title: UACC-62_Input_R1

description:
Input RNA
RIP-seq

data_processing:
RIP-seq processing:
Read files were quality-checked with FastQC
Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.4 (using Bowtie 0.12.7 and Samtools 0.1.16), allowing 2 mismatches
RIP-seq peaks were called with Piranha 1.2.1 using the ZeroTruncatedPoissonRegression distribution, with a bin size of 20 and 0.05 FDR
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Files were generated with Piranha 1.2.1 and contain called peaks

source_name: UACC-62 melanoma cell line

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (Life Technologies) supplemented with 10% fetal bovine serum (Nova-Tech Inc.)

extract_protocol:
RNA was extracted after immunoprecipitation using TRI Reagent (Sigma) including DNase I treatment step.
An estimated mass of 20 ng of RNA per sample was used. Ribosomal RNAs were removed with the Ribo-Zero Gold Kit (Epicentre Cat. No. RZHM11106/RZG1224) and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq RNA Sample Preparation v2 Protocol" (Part # 15026494 Rev. C). Adapter-ligated library was completed by 10 cycles of PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

treatment_protocol: Cell lysates were immunoprecipitated using CUGBP1 antibody (Abcam, ab9549) coupled to Dynabeads Protein A (Invitrogen).

tag: type

value: RIP-seq

value: anti-CUGBP1 (Abcam, ab9549)


title: UACC-62_Input_R3

status: Public on Dec 21 2017

type: SRA

city: Madrid

first: Metehan

last: Cifdaloz

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology Program

country: Spain

institute: CNIO

description:
Input RNA
RIP-seq

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: antibody


title: GHA501A71, Treated single cell RNA-seq

city: London

first: Arsham

last: Ghahramani

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Single cell

data_processing:
Reads were preprocessed using FastQC and Cutadapt. Sequences were aligned to the Mus Musculus genome (GRCm38) using Tophat discarding multiply-mapped reads. Gene level counts were extracted using featureCounts 53. Transcript levels were quantified as transcripts per million (TPM). Genes with a TPM greater than 1 were considered as expressed. We filtered cells for analyses on the basis of number of aligned reads (> 200,000), percentage of ribosomal reads (< 2%) and number of genes expressed (> 2000).
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV containing TPM normalized read count for each gene in each cell

organism: Mus musculus

source_name: Keratinocytes

growth_protocol: Keratinocytes were isolated and cultured from adult dorsal skin in FAD medium (one part Ham’s F12, three parts Dulbecco’s modified Eagle’s medium, 1.8×10-4 M adenine), supplemented with 10% foetal calf serum (FCS) and a cocktail of 0.5 μg/ml hydrocortisone, 5 μg/ml insulin, 1×10-10 M cholera enterotoxin and 10 ng/ml epidermal growth factor (HICE cocktail)

extract_protocol:
Wild type and K14ΔNβ-cateninER keratinocytes were cultured on 12 well plates in a ratio of 9:1 for a total of 200,000 cells per well and allowed to attach for 24 hours. Subsequently, cells were treated with 4-OHT (200nM) or DMSO as a control. After 24 hours of treatment cells were trypsinised and resuspended as a single cell suspension.
Single keratinocytes were captured on a medium-sized (10-17μm) microfluidic chip (C1, Fluidigm). Cells were assessed for viability (LIVE/DEAD assay, Life Technologies) and C1 capture sites were imaged by phase contrast to determine empty and doublet capture sites. Cells were loaded onto the chip at a concentration of 300 cells μl-1. Doublet or non-viable cells were excluded from later analysis. Cell lysis, reverse transcription, and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as per the manufacturer’s instructions. For cDNA synthesis the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) was used. Single cell Illumina NGS libraries were constructed with Nextera XT DNA Sample Prep kit (Illumina). Sequencing was performed on Illumina HiSeq4000 (Illumina) using 100bp paired-end reads.

treatment_protocol: Untreated; DMSO. Treated; 200nM 4OHT for 24 hours.

tag: treatment

value: Treated - 24 hours 4OHT

tag: cell type

value: Keratinocytes


title: UACC-62_aCUGBP1_IP_R1

description:
poly A+ RNA from RIP
RIP-seq


title: UACC-62_aCUGBP1_IP_R3

description:
poly A+ RNA from RIP
RIP-seq


title: SK-Mel-103_aCUGBP1_IP_R1

description:
poly A+ RNA from RIP
RIP-seq

source_name: SK-Mel-103 melanoma cell line


title: GHA501A134, Untreated single cell RNA-seq

description: Single cell

value: UnTreated - 24 hours 4OHT - Control


title: SK-Mel-103_Input_R1

description:
Input RNA
RIP-seq


title: GHA501A191, Untreated single cell RNA-seq

description: Single cell


title: GHA501A95, Treated single cell RNA-seq

description: Single cell


title: GHA501A57, Treated single cell RNA-seq

description: Single cell


title: GHA501A173, Untreated single cell RNA-seq

description: Single cell


title: GHA501A168, Untreated single cell RNA-seq

description: Single cell


title: GHA501A192, Untreated single cell RNA-seq

description: Single cell


title: GHA501A56, Treated single cell RNA-seq

description: Single cell


title: GHA501A36, Treated single cell RNA-seq

description: Single cell


title: GHA501A130, Untreated single cell RNA-seq

description: Single cell


title: GHA501A109, Untreated single cell RNA-seq

description: Single cell


title: GHA501A163, Untreated single cell RNA-seq

description: Single cell


title: GHA501A26, Treated single cell RNA-seq

description: Single cell


title: GHA501A82, Treated single cell RNA-seq

description: Single cell


title: GHA501A179, Untreated single cell RNA-seq

description: Single cell


title: GHA501A51, Treated single cell RNA-seq

description: Single cell


title: GHA501A89, Treated single cell RNA-seq

description: Single cell


title: GHA501A103, Untreated single cell RNA-seq

description: Single cell


title: GHA501A10, Treated single cell RNA-seq

description: Single cell


title: GHA501A101, Untreated single cell RNA-seq

description: Single cell


title: GHA501A121, Untreated single cell RNA-seq

description: Single cell


title: GHA501A53, Treated single cell RNA-seq

description: Single cell


title: R2_TamR_4E_HD

city: New York

first: Robert

middle: J

last: Schneider

state: NY

address: 550 First Ave, MSB 238

department: Microbiology

country: USA

institute: NYU School of Medicine

data_processing:
Sequenced reads were trimmed using trimmomatic v0.33
Reads were aligned using tophat v2.0.9/bowtie v1.0.0.0 to UCSC hg19 genome using UCSC hg19 transcriptome annotations
Aligned reads were quantified using htseq version 0.6.1p1
Differential analysis was performed using voom normalization / Limma linear modeling
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each gene of each sample

molecule: polyA RNA

source_name: MCF7 tamoxifen-resistant breast cancer cells

growth_protocol: MCF7 cells were maintained in Improved MEM with L-glutamine without phenol red (Cellgro), 5% fetal bovine serum (FBS, Gibco), 0.4% gentamicin sulfate (Lonza), 0.5 µg/mL Fungizone (Gibco), and 5 µg/mL plasmocin at 37˚C in a 5% CO2 tissue culture incubator. 1 µM of 4-hydroxytamoxifen was added to TamR cells every 72 h

extract_protocol:
Lysates were either purified (total mRNA) or subjected to polysome profiling.  Polysome profiling samples pertaining to 2-3 ribsomes (light mRNA) were purified or >4 ribosomes were purified (heavy mRNA).  All samples were purified using the RNeasy Mini Kit (Qiagen) as per manufacture instructions.
RNA libraries were prepared for sequencing using poly A enrichment standard Illumina protocols

tag: tissue

value: selected tamoxifen resistant MCF7 breast cancer cells

tag: extraction

value: heavy polysome mRNA

tag: genotype

tag: replicate

value: replicate 2


title: GHA501A40, Treated single cell RNA-seq

description: Single cell


title: GHA501A5, Treated single cell RNA-seq

description: Single cell


title: R2_TamR_4E_LD

value: light polysome mRNA


title: GHA501A141, Untreated single cell RNA-seq

description: Single cell


title: R2_TamS_NS_HD

source_name: MCF7 tamoxifen-sensitive breast cancer cells

value: tamoxifen sensitive MCF7 breast cancer cells

value: non-silencing


title: R2_TamR_4E_T

value: total mRNA


title: R2_TamR_NS_T


title: R2_TamR_NS_LD


title: GHA501A180, Untreated single cell RNA-seq

description: Single cell


title: GHA501A41, Treated single cell RNA-seq

description: Single cell


title: GHA501A138, Untreated single cell RNA-seq

description: Single cell


title: R2_TamR_NS_HD


title: R1_TamS_NS_T

value: replicate 1


title: GHA501A107, Untreated single cell RNA-seq

description: Single cell


title: GHA501A94, Treated single cell RNA-seq

description: Single cell


title: R1_TamS_NS_HD


title: GHA501A102, Untreated single cell RNA-seq

description: Single cell


title: GHA501A143, Untreated single cell RNA-seq

description: Single cell


title: R1_TamS_NS_LD


title: R1_TamR_4E_T


title: GHA501A188, Untreated single cell RNA-seq

description: Single cell


title: GHA501A11, Treated single cell RNA-seq

description: Single cell


title: GHA501A132, Untreated single cell RNA-seq

description: Single cell


title: GHA501A93, Treated single cell RNA-seq

description: Single cell


title: R1_TamR_4E_HD


title: GHA501A90, Treated single cell RNA-seq

description: Single cell


title: R1_TamR_NS_T


title: R2_TamS_NS_T


title: R1_TamR_NS_LD


title: R1_TamR_NS_HD


title: AG2pos_191, Treated single cell RNA-seq

description: Single cell

source_name: Treated single cell

growth_protocol: Keratinocytes were isolated and cultured from adult dorsal skin in FAD medium (one part Ham’s F12, three parts Dulbecco’s modified Eagle’s medium, 1.8×10^-4 M adenine), supplemented with 10% fetal calf serum (FCS) and a cocktail of 0.5 μg/ml hydrocortisone, 5 μg/ml insulin, 1×10^-10 M cholera enterotoxin and 10 ng/ml epidermal growth factor (HICE cocktail)

extract_protocol:
Wild type and K14ΔNβ-cateninER keratinocytes were cultured on 12 well plates in a ratio of 9:1 for a total of 200,000 cells per well and allowed to attach for 24 hours. Subsequently, cells were treated with 4-OHT (200nM) or DMSO as a control. After 24 hours of treatment cells were trypsinized and resuspended as a single cell suspension.
Single keratinocytes were captured on a medium-sized (10-17μm) microfluidic chip (C1, Fluidigm). Cells were assessed for viability (LIVE/DEAD assay, Life Technologies) and C1 capture sites were imaged by phase contrast to determine empty and doublet capture sites. Cells were loaded onto the chip at a concentration of 300 cells μl-1. Doublet or non-viable cells were excluded from later analysis. Cell lysis, reverse transcription, and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as per the manufacturer’s instructions. For cDNA synthesis the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) was used. Single cell Illumina NGS libraries were constructed with Nextera XT DNA Sample Prep kit (Illumina). Sequencing was performed on Illumina HiSeq4000 (Illumina) using 100bp paired-end reads.


title: AG2pos_189, Treated single cell RNA-seq

description: Single cell


title: GHA501A65, Treated single cell RNA-seq

description: Single cell


title: AG2pos_185, Treated single cell RNA-seq

description: Single cell


title: AG1neg_188, Untreated single cell RNA-seq

description: Single cell

source_name: Untreated single cell


title: GHA501A45, Treated single cell RNA-seq

description: Single cell


title: XR_DRB2_R5_60M_1

city: Taichung

first: Yi-Ying

last: Chiou

address: No.145, Xingda Rd., South Dist.

