title: 2-1-0

city: Changsha

first: Qinghua

last: Hu

state: Hunan

address: Xiangya Road

department: Cardiovascular disease

institute: Central south university

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: exosome

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Methods of exosome harvest using ExoQuick Precipitation kit (SBI company, SF，CA, USA) were described previously. Briefly, 1.8 ml plasma was centrifuged at 3000×g for 15 min and supernatant was collected. Then, the supernatant was filtered with 0.22μm filter. After precipitation with the ExoQuick Precipitation kit according to the manufacturer’s instructions and centrifugation at 1500×g for 5 min, exosomes were collected, re-suspended and stored at -80 °C.

value: exosomes derived from serum

value: 53 years


title: root_96hours_control_rep1

status: Public on Apr 19 2019

type: SRA

city: Ann Arbor

first: mehmet

last: tardu

state: MI

address: 930 N University Ave

department: Chemistry

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
Illumina data processing pipeline (v1.5) was used for base calling.
FastQC (v0.11.5) was used to evaluate the initial quality of the raw reads.
The following steps were performed to obtain high quality clean reads using Trimmomatic (v0.35) tool: 1) eliminate low quality reads (phred score <20) and 2) short reads with length <20 nucleotide
All downstream analyses were based on clean, high quality data. De novo assembly of the high quality reads was performed using Trinity, which is composed of three independent software modules: Inchworm, Chrysalis and Butterfly. By Inchworm, RNA-seq data was assembled into unique sequences through establishing a k-mer graph (K = 25). By Chrysalis, the contigs generated in the previous step were clustered, and a de Bruijn graph was constructed for each cluster. Subsequently, by Butterfly, these Bruijn graphs were processed in parallel and the paths were traced according to reads and pairs of reads within graphs to obtain full-length transcripts for alternative splicing isoforms and distinguish transcripts of paralogous genes. Finally, the distributed situation of length of result sequences was counted and analyzed using RSEM method. A Pearson’s correlation analysis was performed to obtain the transcript-level R2 between biological replicates.
For count-based differential expression testing between root and leaf tissues at different time-points, edgeR was used with the following arguments:  min_rowSum_counts of 10, false discovery rate (FDR) < 0.01 and the value of | log2 fold change| ≥ 1
Genome_build: De novo assembly
Supplementary_files_format_and_content: matrix text file (transcript count values of rsem output across samples). The stem samples were used only for de novo transcriptome assembly construction and are not included in the matrix file.

molecule: total RNA

organism: Lens culinaris

source_name: root, 96hours, control

growth_protocol: Seeds of lentil (Lens culinaris Medik. cv. Sultan) were kindly provided by the Southeastern Anatolia Agricultural Research Institute. The seeds were selected for size homogeneity, surface-sterilized for 2–3 min in 1% sodium hypochlorite, rinsed and soaked in distilled water.

extract_protocol:
Total RNA was isolated from 1 gr of root, stem and leaves of Lens culinaris using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. BioAnalyzer (Agilent, USA) was used to measure the quality and the quantity of the isolated total RNAs. After that, total RNA samples were treated with RNase-free DNase I (Thermo Scientific, USA) at a concentration of 1 U/µg to eliminate the genomic DNA. Then, RNA-seq library preparation was performed using TruSeq Stranded RNA LT Kit (Illumina, USA) according to the manufacturer’s instructions.
mRNAs were purified from the 1 µg of total RNA using oligo (dT) magnetic beads and fragmented using fragmentation buffer. Afterthat, the cleaved short RNA fragments were used for first-strand cDNA synthesis using first strand synthesis mix, and the second strand was synthesized using second strand marking master mix. The double strand cDNAs were purified with AMPure XP beads (Beckman Coulter, USA) and eluted with resuspension buffer followed by 3’end adenine nucleotide addition. Finally, sequencing adaptors were ligated to the fragments and cDNA fragments were enriched by PCR amplification. Enriched cDNA libraries were used for cluster generation and sequencing. 100x2 paired-end sequencing of cDNA libraries for control and drought stress exposed samples (1st day and 4th day samples of root and leaf, and 1st day sample of stem) with two biological replicates were performed using the Illumina HiSeq4000 sequencing platform (Illumina, USA).

treatment_protocol: Seeds were surface-sterilized for 5 min in 1% sodium hypochlorite and rinsed with dH2O and then germinated on perlit medium with irrigated everyday by 50 ml Hoagland's nutrient solution (5 mM KNO3, 5 mMCa(NO3)2, 1 mM MgSO4, 5 mM KH2PO4, 0.1 mMFeEDTA, 46 mM H3BO3, 4.5 mM MnCl2, 3.8 mM ZnSO4, 0.3 mM CuSO4, 0.1 mM NH4MoO7). Seven days old seedlings were transferred to hydroponic medium. Control samples were kept in the Hoagland's nutrient solution for the entire hydroponic assay, the drought stress exposed samples were kept in the Hoagland's nutrient solution including 15% PEG 6000, for 5 days. All the experimental pods were aerated through the experiment by air pump and kept in a controlled climate chamber at a temperature of 25/18°C day/night; photoperiod was 16/8 h light/dark, with 10% humidity.

tag: strain

value: Medik. cv. Sultan

tag: tissue

value: root

tag: genotype

value: wild type


title: left tumor (LT) treated with isotype control (A) at 1 wk, biological rep 2

type: RNA

city: New York

first: Nathan

last: Suek

state: NY

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Following fragmentation and labeling, 3.5ug of fragmented and labeled ss-cDNA was hybridized for 16hr at 45C on Clariom S Mouse HT array plates on the GeneTitan MultiChannel Instrument.

scan_protocol: After hybridization was completed the washing, staining and scanning of the arrays was completed on the GeneTitan MultiChannel Instrument.

data_processing: Data was analyzed using the rma() function in R package oligo

label: biotin

organism: Mus musculus

source_name: left tumor treated with isotype at 1 wk

label_protocol: Biotinylated sense-strand DNA targets are generated from 50ng of total RNA following standard protocol using the WT Plus Reagent kit (Applied Biosystems GeneChip WT Plus Reagent Kit Target Preparation Manual).

extract_protocol: not provided

treatment_protocol:
tumor implant protocol: Mice were implanted intradermally with 5x10^5 B16 tumor cells on Day 0.
Mice were injected intratumorally with MPL and CD40 and injected intraperitoneally with PD1 between Day 7-9. Other mice were injected intraperitoneally with PD1 alone. Treatment was given 2x/week and then sacrificed 1 week after start of trx.
organ harvest protocol: Mice were sacrificed and the distant tumors were dissected and mechanically dissociated into single cell suspensions.

tag: strain background

tag: age

value: 8-10 weeks at time of organ harvest

value: tumor


title: 1ALM2

city: Hong Kong

first: Kathy

last: Chan

address: 386, South Block, Science Center, The Chinese University of Hong Kong, Sha Tin

department: School of Life Sciences

country: China

institute: The Chinese University of Hong Kong

data_processing:
Illumina RTA 1.18.54 was used for base-calling
Fastp was used to filter out low quality and unclean reads and Hisat2 was used to align the  high quality and clear reads against the reference genome (Coprinopsis cinerea AmutBmut pab1-1 v1.0) from JGI.
Fragments per kilobase of transcript per million fragments mapped (FPKM) were calculated using Cufflinks protocol form Trapnell C., Nature Protocols, 2012
Genome_build: JGI Coprinopsis cinerea AmutBmut pab1-1 v1.0
Supplementary_files_format_and_content: text files include FPKM values for each Sample

organism: Coprinopsis cinerea

source_name: LiCl-treated , mycelium

growth_protocol: Grown on yeast extract-malt extract-glucose (YMG) medium solidified with 1.5% (w/v) agar

extract_protocol:
Control and LiCl treated samples in two time points of Coprinopsis cinerea were harvested, first one in the mycelium stage were harvested after 4 days of incubation in total darkness, before reaching the edge of plates, whereas second one in the hyphal knot stage were collected after 3-4 days of incubation under the 12/12 h light/dark cycle after the mycelium reached the edge of plates.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: a piece of mycelium 5 mm diameter punch from the stock plates was inoculated on plates spread with 3 μM LiCl and autoclaved water was added in the control plates

tag: developmental stage

value: mycelium

tag: sample type

value: LiCl


title: pBIC_4

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

country: Spain

institute: University of Navarra

description: PolyA RNA

data_processing:
The quality of the samples was verified using FastQC software.
FASTQ files were mapped to mm10 mouse assembly using STAR with default parameters.
featureCounts software and Gencode M13 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Obtained gene counts were normalized using edgeR and voom function of limma.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: B220+GFP+ cells from spleen

extract_protocol:
Murine spleens were submitted to cellular disaggregation, followed by lysis of erythrocytes using ACK buffer. Then, single-cell preparations were stained with B220 and submitted to fresh cellular sorting in a FACSAria Ilu sorter (BD) after exclusion of dead cells with 7AAD. Total RNA was extracted from sorted cells using TRIzol (Invitrogen) as described in manufacturer´s protocol and quality control of extracted RNA was measured using Agilent Bioanalyzer.
General transcriptome library preparation and massive sequencing were performed by BGI Tech (BGI, Shenzhen, China) using the Illumina HiSeq4000 platform with the paired-end 100-bp read option.

tag: murine model

value: ABC-DLBCL lymphoma (pBIC)

tag: genotype/variation

tag: cell type

value: splenic B cells (B220+GFP+)


title: root_96hours_drought_rep2

source_name: root, 96hours, drought


title: 13-N-1

organism: Homo sapiens

tag: Sex

value: Female

value: 57 years


title: 12-N-1

value: Male


title: left tumor (LT) treated with isotype control (A) at 1 wk, biological rep 3


title: 4-1-0

value: 58 years


title: 10-1-0

value: 54 years


title: left tumor (LT) treated with isotype control (A) at 1 wk, biological rep 1


title: C rep3

city: Harbin

first: Zhiyong

last: Wu

address: 600 Changjiang Road, Xiangfang District

institute: Northeast Agricultural University

description: MG infection

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2 with parameters v1.5.2, then mapped to Gallus_gallus-5.0 genome using bowtie2 v2. 2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: csv files include RPKM values for each Sample ...

organism: Gallus gallus

source_name: Lung

growth_protocol: Eighty (1 day old) commercial Leghorn chickens were obtained from Chia Chau Chicken Farm (Harbin, Heilongjiang, China) and were assigned randomly to four groups namely control group, co-infection group, MG group, E.coli group. The chickens were in healthy conditions, MG and E.coli-free and did not undergo vaccination and raised to the 10th day in four separate environmentally controlled chambers (named A, B, C and D).

extract_protocol:
Lungs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent(Invitrogen)
BGISEQ-500 RNA-Seq Library. Library was validated on the Agilent Technologies 2100 bioanalyzer.

treatment_protocol: Control group (A): No treatment control, fed with the same environment, keeping up with the end of the experiment.Co-infection group (B): The infectious dose was diluted into 0.2ml MG medium in left caudal thoracic air sac at the 7th day, and injected intraperitoneally with 0.1 ml of E.coli bacteria at day 10. MG group (C): The MG infection model was constructed one time by left caudal thoracic air sac inoculation with MG Rlow strain 0.2mL at the 7th day. E.coli group (D): The infectious dose was injected intraperitoneally with 0.1 ml of E.coli bacteria at day 10.

