRNA, NCBI RefSeq and Biobases) and mitochondrial tRNA and rRNA sequences (Ensembl ncRNA) using Bowtie allowing 2 mismatch, discarding any mapped reads from further analysis.
The remaining reads were aligned with bowtie against hg38 RefSeq mRNA sequences, allowing 2 mismatches and using 23nt as seed region.
Reads of length 27-30 nt whose 5' end map from 15 nt downstream of the CDS start of a gene and 3' end map from 5 nt upstream of the CDS stop were assigned to that gene.
Codon occupancy was calculated as the codon proportions in the A-site (read start +15-16nt) divided by averaged codon proportions in the 3 codon sites up and dowstream of the ribosome.
For RNA-seq, processing was done similarly except that reads were kept at any mapping position and if read length was at least 25 nt.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files containing codon occupancy, footprint counts (smallRNA counts) assigned to each CDS for all samples, and RNA-seq read counts assigned to each mRNA for all samples.

molecule: cytoplasmic RNA

source_name: rSF+q

growth_protocol: We compared HeLa cells that were cultured 45 days under serum free (SF) conditions with cells that were first cultured under serum free conditions for 30 days and then received 20 nM queuine for 15 days (SF+qR) to rescue any q-dependent defects . Furthermore, a parallel control culture (45 days) was established using SF conditions supplemented with 20 nM queuine (SF+q). HeLa cells grown in standard medium (S) and in standard medium supplemented with 20 nM queuine were included as additional controls.

extract_protocol:
Ribosome footprint was performed according to (Ingolia et al, 2011). 2x107 HeLa cells from each culture condition were treated with cycloheximide (100 µg/ml) for 5 minutes prior to lysis in 800 µl of 20 mM Tris-HCl, pH 7.4, 5 mM MgCl2, 150 mM NaCl, 1% Triton X-100, 100 µg/ml cycloheximide, 1×Complete Protease Inhibitors (Roche). 200 µl aliquot was used to extract cytoplasmic RNA to perform RNAseq.  200 µl aliquot was used to produce ribosome profiling. The left over 400 µl aliquot of lysate was treated with 4 U DNase I (ThermoScientific) and 800 U of RNase I (Ambion), for 45 minutes at room temperature with gentle shaking.   800 U of RNasin ribonuclease inhibitor (Promega) was added to quench the reaction.    The  samples were run on a 17.5-50% sucrose gradient to isolate monosome.  Footprint monosome RNA was end using RNA were end-repaired with T4 polynucleotide kinase (TaKaRa), and size selected 28-31 nucleotide on a 15% polyacrylamide TBE-urea gel.
Small RNA libraries were performed according to the protocol using NEB NEXT Small RNA library Prep Set for Illumina (Multiplex Compatible) E7330, and size-selected (120-170 base pairs) before sequencing. RNA Sequencing libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Illumina) according to the manufacturer's protocol. Briefly, poly(A)+ RNA was purified from 1µg of total RNA using oligo(dT) beads, fragmented and converted to cDNA. The double stranded cDNA fragments were then end-repaired, adenylated on the 3′ end, adapter ligated and amplified with 12 cycles of PCR. The final libraries were validated using Qubit Fluorometer (Life Technologies-Invitrogen) and Agilent TapeStation 4200 (Agilent Technologies). After sizing analysis, multiplexed sequencing libraries were normalized, pooled and clustered on the cBot (Illumina, Inc.) with a final concentration of 10 pM (spiked with 1% PhiX control v3, Cat No. FC-110-3001) using the TruSeq SR Cluster Kit v3 (Cat no. GD-401-3001). Sequencing on HiSeq 2000 (Illumina) was performed using the 50 cycles TruSeq SBS Kit v3 according to the manufacturer's protocol.

value: cervix adenocarcinoma cell line HeLa

tag: treatment

value: Serum free+20nm queuine 45 days


title: flor_amoA

source_name: rhizosphere soil, Edaphic Microbial Communities, flower advent

value: flower advent


title: rSF+q2

description: combinedRNAseqCounts.txt


title: rSF+qR2

description: combinedRNAseqCounts.txt

source_name: rSF+qR

value: Serum free 30 days+20nm queuine 15 days


title: hill_amoA

source_name: rhizosphere soil, Edaphic Microbial Communities, hilling

value: hilling


title: pig_kidney_RNA-seq

value: adult


title: rSF2

description: combinedRNAseqCounts.txt

source_name: rSF

value: Serum free


title: rSF+qR1

description: combinedRNAseqCounts.txt


title: rS2

description: combinedRNAseqCounts.txt

source_name: rS

value: Serum


title: rS+q1

description: combinedRNAseqCounts.txt

source_name: rS+q

value: Serum +20nM queuine


title: fSF+q2

description:
smallRNA-seq
CodonOccupancy.txt
combinedFootprintCounts.txt

source_name: fSF+q


title: rSF1

description: combinedRNAseqCounts.txt


title: rS1

description: combinedRNAseqCounts.txt


title: rS+q2

description: combinedRNAseqCounts.txt


title: fSF+qR1

source_name: fSF+qR


title: fSF1

source_name: fSF


title: fS+q2

source_name: fS+q


title: shNTC_rep1

value: breast cancer cell line

tag: construct/sirna

value: pGIPZ shNTC

tag: induction


title: fSF+qR2

tag: cell line


title: fS+q1


title: fSF+q1


title: fSF2


title: fS2

source_name: fS


title: shNTC_rep2

tag: cell type

tag: replicate


title: Patient 1

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

data_processing:
Cell counter: Cell Ranger
Data filtering: Seurat 2.0.0
Data normalization: Seurat 2.0.0
Genome_build: Hg19
Supplementary_files_format_and_content: tsv and mtx files are tab-separated plain-text tables

source_name: Blood sample

extract_protocol:
For those samples with potential CTCs based on Imagestream analysis, the second aliquot was used for single-cell RNA sequencing (scRNAseq) using Chromium 10X technologies. The cell density was determined using a C-Chip DHC-N01 disposable hemocytometer. A mixture of 5 μl of 0.04% trypan blue (BioRad) and 5 μl of the single cell suspension was loaded unto the hemocytometer and examined at 10X magnification, using the Invitrogen Evos FL Cell Imaging System-digital inverted microscope. The single-cell chip loading, GEM generation & barcoding, post GEM-RT & cDNA amplification, and library construction were performed according to the ChromiumTM Single Cell 3’ Protocol - Chemistry v2. For GEM generation an input of 10,000 cells total, at 1,000 cells/uL density, was targeted for each sample, with a target cell recovery of 6,000 cells.
Library construction, enzymatic fragmentation, End-repair and A-tailing were performed as follows: pre-cool block at 4°C hold, fragmentation at 32°C for 5 minutes; End repair and A-tailing 65°C for 30 minutes and held at 4°C. Post reaction cleanup was performed, followed by Adaptor ligation. Adaptor ligation incubation was done at 20°C for 15 minutes. Post adaptor ligation cleanup was then performed, followed by sample index PCR with the following parameters: 98°C for 45 seconds; followed by 14 cycles: 98°C for 20 seconds; 54°C for 30 seconds; and 72°C for 20 seconds; followed by 72°C for 1 minute and held at 4°C. Quantification of the constructed libraries was evaluated using Qubit dsDNA HS Assay Kit (Thermo Fisher), Agilent cDNA High Sensitivity Kit, and Kapa DNA Quantification Kit for Illumina platforms, following the manufacturer's instructions.
Generated libraries were sequenced on the Illumina HiSeq2500, using the paired-end 2 x 125bp sequencing protocol. Sequencing run parameters were set up according to version 2 chemistry, the number of cycles for each read as follows: Read 1: 26 cycles, i7 index: 8 cycles, i5 index: 0 cycles and Read 2: 98 cycles.

value: circulating tumor cells in hepatocellular carcinoma


title: fS1


title: Patient 2


title: Uninjured Input  Rep3

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

data_processing:
Bowtie2-2.2.3 was used to align the ChIPseq reads to the Ensembl GRCm38 version of the mouse genome.
Duplicate reads were marked with Picard tools 1.1.103 and then removed with Samtools 1.2. Replicate inputs and eluates of each condition were then pooled.
Macs2-2.1.10 was used to call peaks on the pooled replicates using a fragment length of 190bp for each set.
Macs2 bdgdiff command was then used on the bedgraph files of each sample set produced by the callpeaks algorithm. This produced the set of 1046 peaks contained in the processed data file given here.
Genome_build: GRCm38
Supplementary_files_format_and_content: The Jun Differential Peaks.xlsx file contains the peaks called by the Macs2 bdgdiff command (as described above). These are the peaks that were used for all analyses in the associated publication.