department: Graduate Institute of Biochemistry

country: Taiwan

institute: National Chung Hsing University

description:
XR-seq, preDRB, release 5min, UV, 60 min Repair with DRB, Rep 1
ssDNA by NER

library_source: genomic

data_processing:
Library strategy: XR-seq
Reads were trimmed by bbduk tool of BBMap (35.82)  and mapped to the genome by Bowtie2 (2.28) (XR-seq) using the option -- very-sensitive or BBMap (35.82) (NET-seq) using the options maxindel=100000 intronlen=10 ambig=random qin=33
For NET-seq, reads with proper pair were selected and the locations of RNAPII were defined as the positon of first base from the 3’-end of the isolated RNA
Aligned reads were strand-specifically assigned to the genes using Intersect tool of Bedtools (2.25.0) with the option: -c.  For intra-gene distribution, genes with RPKM >=  0.1 in all conditions and the length >= 50 kb were selected (1646 genes). Genes were separated into 250 base per bin and the aligned reads were assigned to each bin using Intersect tool of Bedtools with the options: -c -F 0.5.
Genome_build: human (hg19)
Supplementary_files_format_and_content: Bed files, Number of reads of each gene / each bin of gene

molecule: genomic DNA

source_name: XP-C cells: GM15983

growth_protocol: All cells were grown in DMEM–high glucose (ThermoFisher) supplemented with 10% (v/v) fetal bovine serum (Sigma) and maintained at 37oC in 5% CO2

extract_protocol: XR-seq: protocol from (2015) Genes & development 29, 948-960

treatment_protocol:
UV irradiation: 20J/ m2 UVC
DRB regimens:
a. DMSO: 0.1% DMSO added after UV
b. DRB: 100 uM DRB added after UV
c. DRB2: 100 uM DRB added 2 hrs before UV, released by changing to fresh medium for 5 / 10 min, after UV, cells were incubated in the medium with 100 uM DRB

value: skin fibroblast

value: XPC mutant


title: R1_TamR_4E_LD


title: XR_DRB2_R10_60M_2

description:
XR-seq, preDRB, release 10min, UV, 60 min Repair with DRB, Rep 2
ssDNA by NER


title: AG2pos_183, Treated single cell RNA-seq

description: Single cell


title: AG1neg_184, Untreated single cell RNA-seq

description: Single cell


title: AG1neg_182, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_181, Treated single cell RNA-seq

description: Single cell


title: AG1neg_180, Untreated single cell RNA-seq

description: Single cell


title: XR_DRB_60M_2

description:
XR-seq, DRB after UV,  60 min Repair, Rep 2
ssDNA by NER


title: XR_DRB2_R10_30M_1

description:
XR-seq, preDRB, release 10min, UV, 30 min Repair with DRB, Rep 1
ssDNA by NER


title: AG2pos_193, Treated single cell RNA-seq

description: Single cell


title: AG2pos_175, Treated single cell RNA-seq

description: Single cell


title: AG2pos_177, Treated single cell RNA-seq

description: Single cell


title: XR_DRB_60M_1

description:
XR-seq, DRB after UV,  60 min Repair, Rep 1
ssDNA by NER


title: XR_DMSO_60M_2

description:
XR-seq, No DRB, 60 min Repair, Rep 2
ssDNA by NER


title: AG1neg_190, Untreated single cell RNA-seq

description: Single cell


title: XR_DRB2_R10_60M_1

description:
XR-seq, preDRB, release 10min, UV, 60 min Repair with DRB, Rep 1
ssDNA by NER


title: AG1neg_168, Untreated single cell RNA-seq

description: Single cell


title: XR_DRB_30M_1

description:
XR-seq, DRB after UV,  30 min Repair, Rep 1
ssDNA by NER


title: AG2pos_169, Treated single cell RNA-seq

description: Single cell


title: AG1neg_170, Untreated single cell RNA-seq

description: Single cell


title: XR_DRB2_R10_30M_2

description:
XR-seq, preDRB, release 10min, UV, 30 min Repair with DRB, Rep 2
ssDNA by NER


title: XR_DRB2_R5_60M_2

description:
XR-seq, preDRB, release 5min, UV, 60 min Repair with DRB, Rep 2
ssDNA by NER


title: XR_DRB_30M_2

description:
XR-seq, DRB after UV,  30 min Repair, Rep 2
ssDNA by NER


title: XR_DMSO_30M_2

description:
XR-seq, No DRB, 30 min Repair, Rep 2
ssDNA by NER


title: AG2pos_165, Treated single cell RNA-seq

description: Single cell


title: AG1neg_164, Untreated single cell RNA-seq

description: Single cell


title: XR_DMSO_60M_1

description:
XR-seq, No DRB, 60 min Repair, Rep 1
ssDNA by NER


title: AG2pos_161, Treated single cell RNA-seq

description: Single cell


title: AG1neg_162, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_157, Treated single cell RNA-seq

description: Single cell


title: AG1neg_156, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_167, Treated single cell RNA-seq

description: Single cell


title: AG1neg_160, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_153, Treated single cell RNA-seq

description: Single cell


title: AG1neg_154, Treated single cell RNA-seq

description: Single cell


title: AG1neg_150, Untreated single cell RNA-seq

description: Single cell


title: AG1neg_152, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_143, Treated single cell RNA-seq

description: Single cell


title: AG1neg_148, Untreated single cell RNA-seq

description: Single cell


title: AG1neg_144, Untreated single cell RNA-seq

description: Single cell


title: AG1neg_142, Untreated single cell RNA-seq

description: Single cell


title: AG1neg_138, Untreated single cell RNA-seq

description: Single cell


title: RNAseq_ESC_Hmga1ko_2_b

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
complete coding sequence deletion
mRNA_2_knownGene_mm9.csv

data_processing:
Basecalls were performed using RTA 1.18.64 / bcl2fastq2 v2.17
RNA-seq reads were mapped to the mm9 assembly of the mouse genome using QuasR (PMID: 25417205), which internally uses bowtie (PMID: 19261174). Bowtie was run with mapping parameters "--trim5 3 -m 100 --best --strata". For multi-mapping reads, one randomly chosen alignment was used for quantification.
Gene-level counts were determined using the UCSC knownGene table (PMID: 16500937) via the Rpackage TxDb.Mmusculus.UCSC.mm9.knownGene (Marc Carlson and Bioconductor Package Maintainer (2015). TxDb.Mmusculus.UCSC.mm9.knownGene: Annotation package for TxDb object(s)). Gene counts were determined using the QuasR function qCount (qCount(proj, TxDb.Mmusculus.UCSC.mm9.knownGene, reportLevel="gene", orientation="same”))
Genome_build: mm9
Supplementary_files_format_and_content: Comma-separated text file containing raw alignment counts for each gene and sample as well as gene annotation (width: total number of exonic bases, Entrez gene id , gene symbol)

source_name: Embryonic stem cells

extract_protocol:
RNA was isolated with the RNeasy mini kit (Qiagen) with on-column DNA digestion and was depleted of ribosomal RNA using the Ribo-Zero rRNA removal kit (Epicentre).
Strand-specific RNA-seq libraries were prepared from rRNA-depleted samples using the ScriptSeq v2 protocol (Epicentre) following producer instructions.

value: embryonic stem cells

value: Hmga1 KO


title: AG1neg_140, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_141, Treated single cell RNA-seq

description: Single cell


title: AG1neg_136, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_135, Treated single cell RNA-seq

description: Single cell


title: RNAseq_ESC_Hmga1ko_2_c


title: XR_DMSO_30M_1

description:
XR-seq, No DRB, 30 min Repair, Rep 1
ssDNA by NER


title: AG1neg_134, Untreated single cell RNA-seq

description: Single cell


title: RNAseq_ESC_Hmga1ko_2_a


title: AG2pos_132, Treated single cell RNA-seq

description: Single cell


title: RNAseq_ESC_wt_2_b

value: wild type


title: RNAseq_ESC_wt_2_c


title: RNAseq_ESC_wt_2_a


title: AG1neg_128, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_127, Treated single cell RNA-seq

description: Single cell


title: AG1neg_126, Untreated single cell RNA-seq

description: Single cell


title: RNAseq_ESC_Hmga1koHmga2ab_b

data_processing:
Basecalls were performed using RTA 1.18.64 / bcl2fastq2 v2.17
RNA-seq reads were mapped to the mm9 assembly of the mouse genome using QuasR (PMID: 25417205), which internally uses bowtie (PMID: 19261174). Bowtie was run with mapping parameters "--trim5 3 -m 100 --best --strata". For multi-mapping reads, one randomly chosen alignment was used for quantification. The first 3 nucleotides from the 5’ end were trimmed (“--trim5 3”) as they showed higher error rates in an initial round of mapping without trimming.
Gene-level counts were determined using the UCSC knownGene table (PMID: 16500937) via the Rpackage TxDb.Mmusculus.UCSC.mm9.knownGene (Marc Carlson and Bioconductor Package Maintainer (2015). TxDb.Mmusculus.UCSC.mm9.knownGene: Annotation package for TxDb object(s)). Gene counts were determined using the QuasR function qCount (qCount(proj, TxDb.Mmusculus.UCSC.mm9.knownGene, reportLevel="gene", orientation="same”))
Genome_build: mm9
Supplementary_files_format_and_content: Comma-separated text file containing raw alignment counts for each gene and sample as well as gene annotation (width: total number of exonic bases, Entrez gene id , gene symbol)

value: Hmga1 KO, Hmga2 rescue


title: RNAseq_ESC_Hmga1koHmga1ab_b

value: Hmga1 KO, Hmga1 rescue


title: RNAseq_ESC_Hmga1koHmga2ab_a


title: AG1neg_130, Untreated single cell RNA-seq

description: Single cell

value: Keratinocytes


title: RNAseq_ESC_Hmga1ko_b


title: AG2pos_120, Treated single cell RNA-seq

description: Single cell

value: Treated - 24 hours 4OHT


title: RNAseq_ESC_Hmga1koHmga1ab_a


title: AG2pos_113, Treated single cell RNA-seq

description: Single cell


title: AG1neg_122, Untreated single cell RNA-seq

description: Single cell

value: UnTreated - 24 hours 4OHT - Control


title: RNAseq_ESC_Hmga1ko_a


title: AG2pos_118, Treated single cell RNA-seq

description: Single cell


title: RNAseq_ESC_wt_c


title: RNAseq_ESC_wt_b


title: RNAseq_ESC_wt_a


title: ChIPseq_NP_Hmga2_input_b

data_processing:
Basecalling was performed using RTA 1.18.64 / bcl2fastq2 v2.17
IP and input samples were mapped to the mm9 assembly of the mouse genome using the R package QuasR (PMID: 25417205), which internally uses bowtie (PMID: 19261174). Bowtie was run with QuasR default parameters, allowing only for uniquely mapping reads.
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain the log2 enrichments of wt over the corresponding DNA-binding mutant proteins in 1kb tiling windows.  More precisely, these correspond to the difference in log2 IP/input for wt and log2 IP/input for the DNA-binding mutant using the paired input sample of each IP.

source_name: neural progenitor cells

extract_protocol:
Cells were fixed for 10 minutes with 1% Formaldehyde at room temperature and incubated for 10 min on ice in the presence of 0.125M glycine. Cells were harvested and treated for 10 min with 10mM EDTA, 10mM TRIS, 0.5mM EGTA and 0.25% Triton X-100 and 10 min in 1mM EDTA, 10mM TRIS, 0.5mM EGTA and 200mM NaCl with subsequent nuclear lysis in 50mM HEPES, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS and 150 mM NaCl. DNA was purified with Qiagen columns for PCR Purification. Crosslinked chromatin was subjected to sonication in a Bioruptor instrument (Diagenode). ProteinA (Invitrogen) pre-cleared chromatin was either saved as input or incubated with blocked (1%CFSG, 100ng tRNA) Streptavidin-M280 (Invitrogen) magnetic beads over night at 4°C. Beads were washed and treated with RNaseA for 30 min at 37°C, Proteinase K for 3 hours at 55°C then de-crosslinked over night at 65°C.
Libraries were prepared with the NEBNext (NEB) reagents according to the manufacturer's protocol, with Agencourt AMPure XP (Beckman Coulter) size selection of the fragments (150-200bp) before PCR amplification with indexed primers.