value: Lung

value: Leghorn chicken

value: 13 day old


title: 4CHHK

source_name: Control, hyphal knots

value: hyphal knots

value: Control


title: pBIC_3

description: PolyA RNA


title: 3ALM2

source_name: LiCl-treated, mycelium


title: 3CHHK


title: pBIC_2

description: PolyA RNA


title: 14-N-1

value: exosomes derived from serum

value: 52 years


title: root_24hours_control_rep2

source_name: root, 24hours, control

value: Medik. cv. Sultan

value: root

value: wild type


title: pBIC_1

description: PolyA RNA

value: ABC-DLBCL lymphoma (pBIC)


title: 1CHHK


title: root_96hours_drought_rep1


title: root_24hours_control_rep1


title: C rep2

description: MG infection


title: C rep1

description: MG infection


title: 3LM3A

value: mycelium

value: LiCl


title: BIC_3

description: PolyA RNA

value: ABC-DLBCL lymphoma (BIC)

value: BIC, Blimp1F/FIKK2castopF/stopFCg1Cre/+

value: splenic B cells (B220+GFP+)


title: root_24hours_drought_rep2

source_name: root, 24hours, drought


title: root_96hours_control_rep2


title: 3LM2A


title: B rep2

description: Co-infection


title: 3LM1A


title: B rep1

description: Co-infection


title: BIC_1

description: PolyA RNA


title: BIC_2

description: PolyA RNA


title: root_24hours_drought_rep1


title: AR18_MC_WT_R1

city: Baltimore

first: Jacob

middle: S

last: Heng

state: MD

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: Affinity captured polyribosomes from multiple retinas

data_processing:
scRNA-seq data were pre-processed using the Cell Ranger pipeline (v2.1.0; 10x Genomics) with default settings.  The normalized gene x cell matrix was used as input for the MonocleR/Bioconductor package (Trapnell et al., 2014).  Log-normalized expression estimates (with a pseudocount of 1) were used as input for a modified dpFeature analysis.  For preliminary cell clustering, PCA was performed on the high variance genes, and appropriate components were visualized in two dimensions using UMAP.  Initial clusters were identified from the 2-D embedding using k-means clustering.  Cell type identity was determined by cross-referencing clusters with expression of multiple known cell type markers.
RiboTag, whole retina, and whole brain RNA-seq data were pseudoaligned to the mouse genome (mm10) using the Kallisto software (Bray et al., 2016). Aligned counts were obtained for differential gene expression analysis using EBseq (Leng et al., 2013) and posterior probability ³0.95 that a gene/transcript is differentially expressed was considered statistically significant.
Genome_build: mm10

source_name: adult WT Muller glia Ribotag pulldown

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
6-8 retinas were homogenized in a Dounce homogenizer in 500 μL polysome buffer [50 mM Tris, pH 7.5, 250 mM sucrose, 100 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 200 U/mL RNasin Plus (Promega), 1 mg/mL heparin, 100 g/mL cycloheximide, 0.5 mM spermidine (Sigma),  complete EDTA-free protease inhibitor cocktail (Roche)].  Homogenates were centrifuged at 10,000xg for 10 min to create a postmitochondrial supernatant.  Five μL mouse monoclonal anti-HA antibody (HA.11, ascites fluid; Covance) were added to the supernatants (400 μL) and rotated for 4 hours at 4 °C. 100 μL protein G magnetic beads (Dynabeads; Invitrogen) were washed twice with polysome buffer and added directly to the antibody-coupled polysomes and rotated overnight at 4 °C.  The following day, samples were placed in a magnet on ice and the beads were washed 4x5 minutes in high salt buffer (50 mM Tris, pH 7.5, 300 mM KCl, 12 mM MgCl 2, 1% Nonidet P-40, 1 mM DTT, 20 μg/mL cycloheximide).  To prepare total RNA, 350 μL of Qiagen RLT buffer were added to the beads or to 50 μl of the input samples. Total RNA was prepared according to manufacturer’s instructions using RNeasy Plus Micro kit (Qiagen) and the quantity and quality of the RNA were assessed using Bioanalyzer (Agilent).
Libraries were constructed using the NuGEN single cell RNA-seq library preparation kit as per the manufacturer's protocol.

value: WT

value: 2 month

value: Mixed

value: retina

tag: treatment


title: HM3A

source_name: Control, mycelium


title: A rep3

description: Control

value: Lung

value: Leghorn chicken

value: 13 day old


title: YC_3

description: PolyA RNA

source_name: B220+YFP+ cells from spleen

value: Normal control

value: YC controls, YFPstopF/+Cg1Cre/+

value: splenic B cells (B220+YFP+)


title: HM2A

value: Control


title: YC_2

description: PolyA RNA


title: A rep2

description: Control


title: m_B

city: Seoul

first: Su Jin

last: Yoo

address: Heukseok-ro

department: Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads of which average quality scores of each read is less than 20. The whole filtering process was performed using the in-house scripts.
Filtered reads were mapped to the reference genome related to the species using the aligner TopHat (Trapnell C. et al, 2009).
Gene expression level was measured with Cufflinks v2.1.1 (Trapnell C. et al, 2010) using the gene annotation database of the species. Non-coding gene region was excluded from gene expression measurement using –mask option. To improve the accuracy of the measurement, multi-read-correction and frag-bias-correct options were applied. All other options were set to default values.
Differential expression analysis was performed by Cuffdiff (Trapnell C.et al, 2012). To enhance the analysis accuracy, multi-read-correction and frag-bias-correct options were applied. All other options were set to default values.
Genome_build: Ogataea parapolymorpha DL-1 (GCA_000187245) (Hansenula_2)
Supplementary_files_format_and_content: FPKM

organism: Ogataea parapolymorpha DL-1

source_name: O. parapolymorpha_met4 mutant

growth_protocol: Wild-type and met4Δ strains were inoculated at OD600 = 0.1 in YPD broth and harvested at OD600 = 0.3 (early exponential phase). Then, cells were shifted to B medium or B medium supplemented with 0.5 mM cysteine. After 2 hr incubation, samples were taken.

extract_protocol:
Total RNA was extracted according to the hot phenol extraction method and cleaned-up using QIAGEN RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: leu2 met4::LEU2

tag: culture medium

value: sulfur-limited B medium


title: m_Bcys

value: B medium supplemented with 0.5 mM cysteine


title: WT_Bcys

source_name: O. parapolymorpha_WT

value: leu2 [LEU2]


title: HM1A

value: mycelium


title: B rep3

description: Co-infection


title: YC_1

description: PolyA RNA


title: WT_B


title: Thoracic_3

status: Public on Apr 18 2019

first: Vilas

last: Menon

department: Neurology

institute: Columbia University Medical Center

data_processing:
Adaptor sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were removed from reads using Trimmomatic 0.36
Trimmed reads were mapped using STAR 2.5.3a to the Ensembl mouse genome GRCm38.p5, release 90
Mapped reads were normalized to the total number of reads per sample (counts per million)
Genome_build: GRCm38.p5, release 90
Supplementary_files_format_and_content: STAR 2.5.3a quantification output, expressed as counts and normalized to counts per million

source_name: Labelled SCTNs from thoracic spinal cord

growth_protocol: C57BL mice (P6-7), with injections of CTB-Alexa 555 at P4 in cerebellum

extract_protocol:
For each sample, 50-120 labelled cells were isolated by manual cell sorting on a fluorescence dissecting scope. Following pooling and lysis, total RNA was extracted by Picopure kit (KIT0204; Thermo-Fisher)
Amplified DNA was produced using Ovation RNA-seq System V2 kit (#7102; NuGEN), fragmented to ~200bp, ligated to Illumina sequencing adaptors with Encore Rapid kit (#0314; NuGEN), and sequenced on an Illumina HiSeq 2500 with 4-fold multiplexing (single end, 100bp read length)

tag: section

value: thoracic

tag: fluorescent reporter

tag: injection site

value: Cerebellum


title: Cervical_4

source_name: Labelled SCTNs from cervical spinal cord

value: cervical


title: Cervical_3


title: Thoracic_4


title: Cervical_1


title: Thoracic_1


title: Thoracic_2


title: FS_1190.1_AGN50

city: Cambridge

first: Moran

last: Dvela Levitt

state: MA

address: 415 Main Street

institute: Broad Institute

data_processing:
Illumina HiSeq2500 sequencing system (2x101 Bp Reads) software used for basecalling. The provided data from Sequencing platform  are de-multiplexed and aggregated Picard Bam files.
Bam files received from sequencing platform were reverted to fastq files followed by alignment of paired end reads  to the mm10 mouse or hg19 human reference genome using STAR v2.5.2b.
Quality Control metrics were obtained using RNA-SeQC v2.3.1.
Expression levels were estimated by running RSEM v1.3.0 with default parameters on these alignments.
Genome_build: mm10
Supplementary_files_format_and_content: Raw expression levels produced by RSEM

source_name: MUC1 kidney disease mouse_BRD4780_kidney

extract_protocol:
RNA was extracted from a sagittal section of a half-kidney. Kidney tissue was homogenized using tissue homogenizer  in 1 mL of TRIzol™ Reagent. Following 5 min incubation, 0.2 mL chloroform was added, and samples were vigorously mixed for 30 sec, then centrifuged at 12,000 x g at 4°C for 15 min. The upper aqueous phase containing RNA was then vigorously mixed with 0.5 mL of isopropanol for 30 sec. After 10 min incubation at RT, the samples were centrifuged at 12,000 x g at 4°C for 10 min. The pellet was resuspended in 1 mL of 75% ethanol and centrifuged at 12,000 x g 4°C for 5 min. The RNA pellet was then air dried for 15 min,  dissolved in 50 μL of Nuclease-Free Water, treated with  DNase I, Amplification Grade following the manufacturer’s  protocol and assessed for yield and purity by NanoDrop™ 2000.
Concentrations of purified RNA were measured with the QuantiTTM RiboGreen® RNA Assay Kit  and normalized to 5 ng/μL. An automated variant of the Illumina TruSeqTM Stranded mRNA Sample Preparation Kit was used for library preparation from a 200 ng aliquot of RNA. This method preserves strand orientation of the RNA transcript and uses oligo dT beads to select mRNA from the total RNA sample. Following cDNA synthesis and enrichment, cDNA libraries were quantified with qPCR using the KAPA Library Quantification Kit for Illumina Sequencing Platforms and then pooled equimolarly.

treatment_protocol: BRD4780 (50mg/kg) or vehicle control were applied to 8 month old male knock-in mice  daily during 7 days

value: MUC1 kidney disease mouse model

value: 8 month-old

value: male

value: BRD4780 (50mg/kg) daily for 7 days

value: Kidney


title: FS_1185.1_AGN50


title: FS_1163.2_Saline

source_name: MUC1 kidney disease mouse_saline_kidney

value: saline (vehicle) daily for 7 days


title: FS_1161.3_Saline


title: FS_1161.2_AGN50


title: FS_1157.2_Saline


title: ipsilateral sample from sham-treated animal #4, collected on day 4 after sham

first: Chris

last: Roberts

state: Massachusetts

address: 301 Binney St.