source_name: DRG

extract_protocol:
Seven days after surgery, mice were sacrificed and the three DRGs innervating the sciatic nerve on each side (six ganglia in total) were extracted and placed in HibernateE (BrainBits). Once the DRGs from three mice had been extracted and pooled together, the samples were gently spun down at 80 x g for 2 minutes. The pellet was then resuspended in 10mL of Complete Tissue Fixation Solution (Active Motif) containing 1% fresh formaldehyde and fixed at room temperature for ten minutes. The ActiveMotif ChIP-IT High Sensitivity Kit was then used to perform the remainder of the immunoprecipitation process with the following alterations: 1) TE + 1% SDS was used instead of ActiveMotif’s Chromatin Prep Buffer in Section C step 9; 2) 400µL of ChIP Buffer was used for the sonication, which was carried out in 15mL Bioruptor Pico Tubes with 250mg of sonication beads (Diagenode; Catalog # C01020031); and 3) the sonication was performed on a Bioruptor Pico sonicator for 7 cycles of 30 seconds on and 30 seconds off per cycle with the water bath maintained at 4C continuously (Diagenode). Each chromatin preparation made in this manner yielded enough material for an input and two immunoprecipitation reactions. Immunoprecipitations were carried out according to the ChIP-IT High Sensitivity kit instructions using 4µg of polyclonal rabbit anti-Jun (SantaCruz Biotechnology; Catalog # sc-1694X) antibody. The eluates of each pair of IPs using the anti-Jun antibody from the same chromatin preparation were pooled together.
Kapa Hyperprep was used for library preparation. Samples were sequenced on an Illumina NextSeq 500 generating 75bp single-end reads

treatment_protocol: Mice underwent either bilateral sciatic nerve crush (injured) or sham (uninjured) surgery seven days prior to sacrifice

tag: tag

value: DRG

tag: age

value: 6-8 weeks old

tag: chip antibody


title: human_muscle_RNA-seq

source_name: muscle

value: muscle

value: male

tag: genotype

value: wild type


title: Uninjured Input  Rep2

tag: strain


title: Uninjured Input  Rep1


title: human_muscle_MNase-seq

tag: developmental stage

tag: gender


title: Uninjured Jun ChIPseq Rep1


title: Injured Jun ChIPseq Rep3


title: Uninjured Jun ChIPseq Rep2


title: Injured Input  Rep2


title: Uninjured Jun ChIPseq Rep3


title: human_brain_MNase-seq

source_name: brain

value: brain


title: Injured Input  Rep1


title: mouse_muscle_RNA-seq


title: human_brain_RNA-seq


title: Injured Input  Rep3


title: mouse_heart_RNA-seq

source_name: heart

value: heart


title: mouse_kidney_MNase-seq

source_name: kidney

value: kidney


title: mouse_muscle_MNase-seq


title: Injured Jun ChIPseq Rep2


title: Injured Jun ChIPseq Rep1


title: monkey_muscle_MNase-seq

organism: Macaca mulatta


title: mouse_liver_RNA-seq

source_name: liver

value: liver


title: mouse_brain_RNA-seq


title: mouse_kidney_RNA-seq


title: monkey_kidney_MNase-seq


title: monkey_liver_MNase-seq


title: mouse_liver_MNase-seq


title: monkey_heart_MNase-seq


title: mouse_brain_MNase-seq


title: monkey_liver_RNA-seq


title: mouse_heart_MNase-seq


title: treeShrew_muscle_MNase-seq

organism: Tupaia belangeri


title: H9_spinal cord NSCs_P19 1

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

data_processing:
RNAseq reads were aligned to the hg38 genome assembly using STAR_2.4.0j with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: H9 ESCs

growth_protocol: H9 2iNSCs were induced by small molecules and cultured with small molecules. H9 NSCs were cultured with EGF and LIF. H9 ESCs were cultured with mTeSR. H9- or UCSF4-  spinal cord NSCs were induced by small molecules and cultured with small molecules. Fetal spinal cord NPCs were cultured with FGF2, EGF, and LIF.

extract_protocol:
Total RNA was isolated from cultures using the RNeasy Mini kit (Qiagen) following the manufacturer’s protocol. Fetal brain and spinal cord tissues were purchased from Clontech.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: H9-derived spinal cord NSCs


title: H9_spinal cord NSCs_P12


title: H9_spinal cord NSCs_P6


title: Fetal spinal cord NPCs P16

description: 9 week fetus

source_name: Fetal spinal cord_9 week fetus

value: fetal spinal cord derived NSCs


title: UCSF4_spinal cord NSCs_P6

source_name: UCSF4 ESCs

value: UCSF4-derived spinal cord NSCs


title: H9_spinal cord NSCs_P19 2


title: treeShrew_kidney_MNase-seq

value: adult


title: treeShrew_heart_MNase-seq


title: treeShrew_brain_MNase-seq


title: H9_NSCs p8

value: H9-derived NSCs


title: treeShrew_muscle_RNA-seq


title: Fetal_spinal_cord

description: Normal spontaneously aborted fetal spinal cords from 64 male/female Caucasians, ages: 22-40 weeks

source_name: Fetal spinal cord

value: fetal spinal cord


title: H9_ESCs


title: treeShrew_kidney_RNA-seq


title: Fetal_brain

description: Normal human fetal brains pooled from 59 spontaneously aborted male/female Caucasian fetuses, ages: 20-33 weeks

source_name: Fetal brain

value: fetal brain


title: treeShrew_heart_RNA-seq


title: monkey_brain_MNase-seq


title: treeShrew_brain_RNA-seq


title: Ctrl_rep4

status: Public on Aug 05 2018

city: Dallas

first: Benjamin

last: Nelson

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical School

description: Sample 4

data_processing:
Reads were mapped with TopHat v2.0.9
Transcripts were assembled with Cufflinks v2.1.1
Abundance calculation and pairwise analysis was perfermed with Cuffdiff v2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: Diffdata abundance measurements output from CuffDiff was transferred to Excel.

source_name: Cardiac ventricle

extract_protocol:
Hearts were harvested, atria removed, ventricles rinsed in PBS and flash frozen liquid nitrogen. RNA was isolated using Trizol reagent. 2 ug of total RNA per sample was used for the construction of sequencing libraries.
TruSeq RNA Sample Prep Kit v2, Illumina
Standard Single-end Illumina

value: Cardiac ventricle

value: 4.5 months

tag: genotype/variation

value: Sox5fl/fl, Sox6fl/fl, aMHC-Cre neg


title: DKO_rep4

description: Sample 8

value: Sox5fl/fl, Sox6fl/fl, aMHC-Cre pos


title: DKO_rep3

description: Sample 7


title: Ctrl_rep2

description: Sample 2


title: Fetal spinal cord NPCs P4

description: 9 week fetus


title: DKO_rep1

description: Sample 5


title: H9 2iNSC p8


title: RNA_Esamhi_WT_1

status: Public on Aug 03 2018

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
BCL files were converted to fastq files using bcl2fastq2 Conversion Software ( v2.17)
Single-end RNA-seq reads from were trimmed to remove low quality reads using Trimmomatic (v.0.36)
Trimmed reads were mapped to the Mus musculus  genome (mm10 assembly) using Bowtie2 (v2.2.9).
Reads were counted in exon regions using the summarizeOverlaps function within the GenomicAlignments R package (v1.10.1 )
Genome_build: mm10
Supplementary_files_format_and_content: Table of annotated raw counts using the UCSC mm10 knownGene model.

source_name: spleen

extract_protocol:
Sorted cells were resuspended in Trizol LS and RNA was extracted using the Arcturus PicoPure kit (Thermo Fisher Scientific).
cDNA libraries were prepared using the SMART-seq v4 Ultra Low Input RNA kit and Low Input Library Prep kit (Life Sciences). Libraries were prepared for sequencing using HiSeq SBS v4 Kit.

value: dendritic cells

value: spleen

value: Esamhi

value: WT


title: RNA_Esamhi_WT_2


title: RNA_Esamlo_CKO_2

value: Esamlo

value: CKO


title: DKO_rep2

description: Sample 6


title: H9_spinal cord NSCs_P19 3

value: H9-derived spinal cord NSCs


title: Ctrl_rep3

description: Sample 3


title: RNA_Esamlo_WT_1


title: RNA_Esamlo_WT_2


title: Ctrl_rep1

description: Sample 1


title: RNA_pDC_WT_1

value: pDC


title: RNA_Dec205_CKO_1


title: RNA_Esamhi_CKO_1


title: Input DNA – replicate 1

status: Public on Aug 04 2018

city: Nice

first: Olivier

last: Croce

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

institute: IRCAN

description:
Input_H3K9me3_exp1
Processed data file: H3K9me3_profile.wig
Processed data file: H3K9me3_peaks.bed

data_processing:
Raw fastq files containing reads from SOLiD 5500XL, single-end reads.
Reads were aligned using Bowtie on human hg19 release, with default settings.
Alignments were performed using lifescope chip mapping pipeline. Resulting .bam files were filtered for uniq mapping and QV > 10.
Peak calling was performed with Sicer software with a window of 200 nt and a gap of 600 nt (cut off 10-3 p-value), normalized by corresponding “inputs“ files.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: H3K9me3_profile.wig: Final H9K9me3 profile on hg19.
Supplementary_files_format_and_content: H3K9me3_peaks.bed: Peaks related to profile.