value: neural progenitor cells

tag: pulldown


title: AG2pos_111, Treated single cell RNA-seq

description: Single cell


title: AG1neg_112, Untreated single cell RNA-seq

description: Single cell


title: AG1neg_110, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_NP_Hmga2_input_a

description:
ChIPseq_NP_Hmga2_a.wig.gz
alternative base-calling: RTA 1.18.64 / bcl2fastq v1.8.4


title: ChIPseq_NP_Hmga2_mut_input_b


title: AG2pos_103, Treated single cell RNA-seq

description: Single cell


title: AG1neg_102, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_NP_Hmga2_mut_input_a


title: AG2pos_104, Treated single cell RNA-seq

description: Single cell


title: ChIPseq_NP_Hmga2_mut_b

value: Streptavidin-M280 (Invitrogen) magnetic beads


title: ChIPseq_NP_Hmga2_mut_a


title: AG1neg_100, Untreated single cell RNA-seq

description: Single cell


title: AG1neg_98, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_97, Treated single cell RNA-seq

description: Single cell


title: ChIPseq_NP_Hmga2_a


title: ChIPseq_NP_Hmga2_b

description:
ChIPseq_NP_Hmga2_b.wig.gz
alternative base-calling: RTA 1.18.64 / bcl2fastq v1.8.4


title: AG1neg_94, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_95, Treated single cell RNA-seq

description: Single cell


title: ChIPseq_NP_Hmga1_input_a


title: ChIPseq_NP_Hmga1_mut_input_b


title: ChIPseq_NP_Hmga1_input_b


title: AG2pos_93, Treated single cell RNA-seq

description: Single cell


title: AG2pos_106, Treated single cell RNA-seq

description: Single cell


title: ChIPseq_NP_Hmga1_mut_input_a


title: ChIPseq_NP_Hmga1_mut_b


title: AG2pos_91, Treated single cell RNA-seq

description: Single cell


title: AG1neg_92, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_NP_Hmga1_mut_a


title: ChIPseq_NP_Hmga1_b


title: ChIPseq_ESC_Hmga2_input_b

source_name: embryonic stem cells


title: AG2pos_90, Treated single cell RNA-seq

description: Single cell


title: ChIPseq_NP_Hmga1_a


title: AG1neg_89, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_87, Treated single cell RNA-seq

description: Single cell


title: AG1neg_85, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga2_input_a

description:
ChIPseq_ESC_Hmga2_a.wig.gz
alternative base-calling: RTA 1.18.64 / bcl2fastq v1.8.4


title: ChIPseq_ESC_Hmga2_mut_input_b


title: AG2pos_80, Treated single cell RNA-seq

description: Single cell


title: AG2pos_82, Treated single cell RNA-seq

description: Single cell


title: AG1neg_96, Untreated single cell RNA-seq

description: Single cell


title: AG1neg_83, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga2_b

description:
ChIPseq_ESC_Hmga2_b.wig.gz
alternative base-calling: RTA 1.18.64 / bcl2fastq v1.8.4


title: ChIPseq_ESC_Hmga2_mut_a


title: AG2pos_77, Treated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga2_mut_b


title: ChIPseq_ESC_Hmga2_a


title: AG1neg_79, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga1koHmga2ab_input_a


title: AG1neg_75, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga1koHmga2ab_input_b


title: AG2pos_76, Treated single cell RNA-seq

description: Single cell


title: AG1neg_73, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_72, Treated single cell RNA-seq

description: Single cell


title: AG1neg_71, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga2_mut_input_a


title: ChIPseq_ESC_Hmga1koHmga1ab_input_a


title: AG2pos_70, Treated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga1koHmga1ab_b


title: ChIPseq_ESC_Hmga1koHmga1ab_a


title: AG1neg_69, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga1_input_c

description:
ChIPseq_ESC_Hmga1_c.wig.gz
alternative extract protocol: Chromatin was isolated by resuspending cells in 50 mM Hepes-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100 for 10 min on ice. Nuclei were washed in 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 200 mM NaCl, 0.5 mM EGTA for 10 min RT (removal of detergents) and lysed in 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 0.1% Deoxycholate, 200 mM NaCl, 0.25% N-Lauroylsarcosin, 0.5 mM EGTA. Crosslinked chromatin was subjected to sonication in a Bioruptor instrument (Diagenode). Triton X-100 to 1% final concentration was added before further processing.


title: AG1neg_67, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga1koHmga1ab_input_b


title: AG1neg_65, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga1_input_b


title: AG2pos_74, Treated single cell RNA-seq

description: Single cell


title: AG1neg_64, Untreated single cell RNA-seq

description: Single cell


title: AG1neg_61, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga1_mut_input_b


title: ChIPseq_ESC_Hmga1koHmga2ab_b


title: AG2pos_60, Treated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga1koHmga2ab_a


title: AG2pos_58, Treated single cell RNA-seq

description: Single cell


title: AG2pos_55, Treated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga1_mut_b


title: AG1neg_59, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga1_mut_c


title: ChIPseq_ESC_Hmga1_mut_a


title: ChIPseq_ESC_Hmga1_mut_input_a


title: ChIPseq_ESC_Hmga1_b


title: AG2pos_54, Treated single cell RNA-seq

description: Single cell


title: AG1neg_51, Treated single cell RNA-seq

description: Single cell


title: AG2pos_66, Treated single cell RNA-seq

description: Single cell


title: R2_TamS_NS_LD

value: light polysome mRNA

value: replicate 2


title: ChIPseq_ESC_Hmga1_input_a


title: ChIPseq_ESC_Hmga1_mut_input_c


title: ChIPseq_ESC_Hmga1_c


title: AG1neg_49, Treated single cell RNA-seq

description: Single cell


title: AG2pos_48, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_50, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_GFP

description:
ChIPseq_ESC_GFP.wig.gz
alternative base-calling: RTA 1.18.64 / bcl2fastq v1.8.4


title: AG1neg_47, Treated single cell RNA-seq

description: Single cell


title: 102_3.5_FROZ_L3.D712.star

city: RTP

first: Susan

last: Hester

state: NC

address: 109 TW Alexander Dr

institute: US EPA

data_processing:
After sequencing, basecall files were converted into FASTQ output files using Illumina CASAVA software and other tools developed at EA (available at https://github.com/ExpressionAnalysis/ ea-utils/). FASTQ data were demultiplexed, and sequencing adapters and other low quality bases were clipped to prepare reads for alignment using fastq-mcf --max-ns 4 --qual-mean 25 -H -p 5 -q 7 -l 25 -l 25
Filtered reads were mapped to mm10.fa using Star 2.4 with parameters --readFilesCommand zcat --chimSegmentMin 15 --chimJunctionOverhangMin 17 --chimScoreMin 1 --chimScoreDropMax 20 --chimScoreSeparation 10 --quantMode TranscriptomeSAM --outSAMattributes NH  --alignSJoverhangMin 8 --sjdbScore 3 --outSAMunmapped Within --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --sjdbOverhang 200
BAM files resulting from Star 2.4 were used as input for Partek® expectation maximization algorithm in Partek Flow® (Build version 4.0.16.0128)
Raw read counts were normalized across all samples using reads per kilobase of transcript per million mapped reads (RPKM)
Genome_build: MM10
Supplementary_files_format_and_content: tab-delimited files with estimated counts for all genes and RPKM normalized counts for all genes

source_name: frozen liver (mixed lobes)

growth_protocol: Studies were conducted in 4 week-old male B6C3F1 mice maintained under standard housing conditions at the U.S. Environmental Protection Agency (US EPA) AAALAC-accredited animal facility (Research Triangle Park, NC). Animal care and procedures were conducted under protocols approved by the Institutional Animal Care and Use Committee of the USEPA.

extract_protocol:
For liquid nitrogen frozen (FROZ) liver samples, ~20 mg of liver tissue per sample was homogenized in RNAzol®RT , purified with the Qiagen RNeasy MinElute column protocol, evaluated for integrity using an Agilent 2100 Bioanalyzer, and quantitated using a Qubit fluorometer.
Total RNA was converted into cDNA libraries using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Library Prep Kit (#RS-122-2303, Illumina, San Diego, CA). Briefly, ribosomal RNA (rRNA) was removed from 100 ng of total RNA by hybridization to a biotinylated probe selective for rRNA species, followed by streptavidin bead binding, purification, and fragmentation by heat in the presence of divalent cations. Double-stranded cDNA was generated by removing the RNA template and synthesizing the second strand with dUTP in place of dTTP. A single ‘A’ base was added to the 3’ end to facilitate ligation of sequencing adapters, which contained a single ‘T’ base overhang. Adapter-ligated cDNA was amplified by polymerase chain reaction (PCR) to increase the amount of sequence-ready library. During this amplification the polymerase stalls when it encounters a ‘U’ base, rendering the second strand a poor template. The first strand thus serves as template for amplified sequence, preserving strand information. Final cDNA libraries were analyzed for size distribution and integrity using an Agilent Bioanalyzer (DNA 1000 kit #5067-1504), quantitated by qPCR (KAPA Library Quant Kit #KK4824, KAPA Biosystems, Wilmington, MA), and normalized to 2 nM in preparation for sequencing.Samples were sequenced at EA Genomics (Q2 Solutions, Durham, NC) using the Illumina HiSeq platform

treatment_protocol: Dichloroacetic acid (CAS 79-43-6, Aldrich) was administered in the drinking water at doses of 0, 1.0, 2.0, and 3.5 g/L (as described in DeAngelo et al. 1991).

value: liver

tag: strain

tag: age

value: 4 weeks

tag: Sex

value: male

value: dichloroacetic acid (DCA)

tag: dose


title: AG2pos_46, Untreated single cell RNA-seq

description: Single cell


title: 100_3.5_FROZ_L3.D710.star


title: 99_3.5_FROZ_L3.D709.star


title: AG1neg_53, Untreated single cell RNA-seq

description: Single cell


title: 98_3.5_FROZ_L3.D708.star


title: AG1neg_41, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_40, Treated single cell RNA-seq

description: Single cell


title: 97_3.5_FROZ_L3.D707.star


title: AG1neg_39, Untreated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_Hmga1_a


title: AG2pos_38, Treated single cell RNA-seq

description: Single cell


title: ChIPseq_ESC_GFP_input


title: AG1neg_35, Untreated single cell RNA-seq

description: Single cell


title: 77_2_FROZ_L2.D705.star

value: 2 g/L


title: 76_2_FROZ_L2.D704.star


title: 75_2_FROZ_L2.D703.star


title: AG2pos_36, Treated single cell RNA-seq

description: Single cell


title: 101_3.5_FROZ_L3.D711.star


title: AG1neg_43, Treated single cell RNA-seq

description: Single cell


title: AG2pos_34, Treated single cell RNA-seq

description: Single cell


title: AG1neg_33, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_32, Treated single cell RNA-seq

description: Single cell


title: 73_2_FROZ_L2.D701.star


title: AG1neg_31, Untreated single cell RNA-seq

description: Single cell


title: R5_glucose starvation

first: Anne

last: Spang

institute: Biozentrum, University of Basel

description: column header in processed file: BSSE_QGF_15117

data_processing:
Illumina bcl2fastq-1.8.3 software for base calling
Adapter trimming using Trimmomatic version 0.30 with parameters parameters “SE –s phred33 ILLUMINACLIP:Illumina_smallRNA_adapters.fa:20:5:30 LEADING:30 TRAILING:30 MINLEN:10"
Alignment using Bowtie version 1.0.0 with parameters “-n 0 –l 28 –e 70 –k1 –m 1 --best --strata --sam --nomaqround”
Read counting with htseq-count and default parameters
Normalized read counts from edgeR version 3.0 using default parameters
Genome_build: S. cerevisiae ENSEMBL EF4.72
Supplementary_files_format_and_content: Tab delimited file containing raw read counts

organism: Saccharomyces cerevisiae

source_name: P-bodies_glucose starvation

growth_protocol: Cells expressing Dcp2-HBH or Scd6-HBH were grown to mid-log phase.