institute: Biogen

description:
Hsieh_mouse_TBI_RNAseq_Counts_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_TPM_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_DESeq2Output_day4_13samples
71-493-4-RH-lesion-4d-sham

data_processing:
in-house BCL2FASTQ pipeline
Omicsoft Array Studio aligner OSA4 to generate BAM files
Omicsoft Array Studio quantification algorithm (based on RSEM) to generate counts table
Omicsoft Array Studio DESeq2 algorithm for differential expression analysis
Genome_build: Omicsoft Mouse.B38 which is similar to GRCm38 and mm10
Supplementary_files_format_and_content: processed data tables are Excel files

molecule: polyA RNA

source_name: brain hemisphere

growth_protocol: Standard mouse growth conditions

extract_protocol:
Perfused brain tissues were stored in RNA later at -20C.  RNA was isolated using TRIzol reagent (Invitrogen) and a Kinematica homogenizer (Polytron PT 10-35 GT)
Illumina Truseq Stranded mRNA

treatment_protocol: Controlled cortical impact surgery with anesthesia

tag: animal

value: wild type

value: 12-16 weeks

value: ipsilateral brain hemisphere

value: sham-treated

tag: time

value: day 4 after sham


title: A rep1

description: Control

tag: tissue

value: Lung

tag: strain

value: Leghorn chicken

value: 13 day old


title: ipsilateral sample from sham-treated animal #6, collected on day 4 after sham

description:
Hsieh_mouse_TBI_RNAseq_Counts_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_TPM_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_DESeq2Output_day4_13samples
72-493-6-RH-lesion-4d-sham

tag: genotype


title: ipsilateral sample from CCI-treated animal #2, collected on day 4 after CCI

description:
Hsieh_mouse_TBI_RNAseq_Counts_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_TPM_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_DESeq2Output_day4_13samples
68-493-2-RH-lesion-4d

tag: age

value: CCI-treated

value: day 4 after CCI


title: ipsilateral sample from CCI-treated animal #1, collected on day 4 after CCI

description:
Hsieh_mouse_TBI_RNAseq_Counts_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_TPM_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_DESeq2Output_day4_13samples
67-493-1-RH-lesion-4d


title: contralateral sample from sham-treated animal #6, collected on day 4 after sham

description:
Hsieh_mouse_TBI_RNAseq_Counts_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_TPM_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_DESeq2Output_day4_13samples
22-493-6-LH-4d-sham

value: contralateral brain hemisphere


title: ipsilateral sample from CCI-treated animal #3, collected on day 4 after CCI

description:
Hsieh_mouse_TBI_RNAseq_Counts_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_TPM_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_DESeq2Output_day4_13samples
69-493-3-RH-lesion-4d


title: contralateral sample from sham-treated animal #8, collected on day 4 after sham

description:
Hsieh_mouse_TBI_RNAseq_Counts_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_TPM_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_DESeq2Output_day4_13samples
24-493-8-LH-4d-sham


title: ipsilateral sample from CCI-treated animal #5, collected on day 4 after CCI

description:
Hsieh_mouse_TBI_RNAseq_Counts_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_TPM_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_DESeq2Output_day4_13samples
70-493-5-RH-lesion-4d


title: contralateral sample from sham-treated animal #4, collected on day 4 after sham

description:
Hsieh_mouse_TBI_RNAseq_Counts_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_TPM_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_DESeq2Output_day4_13samples
21-493-4-LH-4d-sham


title: contralateral sample from CCI-treated animal #5, collected on day 4 after CCI

description:
Hsieh_mouse_TBI_RNAseq_Counts_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_TPM_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_DESeq2Output_day4_13samples
20-493-5-LH-4d


title: contralateral sample from CCI-treated animal #3, collected on day 4 after CCI

description:
Hsieh_mouse_TBI_RNAseq_Counts_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_TPM_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_DESeq2Output_day4_13samples
19-493-3-LH-4d


title: contralateral sample from CCI-treated animal #2, collected on day 4 after CCI

description:
Hsieh_mouse_TBI_RNAseq_Counts_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_TPM_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_DESeq2Output_day4_13samples
18-493-2-LH-4d


title: contralateral sample from CCI-treated animal #1, collected on day 4 after CCI

description:
Hsieh_mouse_TBI_RNAseq_Counts_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_TPM_Table_day4_13samples
Hsieh_mouse_TBI_RNAseq_DESeq2Output_day4_13samples
17-493-1-LH-4d


title: Cervical_2

value: cervical

value: Cerebellum


title: FS_1163.1_AGN50

value: MUC1 kidney disease mouse model

value: 8 month-old

value: male


title: FS_1162.1_Saline

value: saline (vehicle) daily for 7 days

value: Kidney


title: WT EpiLC_D4_Rep 2

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

data_processing:
2X100bp paired-end reads were mapped onto the Mouse reference genome (mm10) using STAR v2.5.0a porting unique alignments and allowing at most 6 mismatches per fragment. Tracks were created using HOMER software v4.7
Genome_build: mm10
Supplementary_files_format_and_content: bigWig : coverage

source_name: Epiblast-like Cell

growth_protocol: ES Cells were either cultured in 2+vitC, or differentiated into Epiblast-like cells

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies), then DNase-treated and column purified (Qiagen RNeasy Kit).
RNA-seq libraries were prepared from 500ng of DNase-treated RNA with the TruSeq Stranded mRNA kit (Illumina). Sequencing was performed in 100pb paired-end reads using the Illumina HiSeq2500 platform.

tag: culture

value: Differentiated 4 Days

value: Wild-type


title: WT_EpiLC_D2_Rep_1

value: Differentiated 2 Days


title: WT EpiLC_D4_Rep 1


title: WT_EpiLC_D2_Rep_2


title: WT EpiLC bisulfite-seq

library_source: genomic

data_processing:
The first eight base pairs of the reads were trimmed using FASTX-Toolkit v0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Adapter sequences were removed with Cutadapt v1.3 and reads shorter than 16 bp were discarded. Cleaned sequences were aligned onto the Mouse reference genome (mm10) using Bismark v0.12.5 with Bowtie2-2.1.0 and default parameters. Only reads mapping uniquely on the genome were conserved. Methylation calls were extracted after duplicate removal. Only CG dinucleotides covered by a minimum of 5 reads were conserved.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, methylation percentage

molecule: genomic DNA

growth_protocol: ES Cells were either cultured in 2+vitC, or differentiated for seven days into Epiblast-like cells

extract_protocol:
50ng of bisulfite-converted genomic DNA using the EpiGnome/Truseq DNA Methylation Kit (Illumina) following the manufacturer instructions.
Sequencing was performed in 100pb paired-end reads at a 30X coverage using the Illumina HiSeq2000 platform.

value: Epiblast-like Cell

value: Differentiated 7 Days


title: WT ESC_Rep 2

source_name: Embryonic Stem Cell

value: Embryonic Stem Cell


title: WT EpiLC_D7_Rep 2


title: MUT_3_RNA-seq

first: Marco

last: Seandel

department: Surgery

institute: Weill Cornell Medical College

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs (for RNA-seq samples) (Andrews 2010, Hartley and Mullikin (2015)).
Sequencing reads were aligned with default parameters to the mouse reference genome (GRCm38) using STAR (Dobin et al. 2013). Gene expression estimates were obtained with featureCounts using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M17) (Liao, Smyth, and Shi 2014, Harrow et al. (2012)).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

source_name: adult spermatogonial stem cells

extract_protocol:
Adult mouse testes were enzymatically dissociated and stained for MCAM. Cells were subjected to flow cytometry, gating for MCAM-bright, tdTomato-positive (induced) cells. RNA was isolated using the Arcturus PicoPure kit with DNase I treatment.
Libraries were constructed using TruSeq Stranded mRNA.

value: adult

value: adult spermatogonial stem cells

value: heterozygous Hras G12V mutation

tag: isolation

value: MCAM-bright; tdTomato+

tag: timing

value: isolated 3 months after tamoxifen induction


title: WT_3_RNA-seq

value: wild type


title: MUT_1_RNA-seq


title: WT ESC

data_processing:
2x100bp paired-end reads were aligned onto the Mouse reference genome (mm10) using Bwa mem v0.7.5a with default parameters. Duplicate reads were removed using Picard v1.130 (http://broadinstitute.github.io/picard/). Tracks were created using HOMER software v4.7,
Genome_build: mm10
Supplementary_files_format_and_content: bigWig : coverage

extract_protocol:
Briefly, 50,000 cells were washed, but not lysed. Cells were transposed using the Nextera DNA library prep kit (Illumina) for 30 min at 37º. DNA was immediately purified using Qiagen MinElute Kit (Qiagen).
qPCR was used to determine the optimal cycle number for library amplification. The libraries were sequenced on the Illumina HiSeq2500 platform to obtain 2x100 paired-end reads.


title: MUT_2_RNA-seq


title: WT EpiLC


title: WT_1_RNA-seq


title: WT_2_RNA-seq


title: Eed-/- (J1) ESC_Adam23 VP

data_processing:
Library strategy: 4C-seq
Reverse primer sequences were removed in 3' end of the reads using Cutadapt v1.12. Reads shorter than 15bp were discarded.
Cleaned sequences were aligned onto the Mouse reference genome (mm10) using Bowtie2 v2.1.0 allowing one mismatch in the seed (22bp) and an end to end alignment.
Following steps were performed using the FourCSeq R package (v1.12.0). Mouse reference genome was in-silico digested using the two restriction enzymes. Restriction fragments that do not contain a cutting site of the second restriction enzyme or are smaller than 20bp were filtered out. Fragments 2.5 kb up- and downstream from the viewpoint were excluded during the procedure. Intrachromosomal contacts were kept. Valid fragments were quantified. The fragment counts were then normalized per one million reads. Data were smoothed using a running mean function with 5 informative fragments.
Genome_build: mm10

extract_protocol: Inverse primers with illumina adapter sequences amplified the circular DNA prior to sequencing

treatment_protocol: Cells were cross-linked, digested and ligated twice to make high resolution circular DNA

value: Eed-/-


title: Eed-/- (J1) ESC_Nrp2 VP


title: WT (J1) ESC_Nrp2 VP


title: WT ESC_Rep 1


title: Eed-/- (J1) ESC_pZdbf2 VP


title: Eed-/- (J1) ESC_CTCF_PS VP


title: WT (J1) ESC_pZdbf2 VP


title: WT (J1) ESC_CTCF_PS VP


title: Eed-/- (J1) ESC_pLiz VP


title: WT (J1) ESC_Adam23 VP


title: ∆CTCF_PS (E14) ESC_Nrp2 VP


title: WT (J1) ESC_pLiz VP


title: ∆CTCF_PS (E14) ESC_Adam23 VP


title: ∆CTCF_PS (E14) ESC_pZdbf2 VP


title: WT EpiLC_D7_Rep 1


title: ∆Liz (E14) EpiLC_Nrp2 VP

value: deltaLiz


title: ∆CTCF_PS (E14) ESC_pLiz VP


title: ∆Liz (E14) ESC_Adam23 VP


title: ∆Liz (E14) EpiLC_CTCF_PS VP


title: ∆Liz (E14) ESC_Nrp2 VP


title: WT (E14) EpiLC Rep 1_CTCF_PS VP


title: WT (E14) EpiLC Rep 2_pZdbf2 VP


title: ∆Liz (E14) ESC_CTCF_PS VP


title: WT (E14) EpiLC Rep 2_CTCF_PS VP


title: WT (E14) EpiLC Rep 2_Adam23 VP


title: WT (E14) EpiLC Rep 2_pLiz VP


title: WT (E14) EpiLC Rep 1_pLiz VP


title: ∆Liz (E14) ESC_pZdbf2 VP


title: WT (E14) EpiLC Rep 2_Nrp2 VP


title: WT (E14) EpiLC Rep 1_pZdbf2 VP


title: WT (E14) ESC Rep 3_pZdbf2 VP


title: WT (E14) ESC Rep 3_pLiz VP


title: WT (E14) ESC Rep 2_Adam23 VP


title: WT (E14) ESC Rep 2_Nrp2 VP


title: WT (E14) ESC Rep 3_Nrp2 VP


title: WT (E14) ESC Rep 3_Adam23 VP


title: WT (E14) ESC Rep 1_pLiz VP


title: WT (E14) ESC Rep 2_pLiz VP


title: WT (E14) ESC Rep 2_CTCF_PS VP


title: WT (E14) ESC Rep 1_CTCF_PS VP


title: ∆Liz (E14) EpiLC_Adam23 VP


title: ∆Liz (E14) EpiLC_pZdbf2 VP


title: sciatic nerve input ChIP-Seq, Ep400_cko P9, biological replicate 4

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

description:
input ChIPseq data from P9 sciatic nerve (Ep400 cko)
input_SC_Ep400_cko.bigwig

data_processing:
Reads were mapped to the mouse reference genome (GRCm38/mm10) using Bowtie (version 2.3.4.2).
After removing PCR duplicates with RmDup (version 2.0.1) mapped reads ware converted to BAM format via SAMtools (version 1.1.2).
BAM files were further processed using the BamCoverage tool within the deeptools software (version 3.0.2.0) and normalized to to 1x.
For peak calling Model-based Analysis of ChIP-Seq (MACS2) (version 2.1.1.20160309.0) was used with input samples set as background and default parameters (q-value < 0.05).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using BamCoverage tool after merging bam files which belong together.