source_name: BJ-HELT, input

growth_protocol: Cells were grown in DMEM media supplemented with 10% fetal calf serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and H3K9me3-DNA complexes were isolated with H3K9me3 antibody from Upstate-Millipore (07-442), rabbit polyclonal.
Libraries were prepared according to standard SOLiD's instructions.

value: BJ-HELT

value: immortal fibroblasts

tag: cell origin

value: human foreskin fibroblast expressing hTERT and SV40 early region

tag: passages


title: H3K9me3 ChIPseq – replicate 1

description:
IP_H3K9me3_exp1
Processed data file: H3K9me3_profile.wig
Processed data file: H3K9me3_peaks.bed

source_name: BJ-HELT, H3K9me3 ChIP

value: H3K9me3 antibody (Upstate-Millipore 07-442)


title: H3K9me3 ChIPseq – replicate 2

description:
IP_H3K9me3_exp2
Processed data file: H3K9me3_profile.wig
Processed data file: H3K9me3_peaks.bed


title: Input DNA – replicate 2

description:
Input_H3K9me3_exp2
Processed data file: H3K9me3_profile.wig
Processed data file: H3K9me3_peaks.bed


title: RNA_pDC_CKO_2

tag: tissue


title: RNA_Dec205_CKO_2


title: RNA_pDC_WT_2


title: ATAC_CD11b_WT_1

data_processing:
BCL files were converted to fastq files using bcl2fastq2 Conversion Software ( v2.17)
Paired-end ATAC-seq reads from were trimmed to remove low quality reads using Trimmomatic (v.0.36)
Trimmed reads were mapped to the Mus musculus genome (mm10 assembly) using Bowtie2 (v2.2.9).
Reads were shifted to reflect transposon binding and concordantly mapped pairs were used for peak calling by MACS2 (v2.1.1.20160309)
Irreproducible discovery rate (IDR) calculations were performed on all pairs of replicates and a union of peaks passing a threshold of 0.05 was used as a reference peak list for read counts.
Reads were counted in peak regions using the summarizeOverlaps function within the GenomicAlignments R package (v1.10.1 )
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of normalized counts (scaled using size factors calculated by DEseq2 (v1.14.1)

extract_protocol:
Splenic dendritic cells were sorted as described in the manuscript. Cells were washed with PBS and immediately processed as previously described (Buenostro et al, 2015, PMC4374986)
Libraries were prepared for sequencing using standard Illumina protocols and HiSeq SBS v4 Kit.


title: ATAC_Dec205_CKO_2


title: RNA_pDC_CKO_1


title: ATAC_pDC_WT_2


title: RNA_Dec205_WT_1


title: ATAC_Dec205_WT_2


title: ATAC_CD11b_CKO_1


title: vehicle_MWM_10

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

data_processing:
Raw FASTQ sequencing reads were chastity filtered to remove clusters having outlying intensity corresponding to bases other than the called base.
Filtered reads were assessed for quality using FastQC.
Transcript-level abundances were calculated using Salmon.
Transcript-level abundances were summarized into gene-level counts with tximport.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file with the raw counts.

source_name: wt-vehicle, hippocampus

growth_protocol: All C57BL/6J mice were bred and maintained in standard vivarium conditions

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen)
The Illumina TruSeq Stranded Total RNA Library Prep Kit was used for cDNA library preparation.

treatment_protocol: Intra-cisterna magna injection of Visudyne (verteporfin for injection), or vehicle as control, and photoconversion with 689-nm wavelength non-thermal red light above the intact skull. Procedure was repeated 2 weeks after. Mice performed the MWM test.

value: Brain whole hippocampus

value: 2 months

value: Wild type

tag: treatment

value: Vehicle


title: ATAC_pDC_WT_1


title: ATAC_pDC_CKO_2


title: ATAC_CD11b_WT_2


title: vehicle_MWM_08


title: ATAC_CD11b_CKO_2


title: vehicle_MWM_06


title: ATAC_Dec205_CKO_1


title: old-lec_3

source_name: old, LECs

growth_protocol: Young and old C57BL/6J mice were purchased from Jackson Labs or obtained from the NIH/NIA and maintained in the same vivarium conditions

extract_protocol:
RNA was extracted using Arcturus PicoPure kit (Thermo Fisher)
All RNA sample processing (including linear RNA amplification and cDNA library generation) and RNA-seq was performed by HudsonAlpha Genomic Services Laboratory

treatment_protocol: no treatment

value: Meningeal LECs

value: 20-24 months


title: ATAC_Dec205_WT_1

value: dendritic cells

value: spleen


title: ATAC_pDC_CKO_1


title: RNA_Esamhi_CKO_2

value: Esamhi


title: vehicle_MWM_09


title: vehicle_MWM_07


title: RNA_Dec205_WT_2

value: WT


title: visudyne_MWM_04

source_name: wt-visudyne, hippocampus

value: Visudyne + MWM


title: visudyne_MWM_02


title: visudyne_MWM_01


title: young-lec_2

source_name: young, LECs

value: 2-3 months


title: old-lec_1


title: young-lec_3


title: young-lec_1


title: visudyne_MWM_05


title: visudyne_MWM_03


title: K5 (Asic3-/- #3)

city: Shanghai

first: Xianghua

last: Yi

address: NO.389, Xincun Rd, Putuo distrct

department: pathology

country: China

institute: Tongji hospital

data_processing:
Illumina Casava 1.8.2 software used for basecalling
Sequenced reads were trinned for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse reference genome (GRCm38, Ensembl build) using Tophat version 2.0.12, yielding an average mapping rate of 90.3 ± 2.3%.
Gene expression levels, which represented as fragments per kilo-base per million mapped reads (FPKM), were obtained for 27180 genes/transcripts annotated using Ensemble release 67.

source_name: leukemia-initiating cells from bone marrow

extract_protocol:
LSCs of AML murine model were sortted by FACS, and RNA was harvested using Trizol reagent.  library construction following standard TruSeq RNA sample preparation v2 protocol (Illumina).
library construction following standard TruSeq RNA sample preparation v2 protocol (Illumina).

value: 8 weeks

value: Asic3-/- (Asic3-null)


title: W7 (Asic3+/+ #2)

value: leukemia-initiating cells from bone marrow

value: Asic3+/+ (WT)


title: K3 (Asic3-/- #2)


title: W6 (Asic3+/+ #1)


title: HL-60, DMSO, day 6, replicate 2

city: Davis

first: Sean

middle: R.

last: Collins

state: CALIFORNIA

address: One Shields Ave, 334 Briggs Hall

department: Microbiology & Molecular Genetics

institute: UC Davis

data_processing:
Base calling was performed using bcl2fastq version 2.17.1.14.
Raw RNA-seq reads were aligned to the GRCh38.p5 version of the human genome using the GENCODE GRCh38 (release 24) genome annotations and the STAR two-pass algorithm (STAR version 2.4)
Fragments Per Kilobase of exon per million fragments mapped (FPKM) were calculated using cufflinks v2.2.1 with default paramters.
Normalized expression values were computed from the FPKM values using the "uniform genes" normalization strategy of Glusman et al (PMID: 24223126).
Log10 normalized values were computed, and values of -4 were given to genes with zero read counts.
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: Excel spreadsheet including FPKM and log10 normalized values for each sample

source_name: HL-60 cell line

growth_protocol: Cells were grown in RPMI 1640 media with HEPES and GlutaMAX, supplemented with 9% fetal bovine serum, penicillin and streptomycin. Some samples were then treated with a differentiation protocol to induce neutrophilic differentiation.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. PolyA enrichment was performed by Applied Biological Materials Inc through their Total RNA Sequencing service.
Library construction was performed by Applied Biological Materials using standard Illumina protocols.