extract_protocol:
Cells were lysed in RIPA buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, supplemented with protease inhibitors) with FastPrep machine (MP Biomedicals). To dissolve large RNPs, the supernatants were treated with 50 U/ml RNase T1 (Fermentas) at 22°C for 15 min. Pull-downs were performed with streptavidin agarose beads (Thermo Fisher Scientific) in binding buffer (50 mM NaPi pH 8.0, 300 mM NaCl, 6 M GuHCl, 0.5% Tween-20). The second RNase T1 digestion was performed on the beads with a final concentration of 1 U/μl. Radiolabeling of RNA was performed by adding 0.5 µCi/µl γ 32P-ATP (Hartmann analytic) and 1 U/µl T4 PNK (New England Biolabs). To purify RNA, proteins were digested using 1.2 mg/ml proteinase K (Roche) in 2 x proteinase K buffer (100 mM Tris HCl pH 7.5, 200 mM NaCl, 2 mM EDTA, 1% SDS) for 30 min at 55˚C. The RNA was subsequently isolated using phenol-chloroform-isoamyl alcohol (125:24:1) (Sigma-Aldrich) as described (Schmitt et al., 1990).
Purified RNA was subjected to 3’ and 5’ adapter ligation following Illumina’s TruSeq Small RNA Library Prep Guide. To reduce the rRNA species, RiboMinus transcriptome isolation kit (Invitrogen) was used according to the manufacturer's protocol. Reverse transcription using SuperScript III reverse transcriptase (Invitrogen), oligo dT and random hexamer was performed afterwards. The cDNA libraries were generated by a final PCR amplification step with llumina indexing primer.

treatment_protocol: Cells were subjected to the corresponding stress and crosslinked with 1% formaldehyde for 2 min. Control cells were treated equally except stress application.

tag: tagged p-body component

tag: stress

value: Glucose starvation

tag: clip beads


title: R5_Ca2+

description: column header in processed file: BSSE_QGF_15119

value: 0.2 M CaCl2

value: streptavidin agarose beads (Thermo Fisher Scientific)


title: R5_Na+

description: column header in processed file: BSSE_QGF_15118

value: 0.5 M NaCl


title: R4_Ca2+

description: column header in processed file: BSSE_QGF_14394


title: R5_control

description: column header in processed file: BSSE_QGF_15116

value: Unstressed control


title: R4_glucose starvation

description: column header in processed file: BSSE_QGF_14392


title: 78_2_FROZ_L2.D706.star


title: 54_1_FROZ_L2.D712.star

value: 1 g/L


title: AG2pos_30, Treated single cell RNA-seq

description: Single cell

value: Treated - 24 hours 4OHT

value: Keratinocytes


title: R3_Ca2+

description: column header in processed file: BSSE_QGF_11722


title: 53_1_FROZ_L2.D711.star


title: R4_control

description: column header in processed file: BSSE_QGF_14379


title: 52_1_FROZ_L2.D710.star


title: R4_Na+

description: column header in processed file: BSSE_QGF_14393


title: AG1neg_29, Untreated single cell RNA-seq

description: Single cell

value: UnTreated - 24 hours 4OHT - Control


title: 74_2_FROZ_L2.D702.star


title: 51_1_FROZ_L1.D709.star


title: AG1neg_27, Untreated single cell RNA-seq

description: Single cell


title: 50_1_FROZ_L1.D708.star


title: R3_control

description: column header in processed file: BSSE_QGF_11719


title: R3_Na+

description: column header in processed file: BSSE_QGF_11721


title: AG2pos_28, Treated single cell RNA-seq

description: Single cell


title: R3_glucose starvation

description: column header in processed file: BSSE_QGF_11720


title: R2_Ca2+

description: column header in processed file: BSSE_QGF_11007


title: 49_1_FROZ_L1.D707.star


title: R2_Na+

description: column header in processed file: BSSE_QGF_11006


title: AG2pos_26, Treated single cell RNA-seq

description: Single cell


title: AG1neg_25, Untreated single cell RNA-seq

description: Single cell


title: 8_0_FROZ_L1.D706.star

value: 0 g/L


title: 7_0_FROZ_L1.D705.star


title: R2_control

description: column header in processed file: BSSE_QGF_11004


title: 5_0_FROZ_L1.D703.star


title: AG1neg_23, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_24, Treated single cell RNA-seq

description: Single cell


title: R1_Ca2+

description: column header in processed file: BSSE_QGF_11003


title: 4_0_FROZ_L1.D702.star


title: R2_glucose starvation

description: column header in processed file: BSSE_QGF_11005


title: AG2pos_22, Treated single cell RNA-seq

description: Single cell


title: AG1neg_21, Untreated single cell RNA-seq

description: Single cell


title: 3_0_FROZ_L1.D701.star


title: AG2pos_20, Treated single cell RNA-seq

description: Single cell


title: R1_glucose starvation

description: column header in processed file: BSSE_QGF_11001


title: AG1neg_19, Untreated single cell RNA-seq

description: Single cell


title: R1_control

description: column header in processed file: BSSE_QGF_11000


title: A12dgd

city: hangzhou, Lin an

first: jinsheng

last: yu

address: 88 huan cheng Rd.

country: China

institute: Zhejiang A&F University

description:
Organism: Oryza sativa Indica HT54
Treatment: 1
Sample type: degradome
Processed data file: miRNA_and_dgd_1.xlsx

data_processing:
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis (Li et al. 2010; Wei et al. 2011).
After removing adaptor sequence and low-quality sequencing reads, a public software package, CleaveLand3.0, was used to analyze the Degradome sequencing data. MRNA data from the Rice Genomics Database (ftp://ftp.jgi-psf.org/pub/compgen/phytozome/.v10.0/Osativa_204_v7.0/) was used as reference data to map the degradome sequencing products.
We carried out position normalization for the raw aligned data. Then, we used the normalized data to calculate tags per billion for globe normalization.
Genome_build: Osativa_204_v7.0 (ftp://ftp.jgi-psf.org/pub/compgen/phytozome/.v10.0/Osativa_204_v7.0/)
Supplementary_files_format_and_content: miRNA_and_dgd_1.xlsx: Excel file includes 8 tables:
Supplementary_files_format_and_content: Table 1. Summary of small RNA sequencing and classification of sequences in the CK (D0), heat treatment 12 hr (T12) and heat treatment 24 hr (T24).
Supplementary_files_format_and_content: miR-Table2-Known miRNAs from rice in the CK (D0), T12 and T24 libraries.
Supplementary_files_format_and_content: miR-Table3-Conserved miRNAs from rice in the CK (D0), T12 and T24 libraries.
Supplementary_files_format_and_content: miR-Table4-Novel miRNAs identified in the CK (D0), T12 and T24 libraries from rice.
Supplementary_files_format_and_content: miR-Table5-List of the conserved miRNAs identified in the CK (D0), T12 and T24 libraries and differential expression between the six libraries.
Supplementary_files_format_and_content: DGD Table 1 - Summary of degradome library data.
Supplementary_files_format_and_content: DGD Table 2 - Targets of known and conserved miRNAs from rice in D0, D12 and D24 libraries.
Supplementary_files_format_and_content: DGD Table 3 - Targets of novel miRNAs in the D0, D12 and D24 libraries.

organism: Oryza sativa Indica Group

source_name: rice seedling, leaf, heat shock, 12h

extract_protocol:
To construct nine small RNA libraries, three independent samples from each of the three different time points were harvested and individually subjected to small RNA extraction using an Illumina TruSeq Small RNA Preparation kit (Illumina, San Diego, USA). Total RNA was purified through electrophoretic separation with a 15% TBE-Urea denaturing polyacrylamide gel, and small RNA areas (15-30 nt bands) were excised and recovered. The purified small RNAs were hereafter ligated with 5' adaptors, and the ligation products (40-60 nt in length) were purified on a Novex 15% TBE-Urea gel to abandon un-ligated adaptors. Thereafter, a 3' adaptor was ligated to the 5' ligation products. Following isolation and ligation, the small RNAs were reverse transcribed to cDNAs. The purified cDNAs from the nine RNA libraries were sequenced with an Illumina Genome Analyzer II (LC Sciences, Hangzhou, China) according to the manufacturer's protocols.
For degradome libraries, polyA-enriched RNA was isolated and ligated to oligonucleotide adaptors containing an MmeI recognition site. After reverse transcription, the ligated sequence was used to generate first-strand cDNA. A short PCR was then used to amplify the cDNA. After digestion, ligation and purification, the final cDNA library was sequenced on an Illumina Genome Analyzer II (LC Sciences, Hangzhou, China) following manufacturer's instruction.

treatment_protocol: For heat stress treatment, seeds were soaked in the water at room temperature for 3 days, and then germinated for 2 days at 37°C. The most uniformly germinated seeds were sown in a 96-well plate with the bottom removed. The plate was floated on water for 1 day at 37°C in the dark to encourage root growth before transferring to a growth chamber with a 13-h light (25°C)/11-h dark (25°C) photoperiod. Five days later, the seedlings were placed to Yoshida culture solution. Three-leaf stage seedlings were then treated by heat shock at 45°C for 0, 12 or 24 h. The treated and untreated materials were harvested into liquid nitrogen and stored in -80°C until total RNA extraction.

tag: line

tag: developmental stage

value: three-leaf seedling

value: leaf

tag: treatment duration


title: AG2pos_18, Treated single cell RNA-seq

description: Single cell

tag: treatment


title: Stem

city: Hefei

first: Meiqi

last: Zhou

address: Meishan Road 103

institute: Anhui University of Chinese Medicine

data_processing:
Trim low quality reads and adapters using Trimmomatic software
Transcriptome de novo assembly was implemented by Trinity
Transcripts were performed to cluster and remove redundancy with TGICL
Genome_build: All-Unigene.fa
Supplementary_files_format_and_content: Table-delimited text files include FPKM value of 99807 unigenes across 3 samples

organism: Artemisia argyi

source_name: Tissue

growth_protocol: Artemisia argyi is a mature plant

extract_protocol:
Total RNA was extracted from tissue by using the miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All the samples were histologically confirmed to be normal

tag: species

value: Artemisia argyi Lev. et Vant.