source_name: sciatic nerve P9 (Dhh::Cre, conditional Ep400)

extract_protocol:
Sciatic nerve lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: mixed 129SvJ/C57Bl/6J background

value: postnatal day 9

value: sciatic nerve

value: Dhh::Cre, conditional Ep400

tag: chip antibody


title: WT (E14) ESC Rep 2_pZdbf2 VP

tag: cell type

value: Wild-type


title: sciatic nerve H2A.Z ChIP-Seq, Ep400_cko P9, biological replicate 4

description:
H2A.Z ChIPseq data from P9 sciatic nerve (Ep400 cko)
H2A.Z_SC_Ep400_cko.bigwig


title: WT (E14) ESC Rep 1_pZdbf2 VP


title: sciatic nerve input ChIP-Seq, Ep400_cko P9, biological replicate 3


title: sciatic nerve H2A.Z ChIP-Seq, Ep400_cko P9, biological replicate 3


title: sciatic nerve input ChIP-Seq, Ep400_cko P9, biological replicate 1


title: sciatic nerve H2A.Z ChIP-Seq, Ep400_ctrl P9, biological replicate 4

description:
H2A.Z ChIPseq data from P9 sciatic nerve (ctrl)
H2A.Z_SC_Ep400_ctrl.bigwig

source_name: sciatic nerve P9 (conditional Ep400)

value: conditional Ep400


title: sciatic nerve input ChIP-Seq, Ep400_ctrl P9, biological replicate 3

description:
input ChIPseq data from P9 sciatic nerve (ctrl)
input_SC_Ep400_ctrl.bigwig


title: sciatic nerve input ChIP-Seq, Ep400_cko P9, biological replicate 2


title: sciatic nerve input ChIP-Seq, Ep400_ctrl P9, biological replicate 1


title: sciatic nerve input ChIP-Seq, Ep400_ctrl P9, biological replicate 4


title: sciatic nerve H2A.Z ChIP-Seq, Ep400_cko P9, biological replicate 2


title: sciatic nerve Ep400_ctrl P9, biological replicate 2

description: RNAseq data from P9 sciatic nerve (ctrl)

data_processing:
Sequencing data was pooled using the Illumina HiSeq 2500 platform and converted into fastq files.
Reads from rRNA, tRNA, mt-rRNA and mt-tRNA were purged from demultiplexed reads.
Reads were aligned to mm10 reference genome using STAR (version 2.5.1.b).
Unique maps were generated using HTSeq count relating to Ensembl genes version 85.
Statistical analysis of raw data was done with DESeq2 by R version 1.10.1.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with raw mean counts, log2 foldchange and statistics.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit according to QIAGEN protocol.
RNA libraries were prepared for sequencing using Illumina Stranded mRNA Kit.


title: sciatic nerve H2A.Z ChIP-Seq, Ep400_ctrl P9, biological replicate 2


title: sciatic nerve H2A.Z ChIP-Seq, Ep400_ctrl P9, biological replicate 1


title: sciatic nerve H2A.Z ChIP-Seq, Ep400_cko P9, biological replicate 1


title: sciatic nerve H2A.Z ChIP-Seq, Ep400_ctrl P9, biological replicate 3


title: ChIP_addbackMut_CTCF-IP_1

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
ChIP-seq reads were aligned to the genome using qAlign from the QuasR Bioconductor package version 1.18.0 (Gaidatzis et al, Bioinformatics, 2015) with default parameters, only reporting alignments for reads with a unique match to the genome.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6 and binsize=100. The scores in the wig file therefore represent the number of alignments per 100bp window and per million reads in the library.

growth_protocol: We cultured mouse ES cells as previously described (Mohn et al., 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and Non-essential amino acids (Gibco), beta-mercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). Differentiation of ES cells to neuronal progenitors was performed as previously described (Bibel et al., 2004; Mohn et al., 2008). Cell were grown on plates coated with 0.2% gelatin (Sigma), with the exception of Snf2h ko and ATPase mutant re-expression cell line. Those were grown on MEF feeder cells for (at least) first two passages after thawing.

extract_protocol:
ChIP was carried out as previously described (Weber et al., 2007) with slight modifications. Changes to the protocol were following; (1) chromatin was sonicated for ~50 cycles of 30 sec. using a Diagenode Bioruptor, with 45 sec. breaks in between cycles, (2) protein A/G magnetic Dynabeads Magnetic beads (Thermo Fisher Scientific) were used, (3) DNA was purified using on-column purification instead of chloroform/phenol extraction (Qiagen PCR Purification Kit).
Immunoprecipitated DNA and input DNA were submitted to library preparation (NEBNext Ultra DNA Library Prep Kit, Illumina). In the library preparation protocol, input sample were amplified using 4 PCR cycles, IP sample using 12 cycles.

value: mouse embryonic stem cells

tag: genotype/variation

value: Snf2h ko, Snf2h mutant add-back

value: CTCF (Santa Cruz, Cat. # C-20X)


title: ChIP_addbackWt_CTCF-IP_2

value: Snf2h ko, Snf2h wiltype add-back


title: sciatic nerve Ep400_ctrl P9, biological replicate 1


title: sciatic nerve input ChIP-Seq, Ep400_ctrl P9, biological replicate 2


title: ChIP_addbackMut_CTCF-IP_2


title: sciatic nerve Ep400_ctrl P9, biological replicate 3


title: sciatic nerve Ep400_cko P9, biological replicate 1

description: RNAseq data from P9 sciatic nerve (Ep400 cko)


title: ChIP_addbackWt_CTCF-IP_1


title: ChIP_Brg1ko_CTCF-IP_2

value: Brg1 ko


title: ChIP_Brg1ko_CTCF-IP_1


title: ChIP_Brg1fl_CTCF-IP_2

value: wildtype


title: ChIP_Brg1fl_CTCF-IP_1


title: sciatic nerve Ep400_cko P9, biological replicate 3


title: sciatic nerve Ep400_cko P9, biological replicate 2


title: ChIP_addbackMut_CTCF-input_1


title: ChIP_addbackWt_CTCF-input_1


title: ChIP_Brg1ko_CTCF-input_2


title: ChIP_Brg1fl_CTCF-input_2


title: ChIP_Brg1ko_CTCF-input_1


title: ChIP_Brg1fl_CTCF-input_1


title: ChIP_Brg1fl_REST-IP_2

value: REST (Santa Cruz, Cat. # H-290)


title: ChIP_Brg1fl_REST-IP_1


title: ChIP_Brg1ko_REST-input_1


title: ChIP_Brg1ko_REST-IP_2


title: ChIP_Brg1ko_REST-input_2


title: ChIP_Brg1fl_REST-input_2


title: ChIP_addbackMut_REST-IP_2


title: ChIP_addbackMut_REST-input_1


title: ChIP_Brg1fl_REST-input_1


title: ChIP_addbackWt_REST-IP_1


title: RNA_addbackMut_3

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
RNA-seq reads were aligned to the genome using STAR (Dobin et al., Bioinformatics, 2012, doi:10.1093/bioinformatics/bt-s635, version 2.5.2b), with parameters --outFilterType BySJout --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMmultNmax 1. These parameters report alignments for reads with up to 20 best matches to the genome and report no more than a single, randomly selected alignment per read.
Alignments overlapping the opposite strand of any exon of a known gene (gene annotation from the Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene, version 3.4.0) were counted using the qCount function from the QuasR Bioconductor package version 1.18.0 (Gaidatzis et al, Bioinformatics, 2015) with default parameters. Detected genes were defined as genes with at least 1.0 counts per million in at least two samples of any cell type (n=14,019).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: matrix table with raw alignment counts per gene (rows) for all samples (columns)

source_name: embryonic stem cells

extract_protocol:
RNA for RNA-seq was purified using RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared from purified RNA for at least two biological replicates using TruSeq stranded mRNA Library Prep (Illumina).


title: ChIP_addbackMut_REST-IP_1


title: RNA_addbackMut_1


title: Bis_addbackMut_1

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Bis-seq reads were first trimmed to remove adaptor sequences using cutadapt version 1.15 (Marcel Martin. EMBnet.journal, 17(1):10-12, 2011) with -a AGATCGGAAGAGC -m 10 --overlap=1. Trimmed reads were aligned to the genome using qAlign from the QuasR Bioconductor package version 1.18.0 (Gaidatzis et al, Bioinformatics, 2015) with bisulfite=”dir”.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Total and methylated counts for Cs in CpG context were calculated using the qMeth function from QuasR. The processed data file contains the genomic coordinates for each CpG (columns chr, start and end), and the counts of total and methylated reads that overlap a given CpG (columns n.total and n.methylated).

extract_protocol:
Genomic DNA was isolated using QIAamp DNA mini kit from Qiagen (cat. No 51304) and fragmented using Covaris S220 Focused-ultrasonicator.
500ng of fragmented DNA was then used for library preparation with NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #E7370) and bisulfite treatment with EZ DNA-methylation Gold Kit (Zymo Research #D5005). Final PCR amplification was performed using KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit (KAPA Biosystems #KR0413) and 12 cycles of amplification.


title: Bis_addbackWt_1


title: ChIP_Brg1ko_REST-IP_1


title: ChIP_addbackWt_REST-IP_2


title: RNA_addbackWt_3


title: RNA_addbackWt_1


title: RNA_addbackWt_2


title: RNA_Snf2hko_5

value: Snf2h ko


title: RNA_Snf2hko_2


title: RNA_Snf2hko_3


title: RNA_Snf2hko_4


title: RNA_Snf2hko_1


title: ChIP_addbackWt_REST-input_1


title: RNA_wt_7


title: 0.75h M-,Z+ jumu embryos (replicate 2)

city: Beijing

first: Shunmin

last: He

address: 1 Beichen West Road,  Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
FastQC was used to make sure that the sequencing data were high quality
Reads were aligned to the dm6 genome assembly using Tophat2/STAR
Differential expression analysis was carried out by cuffdiff
Genome_build: dm6

organism: Drosophila melanogaster

source_name: 0.75h M-,Z+ jumu rep 2

extract_protocol:
Total RNAs were isolated from embryos at indicated stages using TRIzol reagent (Invitrogen) and mRNAs were then purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module according to the user manual.
Illumina sequencing libraries were constructed according to the manufacturer’s instructions. The libraries were then sequenced using the Illumina Hiseq2500 V4 and NovaSeq platform

value: M-,Z+ jumu

value: embryo


title: 0.75h M-,Z+ jumu embryos (replicate 1)

source_name: 0.75h M-,Z+ jumu rep 1


title: 0.75h wild type embryos (replicate 2)


title: 0.75h embryo Input

data_processing:
MeDIP-seq reads were aligned to the dm6 genome assembly using bowtie2 with parameters “--no-mixed --no-discordant --non-deterministic --very-sensitive-local”
MACS2 callpeak was used to identify enrichment peaks with parameters “-f BAMPE –B” and a default q-value (FDR) cutoff of 0.05, and used IgG as a control.
Genome_build: dm6
Supplementary_files_format_and_content: Not applicable

source_name: w1118 embryo Input

extract_protocol:
Genomic DNA was extracted from Drosophila and other animal tissues using the Wizard genomic DNA purification Kit (Promega) following the manufacturer’s instructions. 5 µg of fragmented genomic DNA was immunoprecipitated with 5 µg of rabbit 6mA antibody (Abcam) or rabbit IgG overnight at 4°C in a final volume of 500 µl immunoprecipitation buffer. Then the mixture was incubated with 50 µl protein A/G agarose beads for 2 h at 4°C and then washed three times with 1 ml of immunoprecipitation buffer. The beads were then treated with proteinase K and the methylated DNA was purified by phenol-chloroform extraction followed by ethanol precipitation for library construction.
End repair, 3′-adenylation, adaptor ligation, and PCR amplification were performed according to Illumina TruSeq DNA sample preparation procedures. Libraries were sequenced using the Illumina Hiseq2500 V4 platform.