tag: differentiation state

value: Differentiated for 6 days with DMSO

tag: transgene


title: K1 (Asic3-/- #1)


title: HL-60, DMSO+Nutridoma, day 6, replicate 2

value: Differentiated for 6 days with DMSO, Nutridoma-CS (2%), and reduced serum (0.5% FBS)

tag: cell line


title: PLB-985, DMSO+Nutridoma, day 6, replicate 2

source_name: PLB-985 cell line


title: HL-60, not differentiated, replicate 2

value: Undifferentiated


title: HL-60, DMSO, day 6, replicate 1


title: HL-60, not differentiated, replicate 1


title: PLB-985, DMSO+Nutridoma, day 2

value: Differentiated for 2 days with DMSO, Nutridoma-CS (2%), and reduced serum (0.5% FBS)


title: PLB-985, DMSO, day 6, replicate 2


title: old-lec_2

tag: cell type

value: Wild type


title: PLB-985, DMSO+Nutridoma, day 6, replicate 1


title: HL-60, DMSO+Nutridoma, day 6, replicate 1


title: PLB-985, not differentiated, replicate 2


title: PLB-985, DMSO, day 6, replicate 1


title: siNIPBL_HS_CTCF_Hi-ChIP

city: XIAMEN

first: XIAOWEN

last: LYU

state: FUJIAN

address: No.4221, Xiang'an South Road, Xiang'an District

institute: XIAMEN UNIVERSITY

description:
Hi-ChIP
Hi-ChIP under heat shock conditions
siNIPBL_HS_CTCF_HiChIP.hic

data_processing:
Library strategy: HiChIP
All experiments results are mapped to human hg38 genome build. ChIP-Seq and ATAC-Seq were paired end mapped using bowtie and PCR duplicates were removed. Hi-C and HiChIP reads were processed using the Juicer pipeline. eU-Seq were mapped by TOPHAT using default parameters, and FPKM were calculated by Cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig containing coverage of ChIP-seq or ATAC-seq and .hic files containing Hi-C and contact matrices.

source_name: H9 hESCs

extract_protocol:
For Hi-C, cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched with glycine, nuclei were isolated and chromatin digested by HindIII, filled in with biotin-dCTP, and ligated. After ligation, nuclei were digested by ProteinaseK and chromatin were reverse-crosslinked overnight, followed by ethanol precipitation to get purified DNA. DNA were sonicated to 200-500 bp fragment and enriched with streptavidin dynal beads, followed by illumina library preparation. For ChIP-seq, nuclear lysates were sonicated to generate 200-500 bp fragments . Chromatin was precleared with Protein A or G Dynabeads at 4°C for 2 hours and incubated with antibody overnight at 4°C. Immunoprecipitated chromatin was eluted, reverse crosslinked and purified by standard methods, followed by illumina library preparation. For HiChIP nuclei were isolated and chromatin digested by DpnII, filled in with biotin-dCTP, and ligated. After ligation, chromatin was sonicated and precleared with Protein A and G Dynabeads at 4°C for 2 hours, then precipitated using Protein A or G dynalbeads pre-incubated with proper antibodies  overnight. Immunoprecipitated chromatin was eluted, reverse crosslinked and purified by standard methods, followed by streptavidin beads pull down and illumina library preparation. For ATAC-seq, H9 cells grown to exponential stage in 96-well plates cultured at 37°C or heat stressed at 42°C were collected and used for Fast-ATAC and OMNI-ATAC protocol. For fast-ATAC, cells on 96-well plate were washed with PBS and incubated in 50 µl transposes Tn5 mixture (0.01% digitonin for permeabilizing cell membrane, 2.5 µl Tn5, 25 µl TD buffer) at 37°C for 20 min with occasional shaking. For OMNI-ATAC, cells on 96-well plate were washed with PBS and nuclear membrane was disrupted by soaking in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin) on ice, nuclei was washed once in cold lysis buffer without NP40 or digitonin, and then incubated in Tn5 transposes mixture (25 ul 2x TD buffer, 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O) at 37°C for 20 min with occasional shaking. After the reaction is over, DNA was directly extracted by Minelute Kit (Qiagen). Purified tagmented DNA were used to make illumina Nextera libraries. For eU-Seq, Ctrl and HS cells were labeled with EU in growth medium for 30 min at 37°C and 42°C respectively before RNA extraction with TRIZOL reagent. Purified RNAs were converted by click-chemistry into Biotin-U labeled RNAs and pulled down with streptavidin beads, followed by fragmentation and reverse transcription into cDNA. Illumina libraries were made from dsDNAs after second strand synthesis on cDNA and amplified with barcoded primers for sequencing.
Libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding  adenosine to  the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligatedat room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix. Nextera libraries were amplified with Nextera barcoded primers using the KAPA SYBR FAST qPCR Master Mix.

value: H9 human Embryonic Stem Cell Line

tag: chip-antibody

value: CTCF


title: HS H3K4me1 Hi-ChIP Rep2

description:
Hi-ChIP
Hi-ChIP under heat shock conditions
HS_H3K4me1_HiChIP.hic


title: HS H3K4me1 Hi-ChIP Rep1


title: siNIPBL_HS_H3K4me1_Hi-ChIP

description:
Hi-ChIP
Hi-ChIP under heat shock conditions
siNIPBL_HS_H3K4me1_HiChIP.hic


title: H3K4me1 Hi-ChIP Rep2

description:
Hi-ChIP
Hi-ChIP under normal conditions
H3K4me1_HiChIP.hic


title: W9 (Asic3+/+ #3)


title: KLF4 Hi-ChIP Rep2

description:
Hi-ChIP
Hi-ChIP under normal conditions
KLF4_HiChIP.hic


title: KLF4 Hi-ChIP Rep1


title: HS NANOG Hi-ChIP Rep2

description:
Hi-ChIP
Hi-ChIP under heat shock conditions
HS_NANOG_HiChIP.hic

value: NANOG


title: HS KLF4 Hi-ChIP

description:
Hi-ChIP
Hi-ChIP under heat shock conditions


title: NANOG Hi-ChIP Rep2

description:
Hi-ChIP
Hi-ChIP under normal conditions
NANOG_HiChIP.hic


title: NANOG Hi-ChIP Rep1


title: OCT4 Hi-ChIP Rep1

description:
Hi-ChIP
Hi-ChIP under normal conditions
OCT4_HiChIP.hic


title: HS NANOG Hi-ChIP Rep1


title: HS OCT4 Hi-ChIP Rep1

description:
Hi-ChIP
Hi-ChIP under heat shock conditions
HS_OCT4_HiChIP.hic


title: PLB-985, DMSO+Nutridoma, day 4

value: Differentiated for 4 days with DMSO, Nutridoma-CS (2%), and reduced serum (0.5% FBS)


title: CTCF Hi-ChIP Rep2

description:
Hi-ChIP
Hi-ChIP under normal conditions
CTCF_HiChIP.hic


title: PLB-985, not differentiated, replicate 1


title: HS CTCF Hi-ChIP Rep2

description:
Hi-ChIP
Hi-ChIP under heat shock conditions
HS_CTCF_HiChIP.hic


title: HS KI Rad21 Hi-ChIP


title: CTCF Hi-ChIP Rep1


title: HS CTCF Hi-ChIP Rep1


title: CTCF Hi-ChIP Rep3


title: HS Rad21 Hi-ChIP Rep4

description:
Hi-ChIP
Hi-ChIP under heat shock conditions
HS_Rad21_Hi-ChIP.hic


title: HS Rad21 Hi-ChIP Rep1 and Rep2 technical replicate


title: HS Rad21 Hi-ChIP Rep2


title: Rad21 Hi-ChIP Rep4

description:
Hi-ChIP
Hi-ChIP under normal conditions
Rad21_Hi-ChIP.hic


title: HS Rad21 Hi-ChIP Rep3


title: R01-104

city: Stanford

first: Shaimaa

last: Bakr

address: 4450 Serra Mall, Stanford, CA 94305

department: Electrical Engineering

institute: Stanford University

data_processing:
Raw reads preprocessing and quality control:
a. Paired-end reads were filtered and trimmed using software Trimmomatic
b. Quality control before and after raw reads preprocessing was done using software FastQC
Raw reads alignment:
a. Trimmed fastq reads were aligned to human hg19 reference genome using software TopHat2 and indexed with SAMtools.
b. RNAseq alignment QC metrics were collected using software PICARD
Transcripts assembly and expression estimation:
a. Gene and isoform assembly and expression level estimation was done using Cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing expression level for each gene per sample

source_name: Non-Small Cell Lung Cancer

extract_protocol:
Following surgical excision of tumor, necrotic debris and sampled cavitary lesions were removed to include a sufficient solid component.  Next, the surgeon cut a 3-5-mm-thick slice along the longest axis of the excised tissue, which was frozen within 30 minutes of excision and later retrieved for RNA extraction
For library preparation, the TruSeq Total Stranded RNA with Ribo-Zero Reduction (Illumina) was used following manufacturer’s instructions.