tag: developemental stage

value: mature plant

value: Stem


title: Root

tag: tissue

value: Root


title: A24dgd

source_name: rice seedling, leaf, heat shock, 24h


title: AG1neg_17, Untreated single cell RNA-seq

description: Single cell

tag: cell type


title: A0dgd

description:
Organism: Oryza sativa Indica HT54
Treatment: 3
Sample type: degradome
Processed data file: miRNA_and_dgd_1.xlsx

source_name: rice seedling, leaf, heat shock, 0h


title: A24_3miRNA

description:
Organism: Oryza sativa Indica HT54
Treatment: 1
Sample type: miRNA
Processed data file: miRNA_and_dgd_1.xlsx


title: Leaf

value: Leaf


title: AG1neg_15, Untreated single cell RNA-seq

description: Single cell


title: 6_0_FROZ_L1.D704.star

value: liver

value: 4 weeks

value: male

value: dichloroacetic acid (DCA)


title: A24_1miRNA

description:
Organism: Oryza sativa Indica HT54
Treatment: 3
Sample type: miRNA
Processed data file: miRNA_and_dgd_1.xlsx


title: AG2pos_14, Treated single cell RNA-seq

description: Single cell


title: AG1neg_13, Untreated single cell RNA-seq

description: Single cell


title: A0_3miRNA


title: AG2pos_12, Treated single cell RNA-seq

description: Single cell


title: AG2pos_10, Treated single cell RNA-seq

description: Single cell


title: A0_1miRNA


title: A12_1miRNA


title: A12_3miRNA


title: AG2pos_8, Treated single cell RNA-seq

description: Single cell


title: AG2pos_6, Treated single cell RNA-seq

description: Single cell


title: AG1neg_9, Untreated single cell RNA-seq

description: Single cell


title: AG1neg_7, Untreated single cell RNA-seq

description: Single cell


title: AG1neg_5, Untreated single cell RNA-seq

description: Single cell


title: AG1neg_11, Untreated single cell RNA-seq

description: Single cell


title: AG2pos_4, Treated single cell RNA-seq

description: Single cell


title: AG2pos_86, Treated single cell RNA-seq

description: Single cell


title: AG1neg_1, Untreated single cell RNA-seq

description: Single cell


title: R3_total_Ca2+

description: column header in processed file: BSSE_QGF_73027

data_processing:
Total RNA-Seq: Illumina bcl2fastq-2.19.1.403 software for base calling. apter trimming using Trimmomatic version 0.30 with parameters parameters “SE –s phred33 ILLUMINACLIP:Illumina_smallRNA_adapters.fa:1:20:5. Alignment using Bowtie version 1.0.0 with parameters “-n 0 –l 28 –e 70 –k1 –m 1 --best --strata --sam --nomaqround”. Read counting with htseq-count and default parameters.
Genome_build: Total RNA-Seq: S. cerevisiae ENSEMBL EF4.72
Supplementary_files_format_and_content: Total RNA-Seq: one processed data file: TotalmRNA_counts_raw, Tab delimited file containing raw counts.

source_name: whole yeast cell_total RNA

growth_protocol: Total RNA-Seq: Cells expressing Dcp2-HBH were grown to mid-log phase.

extract_protocol:
Total RNA-Seq: Total RNA was extracted using phenol-chloroform-isoamyl alcohol method (125:24:1) (Sigma-Aldrich) as described  in Schmitt et al., 1990.
Total RNA-Seq: Library preparation was performed with 1µg total RNA using the TruSeq Stranded mRNA Library Prep Kit High Throughput with D501-D508, D701 and D702 adapters (Illumina). Libraries were quality-checked on the Fragment Analyzer (Advanced Analytical) using the Standard Sensitivity NGS Fragment Analysis Kit (Advanced Analytical).

treatment_protocol: Total RNA-Seq: Cells were subjected to the corresponding stresses for 10 min except for unstress control.

value: Ca+

tag: replicate

value: Replicate 3


title: AG2pos_2, Treated single cell RNA-seq

description: Single cell

value: Treated - 24 hours 4OHT


title: noTF-condition_SUV39H1-siRNA_rep1

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description: noTF-condition_SUV39H1-siRNA_pooledReps.bw

data_processing:
Samples were demultiplexed (bcl2fastq using BaseSpace) to produce FASTQ files.
Sequenced reads were aligned to the hg19 Refseq gene model, in a strand-specific manner, using TopHat v2.0.11 (parameters: --b2-very-sensitive --library-type fr-firststrand).
To generate genome coverage tracks, BED files were first pooled between biological replicates. Reads aligning to genomic regions longer than the sequencing length (75 bp), due to spanning of splice junctions, were discarded. Pooled BED files were then converted to BedGraph files using genomeCoverageBed (bedtools v2.20.1) and normalized to the number of millions of reads sequenced, to correct for lane or sample biases. The resulting subtracted BedGraph was converted to a bigWig file using bedGraphToBigWig (v4).
Genome_build: hg19
Supplementary_files_format_and_content: bigWIg

source_name: BJ foreskin fibroblasts

growth_protocol: Human BJ foreskin fibroblasts were obtained from Stemgent (08-0027) at passage 6 and cultured in Eagle’s Minimum Essential Medium (Sigma M2279) supplemented with 10% fetal bovine serum (FBS, Hyclone SH30071) and 2mM L-glutamine (Gibco) at 37°C and 5% CO2.

extract_protocol:
RNA was purified using the ZR-96 Quick-RNA kit (Zymo Research R1052) and was polyA-selected using Oligo(dT)25 Dynabeads (Thermo Fisher Scientific, #61002).
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7420S)

treatment_protocol: Cells were treated with two rounds of transfection with 10nM Silencer Silect siRNAs (Thermo Fisher Scientific) and 2.5 μl Lipofectamine RNAiMAX (Thermo Fisher #13778150), for 3 days per transfection. RNA was harvested at day 6 after the first transfection. For samples in the "hepatic TF" protocol, cells were first infected with lentiviruses delivering the human hepatic transcription factors FOXA3, HNF1A, and HNF4A (MOI 1.25 per virus) the day before the first siRNA transfection (day -1), or 7 days before RNA harvest.

tag: viral infection

tag: sirna

value: SUV39H1 (10nM Silencer Select s13660)


title: noTF-condition_RBMX-siRNA_rep2

value: RBMX/RBMXL1 (10nM Silencer Select s56035)


title: noTF-condition_SUV39H1-siRNA_rep2


title: R2_total_Ca2+

description: column header in processed file: BSSE_QGF_73026

value: Replicate 2


title: AG1neg_3, Untreated single cell RNA-seq

description: Single cell

value: UnTreated - 24 hours 4OHT - Control

value: Keratinocytes


title: R3_total_Na+

description: column header in processed file: BSSE_QGF_73024

value: Na+


title: noTF-condition_control-siRNA_rep2

description: noTF-condition_control-siRNA_pooledReps.bw

value: Non-targeting control #1 (10nM Silencer Select)


title: R2_total_Na+

description: column header in processed file: BSSE_QGF_73023


title: hepaticTF-condition_SUV39H1-siRNA_rep2

description: hepaticTF-condition_SUV39H1-siRNA_pooledReps.bw

value: FOXA3, HNF1A, HNF4A lentiviruses


title: R2_total_glucose starvation

description: column header in processed file: BSSE_QGF_73020

value: glucose starvation


title: R3_total_glucose starvation

description: column header in processed file: BSSE_QGF_73021


title: R1_total_Na+

description: column header in processed file: BSSE_QGF_73022

value: Replicate 1


title: R1_total_glucose starvation

description: column header in processed file: BSSE_QGF_73019


title: R3_total_control

description: column header in processed file: BSSE_QGF_73018

value: unstressed control


title: R2_total_control

description: column header in processed file: BSSE_QGF_73017


title: hepaticTF-condition_control-siRNA_rep1

description: hepaticTF-condition_control-siRNA_pooledReps.bw


title: hepaticTF-condition_control-siRNA_rep2


title: SonicationResistantHeterochromatin_fraction_rep2

description: Sonication-Resistant Heterochromatin fraction (fractions #10-17) isolated from a sucrose gradient loaded with crosslinked, sonicated BJ fibroblast chromatin

data_processing:
Samples were demultiplexed (bcl2fastq using BaseSpace) to produce FASTQ files.
Sequenced reads were aligned to the hg19 assembly of the human genome using bowtie2 v2.1.0 (parameters: --very-sensitive). Bowtie output files were converted to .bam files using samtools v1.1, and then to .bed files using bedtools v2.20.1 (bamtobed).
For each sample, reads mapping to the same genomic position (duplicate reads) were collapsed to a single entry (unique reads).
75bp sequencing reads were extended to 200bp, to match the average size of DNA prior to library preparation.
To generate input-normalized genome coverage tracks, BED files were converted to BedGraph files using genomeCoverageBed (bedtools v2.20.1) and normalized to the number of millions of reads sequenced, to correct for lane or sample biases. For each sample’s normalized BedGraph, the corresponding input sample was subtracted on a basepair-by-basepair basis. The resulting subtracted BedGraph was converted to a bigWig file using bedGraphToBigWig (v4).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
Crosslinked chromatin was sonicated using a Diagenode Bioruptor and sedimented on a 6-40% sucrose gradient for 3 hours at 41K rpm (see Methods of text for full details). Fraction #2 (near top of the gradient) containing highly sonicated fragments was harvested as the Euchromatin fraction, while Fractions #10-17 containing larger chromatin fragments was pooled as the Euchromatin fraction. Alternatively, chromatin was immunoprecipitated using Dynabead Protein G beads saturated with anti-H3K9me3 antibodies (abcam 8898, lot GR164997-3). H3K9me3-directed IPs were also performed using chromatin from the Euchromatin and Sonication-Resistant Heterochromatin fractions. DNA was purified by reversing crosslinks overnight, treating with RNase A and Proteinase K, and performing phenol-chloroform extraction.
50 ng of purified DNA was used to prepare libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370S). For samples containing larger DNA fragments (gradient input, Sonication-Resistant Heterochromatin fraction, and IP from the Sonication-Resistant Heterochromatin fraction), the purified DNA was sheared to 100-300bp with a Covaris sonicator prior to library preparation.

treatment_protocol: Cells at passage 12 were grown to ~80% confluence and crosslinked with 1% formaldehyde.

tag: antibody

tag: sonication of purified dna prior to library prep

value: yes


title: hepaticTF-condition_RBMX-siRNA_rep1

description: hepaticTF-condition_RBMX-siRNA_pooledReps.bw


title: hepaticTF-condition_RBMX-siRNA_rep2


title: R1_total_control

description: column header in processed file: BSSE_QGF_73016


title: human_BJ_fibroblast_H3K9me3_ChIP_rep2

description: H3K9me3-directed ChIP


title: human_BJ_fibroblast_ChIP_Input_rep2

description: Input chromatin used for H3K9me3 ChIP-seq studies


title: SonicationResistantHeterochromatin_fraction_rep1


title: human_BJ_fibroblast_H3K9me3_ChIP_rep1

description: H3K9me3-directed ChIP


title: R1_total_Ca2+

description: column header in processed file: BSSE_QGF_73025


title: noTF-condition_control-siRNA_rep1


title: human_BJ_fibroblast_ChIP_Input_rep1


title: H3K9me3_IP_from_Euchromatin_fraction_rep1

description: H3K9me3 IP performed using chromatin from the Euchromatin fraction (fraction #2 of a sucrose gradient loaded with crosslinked, sonicated BJ fibroblast chromatin)


title: H3K9me3_IP_from_SonicationResistantHeterochromatin_fraction_rep1

description: H3K9me3 IP performed using chromatin from the Sonication-Resistant Heterochromatin fraction (fractions #10-17 of a sucrose gradient loaded with crosslinked, sonicated BJ fibroblast chromatin)


title: H3K9me3_IP_from_SonicationResistantHeterochromatin_fraction_rep2


title: H3K9me3_IP_from_Euchromatin_fraction_rep2


title: gradientInput_rep1

description: Input chromatin used for sucrose gradient studies


title: gradientInput_rep2


title: hepaticTF-condition_SUV39H1-siRNA_rep1


title: Euchromatin_fraction_rep2

description: Euchromatin fraction (fraction #2) isolated from a sucrose gradient loaded with crosslinked, sonicated BJ fibroblast chromatin


title: Control (BKO) replicate1

first: KUNHUA

last: QIN

email: qink@chop.edu, kunhua.qin@gmail.com

address: 3615 Civic Center Blvd, 315H

institute: Children's Hospital of Philadelphia

description:
mRNA
Processed data file: All_Genes_ReadCount.txt

data_processing:
After sequencing, short sequence reads were first aligned to mouse genome (UCSC mm9) using TopHat aligner, then reads aligned to known transcripts were counted using HTSeq.
Expression abundance of each gene was quantitated both by the total reads aligned to the gene (read count) and by RPKM (read per kilobase of transcript per million reads mapped).
Genome_build: UCSC mm9 (MGSCv37)
Supplementary_files_format_and_content: All_Genes_ReadCount.txt: Tab-delimited text file includes raw reads for each Sample.

source_name: Primary islets

growth_protocol: Islets were isolated through collagenase perfusion and recovered in RPMI 1640 with 10% fetal bovine serum (FBS) for 4 hours.

extract_protocol:
RNA was extracted with Quick-RNA™ MicroPrep kit (ZYMO RESEARCH).
Approximately 100ng Total RNA was used for RNA-Seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide.