title: RNA_wt_3


title: 6h DMADKD embryos (replicate 2)

source_name: 6h DMADKD rep 2

value: DMAD knockdown


title: RNA_wt_2


title: 6h wild type embryos (replicate 2)


title: 6h wild type embryos (replicate 1)


title: RNA_wt_4


title: RNA_wt_6


title: Mnase_Snf2hko_2

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
MNase-seq reads were aligned to the genome using qAlign from the QuasR Bioconductor package version 1.18.0 (Gaidatzis et al, Bioinformatics, 2015) with default parameters, only reporting alignments for reads with a unique match to the genome.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6, binsize=100 and shift=80. The scores in the wig file therefore represent the number of alignment starts, shifted by 80bp towards their 3'-end, per 100bp window and per million reads in the library.

extract_protocol:
A custom MNase protocol was used combining previously published methods (Cui and Zhao, 2012; Gaidatzis et al., 2014). Cells were resuspended in 1mL of Buffer 1 (0.3M Sucrose, 15mM Tris pH 7.5, 60mM KCl, 15mM NaCl, 5mM MgCl2, 2mM EDTA, 0.5mM DTT, 1x PIC, 0.2mM spermine, 1mM spermidine) w/ detergent (Buffer 1 + 0.02% NP-40) and incubated on ice for 5min. Nuclei were then pelleted at 300g for 5min at 4ºC. Nuclei were gently resuspended in 1mL of Buffer 2 (0.3M Sucrose, 15mM Tris pH 7.5, 60mM KCl, 15mM NaCl, 5mM MgCl2, 0.5mM DTT*, 1 x PIC, 0.2mM spermine, 1mM spermidine). Nuclei integrity was checked at this point using the TC20 cell analyzer (BioRad). We made sure to recover no less than 75% of nuclei compared to the starting cell number. Nuclei were then pelleted for 5 min. at 300g at 4ºC. Pallets were resuspended in 400 μl MNase buffer (0.3M Sucrose, 50mM Tris ph 7.5, 4mM MgCl2, 1mM CaCl2, 1 x PIC). Varying concentration of MNase S7 micrococcal nuclease (Roche) was added. Optional concentration was later determined to be 5U. Nuclei were then incubated for 30min. at 37ºC. Reaction was stopped by adding 4μl of EDTA at 5 mM (0.5M solution). 20μl of SDS at 1% (20% stock solution) and 8μl of Proteinase K at 200 μg/mL (10 mg/mL stock concentration) were added to the sample. Samples were incubated at 55ºC for 1h with shaking. DNA was purified using PCR Purification Kit (Qiagen). Purified DNA was loaded on a 1% agarose gel or on the Agilent Bioanalyzer to determine digestion efficiency. Mononculesomal fraction was isolated using AMPure XP beads (1/1 radio, Beckman Coulter).
Libraries were prepared with NEBUltra Library Preparation Kit (NEB), using 4 PCR cycles and 1 μg of starting DNA.


title: Mnase_addbackWt_2


title: Mnase_addbackWt_1


title: 6h embryo RNAseq (replicate 1)

description: processed data file: 6h_FPKM.txt

data_processing:
FastQC was used to make sure that the sequencing data were high quality
Reads were aligned to the dm6 genome assembly using STAR or Tophat2
Differential expression analysis was carried out by cuffdiff
Genome_build: dm6

source_name: w1118 6h RNAseq

extract_protocol:
Total RNAs were isolated from embryos at indicated stages using TRIzol reagent (Invitrogen) and mRNAs were then purified using a Dynabeads mRNA DIRECT Kit (Invitrogen) according to the user manual.
Illumina sequencing libraries were constructed according to the manufacturer’s instructions. The libraries were then sequenced using the Illumina Hiseq2500 V4 platform

value: wild type


title: 6h embryo RNAseq (replicate 2)

description: processed data file: 6h_FPKM.txt


title: RNA_wt_1


title: Mnase_addbackMut_2


title: Mnase_addbackMut_1


title: 3h embryo RNAseq (replicate 2)

description: processed data file: 3h_FPKM.txt

source_name: w1118 3h RNAseq


title: Mnase_Snf2hko_1


title: RNA_wt_8


title: 3h embryo RNAseq (replicate 1)

description: processed data file: 3h_FPKM.txt


title: Mnase_wt_2


title: 0.75h embryo RNAseq (replicate 2)

description: processed data file: 0.75h_FPKM.txt

source_name: w1118 0.75h RNAseq


title: RNA_wt_5


title: 0.75h wild type embryos (replicate 1)


title: 0.75h embryo RNAseq (replicate 1)

description: processed data file: 0.75h_FPKM.txt


title: Mnase_wt_1


title: 6h DMADKD embryos (replicate 1)

source_name: 6h DMADKD rep 1


title: ChIP_Snf2hko_REST-input_1

tag: antibody


title: 6h embryo DNA and Jumu pull down seq

source_name: w1118 6h jumu pull down


title: ChIP_wt_REST-input_1


title: ChIP_Snf2hko_REST-IP_1


title: ChIP_wt_REST-IP_2


title: 6h embryo IgG MeDIP-seq

data_processing:
MeDIP-seq reads were aligned to the dm6 genome assembly using bowtie2 with with parameters “--no-mixed --no-discordant --non-deterministic --very-sensitive-local”
MACS2 callpeak was used to identify enrichment peaks with parameters “-f BAMPE –B” and a default q-value (FDR) cutoff of 0.05, and used IgG as a control
Genome_build: dm6
Supplementary_files_format_and_content: bed file of the callpeak result

source_name: w1118 embryo IgG


title: 6h embryo 6mA MeDIP-seq

source_name: w1118 embryo 6mA


title: 0.75h embryo DNA and Jumu pull down seq

source_name: w1118 embryo jumu pull down


title: ChIP_wt_REST-IP_1


title: 3h embryo IgG MeDIP-seq


title: ChIP_Snf2hko_CTCF-input_1


title: 0.75h embryo IgG MeDIP-seq


title: ChIP_wt_CTCF-input_1


title: 0.75h embryo 6mA MeDIP-seq


title: SY5Y-NOTCH3IC-off input

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

data_processing:
Peaks were called using the RSEG algorithm using the following arguments (rseg-diff -d k41.hg19.bed  -m 2 -v -i 20 -c human.hg19.size.bed -o )
bed files: rseg-files.
Genome_build: hg19
Supplementary_files_format_and_content: bed files: rseg-files.

source_name: Neuroblastoma cell  line

growth_protocol: DMEM, 10% FCS

extract_protocol: Cultured cells were fixed with 1% formaldehyde. Nuclei were isolated and the DNA was sheared to 200 to 300 bp fragments. Histon-bound DNA was precipitated using H3K27ac antibody (#4729, Abcam). De-crosslinked DNA was purified using Qiagen PCR purification kit (Qiagen) and quantified with Quant-IT Picogreen (Invitrogen). The DNA was used to generate sequencing libraries according to the manufactures procedure (Life Technologies): The DNA was end-polished, dA-tailed and adaptors with barcodes were ligated. The fragments were amplified (8 cycles) and quantified with a Bioanalyzer (Agilent). The libraries were prepped with the HiSeq PE cluster kit v4 (Illumina) and sequenced with the HiSeq4000 (Illumina) resulting in 125 bp reads.

tag: growth medium

value: DMEM, 10 percent FCS


title: SY5Y-NOTCH3IC-on7d input


title: SY5Y-NOTCH3IC-off_H3K27Ac

source_name: Neuroblastoma cell line


title: ATAC_wt_1

data_processing:
Illumina RTA 1.18.64 (HiSeq 2500) or RTA 2.4.1 (NextSeq 500) and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Paired ATAC-seq reads were first trimmed to remove adaptor sequences using cutadapt version 1.15 (Marcel Martin. EMBnet.journal, 17(1):10-12, 2011) with -a CTGTCTCTTATA -m 10 --length=51. Trimmed reads were aligned to the genome using bowtie2 version 2.3.0 ( Langmead B, Salzberg S. Nature Methods. 2012, 9:357-359). with --sensitive-local --minins 0 --maxins 1000 –dovetail and converted to bam format.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package (Gaidatzis et al, Bioinformatics 2015) version 1.18.0 with default parameters except scaling=1e6, binsize=100 and pairedAsSingle=TRUE. The scores in the wig file therefore represent the number of 5'-read ends (Tn5 insertion sites) per 100bp window and per million reads in the library.

growth_protocol: We cultured mouse ES cells as previously described (Mohn et al., 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and Non-essential amino acids (Gibco), beta-mercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). Differentiation of ES cells to neuronal progenitors was performed as previously described (Bibel et al., 2004; Mohn et al., 2008). Cell were grown on plates coated with 0.2% gelatin (Sigma), with the exception of Snf2h ko and ATPase mutant re-expression cell line. Those were grown on MEF feeder cells for (at least) first two passages after thawing. Brg1fl/fl ESCs were previously described (Ho et al., Nat. Cell Biol. 2011).

extract_protocol:
ATAC-seq was performed according to the previously described protocol (Buenrostro et al., 2015) with modifications. Briefly, 50,000 cells were washed with cold PBS and resuspended in lysis buffer to extract nuclei. The nuclei were cold-centrifuged at 500 x g for 10 min. The nuclei pellet was incubated with transposition reaction buffer for 30 min. at 37 °C. The DNA was purified using the PCR Purification Kit (Qiagen).
The eluted transposed DNA was submitted to the PCR using Q5 High-Fidelity Polymerase (NEB). DNA was amplified with 12 cycles of PCR.

treatment_protocol: To induce deletion of Brg1 (Brg1 fl/fl ECSs), cells were treated with 1μM 4-hydroxytamoxifen for 72h. Correct depletion of Brg1 was checked by genotyping and Western Blot.


title: 3h embryo 6mA MeDIP-seq


title: ChIP_Snf2hko_CTCF-IP_1


title: RIPseq with hnRNPK antibody, MCF10A cells, repeat2

city: Bethesda

first: Jing

last: Huang

institute: National Cancer Institute

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases  using Trimmomatic software before alignment with the reference genome (Human - hg19) and the annotated  transcripts using STAR.
Both the  normalized count and the raw count are provided as part of the data delivery.
Genome_build: hg19
Supplementary_files_format_and_content: The gene expression quantification analysis (RSEM) was performed for all samples using STAR/RSEM tools.