tag: disease state

value: Non-Small Cell Lung Cancer (NSCLC)

tag: histology

value: Adenocarcinoma

tag: histopathological grade

value: G2 Moderately differentiated

value: Male


title: R01-106

value: G3 Poorly differentiated


title: R01-105

value: Female


title: R01-103


title: OCT4 Hi-ChIP Rep2


title: HS BRG1-KO_H3K27ac

description: ChIP-Seq under heat shock conditions

data_processing:
All experiments results are mapped to human hg38 genome build. ChIP-Seq and ATAC-Seq were paired end mapped using bowtie and PCR duplicates were removed. Hi-C and HiChIP reads were processed using the Juicer pipeline. eU-Seq were mapped by TOPHAT using default parameters, and FPKM were calculated by Cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig containing coverage of ChIP-seq or ATAC-seq and .hic files containing Hi-C and contact matrices.


title: R01-102

value: Squamous cell carcinoma

value: Other, Type I:Well to moderately differentiated


title: Rad21 Hi-ChIP Rep1


title: Rad21 Hi-ChIP Rep2


title: HS OCT4 Hi-ChIP Rep2


title: BRG1-KO_H3K27ac

description: ChIP-Seq under normal conditions


title: R01-146


title: HS BRG1-KO_ATAC-Seq

description:
OMNI ATAC-Seq
OMNI ATAC-Seq under heat shock conditions


title: HS Fast ATAC-Seq Rep2

description:
fast ATAC-Seq
Fast ATAC-Seq under heat shock conditions
HS_ATAC-Seq.bw


title: OMNI ATAC-Seq

description:
OMNI ATAC-Seq
OMNI ATAC-Seq under normal conditions


title: HS Rad21 Hi-ChIP Rep1


title: R01-144


title: R01-145

value: Other, Type II:Moderately to poorly differentiated


title: Fast ATAC-Seq Rep2

description:
fast ATAC-Seq
Fast ATAC-Seq under normal conditions
ATAC-Seq.bw


title: R01-142


title: HS Fast ATAC-Seq Rep1


title: HS OMNI ATAC-Seq


title: R01-101


title: R01-137


title: H3K4me3 ChIP-Seq

description: ChIP-Seq under normal conditions

tag: condition

value: under normal conditions


title: R01-135


title: H3K4me1 ChIP-Seq

description: ChIP-Seq under normal conditions


title: R01-140


title: HS H3K27me3 ChIP-Seq

description: ChIP-Seq under heat shock conditions

value: under heat shock conditions


title: Rad21 Hi-ChIP Rep3


title: R01-141


title: R01-138


title: R01-139


title: H3K27me3 ChIP-Seq

description: ChIP-Seq under normal conditions


title: HS H3K27ac ChIP-Seq Rep

description:
ChIP-Seq under heat shock conditions
H3K27ac_HS.bw


title: R01-133


title: R01-128


title: Fast ATAC-Seq Rep1


title: HS H3K4me3 ChIP-Seq

description: ChIP-Seq under heat shock conditions


title: R01-136

value: G1 Well differentiated


title: R01-127


title: HS H3K4me1 ChIP-Seq

description: ChIP-Seq under heat shock conditions


title: HS CTCF ChIP-Nexus

description: ChIP-Nexus under heat shock conditions


title: R01-100


title: R01-126


title: CTCF ChIP-Nexus

description: ChIP-Nexus under normal conditions


title: R01-134


title: HS NIPBL ChIP-Seq

description: ChIP-Seq under heat shock conditions

value: NIPBL


title: BRG1-KO_ATAC-Seq

value: H9 human Embryonic Stem Cell Line


title: HS WAPL ChIP-Seq

description: ChIP-Seq under heat shock conditions

value: WAPL


title: R01-132


title: R01-131


title: WAPL ChIP-Seq

description: ChIP-Seq under normal conditions


title: HS KI HSF1 ChIP-Seq

description: ChIP-Seq under heat shock conditions plus kinase inhibitors


title: H3K27ac ChIP-Seq Rep

description:
ChIP-Seq under normal conditions
H3K27ac_NT.bw


title: R01-120


title: R01-119


title: R01-130


title: HSF1 ChIP-Seq

description: ChIP-Seq under normal conditions


title: HS H3K27ac ChIP-Seq


title: Brg1 ChIP-Seq

description: ChIP-Seq under normal conditions


title: HS RING1B ChIP-Seq

description: ChIP-Seq under heat shock conditions


title: R01-129


title: R01-115


title: H3K27ac ChIP-Seq


title: RING1B ChIP-Seq

description: ChIP-Seq under normal conditions


title: H3K4me1 Hi-ChIP Rep1

description:
Hi-ChIP
Hi-ChIP under normal conditions
H3K4me1_HiChIP.hic


title: HS Rad21 ChIP-Nexus

description: ChIP-Nexus under heat shock conditions


title: R01-125


title: R01-111


title: Rad21 ChIP-Nexus

description: ChIP-Nexus under normal conditions


title: HS KLF4 ChIP-Seq

description: ChIP-Seq under heat shock conditions


title: R01-124


title: NIPBL ChIP-Seq

description: ChIP-Seq under normal conditions


title: R01-123


title: R01-122


title: R01-121


title: HS HSF1 ChIP-Seq

description: ChIP-Seq under heat shock conditions


title: R01-118


title: R01-110


title: HS Brg1 ChIP-Seq

description: ChIP-Seq under heat shock conditions


title: R01-117


title: R01-109


title: KLF4 ChIP-Seq

description: ChIP-Seq under normal conditions


title: R01-108


title: HS cFos ChIP-Seq

description: ChIP-Seq under heat shock conditions

value: cFos


title: R01-099


title: R01-114


title: R01-113


title: R01-107


title: HS OCT4 ChIP-Seq

description: ChIP-Seq under heat shock conditions


title: R01-116


title: R01-091


title: R01-112


title: HS RNAPol II ChIP-Seq

description: ChIP-Seq under heat shock conditions

value: RNA polymerase II


title: HS ZNF143 ChIP-Seq

description: ChIP-Seq under heat shock conditions


title: ZNF143 ChIP-Seq

description: ChIP-Seq under normal conditions


title: RNA_Esamlo_CKO_1

value: dendritic cells

value: spleen

value: Esamlo

tag: genotype

value: CKO

tag: replicate


title: OCT4 ChIP-Seq

description: ChIP-Seq under normal conditions


title: cFos ChIP-Seq

description: ChIP-Seq under normal conditions


title: HS NANOG ChIP-Seq

description: ChIP-Seq under heat shock conditions

value: NANOG


title: NANOG ChIP-Seq

description: ChIP-Seq under normal conditions


title: R01-098

value: Non-Small Cell Lung Cancer (NSCLC)

value: Adenocarcinoma

value: G2 Moderately differentiated

tag: gender

value: Female


title: RNAPol II ChIP-Seq

description: ChIP-Seq under normal conditions

value: under normal conditions


title: HS CTCF ChIP-Seq

description: ChIP-Seq under heat shock conditions

value: CTCF

value: under heat shock conditions


title: R01-158

value: Squamous cell carcinoma

value: Male


title: HS Rad21 ChIP-Seq Rep2

description:
ChIP-Seq under heat shock conditions
Rad21_HS.bw

value: H9 human Embryonic Stem Cell Line


title: R01-157

value: G3 Poorly differentiated


title: R01-152

value: G1 Well differentiated


title: R01-089

value: Other, Type II:Moderately to poorly differentiated


title: HS Rad21 ChIP-Seq Rep1


title: Rad21 ChIP-Seq Rep2

description:
ChIP-Seq under normal conditions
Rad21_NT.bw


title: R01-150


title: R01-079


title: Rad21 ChIP-Seq Rep1


title: R01-151


title: HS eU-Seq

description: eU-Seq under heat shock conditions. nascent transcribed RNA

data_processing:
Library strategy: eU-Seq
All experiments results are mapped to human hg38 genome build. ChIP-Seq and ATAC-Seq were paired end mapped using bowtie and PCR duplicates were removed. Hi-C and HiChIP reads were processed using the Juicer pipeline. eU-Seq were mapped by TOPHAT using default parameters, and FPKM were calculated by Cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig containing coverage of ChIP-seq or ATAC-seq and .hic files containing Hi-C and contact matrices.