treatment_protocol: Purified islets were picked in low-retention Ep tubes, washed with PBS, and homogenized in TRIzol reagent (Invitrogen).

tag: strain/background

value: mix

tag: genotype/variation

value: MIP1-CreERT Sirt6 f/+

tag: gender

value: male

tag: age

value: 8-9 weeks

value: Primary islets


title: L-GFP+

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to mouse genome (mm10) by TopHat (version 2.0.10) and Bowtie2 (version 2.1.0).
The number of fragments in each known gene from GENCODE Release M7 was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.16.0).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are normalized expression values (estimated by DESeq) for all the samples.

source_name: Freshly purified mouse luminal label-retaining cells

extract_protocol:
The FACS purified mouse prostate luminal GFP+ and luminal GFP- epithelial cell populations are subject to total RNA extraction by RNeasy mini kit (Qiagen, Valencia, CA). Illumina TruSeq Stranded Total RNA Preparation Kit (Illumina, cat#: RS-122-2301) was used with 400~1000 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Prostate

value: luminal

value: 18 weeks


title: BKO replicate2

value: MIP1-CreERT Sirt6 f/f


title: BKO replicate1


title: Control (BKO) replicate2

value: MIP1-CreERT Sirt6 +/+


title: EKO replicate1

value: Ngn3-Cre Sirt6 f/f


title: CDH23 negative control, biological rep 1

status: Public on Dec 20 2017

city: Pozzuoli

first: Margherita

last: Mutarelli

address: Via Campi Flegrei 34

department: ISASI

country: Italy

institute: CNR

description: Gene expression data from HEK293 WT cells

data_processing:
Sequence reads were trimmed using Trim Galore! software
Reference-guided alignment was performed with HISAT2 on hg19 genome sequence plus a custom reference containing the three vector inserts of each transgene pasted sequentially side by side
Each sample transcript assembly prediction was performed with Stringtie and merged with Stringtie merge function
The expression levels of each transcript in the assembled consensus was estimated with Stringtie
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include assembled gene id, gene name, assembled transcript id and raw counts for each Sample

source_name: HEK293 cells

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) and 2 mM L-glutamine (GIBCO)

extract_protocol:
Total RNA was extracted using the RT–PCR RNeasy MiniKit according to the manufacturer's instructions (Qiagen). RNA (500 ng) was submitted to DNase I digestion (Qiagen) and 20 μl cDNA was generated using the SuperScript™ III Reverse Transcriptase kit (Thermo Fisher) using oligo dT primers.
A total of 47.5 ng of RNA was used as input for the synthesis of cDNA with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara). Manufacturer suggested protocol was followed, with minor modifications. The second strand synthesis of cDNA was performed by replacing the SMART-Seq v4 Oligo with custom primers, specific for the transgenes of interest [CDH23 oligo – 5’-AAGCAGTGGTATCAACGCAGAGTacttgttgatctccgaagataccc-3’; ALMS1 oligo – 5’-AAGCAGTGGTATCAACGCAGAGTtagtggtggaggaagtagaggag-3’ (bp in capital letters belong to the RNAseq adapter)]. Seventy-five pg of cDNA generated with SMART-Seq v4 Kit were used for library preparation using the NEXTERA XT DNA Library Preparation kit (Illumina), following suggested protocol.

treatment_protocol: Plated cells were first transfected with 1.5 μg/1x106 cells of pDeltaF6 helper plasmid. After 4 h, cells were washed once with serum-free DMEM and incubated with AAV2/2 vectors (m.o.i. 5x104 GC/cell of each vector) in a final volume of 700 µl of serum-free DMEM. Two hours later, 1.3 ml of complete DMEM were added to the cells.

tag: cell line

value: WT


title: CDH23 negative control, biological rep 2


title: ALMS1 negative control, biological rep 3


title: cells infected with CDH23 triple AAV, biological rep 1

description: Gene expression data from cells infected with ALMS1 triple AAV

value: CDH23 triple AAV


title: cells infected with CDH23 triple AAV, biological rep 3


title: ALMS1 negative control, biological rep 1


title: ALMS1 negative control, biological rep 2


title: Control (EKO) replicate2

value: Ngn3-Cre Sirt6 +/+


title: cells infected with ALMS1 triple AAV, biological rep 3

value: Alms1 triple AAV


title: cells infected with ALMS1 triple AAV, biological rep 2


title: cells infected with ALMS1 triple AAV, biological rep 1


title: Control (EKO) replicate1


title: EKO replicate2


title: Euchromatin_fraction_rep1


title: RAD21

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v1.1.1. and normalized to the sample with the smallest number of mapped reads (10.8 million reads for TFIIIC5 and NMYC samples, 11 million reads for RNAPII samples, 51 million reads for CTCF and RAD21 samples).
Wiggle files were generated using MACS v1.4.2 with default parameters but a p-value cutoff of 1e-6 (N-MYC, TF3C5) and keep-dup parameter =1. .bedGraph files were generated using bedtools genomecov.
Genome_build: hg19
Supplementary_files_format_and_content: Fixed step wiggle files with a resolution of 10bp or bedgrpah files (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

growth_protocol: Neuroblastoma cells were grown in RPMI-1640 (Sigma). Medium was supplemented with 10% fetal calf serum (Biochrom) and penicillin/streptomycin (Sigma).

extract_protocol:
Cells were treated with 1% formaldehyde for 10 min at 37 °C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <500 bp using a Branson sonifier. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Qiagen gel extraction kit. DNA fragments were amplified by 18 cycles of PCR and library size was tested with the Biorad Experion system. The amount of library DNA was quantified using a picogreen assay

treatment_protocol: For siRNA transfections, cells were transfected using the RNAiMAX reagent and OptiMem medium (LifeTechnologies) according to the manufacturer's instructions. Cells were harvested 48 h after transfection. Cells were treated with CD532 (1µM) or DMSO for 4 (ChIP-seq) or 4 and 8 (RNA-seq) hours.To activate N-MYC-ER in SH-EP cells, cells were treated with 4-OHT (200nM) for 5 hours. Conditional shRNA-mediated depletion of TFIIIC5 was induced with doxycycline (1 µg/ml) for 48 hours.


title: CTCF

value: CTCF (abcam, ab70303)


title: SHEP_NMYCER_TF3C5depletion_RNAPII_N20_plusOHT_DOX

data_processing:
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v1.1.1. and normalized to the sample with the smallest number of mapped reads.
Wiggle files were generated using MACS v1.4.2 with default parameters but a p-value cutoff of 1e-6 (N-MYC, TF3C5) and keep-dup parameter =1. .bedGraph files were generated using bedtools genomecov.
genome build: hg20
Fixed step wiggle files with a resolution of 10bp.
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.

source_name: SH-EP-NMYCER

tag: treatment 1

tag: treatment 2

value: DOX

value: RNAPII (N20, Santa Cruz, sc-899)


title: SHEP_NMYCER_TF3C5depletion_RNAPII_N20_minusOHT_DOX

value: EtOH


title: input_CTCF_RAD21


title: L-GFP-

source_name: Freshly purified mouse luminal non-label-retaining cells


title: CDH23 negative control, biological rep 3


title: SHEP_NMYCER_TF3C5depletion_input


title: SHEP_NMYCER_TF3C5depletion_RNAPII_N20_minusOHT_EtOH


title: SHEP_NMYCER_Sphase_arrested_RNAPII_N20_plusOHT_CD532


title: SHEP_NMYCER_Sphase_arrested_RNAPII_N20_minusOHT_CD532


title: SHEP_NMYCER_Sphase_arrested_RNAPII_N20_plusOHT_DMSO

value: DMSO


title: SHEP_NMYCER_Sphase_arrested_input


title: SHEP_NMYCER_Sphase_arrested_RNAPII_N20_minusOHT_DMSO


title: SHEP_NMYCER_plusOHT_rep3

data_processing:
Reads per gene were counted using the countOverlaps function from the R package {GenomicRanges}.
Weakly expressed genes were removed(mean count over all samples <1.5) and differentially expressed genes were called using EdgeR.
genome build: hg19
txt files containing Ensembl gene ID, gene symbol, gene description, log2FC, p-value and q-value (FDR) for all comparisons. A matrix file containing raw read counts for all samples.
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.

extract_protocol:
Total RNA was isolated using RNeasy mini columns (Qiagen) including on-column DNase I digestion.
mRNA was extracted using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB). Library preparation was performed with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the instruction manual. Size-selection of libraries was performed using Agencourt AMPure XP Beads (Beckman Coulter) followed by amplification with 12 PCR cycles. Afterwards libraries were quantified and the size was determinded using Experion Automated Electrophoresis System (Bio-Rad).


title: SHEP_NMYCER_plusOHT_rep2


title: SHEP_NMYCER_plusOHT_rep1


title: SHEP_NMYCER_minusOHT_rep1

extract_protocol:
Total RNA was isolated using RNeasy mini columns (Qiagen) including on-column DNase I digestion.
mRNA was extracted using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB). Library preparation was performed with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the instruction manual. Size-selection of libraries was performed using Agencourt AMPure XP Beads (Beckman Coulter) followed by amplification with 12 PCR cycles. Afterwards libraries were quantified and the size was determinded using Experion Automated Electrophoresis System (Bio-Rad).
For RNA-seq, reads were mapped to hg19 with Tophat2 and Bowtie1 with default settings.


title: SHEP_NMYCER_minusOHT_rep3


title: SHEP_NMYCER_minusOHT_rep2


title: R1_Na+

description: column header in processed file: BSSE_QGF_11002

tag: tagged p-body component

tag: stress

value: 0.5 M NaCl

tag: clip beads

value: streptavidin agarose beads (Thermo Fisher Scientific)


title: CD532_4h_rep2

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For RNA-seq, reads were mapped to hg19 with Tophat2 and Bowtie1 with default settings.
Reads per gene were counted using the countOverlaps function from the R package {GenomicRanges}.
Weakly expressed genes were removed(mean count over all samples <1.5) and differentially expressed genes were called using EdgeR.
Genome_build: hg19
Supplementary_files_format_and_content: txt files containing Ensembl gene ID, gene symbol, gene description, log2FC, p-value and q-value (FDR) for all comparisons. A matrix file containing raw read counts for all samples.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v1.1.1. and normalized to the sample with the smallest number of mapped reads.
Wiggle files were generated using MACS v1.4.2 with default parameters but a p-value cutoff of 1e-6.
Genome_build: hg19
Supplementary_files_format_and_content: Fixed step wiggle files with a resolution of 10bp.

treatment_protocol: For siRNA transfections, cells were transfected using the RNAiMAX reagent and OptiMem medium (LifeTechnologies) according to the manufacturer's instructions. Cells were harvested 48 h after transfection. Cells were treated with CD532 (1µM) or DMSO for 4 (ChIP-seq) or 4 and 8 (RNA-seq) hours.

tag: treatment


title: siRAD21_rep2


title: DMSO_rep1


title: DMSO_rep2


title: CD532_8h_rep2


title: siAURKA_rep3

value: siAURKA


title: siRAD21_rep1


title: siAURKA_rep1


title: CD532_8h_rep1


title: SHEP_NMYCER_TF3C5depletion_RNAPII_N20_plusOHT_EtOH


title: siAURKA_rep2


title: CD532_4h_rep1


title: siTF3C5_rep1


title: siTF3C5_rep3


title: siTF3C5_rep2


title: siCTR_rep6

value: siCTR


title: siCTR_rep7


title: siCTR_rep8


title: siCTR_rep4


title: siCTR_rep5


title: siCTR_rep3


title: siCTR_rep2


title: siAURKA_rep4


title: cells infected with CDH23 triple AAV, biological rep 2


title: Id3hi Treg rep3

city: Freiburg

first: Kristina

last: Schachtrup

address: Breisacher Str. 117

department: Center for Chronic Immunodeficiency

institute: University Medical Center Freiburg

data_processing:
Reads mapped against mouse (mm10) genome using the STAR aligner application on Illumina BaseSpace
Differential gene analaysis performed using DeSeq2 application on Illumina BaseSpace.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts of sequencing reads

source_name: splenic Treg cells (CD4+CD25+CD45RBlo)

extract_protocol:
Treg cells were FACS sorted directly into RLT lysis buffer and RNA extracted using RNAeasy MicroKit (Qiagen) according to manufacturer’s recommendations. cDNA was generated using Ovation RNA-seq system V2 (NuGEN).
Libraries were constructed with Ovation Ultralow System V2 1-16 (NuGEN) according to the manufacturer’s instructions.
The libraries were subjected to 50 cycles of NextSeq 500 sequencing from 2-3 samples per cell type.