source_name: MCF10A cells (ATCC® CRL-10317)

growth_protocol: MCF10A cells were cultured in DMEM/F12 media supplemented with 5% horse serum, 10 µg/ml human recombinant insulin, 20 ng/ml human EGF, 500 ng/ml Hydrocortisone, 100ng/ml Cholera toxin and antibiotics.

extract_protocol:
RNA were extracted with Trizol followed by cleanup using the Qiagen's Rneasey kit .
TruSeq mRNA Prep Kit  RS-122-2101
illumina TruSeq mRNA Prep Kit RS-122-  2101

treatment_protocol: No treatment

tag: passages

value: less than 20

tag: cell line

value: hnRNPK


title: RIPseq with hnRNPK antibody, MCF10A cells, repeat1


title: 6h embryo DMAD knock down 6mA MeDIP-seq

source_name: w1118 embryo DMAD KD


title: ChIP_Snf2hko_REST-IP_2

source_name: embryonic stem cells


title: Input, MCF10A expressing FLAG-CBFB


title: Input, MCF10A


title: LEC-enriched hepatic non-parenchymal cells (Non-Diseased, rep 1)

city: Aurora

first: Matthew

middle: Alan

last: Burchill

state: Colorado

department: Department of Medicine

institute: University of Colorado - Anschutz Medical Campus

description:
count_matrix.tsv.gz
cell_metadata.tsv.gz
nd1

data_processing:
UMI count matrices were generated using the 10x genomics CellRanger count (3.0.1) pipeline with default parameters.
The count matrices were combined and normalized using Seurat.
The combined matrix was then further filtered to exclude cells not passing the following QC measures: at least 250 genes detected (UMI > 0) and proportion of UMIs derived from mitochondia less than 20%. Genes were also excluded  if they were not expressed in at least  3 cells (UMI count > 0).
After filtering, this matrix was used for tSNE projection and graph based clustering. Following cell-embeddings and clustering, the original non-downsampled UMI data was used for all analysis and is provided as the count_matrix.tsv.gz.
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix with UMI counts per gene per cell. Cell_metadata.tsv contains information about each cell in the count matrix

source_name: LEC-enriched hepatic non-parenchymal cells (Non-Diseased)

growth_protocol: Transplanted livers were harvested and non-parenchymal cells (NPCs) were isolated and frozen in a single cell suspension as previously described. Additionally, non-diseased NPCs were purchased from Triangle research laboratories.

extract_protocol:
To enrich LECs from hepatic NPCs we thawed frozen samples in RPMI containing 10% Human Serum AB (Gemini Bio-products, West Sacramento, CA) and 1% DNASE (MP Biomedicals, Santa Ana, CA). Cells were washed 2x with PBS containing 2% FBS (Atlas Biologicals, Fort Collins, CO) and stained with antibodies against CD45 (clone HI30), CD31 (PECAM1, clone WM59), Podoplanin (clone NC-08) and CD146 (clone P1H12) from Biolegend (San Diego, CA) and CD68 (clone KP1) from abcam (San Francisco, CA). Cells from either Non-diseased, NASH or HCV were sorted using an Aria Fusion sorter (BD Biosciences, Franklin lakes, NJ) and enriched LECs were sorted into RPMI containing 50% human serum AB. Approximately 10,000 LEC-enriched hepatic NPCs were loaded onto a 10x genomics (San Francisco, CA) controller per manufacturer instructions to generate barcoded single cell GEMs using the 10x genomics 3’ kit.
10x Genomics 3' end library kit

tag: disease state

value: Non-diseased

value: liver


title: TMD8 Input

city: HOUSTON

last: Green

state: TEXAS

address: 7455 fannin street, SCR2.2026, Department of Lymphoma/Myeloma

institute: MD Anderson Cancer Center

data_processing:
Sequencing reads were aligned to the human genome (hg19) using BWA-Mem, realigned around InDels using GATK, sorted and deduplicated using Piccard tools. Peaks were called in TCF4 ChIP samples compared to their input control using EaSeq with global thresholding.
Peaks were annotated according to the transcription start site of the nearest RefSeq gene and filtered based upon FDR (<0.1), log2ratio of TCF4 ChIP vs. isotype control (≥2.0), peaks that overlapped between TMD8 and SUDHL2, and peaks corresponding to genes with differential expression between ABC-like DLBCL tumors with or without TCF4 DNA copy number gain. For visualization, files were converted to wiggle format and viewed using the Integrative Genomics Viewer.
Genome_build: hg19
Supplementary_files_format_and_content: wiggle plot of read density

source_name: ABC-DLBCL cell line

growth_protocol: DLBCL cell lines were mantained in RPMI-1640 media supplemented with 10%FBS and 1% penecilin/streptomycin. Cell authentication by short tandom repeat and mycoplasma testing were performed regularly during cell line maintanance.

extract_protocol:
For chromatin immuno-precipitation, cells were fixed with 1% formaldehyde, quenched by addition of 125 mM Glycine, 5µg of TCF4 antibody (The antibody is not commercially available. It is described in PMID 27846392 and was kindly shared by Dr. Michele Ceribelli) was used to perform ChIP overnight at 4ºC. Note; for Chip normalization, spike in chromatin/antibody was added to sonicated lysates (53083/61686; Active Motif). ChIP genomic DNA libraries were prepared using KAPA Hyper Prep kit (KK8502). Input represent the whole cell extract was used to prepare the genomic DNA library.
DNA libraries were prepared for sequencing using KAPA Hyper Prep Kit (Roche) with TruSeq indexes according to manufacturer's protocol.

treatment_protocol: Cell were seeded at 0.5 million cells/ml and treated with 60ng/ml concentartion of doxycycline for 24 hours.

value: activated B cell-like (ABC) diffuse large B-cell lymphoma (DLBCL) cell line

tag: treatment

value: Tetracyclin inducible TCF4 expression

tag: chip  antibody

value: none (WCE)


title: ChIP_wt_CTCF-IP_1

tag: tissue

value: mouse embryonic stem cells

value: CTCF (Santa Cruz, Cat. # C-20X)


title: SY5Y-NOTCH3IC-on7d_H3K27Ac


title: TMD8 TCF4 ChIP-seq


title: SU-DHL-2 TCF4 ChIP-seq


title: SU-DHL-2 Input


title: U2932 ARV771 RNAseq

data_processing:
Fastq files were aligned with STAR 2.6.0 using GENCODE27lift37 annotations with the arguments --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFilterType BySJout --outSAMtype BAM SortedByCoordinate --outSJfilterReads All --quantMode TranscriptomeSAM
The bam file with transcriptome coordinates were pre-processed with RSEM version 1.2.31's convert-sam-for-rsem tool with arguments -p 7 --memory-per-thread 1G
rsem-calculate-expression from RSEM 1.2.31 was used to quantify transcript expressions, with index similarly derived from GENCODE27lift37, using the parameters --paired-end --forward-prob 0.5 -p 7 --seed 20021208 --calc-pme --calc-ci --estimate-rspd
Tximport version 1.6.0 was used under R version 3.4.3 to aggregate the FPKM values from individual outputs, and then expression abundence from transcripts associated with the same HUGO symbol, as listed in ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_27/GRCh37_mapping/gencode.v27lift37.metadata.HGNC.gz, were summed to form gene-level expression data.
Genome_build: GRCh37
Supplementary_files_format_and_content: Comma-separated file representing the FPKM of the genes in HUGO symbols.

extract_protocol:
Total RNA isolated using All prep DNA/RNA kit from Qiagen Cat:80204
RNA libraries were prepared for sequencing using KAPA RNA Hyper Prep with RiboErase (HMR) KR1351 according to kit protocol.

treatment_protocol: Cell were seeded at 0.5 million cells/ml and treated with 50nM concentartion of ARV771 for 24 hours. Control cells were treated with equal volume of DMSO.

value: ABC-DLBCL cell line


title: RIVA ARV771 RNAseq

value: RIVA


title: HeLa NSUN2 KO rescue

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

data_processing:
Basecalls performed using illumina bcl2fastq 2.17.
Adapters were trimmed with cutadapt. Adapter-trimmed reads were quality trimmed with Trimmomatic.
Clean reads were firstly mapped to the genome and then transcriptome with hisat2-2.10
Pileup was performed using samtools API pysam.
Customized scripts were used to call m5C sites from samples
Genome_build: hg19
Supplementary_files_format_and_content: CSV files recording the coverage, m5C level, P-value for m5C sites

source_name: HeLa

extract_protocol:
Total RNA was isolated from tissues or cultured cells using chloroform and isopropanol following the manufacturer’s protocol. Polyadenylated RNA was separated from total RNA using either GenElute mRNA miniprepKit (Sigma-Aldrich) or Oligo dT Magnetic Beads (Vazyme).
Bisulfite treatment was performed using the EZ RNA methylation kit (Zymo Research) with some modifications. In brief, 1μg of polyadenylated RNA was converted using three different conversion conditions. The quantity of the converted RNA was determined by Qubit. Libraries were then constructed using VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). In short, 20ng converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 3min in 2× frag/prime buffer. The fragmented RNA was then used for library construction, following the manufacturer’s protocol.

value: HeLa

value: NSUN2 knockout, rescue


title: RIVA DMSO RNAseq

value: DMSO


title: HeLa NSUN2 KO rep2

value: NSUN2 knockout


title: AB5876 scRNA-seq

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Note: Second read contained only cell and molecule barcodes.

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: metadata.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts

source_name: brain immune cells

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Murine thymi were treated with enzymes cocktail (Collagenase, Dispase and Dnase) at 37C. Cells were separated by Percoll gradient density centrifugation, filtered and stained with Flow cytometry antibodies.
Murin small intestines were flushed with PBS, treated with EDTA, Dispase and Dnase, filtered and stained with Flow cytometry antibodies.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Mice were sacrified by CO2

tag: strain

value: DM-hTAU mice

value: brain

tag: selection marker

value: brain immune cells

value: 9 month


title: HeLa NSUN2 KO rep1

tag: genotype


title: AB5867 scRNA-seq

tag: age


title: ATAC_Snf2hko_1

value: Snf2h ko


title: LEC-enriched hepatic non-parenchymal cells (HCV)

description:
count_matrix.tsv.gz
cell_metadata.tsv.gz
hcv

value: HCV

value: liver


title: AB5865 scRNA-seq


title: AB5864 scRNA-seq


title: HeLa control rep2

description: Ctrl.csv

value: wild type


title: RIPseq with FLAG antibody, MCF10A expressing FLAG-CBFB

value: less than 20

value: FLAG


title: HeLa control rep1

description: Ctrl.csv


title: AB5863 scRNA-seq


title: Sample_c4

city: La Tronche

first: arnaud

last: MILLET

address: Allée des Alpes

institute: Institute for Advanced Studies

description: M1 2D=1, M1 3D=2, M2 2D=3, M2 3D=4

data_processing:
Fastq files were aligned to the reference human genome hg19/GRCh37 with tophat2 (-p 16 -r 150 -g 2 --library-type fr-firststrand) (Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
We removed reads mapping to multiple locations. We used HTSeq (Anders, S., Pyl, P. T. & Huber, W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinforma. Oxf. Engl. 31, 166–169 (2015) to obtain the number of reads associated to each gene in the Gencode v24lift37.
We used the Bioconductor DESeq package (Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010) to import raw HTSeq counts for each sample into R statistical software and extract the count matrix.
After normalizing for library size factors, we normalized the count matrix by the coding length of genes to compute FPKM scores (number of fragments per kilobase of exon model and millions of mapped reads).
Bigwig visualization files were generated using the bam2wig python script (Wang, L., Wang, S. & Li, W. RSeQC: Quality Control of RNA-seq experiments. Bioinformatics bts356 (2012).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt files include FPFM for each samples and conditions

source_name: Blood

growth_protocol: Peripheral blood mononuclear cells (PBMC) were obtained from whole blood (leukocyte reduction system cones) by density gradient centrifugation.Monocytes were isolated from PBMCs using CD14 magnetic beads.Polarization was subsequently obtained by seeding cells in the same concentration of M-CSF and adding specific stimulations for a total of 48 h. Polarization states were induced as follows M1 macrophages: IFNγ 10 ng/ml + LPS 1 ng/ml and M2 macrophages: IL-4 20 ng/ml + IL-13 20 ng/ml.