title: R01-148


title: CTCF ChIP-Seq

description: ChIP-Seq under normal conditions


title: HS IgG ChIP-Seq

description: ChIP-Seq under heat shock conditions

value: IgG


title: R01-149


title: eU-Seq

description: eU-Seq under normal conditions. nascent transcribed RNA


title: R01-033

value: Other, Type I:Well to moderately differentiated


title: R01-073


title: HS HiC _Rep2

description:
in-situ Hi-C under heat shock conditions
HS_H9_Hi-C.1kb.intra.hic

data_processing:
Library strategy: HiC-Seq
All experiments results are mapped to human hg38 genome build. ChIP-Seq and ATAC-Seq were paired end mapped using bowtie and PCR duplicates were removed. Hi-C and HiChIP reads were processed using the Juicer pipeline. eU-Seq were mapped by TOPHAT using default parameters, and FPKM were calculated by Cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig containing coverage of ChIP-seq or ATAC-seq and .hic files containing Hi-C and contact matrices.


title: R01-069


title: HiC _Rep2

description:
in-situ Hi-C under normal conditions
H9_Hi-C.1kb.intra.hic


title: HS HiC _Rep1


title: R01-065


title: R01-064


title: R01-055


title: R01-032


title: R01-041


title: R01-076


title: IgG ChIP-Seq

description: ChIP-Seq under normal conditions


title: R01-040


title: R01-156


title: R01-160


title: R01-049


title: R01-071


title: R01-039


title: R01-046


title: R01-038


title: R01-042


title: R01-029

value: NSCLC NOS (not otherwise specified)


title: HiC _Rep1


title: R01-054


title: R01-014


title: R01-026


title: R01-004


title: R01-022


title: R01-015


title: R01-027


title: R01-021


title: R01-031


title: R01-016


title: R01-018


title: R01-048


title: R01-078


title: R01-153


title: R01-017


title: R01-081


title: R01-013


title: R01-012


title: R01-077


title: R01-066


title: R01-007


title: R01-083


title: R01-003


title: R01-154


title: R01-080


title: R01-072


title: R01-024


title: R01-059


title: R01-061


title: R01-068


title: R01-067


title: R01-043


title: R01-037


title: R01-006


title: R01-084


title: R01-062


title: R01-063


title: R01-057


title: R01-097


title: R01-159


title: R01-093


title: R01-094


title: R01-052


title: R01-056


title: 16-126B CA1 WT

first: Rayna

middle: Michelle

last: Harris

address: 1 Shields Ave

institute: University of California Davis

description:
16-126B
yoked controls in active place avoidance task

data_processing:
Raw reads were downloaded from the Amazon cloud server to the Stampede Cluster at the Texas Advanced Computing Facility for processing and analysis.
RNA quality was checked using the bioinformatic program FASTQC.
Low quality reads and adapter sequences were removed using the program Cutadapt.
To explore gross patterns at the whole transcriptome level, we used a Kallisto for read counting and mapping.
We used DESeq2 for gene expression normalization and quantification
We used the a rank-based gene ontology analysis of gene expression data using the R package GO MWU
Statistics on the principal component analyses were conduct in R
Genome_build: Gencode M11 mouse transcriptome
Supplementary_files_format_and_content: raw fastq files, fastqc qualtiry control files, kallisto count files, input files for DESeq2

source_name: hippocampus; CA1 subfield

extract_protocol:
RNA from the CA1 subfield of the hippocampus was isolated using the Maxwell 16 LEV RNA Isolation Kit (Promega).
RNA libraries were prepared by the Genomic Sequencing and Analysis Facility at the University of Texas at Austin using the Illumina HiSeq platform.

treatment_protocol: WT and Fmr1-KO mice were uses as controls in the active place avoidance paradigm

value: hippocampus; CA1 subfield

tag: genotype/variation


title: 16-125D CA1 WT

description:
16-125D
yoked controls in active place avoidance task


title: R01-023

value: Non-Small Cell Lung Cancer (NSCLC)


title: R01-147

value: Adenocarcinoma


title: R01-051

value: G2 Moderately differentiated


title: R01-005


title: 16-125B CA1 WT

description:
16-125B
yoked controls in active place avoidance task


title: R01-035


title: 16-124D CA1 WT

description:
16-124D
yoked controls in active place avoidance task


title: 16-122D CA1 WT

description:
16-122D
yoked controls in active place avoidance task


title: 16-122B CA1 WT

description:
16-122B
yoked controls in active place avoidance task


title: R01-096


title: 16-120B CA1 FMR1

description:
16-120B
yoked controls in active place avoidance task


title: R01-034


title: R01-028


title: R01-060

value: Female


title: 16-119D CA1 FMR1

description:
16-119D
yoked controls in active place avoidance task


title: 16-118D CA1 FMR1

description:
16-118D
yoked controls in active place avoidance task


title: 16-123D CA1 WT

description:
16-123D
yoked controls in active place avoidance task


title: Differentiated Ctrl sgRNA 3

city: South San Francisco

middle: John

last: Bohlen

address: Room 15-2006, Genentech Building 15

institute: Genentech

data_processing:
RNA-seq data was mapped to the human genome annotation hg38 using HISAT2 version 2.0.3 (Kim et al., 2015) via the Galaxy platform (https://usegalaxy.org/) (Afgan et al., 2016), resulting in 8 to 12 million mapped reads per sample. Transcript FPKM (fragments per kilobase of transcript sequence per million mapped fragments) scores were obtained using Cufflinks version 2.2.1 (Trapnell et al., 2010) with the iGenomes hg38 gtf file as a reference annotation.
The counts and FPKM tables do not contain processed data for D_GFP_1. This was omitted due to a processing error and was left out of the analysis.
Genome_build: hg38
Supplementary_files_format_and_content: CBMH2_Counts_GEO.xlsx and CBMH2_FPKM_GEO.xlsx contain counts from DESeq2 and FPKM values from Cufflinks respectively

source_name: U937 cell line

growth_protocol: U937 cells were acquired from ATCC (CRL-1593.2). Cells were maintained in suspension culture using spinner flasks for library propagation and tissue culture plates for single-gene knockout lines, all in sterile-filtered U937 growth medium (RPMI1640 supplemented with 2 mM glutamine, 100 units/mL penicillin, 100 mg/mL streptomycin, and 10% heat-inactivated fetal calf serum). Cells were cultured in a humidified 37°C incubator set at 5% CO2. Cells were passaged 2-3 times weekly.

extract_protocol:
Differentiated and undifferentiated U937 cells were seeded at a density of 50,000 cells per well in a 24-well plate. Two days later, cells were lysed in RLT buffer and RNA was isolated using the RNeasy Micro Kit (Qiagen).
cDNA libraries were prepared and adapted for sequencing using a modified Smart-seq2 protocol (Picelli et al., 2014). In short, 10 ng of purified RNA was mixed with RNase Inhibitor, Oligo-dT30 primer, and dNTPs and heat-denatured before addition to a SuperScriptII template-switching reverse transcription reaction mixture. cDNA was amplified in a 12-cycle KAPA HiFi HotStart PCR reaction and purified using Ampure XP SPRI beads. 0.5 ng of cDNA was fragmented for sequencing using the Nextera XT DNA sample preparation kit. After tagmentaion and amplification of adapter-ligated, indexed fragments, DNA was purified using Ampure XP SPRI beads and sequenced on a NextSeq 550 (Illumina) to obtain 75 bp paired-end reads.

treatment_protocol: For differentiation, U937 cells were diluted to a density of 1-2 million cells per mL in U937 growth medium containing phorbol myristate acetate (PMA) to achieve a final concentration of 50 nM PMA. Cells were plated on tissue culture plastic and allowed to differentiate and adhere for 3 days. After differentiation, cells were recovered by harvesting supernatants and trypsinizing adherent cells. For trypsinization, cells were washed three times with phosphate buffered saline (PBS; 137 mM NaCl, 2.7 mM KCl, 8 mM sodium phosphate dibasic, 2 mM potassium phosphate monobasic, pH 7.4), incubated in PBS containing 300 units/mL trypsin for 7 min at 37°C, then recovered from the plate by repeatedly pipetting the solution to dislodge cells. Trypsinized adherent and non-adherent supernatant cells were pooled, pelleted by centrifugation (300g, 7 min, room temperature), and resuspended in fresh U937 growth medium. Cells were then plated and allowed to recover for two days before further processing.