tag: strain

tag: cell type

value: splenic Treg cells (CD4+CD25+CD45RBlo)


title: Id3lo Treg rep4


title: Id3hi Treg rep4


title: Id3lo Treg rep3


title: Id3lo Treg rep2


title: Id3lo Treg rep1


title: MAA4 RNAseq

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

description: rRNA depleted total RNA

data_processing:
RNA-seq reads were analyzed for both quality and adapter contamination using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
All reads were trimmed using Trimmomatic using Illuminaclip single end adapter trimming, a removal of the first three bp from the 5’ as recommended for SMARTer libraries, and a 4 bp sliding window trim for quality scores less than 15.  All remaining reads greater than 15 bp were then reanalyzed using FASTQC to verify quality.
RNA-seq reads were aligned to mouse genome mm10 using the splicing-aware aligner Tophat2 (v2.0.14/bowtie2.2.5, stranded, Single End) and reads aligning to each gene will were counted using FeatureCounts with exclusion of multimapping reads
Genome_build: mm10
Supplementary_files_format_and_content: FeatureCounts raw counts per gene

source_name: acutely isolated microglia, P35 brain

extract_protocol:
P35 female mice were deeply anaesthetized with CO2 and then quickly perfused intracardially with ice-cold PBS. Whole brains were removed and stored on ice in HBSS w/out Ca/Mg until processed. Each brain was gently homogenized to a single cell solution using a dounce, then added to 1.8ml of isotonic Percoll to form a 30% isotonic Percoll solution.  Isotonic Percoll gradients were then constructed with layers of 70% with 1x phenol red, 37% and the top layer of brain/30%.  The resulting gradients were spun in a swinging bucket centrifuge for 30min at 500xg at room temperature. The top layer of myelin and non-microglial cells were discarded and the microglia at the interface between the 37% and 70% layers were collected. The resulting microglia were then washed in HBSS and counted.  An additional animal was run in parallel and harvested microglia were used to assess purity by flow cytometry for CD45.2 and CD11b. The collected cells were immediately flash frozen for RNA/DNA extraction.
Duet RNA/DNA kit (Zymo, D7001) with on-column DNase digestion (Qiagen, 79254) for RNA extraction.  RNA and DNA were quantified using Qubit High Sensitivity assays.  RNA quality was assessed by Bioanalyzer and only samples with RIN scores greater than 7 were used for library preparation.  60-100 ng of input RNA per sample were used for RiboGone rRNA removal (Clonetech, 634847).  2 ng of rRNA depleted RNA per sample was then used for library construction using the SMARTer Stranded RNA-Seq kit (Clontech, 634836) and 14 cycles of PCR amplification.  Library quality was assessed using a bioanalyzer and quantified by Qubit high sensitivity assay.
All samples were barcoded, pooled, and run on a single sequencing lane of a HiSeq3000 to generate 50 bp single end reads.

treatment_protocol: Briefly, on postnatal day (P) 42 and 49 sexually naive female C57Bl/6J mice were sensitized with a single intraperitoneal injection of 10μg ovalbumin (OVA, Sigma, St. Louis, MO USA) in 1mg (Al)OH3 (InvivoGen, San Diego, CA USA) dissolved in 200μl phosphate buffered saline (PBS). One week following the second sensitization treatment, female mice were mated overnight and checked daily for the presence of a seminal plug, noted as gestational day 0.5 (G0.5). Pregnant mice were randomly assigned to either the allergic asthma or control group and exposed to either an aerosolized solution of 1% (wt/vl) OVA in PBS (maternal allergic asthma (MAA) group) or vehicle control for three 45-minute induction on gestational days 9.5, 12.5, and 17.5, to correspond with early, middle, and late gestation.  Following the final induction, mice were returned to their home cages, single housed, and left undisturbed until the birth of their litters. Pups remained with their mother until weaning on P21, at which time the offspring were group housed with same-sex littermates.

value: postnatal day 35

tag: Sex

value: female

tag: index

value: CAGATC

tag: group

value: Mother given maternal allergic asthma inflammation on gestation day 9,12, and 17


title: Id3hi Treg rep1


title: MAA1 RNAseq

description: Mother given maternal allergic asthma inflammation on gestation day 9,12, and 17

value: ATCACG


title: MAA2 RNAseq

value: CGATGT


title: input_D12_rep4_ChIPSeq

city: Ithaca

first: Siu

middle: Sylvia

last: Lee

address: 520 Campus road

institute: Cornell University

description: glp-1 stands for the mutant abnormal Germ Line Proliferation

data_processing:
Basecalls performed using CASAVA version 1.8
For RNAseq: tRNA and rRNA reads were first filtered out using Bowtie2 (2.2.6)  using the parameters --un-gz --al-gz -x–U –S. Libraries were stranded. RNA-seq reads  were further aligned to WBcel235 transcript annotation by TopHat2 (v2.1.0) (--min-segment-intron 20 --library-type fr-secondstrand --no-novel-juncs --transcriptome-index=transcriptome_data/known) with no novel junctions allowed
For ChIPseq: Sequencing reads were filtered by FASTX_toolkit (-q 20 –p 80) and mapped to C. elegans reference genome ce10 by bowtie2 (2.2.6) with the default setting (bowtie2 -x ce10 –U –S). Mapped reads were extracted (samtools view -hS -F 4) and PCR duplicates were removed with samtools (samtools rmdup -s). aligned reads were expressed as normalized bigwig using the deepTools utility bamCompare using the parameters --binSize 25 --fragmentLength 200 --missingDataAsZero no --ratio subtract --scaleFactorsMethod readCount --normalizeUsingRPKM
Genome build: ce10, WBcel235
Processed data files format and content: for ChIP-seq,bigwig files were generated to present H3K4me3 enrichment normalized to H3 by subtraction (Deeptools, bamCompare function). For ribo-RNAseq, tab-delimited text files include FPKM values from Cuffdiff (v2.1.1) analysis are used to present expression level.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans strain glp-1(e2141)  stocks were kept at 16°C and grown under standard growth condition (Brenner 1974).  For ChIP-seq and ribo-RNAseq experiments, embryos prepared from 16°C glp-1(e2141)  stocks by bleaching were hatched and cultured at 25°C with about 3,000 embryos per 15 cm Nematode Growth Media (NGM) plate seeded with concentrated E. coli OP50 (1.5 mL 30 x overnight culture) with carbenicillin (50 μg/mL) and tetracycline (15 μg/mL).  For day 12 samples, worms were re-fed once on day 4.

extract_protocol:
For ChIP-seq,chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012).  Chromatin extract was incubated with H3 antibody, H3K4me3 antibodies overnight at 4°C.  Antibodies used were prescreened for specificity using dot blots.  The optimal amounts of antibodies used were determined by titration in preliminary experiment with ChIP-qPCR.  5-15 ng precipitated DNA from each sample was used for illumina sequencing library preparation.  DNA from ChIP was first end-repaired to generate blunt end, followed by adding single adenine base for adaptor ligation. Ligation product with adaptor was size selected and amplified by PCR with primers targeting adaptor.
Worms at L3,adult day 2, and adult day 12 stages were washed with ice cold M9 three times.  Worm pellets were stored at -80°C before chromatin immunoprecipitation and RNA extraction. For ChIP-seq, chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012).  Worm pellet was grinded with mortar/pestle and cross-linked with 1% formaldehyde in PBS at room temperature for 10 min.  Worm fragments were collected by spinning at 3,000 g for 5 min and resuspended in FA buffer followed by sonication with Bioruptor. For ribo-RNAseq, total RNA was extracted from worms harvested at the same stages at adult day 2 and day 12 as ChIP-seq sample preparation.

value: D12 old adult

tag: tissue

value: whole animal


title: PBS1 RNAseq

description: Mother given PBS on gestation day 9,12, and 17

value: ACAGTG


title: PBS2 RNAseq

value: GCCAAT

value: Mother given PBS on gestation day 9,12, and 17


title: input_D2_rep4_ChIPSeq

value: D2 young adult


title: input_D2_rep3_ChIPSeq


title: input_D2_rep5_ChIPSeq


title: PBS4 RNAseq

value: ACTTGA


title: NHLF_siTBX4

city: Tokyo

first: Akira

last: Saito

address: 7-31-, Hongo, Bunkyo

country: Japan

institute: Tokyo University

data_processing:
CLC Genomics workbench software (Qiagen) was used to generate RPKM data.
Adapter sequences were removed, and read mapping was carried out using the default settings of RNA-Seq analysis package (mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8, and maximum number of hits for a read set to: 30).
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel

source_name: NHLF

growth_protocol: Normal human lung fibroblasts (NHLFs) were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from NHLFs 24 h after siRNA transfection using the RNeasy Mini Kit (Qiagen).
The mRNA from eukaryotic organisms was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: Small interfering RNAs (siRNAs) for human TBX4 was purchased from Life technologies. NHLFs were transfected with 20 nM siRNA using Lipofectamine RNAiMAX.

tag: sirna

value: transfected with TBX4 siRNAs


title: input_D12_rep3_ChIPSeq


title: H3_D12_rep4_ChIPSeq

description:
glp-1 stands for the mutant abnormal Germ Line Proliferation
processed data file:
subtract_D12K4rep4ChIP_vs_H3_rmdup.bw.gz

tag: chip-antibody

tag: antibody source

value: H3 (ab1791, Abcam)


title: PBS3 RNAseq

tag: age

value: TGACCA


title: input_D12_rep5_ChIPSeq


title: H3_D12_rep5_ChIPSeq

description:
glp-1 stands for the mutant abnormal Germ Line Proliferation
processed data file:
subtract_D12K4rep5ChIP_vs_H3_rmdup.bw.gz


title: H3_D12_rep3_ChIPSeq

description:
glp-1 stands for the mutant abnormal Germ Line Proliferation
processed data file:
subtract_D12K4rep3ChIP_vs_H3_rmdup.bw.gz


title: NHLF_siNC

value: transfected with control siRNAs


title: siCTR_rep1

value: siCTR

tag: cell line


title: H3_D2_rep3_ChIPSeq

description:
glp-1 stands for the mutant abnormal Germ Line Proliferation
processed data file:
subtract_D2K4rep3ChIP_vs_H3_rmdup.bw.gz


title: H3K4me3_D12_rep5_ChIPSeq

value: H3K4me3 (17-614,millipore)


title: H3K4me3_D12_rep4_ChIPSeq

value: H3K4me3 (ab9050, Abcam)


title: H3K4me3_D12_rep3_ChIPSeq


title: opaque cells a only biological rep 2

city: Providence

first: Christine

middle: Maria

last: Scaduto

state: RI

address: 171 Meeting Street

department: Molecular Microbiology and Immunology

institute: Brown University

description: a cells only

data_processing:
base calling by Illumina HiSeq software
sequenced reads were mapped to C. albicans genome (Assembly 21) using TopHat2
fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks
Genome_build: C albicans SC5314 Assembly 21
Supplementary_files_format_and_content: tab delimited text files of FPKM values for each sample

organism: Candida albicans

source_name: C. albicans opaque cells grown on Spider medium

growth_protocol: Spider agar for 8 hours

extract_protocol:
Cells were scraped off plates after 8 hours on mating media and flash frozen in liquid nitrogen. RNA was extracted using the RiboPure RNA purificaiton kit for yeast (Thermo Scientific).
Libraries were constructed using the Illumina TrueSeq Stranded mRNA Library Prep Kit (cat # RS-122-2103).