extract_protocol:
RNA was isolated from 106 cells for each polarization using the MirVana isolation kit™
RNA libraries were prepared for sequencing using standard Illumina protocols

value: J7 differetiated macrophages

tag: donor

value: Donor c


title: Sample_c3

description: M1 2D=1, M1 3D=2, M2 2D=3, M2 3D=4


title: Sample_c2

description: M1 2D=1, M1 3D=2, M2 2D=3, M2 3D=4


title: U2932 DMSO RNAseq

value: ABC-DLBCL cell line


title: Sample_c1

description: M1 2D=1, M1 3D=2, M2 2D=3, M2 3D=4


title: Sample-8

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

data_processing:
The RNA-seq data analysis was performed using the new version of the Tuxedo protocol with HISAT, StringTie and Ballgown
Sequences were then aligned to the mouse genome (prebuilt indexes downloaded from HISAT2 website) using the hierarchical indexing for spliced alignment of transcripts program HISAT2
StringTie was used to assemble and quantify the transcripts in each sample using the mouse genome database
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with Ballgown following the protocol described in the Tuxedo protocol publication (Nat Protoc. 2016 Sep; 11(9): 1650–1667.)
Genome_build: M. musculus, GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: The murine fibroblast 3T3-L1 cell line was purchased from ZenBio (Cambridge Bioscience, Cambridge, UK) and was not used past passage 10. Undifferentiated 3T3-L1 cells were grown at 37°C (5% CO2) in 75 cm² flasks (Corning, Tewksbury, USA) in a maintenance medium composed of phenol red free DMEM (Life Technologies, Warrington, UK), 10% newborn calf serum (New Zealand origin, Thermo Fisher Scientific (Life Technologies)), 2mM glutamine (GE Healthcare Life Sciences) and 10 µg/ml penicillin/streptomycin (Life Technologies). For differentiation of 3T3-L1 cultures to adipocytes, cells were seeded into 96 well plates (Dutscher Scientific, Brentwood, UK) at a density of 20,000 cells per well in 100 µl maintenance medium.

extract_protocol:
RNA extraction was performed using the Qiagen RNeasy kit (Qiagen, Manchester, UK) according to the manufacturer's instructions. RNA samples were assessed for quantity and integrity using the NanoDrop 8000 spectrophotometer V2.0 (ThermoScientific, USA) and Agilent 2100 Bioanalyser (Agilent Technologies, Waldbronn, Germany), respectively. All samples displayed a RIN score of 10 and were taken forward for RNA library preparation.
A 100ng aliquot of total RNA from each sample was used to prepare mRNA libraries using the NEBNext mRNA isolation kit in conjunction with the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs, Massachusetts, USA), and samples randomised before preparation. Fragmentation of isolated mRNA prior to first strand cDNA synthesis was conducted using incubation conditions recommended by the manufacturer for a fragment size of 300bp (94°C for 10 minutes). A total of 13 cycles of PCR were performed for final library amplification. Resulting libraries were quantified using the Qubit 2.0 spectrophotometer (Life Technologies, California, USA) and average fragment size assessed using the Agilent 2200 Tapestation (Agilent Technologies, Waldbronn, Germany). A final sequencing pool was created using equimolar quantities of each sample with compatible indexes. Paired-end reads of 75bp were generated for each library using the Illumina NextSeq®500 in conjunction with the NextSeq®500 v2 High-output 150-cycle kit (Illumina Inc., Cambridge, UK).

treatment_protocol: Following a 2-day stabilization period, they were switched to a differentiation medium containing DMEM, 2mM glutamine, 10 µg/ml penicillin/streptomycin, 10% fetal bovine calf serum (GE Healthcare Life Sciences, Buckinghamshire, UK), 500 μM 3isobutyl1methylxanthine (Sigma-Aldrich Ltd, Gillingham, Dorset, UK) and 100 nM insulin from bovine pancreas (Sigma-Aldrich Ltd). After a further 2-day incubation, the medium was refreshed to start the incubation with quizalofop-p-ethyl at the concentration of 50 uM. Dexamethasone was used as a positive control. Media were replenished every 2 days for a further 6 days.

value: Quizalofop-p-ethyl 0.05mM 6hrs

value: differentiated 3T3-L1 cells

tag: culture replicate


title: Sample-9

value: Control 24 hrs


title: Sample-5

value: Control 12 days


title: Sample-6

value: Quizalofop-p-ethyl 0.05mM 12 days


title: Sample-7

value: Control 6 hrs


title: Sample_b4

description: M1 2D=1, M1 3D=2, M2 2D=3, M2 3D=4

value: Donor b


title: Sample-4

value: Quizalofop-p-ethyl 0.05mM 24hrs


title: Sample_b2

description: M1 2D=1, M1 3D=2, M2 2D=3, M2 3D=4


title: Sample_b1

description: M1 2D=1, M1 3D=2, M2 2D=3, M2 3D=4


title: Sample-30


title: Sample_a3

description: M1 2D=1, M1 3D=2, M2 2D=3, M2 3D=4

value: Donor a


title: Sample-27


title: Sample-29


title: Sample-28


title: Sample_a2

description: M1 2D=1, M1 3D=2, M2 2D=3, M2 3D=4


title: Sample_a1

description: M1 2D=1, M1 3D=2, M2 2D=3, M2 3D=4


title: Sample-26


title: HeLa_m5C_mix_IP (RIP-seq)

data_processing:
Basecalls performed using illumina bcl2fastq2.
Adapters were trimmed with cutadapt.
Clean reads were mapped to the reference genome with Tophat2
m5C peak analysis was then performed. Each gene was split into the 100-nucleotide sliding windows and an enrichment fold (winscore) was calculated for each window
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: HeLa, cell line

extract_protocol:
Total RNA was isolated from cultured cells using chloroform and isopropanol following the manufacturer’s protocol. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
Polyadenylated mRNA was first fragmented with Magnesium RNA Fragmentation Module and then cleaned up using ethanol precipitation. 100ng RNA was saved to serve as input control and the rest was incubated with 5ug anti-m5C antibody in IPP buffer overnight at 4℃. 60μl Protein-G magnetic beads was pre-blocked with 0.5mgml-1 BSA at 4℃ for 2h and then added for immunoprecipitating m5C-Ab mixture at 4℃ for another 2h. After washing with IPP buffer 3 times, RNA was competitively eluted from the beads with 20mM 5-Methylcytosine hydrochloride , followed by ethanol precipitation. RNA was resuspended in 8μl water. VAHTS Stranded mRNA-seq library prep kit (Vazyme) was used for library construction of both IP and input RNAs.

value: HeLa

tag: spike-ins

value: With in vitro transcribed m5C spike-ins

tag: rip antibody

value: 5-mC antibody, Diagenode, catalog:C15200003, lot:003


title: Sample-25

tag: cell type


title: HeLa_m5C_mix_input (RIP-seq)


title: HeLa_C_mix_IP (RIP-seq)

value: With in vitro transcribed non-m5C spike-ins


title: Sample-24


title: Sample-23


title: HeLa_C_mix_input (RIP-seq)


title: Sample-22


title: Sample_b3

description: M1 2D=1, M1 3D=2, M2 2D=3, M2 3D=4


title: Testis_N2 (human_BS)

data_processing:
Basecalls performed using illumina bcl2fastq 2.17.
Adapters were trimmed with cutadapt. Adapter-trimmed reads were quality trimmed with Trimmomatic.
Clean reads were firstly mapped to the genome and then transcriptome with hisat2-2.10
Pileup was performed using samtools API pysam.
Customized scripts were used to call m5C sites from samples
Genome_build: hg19

source_name: Testis

value: Testis


title: Testis_N7 (human_BS)


title: Sample-20


title: Sample-21


title: Spleen_N6 (human_BS)

source_name: Spleen

value: Spleen


title: Spleen_N1 (human_BS)


title: Sample_a4

description: M1 2D=1, M1 3D=2, M2 2D=3, M2 3D=4

value: J7 differetiated macrophages


title: Muscle_N5 (human_BS)

source_name: Muscle

value: Muscle


title: Muscle_N2 (human_BS)


title: Sample-3


title: Sample-2

value: Quizalofop-p-ethyl 0.05mM 6hrs


title: Sample-18

value: differentiated 3T3-L1 cells


title: Sample-17


title: Lung_N1 (human_BS)

source_name: Lung

value: Lung


title: Sample-15

value: Control 24 hrs


title: Sample-13


title: Sample-16


title: Liver_N1 (human_BS)

source_name: Liver

value: Liver


title: Sample-14


title: Heart_N5 (human_BS)

source_name: Heart

value: Heart


title: Sample-12

value: Quizalofop-p-ethyl 0.05mM 12 days


title: Sample-11

value: Control 12 days


title: Frontal_cortex_N4 (human_BS)

source_name: Frontal cortex

value: Frontal cortex


title: Sample-10

value: Quizalofop-p-ethyl 0.05mM 24hrs


title: Sample-1

value: Control 6 hrs


title: HiC_Brg1ko_2

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
HiC-seq reads were aligned to the genome, paired and filtered using HiC-Pro version 2.10 (Servant N et al, Genome Biology 2015, 16:259) with default parameters and using MboI as restriction enzyme with LIGATION_SITE = GATCGATC.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Files with extension .matrix: Processed, iterative corrected (iced) sparse Hi-C matrix at 150kb resolution. Files with extension .bed: Bin file for genomic positions of 150kb bins in bed format (NOTE: the  HiC-seq bed files are  identical since the same binning applied to all HiC-seq samples).

extract_protocol:
Hi-C was performed as previously described (Rao et al., 2014) with modifications. In brief, 5 million mouse ES cells were fixed using formaldehyde and lysed in 500μl of Lysis Buffer (10 mM Tris-HCl pH8.0; 10 mM NaCl; 0.2% NP40; 1X Protease inhibitors). Nuclei were permeabilised and digested with 400U of MboI restriction enzyme (NEB #R0147M). 5’overhangs were filled with incorporation of biotin-14-dATPs (ThermoFisher #19524016) using DNA Polymerase I Large (Klenow) fragment (NEB #M0210L) and resulting blunt-ends were ligated with T4 DNA Ligase (NEB #M0202T). After reverse-crosslinking, RNAseA and Proteinase K treatment, DNA was purified using AMPure XP beads and 2μg of purified DNA was sheared using Covaris S220 Focused-ultrasonicator to an average size of 300-500bp. The biotin ligation junctions were then captured using Dynabeads MyOne Streptavidin T1 beads (ThermoFisher #65601).
End-repairing, A-tailing, Illumina adapter ligation and indexing PCR amplification (8-10 cycles) were performed on beads before final purification with AMPure XP beads. Resulting libraries were analysed and quantified using Agilent Bioanalyzer and sequenced.