tag: protocol

value: Differentiated Ctrl sgRNA


title: Differentiated Ctrl sgRNA 2


title: Differentiated Ctrl sgRNA 1


title: Undifferentiated Ctrl sgRNA 2

value: Undifferentiated Ctrl sgRNA


title: Undifferentiated Ctrl sgRNA 3


title: 16-123B CA1 WT

description:
16-123B
yoked controls in active place avoidance task


title: Undifferentiated GFP 3

value: Undifferentiated GFP


title: 16-119B CA1 FMR1

description:
16-119B
yoked controls in active place avoidance task


title: 16-120D CA1 FMR1

description:
16-120D
yoked controls in active place avoidance task


title: Mnase-seq.BG3C2.Ctrl2.fastq

status: Public on Aug 02 2018

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

data_processing:
Basecalls performed using CASAVA version 1.4
6mA-IP-seq and ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.9 with the standard parameters.
RNA-seq reads were aligned using tophat v2.0.8 and differential RPKM expression values were extracted using cuffdiff v2.2.1
Peaks were called using MACS version 1.4.2 with the following setting: BW (200), GSIZE (mm). MACS identfied peaks were merged by bedtools. Gain-of-6mA regions in brains were identified by bedtools. Gain-of-6mA regions in BG3C2 cells were identified by published computational algorithm (R/Bioconductor package DSS)
Genome_build: dm3

organism: Drosophila melanogaster

source_name: BG3C2 cells

growth_protocol: BG3C2 fly neuronal cells was maintained in 1× Schneider's medium (GIBCO) supplemented with 10% Fetal Bovine Serum (Hyclone) and 100 μg/mL human recombinant insulin (Sigma).

extract_protocol:
Genomic DNA was prepared following regular protocol as described previously4 with some modifications. Add 600 μl of lysis buffer containing 100mM Tris-HCl, pH 8.5, 5mM EDTA pH8.0, 0.2% SDS, 200mM NaCl, and 20-25 μl of protease K @ 20mg/ml to the ground tissues or cells, mix well, and incubate at 55°C overnight. After the overnight digestion was cooled down to room temperature, add 5 μl of RNase A solution @ 20mg/ml for at least 1hr at RT. Following extraction with equal volume of phenol: chloroform: isoamyl alchohal =25:24:1, precipitation was carried out using equal volume of isopropanol. If flocky DNA forms, transfer it to a new tube containing 1ml of 70% ethanol. If necessary, spin down to collect the remained DNA in the precipitation solution followed by washing with 70% ethanol. If no flocky DNA appears, spin down @maximum speed for 10 min to collect gDNA pellet.
25ng of input genomic DNA or experimental enriched DNA were utilized for each library construction. 150-300 bp DNA fragments were selected by AMPure XP Beads (Beckman Coulter) after the adapter ligation. An Agilent 2100 BioAnalyzer was used to quantify the amplified DNA, qPCR was applied to accurately quantify the library concentration. 20 pM diluted libraries were used for sequencing. 50-cycle single-end sequencings were performed using Illumina HISeq 2000. Image processing and sequence extraction were done using the standard Illumina Pipeline. RNA-seq libraries were generated from duplicated samples per condition using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer’s protocol. The RNA-seq libraries were sequenced as 50-cycle pair-end runs using Illumina HiSeq 2000.

treatment_protocol: The 580bp of dsRNA fragments corresponding to CG2083 mRNA was generated via T7 promoter-driven in vitro transcription using RT-PCR product as template with T7 promoters located at both of 5’ and 3’ ends. The following primers were used for RT-PCR: forward -5’gaaatCTCGAGtaatacgactcactatagggCGGAGCCAGTAGTTTTCAGC3’and reverse - 5’gaaatGAATTCtaatacgactcactatagggCATGGGGTTGATCTTCTCGT3’. The gel purified PCR products were applied for in vitro transcription using HiScribe T7 High Yield RNA Synthesis Kit from NEB per se manufacturer’s  instructions. The generated dsRNA was purified by two - step extractions with phenol: chloroform: isoamyl alchohol =25:24:1 first and then followed by chloroform alone. The extracted dsRNA was precipitated with absolute ethanol. The dsRNA-mediated knock down was conducted for 144hr by adding dsRNA to the BG3C2 cells growing in the Shields and Sang M3 insect medium under FBS starvation at least 24hr in advance. 24hr post incubation with dsRNA, add FBS to the culture media to final 3%. Every 48hr the media and dsRNA were changed.

tag: antibody

value: Total nucleosome


title: Mnase-seq.BG3C2.KD2.fastq


title: Mnase-seq.BG3C2.Ctrl1.fastq


title: H3K27me3.ChIPseq.BG3C2.KD.fastq

value: anti-H3K27me3 (Cat# ab6002) Abcam


title: 16-117D CA1 FMR1

description:
16-117D
yoked controls in active place avoidance task

tag: tissue


title: Differentiated Ctrl sgRNA 4


title: H3K4me3.ChIPseq.BG3C2.KD.fastq

value: Anti-H3K4me3 (Cat# ab8580) Abcam


title: Differentiated GFP 4

value: Differentiated GFP


title: Differentiated GFP 3


title: Wds.ChIPseq.BG3C2.Ctrl.fastq

value: Anti-Wds antibody (Cat# 40630002) Novus Biologicals


title: Brain.Ctrl2.RNAseq

data_processing:
Basecalls performed using CASAVA version 1.4
6mA-IP-seq and ChIP-seq reads were aligned to the dm3 genome assembly using bowtie version 0.12.9 with the standard parameters.
RNA-seq reads were aligned using tophat v2.0.8 and differential RPKM expression values were extracted using cuffdiff v2.2.1
Peaks were called using MACS version 1.4.2 with the following setting: BW (200), GSIZE (mm).
genome build: dm3
Supplementary_files_format_and_content: BG3C2.Ctrl.KD.RNAseq.cuffdiff.txt: BG3C2.Wildtype and DMAD-KD RNA-seq cuffdiff output file
Supplementary_files_format_and_content: Brain.Ctrl.KO.RNAseq.cuffdiff.txt: Fly brain.Wildtype and DMAD-KO RNA-seq cuffdiff output file
Supplementary_files_format_and_content: Brain.6mA.WT_peaks.bed: Brain.6mA.wildtype peaks
Supplementary_files_format_and_content: Brain.6mA.DMAD.KD.comb_peaks.bed: Brain.6mA.DMAD-KD peaks
Supplementary_files_format_and_content: Brain.6mA.DMAD.KO_peaks.bed: Brain.6mA.DMAD-KO peaks
Supplementary_files_format_and_content: WT.BG3.6mA.comb_peaks.bed: BG3C2.6mA.wildtype peaks
Supplementary_files_format_and_content: KD.BG3.6mA.comb_peaks.bed: BG3C2.6mA.DMAD-KD peaks
Supplementary_files_format_and_content: DMAD.ChIP.BG3C2.comb_peaks.bed: DMAD ChIPseq in wildtype BG3C2 peaks
Supplementary_files_format_and_content: ChIP.Pc.ctrl.BG3C2.comb_peaks.bed: Pc ChIPseq peaks in wildtype BG3C2 cells
Supplementary_files_format_and_content: ChIP.Pc.dTetKD.BG3C2.comb_peaks.bed: Pc ChIPseq peaks in DMAD-KD BG3C2 cells
Supplementary_files_format_and_content: BG3.ChIP.H3K27ac.Ctrl_peaks.bed: H3K27ac. ChIPseq peaks in wildtype BG3C2 cells
Supplementary_files_format_and_content: BG3.ChIP.H3K27ac.DMAD.KD_peaks.bed: H3K27ac. ChIPseq peaks in DMAD-KD BG3C2 cells
Supplementary_files_format_and_content: BG3.H3K4me3.Ctrl_peaks.bed: H3K4me3. ChIPseq peaks in wildtype BG3C2 cells
Supplementary_files_format_and_content: BG3.H3K4me3.DMAD.KD_peaks.bed: H3K4me3. ChIPseq peaks in DMAD-KD BG3C2 cells
Supplementary_files_format_and_content: BG3C3.ChIP.Pol_II.Ctrl_peaks.bed: PolII. ChIPseq peaks in wildtype BG3C2 cells
Supplementary_files_format_and_content: BG3C2.ChIP.Pol.II.DMAD.KD_peaks.bed: PolII. ChIPseq peaks in DMAD-KD BG3C2 cells

source_name: Drosophila brains

value: Wildtype


title: Brain.KO2.RNAseq

value: DMAD-knockout


title: BG3C2.KD3.RNAseq

value: DMAD-siRNA knockdown


title: Brain.Ctrl1.RNAseq


title: Differentiated GFP 2


title: Differentiated GFP 1


title: Stroke patient 32

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

institute: University of Pennsylvania

description: 50,000 cells

data_processing:
Clean reads were mapped to human reference genome hg38/Grch38 using Bowtie. RNA species was determined using Ensembl genome annotation version 84 and counted using HTSeq-count. A replicated differential expression analysis was performed on the miRNA expression data. The following comparisons were performed: “Good” vs “Bad”.
Genome_build: hg38/Grch38
Supplementary_files_format_and_content: miRNA.counts

source_name: CD34+ hematopoietic stem cells

growth_protocol: N/A (The cells were isolated and frozen in RNAProtect Cell Reagent from Qiagen. No further culture of cells was performed).