tag: cell state

value: opaque

tag: genotype

value: WT


title: white cells a only biologial rep 2

description: a cells only

source_name: C. albicans white cells gown on Spider medium

value: white


title: H3K4me3_D2_rep3_ChIPSeq


title: H3K4me3_D2_rep5_ChIPSeq

description:
glp-1 stands for the mutant abnormal Germ Line Proliferation
processed data file:
subtract_D2K4rep5ChIP_vs_H3_rmdup.bw.gz

value: H3K4me3 (17-614),millipore)


title: H3K4me3_D2_rep4_ChIPSeq

description:
glp-1 stands for the mutant abnormal Germ Line Proliferation
processed data file:
subtract_D2K4rep4ChIP_vs_H3_rmdup.bw.gz

value: whole animal


title: white cell crosses biological rep 2

description: mix of a cells and alpha cells

source_name: C. albicans white a and alpha cells grown on Spider agar


title: opaque cells a only biological rep 1

description: a cells only


title: triple OE crosses biological rep 2

description: mix of a cells and alpha cells

source_name: C. albicans engineered white a and alpha cells grown on Spider agar

value: wor1_delta/wor1_delta, ACT1p-STE4, ADH1-CEK2, ACT1-CST5


title: white cells a only biologial rep 1

description: a cells only


title: opaque cell crosses biological rep 1

description: mix of a cells and alpha cells

source_name: C. albicans opaque a and alpha cells grown on Spider medium


title: glp1_D12_rep2_ribo-RNASeq

description:
glp-1 stands for the mutant abnormal Germ Line Proliferation
processed data file:
ribo_RNAseq_glp-1_D2_D12_genes.fpkm_tracking.gz

extract_protocol:
For ribo-RNAseq, the libraries were prepared by Ovation Human FFPE RNA-Seq Library Systems from NuGEN.
Worms at L3,adult day 2, and adult day 12 stages were washed with ice cold M9 three times.  Worm pellets were stored at -80°C before chromatin immunoprecipitation and RNA extraction. For ChIP-seq, chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012).  Worm pellet was grinded with mortar/pestle and cross-linked with 1% formaldehyde in PBS at room temperature for 10 min.  Worm fragments were collected by spinning at 3,000 g for 5 min and resuspended in FA buffer followed by sonication with Bioruptor. For ribo-RNAseq, total RNA was extracted from worms harvested at the same stages at adult day 2 and day 12 as ChIP-seq sample preparation.

value: D12 old adult


title: white cell crosses biological rep 1

description: mix of a cells and alpha cells


title: glp1_D12_rep1_ribo-RNASeq


title: H3_D2_rep4_ChIPSeq


title: wildtype mouse fetal liver small RNA replicate 1

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

data_processing:
3' adapter sequences were  trimmmed using the cutadapt utility
reads < 17nt in size were filtered
identical read sequences were collapsed using the fastq_collapser utility
Supplementary_files_format_and_content: read count table files (columns are read sequence and number of reads)

source_name: mouse fetal liver

extract_protocol:
wildtype and Ago2 catalytic dead mouse fetal livers were dissected and flash frozen in liquid nitrogen. Total RNA was extracted using Trizol as per manufacturer's instructions.
For Illumina HiSeq Library: Libraries were created with the Illumina truseq small RNA cloning kit using a modified protocol (PMID: 25490151). All enzymatic reactions and oligos were used as indicated by manufacturer.

value: fetal liver


title: Ago2 CD mouse fetal liver small RNA replicate 2


title: glp1_D2_rep2_ribo-RNASeq

value: D2 young adult


title: PBS4 WGBS

data_processing:
Filter using Illumina flag
Separate and trim reads based on adapter contamination
Alignto mouse genome (mm10) using the Bisulfite Seeker2 program (v2.0.8 with bowtie1.1.1)
Combine aligned reads, both trimmed and no adapter contamination
Convert sam files to percent methylation bed files
Combine all chromosome percent methylation bed files into a single file
Convert bed file to bigwig
Genome_build: mm10
Supplementary_files_format_and_content: percent methylation in bigwig

extract_protocol:
P35 female mice were deeply anaesthetized with CO2 and then quickly perfused intracardially with ice-cold PBS. Whole brains were removed and stored on ice in HBSS w/out Ca/Mg until processed. Each brain was gently homogenized to a single cell solution using a dounce, then added to 1.8ml of isotonic Percoll to form a 30% isotonic Percoll solution.  Isotonic Percoll gradients were then constructed with layers of 70% with 1x phenol red, 37% and the top layer of brain/30%.  The resulting gradients were spun in a swinging bucket centrifuge for 30min at 500xg at room temperature. The top layer of myelin and non-microglial cells were discarded and the microglia at the interface between the 37% and 70% layers were collected. The resulting microglia were then washed in HBSS and counted.  An additional animal was run in parallel and harvested microglia were used to assess purity by flow cytometry for CD45.2 and CD11b. The collected cells were immediately flash frozen for RNA/DNA extraction.
DNA was isolated from the microglia samples using ZR-Duet RNA/DNA kit (Zymo, D7001). WGBS libraries were constructed using the Illumina EpiGnome/TruSeq DNA Methylation kit (Illumina, EGMK81312) with indexing barcodes (Illumina, EGIDX81312). 100 ng of DNA from each sample was bisulfite converted using the EZ DNA Methylation-Lightning kit (Zymo, D5030.  Each library was given a unique barcode identifier and 14 cycles of PCR amplification. Libraries were quantified by Quibt and quality was assessed by Bioanalyzer.
Sequencing of barcoded and pooled libraries was performed across two lanes of two runs on the Illumina HiSeq4000 to obtain 100 bp single end reads.

value: postnatal day 35

value: female

value: GGCTAC

value: Mother given PBS on gestation day 9,12, and 17


title: PBS2 WGBS

value: ACAGTG


title: PBS3 WGBS

value: ACTTGA


title: PBS1 WGBS

value: GATCAG


title: MAA4 WGBS

value: TAGCTT

value: Mother given maternal allergic asthma inflammation on gestation day 9,12, and 17


title: MAA3 WGBS

value: ATCACG


title: Ago2 CD mouse fetal liver small RNA replicate 1


title: MAA1 WGBS

value: CGATGT


title: U87MG shFUBP1 3

city: Cambridge

first: Silvia

last: Buonamici

state: MA

address: 300 Technology Square #5

institute: H3 Biomedicine

description:
GS044838
Junction PSI

data_processing:
Raw data were aligned to hg19 using the STAR alignment package
Junction counts and reads across exon-intron boundaries are converted to percent spliced-in (PSI)
Genome_build: hg19
Supplementary_files_format_and_content: PSI values for each junction within each sample

source_name: GBM

extract_protocol:
Total RNA was harvested and Poly A selected
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: biomaterial provider

value: ATCC

tag: genotype/variation

value: FUBP1 knockdown via shRNA


title: triple OE crosses biological rep 1

description: mix of a cells and alpha cells

value: white

value: wor1_delta/wor1_delta, ACT1p-STE4, ADH1-CEK2, ACT1-CST5


title: U87MG shFUBP1 2

description:
GS044837
Junction PSI


title: MAA2 WGBS

value: TGACCA


title: STAT4WT_HPOS_D2_002

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

description: STAT4KOChimera_MCMV_Stat4HposHneg_rawCounts_knownGene.txt

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.16-2.19)
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Genome_build: mm10
Supplementary_files_format_and_content: Text files are raw counts (1 count per pair of reads) calculated using the summarizeOverlaps function from the GenomicAlignments R package (v10.10.1)

source_name: splenic NK cells

extract_protocol:
Cells were sorted directly into Trizol and total RNA underwent amplification using SMART-seq V4 (Clontech) Ultra Low Input RNA kit.
Subsequently, 10 ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on Hiseq 2500 1T, in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 47 million paired reads were generated per sample and the percent of mRNA bases was over to 72% on average.

tag: replicate

value: HPOS

tag: condition

value: splenic NK cells


title: U87MG shCTRL 2

description:
GS044834
Junction PSI

value: Non-specific shRNA


title: U87MG shCTRL 3

description:
GS044835
Junction PSI


title: glp1_D2_rep1_ribo-RNASeq

tag: strain

value: D2 young adult

value: whole animal


title: STAT4KO_HPOS_D2_002

tag: cell type


title: U87MG shCTRL 1

description:
GS044833
Junction PSI


title: STAT4WT_HNEG_D2_003

value: HNEG


title: STAT4WT_HNEG_D2_002


title: STAT4KO_HNEG_D2_003


title: STAT4WT_HNEG_D2_001


title: STAT4KO_HNEG_D2_002


title: STAT4WT_HPOS_D2_001


title: STAT4KO_HPOS_D2_003


title: STAT4WT_HPOS_D0_001


title: STAT4WT_HPOS_D0_002


title: STAT4WT_HNEG_D0_001


title: STAT4KO_HPOS_D0_002


title: STAT4KO_HPOS_D2_001


title: STAT4KO_HNEG_D0_002


title: WT_M2

description: RUNX1KOChimera_MCMV_F1M1M2_rawCounts_knownGene.txt


title: RUNX1KO_M2


title: STAT4KO_HPOS_D0_001


title: STAT4KO_HNEG_D0_001


title: WT_M1


title: RUNX1KO_F1


title: unstim_02

description: ExVivoCytokineStim_unstimIL1218IL15only_rawCounts_knownGene.txt

value: WT

value: HPOSNEG

value: unstim


title: STAT4KO_HNEG_D2_001


title: unstim_01


title: IL15_02


title: IL15_01


title: NK_d2_1

description:
MCMV_RNA_d0d2Only_rawCounts_knownGene.txt
MCMV_RNA_NKCD8m45_rawCounts_knownGene.txt


title: NK_d0_2


title: NK_d2_2


title: RUNX1KO_M1


title: IL12IL18_01


title: aH3K4me3_STAT4WT_UNSTIM_1_CHIP

data_processing:
BCL files were converted to fastq using bcl2fastq (v1.8.3 and v1.8.4)
ChIP-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated by converting BAM files to size-normalized BEDGRAPH files using bedtools (v2.26.0) and converted to bigWig using UCSC's bedGraphToBigWig (v4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files normalized by size factors calculated by DESeq2 among all ChIP (non-input) samples in peak regions or flank regions (see manuscript)

extract_protocol:
Protein was cross-linked to DNA with 0.75% formaldehyde. Clarified supernatant from sonicated nuclei were applied to antibody-bound beads. After de-crosslinking and elution, DNA was isolated using Qiagen Gel Extraction Kit. Input samples were clarified supernatant that were not applied to antibody-bound beads.
Immunoprecipitated DNA was quantified by Picogreen and size was evaluated on a HighSense BioAnalyzer chip. When possible, fragments between 100 and 600 bp were size selected and Illumina Hiseq libraries were prepared using the Kapa DNA library preparation chemistry (Kapa Biosystems) using 12-15 cycles of PCR. Adaptors were diluted 1/10 or  1/50 depending on the starting amount of material available. Barcoded libraries were run on Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 57 million paired reads were generated per sample.

tag: chip antibody


title: aH3K4me3_STAT4WT_STIM_1_CHIP


title: aH3K4me3_STAT4WT_UNSTIM_1_INPUT


title: aH3K4me3_STAT4KO_STIM_1_INPUT


title: NK_d0_1


title: aH3K4me3_STAT4KO_UNSTIM_1_INPUT


title: aSTAT4_STAT4WT_STIM_3_INPUT


title: IL12IL18_02


title: aH3K4me3_STAT4WT_STIM_1_INPUT


title: aH3K4me3_STAT4KO_UNSTIM_1_CHIP


title: aH3K4me3_STAT4KO_STIM_1_CHIP