value: mouse embryonic stem cells

tag: genotype/variation

value: Brg1 ko


title: Spleen_M1 (mouse_BS)

data_processing:
Basecalls performed using illumina bcl2fastq 2.17.
Adapters were trimmed with cutadapt. Adapter-trimmed reads were quality trimmed with Trimmomatic.
Clean reads were firstly mapped to the genome and then transcriptome with hisat2-2.10
Pileup was performed using samtools API pysam.
Customized scripts were used to call m5C sites from samples
Genome_build: mm10

source_name: spleen

extract_protocol:
Total RNA was isolated from tissues or cultured cells using chloroform and isopropanol following the manufacturer’s protocol. Polyadenylated RNA was separated from total RNA using either GenElute mRNA miniprepKit (Sigma-Aldrich) or Oligo dT Magnetic Beads (Vazyme).
Bisulfite treatment was performed using the EZ RNA methylation kit (Zymo Research) with significant modifications.

tag: gender

value: male

value: 8-10 weeks

value: WT

value: spleen


title: HEK293T (human_BS)

source_name: HEK293T, cell line


title: Sample-19


title: Small_intestine_M1 (mouse_BS)

source_name: small intestine

value: small intestine


title: Spleen_F1 (mouse_BS)

value: female


title: HiC_Brg1fl_2

value: wildtype


title: Small_intestine_F1 (mouse_BS)


title: HiC_Brg1ko_1


title: HiC_Brg1fl_1


title: Lung_N7 (human_BS)

value: Lung


title: Liver_N6 (human_BS)

value: Liver


title: Muscle_F3 (mouse_BS)

source_name: muscle

value: muscle


title: Muscle_F4 (mouse_BS)


title: HiC_wt_2


title: Muscle_F2 (mouse_BS)


title: Heart_N1 (human_BS)

value: Heart


title: Bis_Snf2hko_1

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Bis-seq reads were first trimmed to remove adaptor sequences using cutadapt version 1.15 (Marcel Martin. EMBnet.journal, 17(1):10-12, 2011) with -a AGATCGGAAGAGC -m 10 --overlap=1. Trimmed reads were aligned to the genome using qAlign from the QuasR Bioconductor package version 1.18.0 (Gaidatzis et al, Bioinformatics, 2015) with bisulfite=”dir”.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Total and methylated counts for Cs in CpG context were calculated using the qMeth function from QuasR. The processed data file contains the genomic coordinates for each CpG (columns chr, start and end), and the counts of total and methylated reads that overlap a given CpG (columns n.total and n.methylated).

source_name: embryonic stem cells

extract_protocol:
Genomic DNA was isolated using QIAamp DNA mini kit from Qiagen (cat. No 51304) and fragmented using Covaris S220 Focused-ultrasonicator.
500ng of fragmented DNA was then used for library preparation with NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #E7370) and bisulfite treatment with EZ DNA-methylation Gold Kit (Zymo Research #D5005). Final PCR amplification was performed using KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit (KAPA Biosystems #KR0413) and 12 cycles of amplification.

value: Snf2h ko


title: Lung_M1 (mouse_BS)

source_name: lung

value: lung


title: Lung_F1 (mouse_BS)


title: Bis_wt_1


title: Muscle_F1 (mouse_BS)


title: ATAC_Brg1ko_3


title: HiC_wt_1


title: HiC_Snf2hko_2


title: ATAC_Brg1ko_2


title: Heart_F1 (mouse_BS)

source_name: heart

value: heart


title: ATAC_Brg1ko_1


title: ATAC_Brg1ctrl_3

value: Brg1 fl/fl (control)


title: HiC_Snf2hko_1

value: mouse embryonic stem cells


title: ATAC_Brg1ctrl_2


title: Sox1posGP 2

city: Planegg-Martinsried

first: Valentin

middle: Claude Vincent

last: Baumann

address: Grosshaderner Strasse 9

department: Physiologicl Genomics

institute: Biomedical Center, LMU Munich

data_processing:
reads were mapped to the mm10 genome using STAR v2.6 RNA-seq aligner (RRID:SCR_015899)
TPM were calculated using RSEM v1.1.14 (RRID:SCR_013027)
A matrix with the raw counts of reads per transcript in each sample was generated using R Studio v 1.1.442 (RRID:SCR_000432)
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts of reads per transcript of each sample; .csv

source_name: Neural progenitor cells

extract_protocol:
Total RNA was isolated using the  PicoPureTM RNA Isolation Kit (ThermoFisher, KIT0204)
cDNA was synthesized and amplified using the SMART-SeqTM v4 UltraTM Low Input RNA Kit (TaKaRa, 634894), and libraries were prepared using the MicroPlex Library Preparation Kit v2 (Diagenode, C05010012)

tag: sox1 epression

value: ES-derived neural progenitor cells

tag: sorted

value: yes

value: Sox1 positive glial progenitors


title: Sox1posGP 1


title: Baseline 3

value: no

value: Baseline (=Sox1 negative) glial progenitors


title: ATAC_Brg1ctrl_1


title: Sox1posGP 3


title: Liver_F1 (mouse_BS)

source_name: liver

value: 8-10 weeks

value: WT

value: liver


title: ATAC_addbackMut_1

value: Snf2h ko, Snf2h mutant add-back


title: Baseline 1


title: ATAC_addbackMut_2


title: NR 2

source_name: Neural stem cells

value: ES-derived neural stem cells

value: neural rosettes (GFP sorted neuroepithelial cells)


title: ATAC_addbackWt_1

value: Snf2h ko, Snf2h wiltype add-back


title: ATAC_Snf2hko_2

value: Snf2h ko


title: NR 1


title: ATAC_wt_2

value: wildtype


title: NSC 3

value: neural stem cells (unsorted neuroepithelial cells)


title: NSC 2


title: NSC 1


title: F49TH1

city: Riversidy

first: Giovanna

last: Pozuelos

state: California

address: 3401 Watkins Drive

institute: University of California, Riverside

description:
F49THS1: Female, age 49, before third hand smoke exposure
Final_supplemental_counts_rpkm_cpm_edger_ThirdhandSmoke.txt

data_processing:
Libraries were sequenced as single-end 75 base pair reads using an Illumina NextSeq500 following the manufacturer's instructions.
The RNA-Seq analysis workflow implemented by systemPipeR was used to perform all the downstream data processing.
Adapter sequences and low quality tails were removed from the raw reads using the Trimmomatic package
The preprocessed reads were then aligned against the UCSC hg19 human reference genome using Tophat2 package (Version 2.0.14)
Read counting was performed with the summarizeOverlaps function of the GenomicsAlignment package
Using a cut-off value of at least 1 RPKM average in all the samples, the raw expression counts of the remaining 10,938 genes passing this filter were used for differential gene expression analysis using EdgeR29
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts, RPKM, CPM values and edgeR differential gene expression calls for every gene in each Sample.

source_name: Nasal Epithelium

extract_protocol:
RNA was isolated from human nasal scrapes using RNeasy micro kits (Catalogue #74034, Germantown, MD) and the isolated RNA was stored at -80oC untill further processing
Libraries were sequenced as single-end 75 base pair reads using an Illumina NextSeq500 following the manufacturer's instruction
poly-A RNA-Seq

treatment_protocol: Four non-smoker females were individually exposed to clean air using a helmet for a total of ~3 hours. The same individuals returned after ~21 days or more, and were exposed to THS using the same laboratory conditions (wearing the helmet). Nasal scrapes were collected before and after each with the end goal to peform RNAseq.

value: Nasal Epithelium

value: female

tag: exposure

value: before third hand smoke exposure


title: F49TH2

description:
F49THS2: Female, age 49, after third hand smoke exposure
Final_supplemental_counts_rpkm_cpm_edger_ThirdhandSmoke.txt

value: after third hand smoke exposure


title: F44TH2

description:
F44THS2: Female, age 47, after third hand smoke exposure
Final_supplemental_counts_rpkm_cpm_edger_ThirdhandSmoke.txt


title: Baseline 2

value: ES-derived neural progenitor cells


title: P1A8_Pool_No_Dox_3

last: Dvela Levitt

data_processing:
Illumina HiSeq2500 sequencing system (2x101 Bp Reads) software used for basecalling. The provided data from Sequencing platform  are de-multiplexed and aggregated Picard Bam files.
Bam files received from sequencing platform were reverted to fastq files followed by alignment of paired end reads  to the mm10 mouse or hg19 human reference genome using STAR v2.5.2b.
Quality Control metrics were obtained using RNA-SeQC v2.3.1.
Expression levels were estimated by running RSEM v1.3.0 with default parameters on these alignments.
Genome_build: hg19
Supplementary_files_format_and_content: Raw expression levels produced by RSEM

growth_protocol: 200,000 cells/well were plated on 12-well filter plates, cells were grown for 4 days before RNA extraction

extract_protocol:
RNaesy- Qiagen kit-(#74106) was used for RNA extraction
Concentrations of purified RNA were measured with the QuantiTTM RiboGreen® RNA Assay Kit  and normalized to 5 ng/μL. An automated variant of the Illumina TruSeqTM Stranded mRNA Sample Preparation Kit was used for library preparation from a 200 ng aliquot of RNA. This method preserves strand orientation of the RNA transcript and uses oligo dT beads to select mRNA from the total RNA sample. Following cDNA synthesis and enrichment, cDNA libraries were quantified with qPCR using the KAPA Library Quantification Kit for Illumina Sequencing Platforms and then pooled equimolarly.

value: MUC1 kidney disease patient derived kidney epithelial cells


title: F44TH1

description:
F44THS1: Female, age 47, before third hand smoke exposure
Final_supplemental_counts_rpkm_cpm_edger_ThirdhandSmoke.txt


title: F48TH2

description:
F48THS2: Female, age 48, after third hand smoke exposure
Final_supplemental_counts_rpkm_cpm_edger_ThirdhandSmoke.txt


title: ATAC_addbackWt_2

data_processing:
Illumina RTA 1.18.64 (HiSeq 2500) or RTA 2.4.1 (NextSeq 500) and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Paired ATAC-seq reads were first trimmed to remove adaptor sequences using cutadapt version 1.15 (Marcel Martin. EMBnet.journal, 17(1):10-12, 2011) with -a CTGTCTCTTATA -m 10 --length=51. Trimmed reads were aligned to the genome using bowtie2 version 2.3.0 ( Langmead B, Salzberg S. Nature Methods. 2012, 9:357-359). with --sensitive-local --minins 0 --maxins 1000 –dovetail and converted to bam format.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package (Gaidatzis et al, Bioinformatics 2015) version 1.18.0 with default parameters except scaling=1e6, binsize=100 and pairedAsSingle=TRUE. The scores in the wig file therefore represent the number of 5'-read ends (Tn5 insertion sites) per 100bp window and per million reads in the library.

value: mouse embryonic stem cells


title: P1A8_Pool_No_Dox_2


title: NR 3

value: yes


title: F48TH1

description:
F48THS1: Female, age 48, before third hand smoke exposure
Final_supplemental_counts_rpkm_cpm_edger_ThirdhandSmoke.txt


title: F27TH2

description:
F27THS2: Female, age 27, after third hand smoke exposure
Final_supplemental_counts_rpkm_cpm_edger_ThirdhandSmoke.txt


title: N1H1_Pool_No_Dox_2

value: normal kidney cells


title: P1A8_Pool_No_Dox_1


title: F27TH1

description:
F27THS1: Female, age 27, before third hand smoke exposure
Final_supplemental_counts_rpkm_cpm_edger_ThirdhandSmoke.txt


title: N1H1_Pool_No_Dox_1


title: F49CA2

description:
F49CA2: Female, age 49, after clean air exposure
Final_supplemental_counts_rpkm_cpm_edger_ClearAir.txt

value: after clean air exposure