extract_protocol:
Total RNA isolation was performed by Seqmatic LLC (Fremont, CA). Briefly, TRIzol reagent (Thermo Fisher) was used to extract RNA from the cell samples
Libraries were generated using total RNA prepared by SeqMatic. The SeqMatic Tailormix miRNA library prep kit V2 was used to create libraries that are compatible with Illumina sequencing. Each sample was validated for yield and quality using a BioAnalyzer High Sensitivity DNA assay. Libraries were normalized and pooled in equal molar ratios. The pool was gel purified and the purified product was quantified using the SeqMatic TailorMix HT1 qPCR assay. A single end read 50bp sequencing run was performed using the Illumina MiSeq instrument. Reads were demultiplexed by barcode and output into FASTQ format for subsequent analysis. Raw sequence data was trimmed of adapters and low quality sequences using Trimmomatic. Only reads with a minimum Qscore of 15 and length of 16nt were kept for downstream processing.

treatment_protocol: N/A (The cells from stroke patients were isolated and frozen in RNAProtect Cell Reagent from Qiagen. No further treatment was performed).

tag: clinical outcome

value: Patient with "good" clinical outcome


title: Stroke patient 45

description: 25,000 cells


title: Undifferentiated Ctrl sgRNA 1


title: Undifferentiated GFP 4


title: Undifferentiated GFP 2


title: 16-118B CA1 FMR1

description:
16-118B
yoked controls in active place avoidance task

value: hippocampus; CA1 subfield


title: Stroke patient 25

description: 40,000 cells

value: Patient with "bad" clinical outcome


title: Pc.ChIPseq.BG3C2.KD2

value: Pc, Santa Cruz #sc-25762


title: Pc.ChIPseq.BG3C2.KD1


title: DMAD.ChIPseq.BG3C2.rep3

value: The anti-DMAD antibody was generated by immunizing rabbit and mouse with the recombinant protein GST-DMAD (amino acids 959–1108) produced in E. coli


title: DMAD.ChIPseq.BG3C2.rep2


title: 16-116B CA1 FMR1

description:
16-116B
yoked controls in active place avoidance task


title: Mnase-seq.BG3C2.KD1.fastq


title: Undifferentiated Ctrl sgRNA 4


title: Undifferentiated GFP 1


title: Brain.m6A.IP.Ctrl

value: m6A, Synaptic Systems # 202003


title: H3K27me3.ChIPseq.BG3C2.Ctrl.fastq


title: BG3C2.m6A.IP.Ctrl1-2


title: BG3C2.m6A.IP.Ctrl1-1


title: BG3C2.KD1.RNAseq


title: Stroke patient 34

description: 35,000 cells


title: Stroke patient 31

description: 37,500 cells


title: DMAD.ChIPseq.BG3C2.rep1


title: BG3C2.Ctrl3.RNAseq


title: Wds.ChIPseq.BG3C2.KD.fastq


title: BG3C2.Ctrl1.RNAseq


title: Pc.ChIPseq.BG3C2.Ctrl2


title: H3K4me3.ChIPseq.BG3C2.Ctrl.fastq


title: Stroke patient 29

description: 35,000 cells


title: Brain.KO1.RNAseq


title: BG3C2.KD2.RNAseq


title: BG3C2.Ctrl2.RNAseq


title: Pdgfra-GFP positive cells P7 Brain 22

city: Stockholm

first: David

last: van Bruggen

state: Stockholm

address: Scheeles väg 2

department: MBB

institute: Karolinska Institutet

description: STRT fluidigm sequence prep

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), RNA molecules (UMIs) supported only by a single read ("singleton molecules") were removed.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: Genome_build: UCSC mm10
Supplementary_files_format_and_content: Total transcript counts per gene for each individual cell

source_name: Pdgfra-GFP positive cells from Mouse Brain

extract_protocol:
Forebrain and spinal cord were excised and dissociated with the Papain Neural dissociation kit from Miltenyi, following the manufacturer’s instructions.
Variable, see sample
Illumina’s TruSeq Stranded Total RNA Library Prep Kit was used according to manufacturer’s instructions. Three pooled biological replicates were sequenced for each developmental stage and brain region, and a total of 38 - 66 million 150 bp strand-specific paired-end reads were generated for each replicate, comprising a total of 620.5 million reads across all datasets

tag: strain


title: Pdgfra-GFP positive cells P7 Brain 21

description: STRT fluidigm sequence prep


title: Pdgfra-GFP positive cells P7 Spinal Cord 26

description: STRT fluidigm sequence prep

source_name: Pdgfra-GFP positive cells from Mouse Spinal Cord


title: Pc.ChIPseq.BG3C2.Ctrl1


title: BG3C2.m6A.IP.KD2


title: Brain.m6A.IP.KO


title: BG3C2.m6A.IP.KD1-2


title: BG3C2.m6A.IP.Ctrl2


title: Pdgfra-GFP positive cells P7 Spinal Cord 23

description: STRT fluidigm sequence prep


title: BG3C2.m6A.IP.KD1-1


title: Pdgfra-cre-GFP positive cells 20

description: STRT fluidigm sequence prep

source_name: P7 timepoint Pdgfra-cre-GFP positive cells from P3 Tamoxifen injected mouse brain

value: Pdgfra-cre-ERT/RCE


title: Pdgfra-cre-GFP positive cells 19

description: STRT fluidigm sequence prep


title: Pdgfra-GFP positive cells E13.5 Brain 24

description: STRT fluidigm sequence prep

extract_protocol:
Forebrain and spinal cord were excised and tissue was mechanical dissociated in HBSS with ions using 3 different Pasteur pipettes of decreasing diameter
Variable, see sample
Illumina’s TruSeq Stranded Total RNA Library Prep Kit was used according to manufacturer’s instructions. Three pooled biological replicates were sequenced for each developmental stage and brain region, and a total of 38 - 66 million 150 bp strand-specific paired-end reads were generated for each replicate, comprising a total of 620.5 million reads across all datasets


title: Pdgfra-GFP positive cells E13.5 Brain 25

description: STRT fluidigm sequence prep


title: Pdgfra-cre-GFP positive cells 17

description: STRT fluidigm sequence prep

source_name: P7 timepoint Pdgfra-cre-GFP positive cells from E12.5 Tamoxifen injected mouse brain


title: Pdgfra-cre-GFP positive cells 18

description: STRT fluidigm sequence prep


title: Pdgfra-GFP positive cells E13.5 Spinal Cord 7

description: STRT fluidigm sequence prep


title: Pdgfra-GFP positive cells P7 Spinal Cord 9

description: STRT fluidigm sequence prep


title: Pdgfra-cre-GFP positive cells 14

description: STRT fluidigm sequence prep


title: Pdgfra-GFP positive cells E13.5 Spinal Cord 8

description: STRT fluidigm sequence prep


title: Pdgfra-cre-GFP positive cells 15

description: STRT fluidigm sequence prep


title: Pdgfra-cre-GFP positive cells 16

description: STRT fluidigm sequence prep


title: Pdgfra-GFP positive cells E13.5 Spinal Cord 4

description: STRT fluidigm sequence prep


title: Pdgfra-GFP positive cells P7 Spinal Cord 12

description: STRT fluidigm sequence prep


title: Pdgfra-GFP positive cells E13.5 Brain 2

description: STRT fluidigm sequence prep


title: I2 TElo

city: Houston

first: Maria

last: Bettini

state: TX

address: 1102 Bates St

institute: Baylor College of Medicine

data_processing:
NextSeq Control Software v2.0 used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using TopHat Alignment v1.0.0
Fragment per kilobase million of library size (FPKM) were calculated using Cufflinks Assembly & DE v1.1.0
Genome_build: RefSeq mm10

source_name: conventional T cells

extract_protocol:
TritonX-100 cell lysis, reverse transcription, cDNA amplification
Nextera XT

value: NOD

value: pancreatic islets

tag: age

value: NOD (WT)

value: conventional T cells


title: I1 TElo


title: Pdgfra-cre-GFP positive cells 5

description: STRT fluidigm sequence prep


title: I4 TRlo

source_name: regulatory T cells

value: regulatory T cells


title: I1 TEhi


title: Pdgfra-GFP positive cells E13.5 Brain 6

description: STRT fluidigm sequence prep


title: Pdgfra-GFP positive cells P7 Spinal Cord 10

description: STRT fluidigm sequence prep


title: I2 TEhi


title: S2 TRhi

value: spleen


title: I1 TRhi


title: Pdgfra-cre-GFP positive cells 13

description: STRT fluidigm sequence prep


title: I4 TRhi


title: I2 TRlo


title: S1 TRhi


title: Pdgfra-GFP positive cells E13.5 Brain 3

description: STRT fluidigm sequence prep


title: Pdgfra-GFP positive cells P7 Spinal Cord 11

description: STRT fluidigm sequence prep