title: TKO_ES_K27_rep1

source_name: H3K27me3 ChIP DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 1

source_name: MNase digested input DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells for H3K27me3 ChIP, replicate 1


title: NT_2

status: Public on Feb 17 2021

type: SRA

city: Shanghai

first: xiangyang

last: wu

address: 507 Zhengmin Road, Shanghai, China

country: China

institute: Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data contained low quality reads, contaminated joints, and unspecified high N base reads. These reads need to be removed by using SOAPnuke v1.5.2 solfware with parameters -l 15 -q 0.2 -n 0.1 (BGI Platform: https://github.com/BGI-flexlab/SOAPnuke) before data analysis to ensure the reliability of the results (QC).
After we got clean reads, we used HISAT(Hierarchical Indexing for Spliced Alignment of Transcripts) (Kim, Langmead et al. 2015) v2.0.4 software with parameters -p 8 --phred64 --sensitive -I 1 -X 1000 (http://www.ccb.jhu.edu/software/hisat) to compare clean reads to the reference genome sequence (May need to QC of alignment).
Clean reads were aligned to the reference sequence by using Bowtie2 (Langmead and Salzberg 2012) v2.2.5 software with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200 (http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml), and then RSEM (Li and Dewey 2011) v1.2.12 software with the default parameters (http://deweylab.biostat.wisc.edu/ RSEM) was used to calculate the expression levels of genes and transcripts.
We used DEGseq algorithm with parameters Fold Change >= 2 and Adjusted Pvalue <= 0.001  for differential gene analysis a protocol from (Wang, Feng et al. 2010).
Genome_build: mm10
Supplementary_files_format_and_content: differential expression statistics

molecule: total RNA

organism: Mus musculus

source_name: peritoneal macrophage

growth_protocol: Peritoneal macrophages were isolated as described (Kong et al, 2009). Briefly, mice received intraperitoneally 2.0 ml of 4% Brewer’s thioglycollate medium (B2551, Sigma-Aldrich). After 3 days, peritoneal exudate cells were collected from euthanized animals using 10 ml cold PBS. Subsequently, cells were plated in 12-well plates at 106 cells/well in RPMI 1640 supplemented with 10% FBS plus penicillin/streptomycin and were incubated at 37°C in 5% CO2 for 2 hours. Cultures were washed three times with PBS to remove non-adherent cells, and the remaining adherent monolayer cells were used as primary peritoneal macrophages.

extract_protocol:
Total RNA was isolated, its concentration, RIN value, and 28S/18S fragment size were measured, used for RNA-seq analysis. cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ-500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NT(no treatment); AG(arabinogalactan, 1μg/ml, 24h); Mtb(H37Rv, MOI=5,24h); Mtb_AG(H37Rv MOI 5 for 24, plus arabinogalactan, 1μg/ml for 24h). Before infection, Mtb organisms were suspended in a complete medium without antibiotics. Peritoneal macrophages were infected with Mtb at an MOI of 5.

tag: strain

tag: cell type

value: peritoneal macrophage


title: TKO_ES_K9_rep1

type: genomic

city: Kobe

first: Yuichi

last: Kumaki

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description: H3K9me2 ChIP-chip data from Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells

hyb_protocol: Approximately 4 ug each of Cy3 and Cy5 labeled DNA were hybridized in Agilent hybridization chambers for 40.5-41.0 hours at 65 degrees C and 20 rpm according to the manufacturer's instructions (G4481-90010 Agilent Mammalian ChIP-on-chip Protocol Version 10.11).

scan_protocol: Slide scanning was performed using the Agilent DNA Microarray Scanner G2505C with 5 um resolution and 20-bit dynamic range.

data_processing: The scanned images were processed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol ChIP_107_Sep09 and Grid 027128_D_F_20100129) to generate background subtracted and spatially detrended Processed Signal intensities and log 10 ratios with the linear normalization.  Data was processed by a) change log base from 10 to 2, b) removal of data of control probes, c) removal of data of outlier probes (gIsFeatNonUnifOL flag = 1,  gIsFeatPopnfOL flag = 1, gIsPosAndSignif flag = 0, rIsFeatNonUnifOL = 1 or rIsFeatPopnfOL = 1 in any of samples).

molecule: genomic DNA

source_name: H3K9me2 ChIP DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 1

label_protocol: Without amplification, ChIP DNA and input MNase digested DNA were labeled with Cy5 and Cy3, respectively, using the Genomic DNA Enzymatic Labeling Kit (Agilent) according to the manufacturer's instructions (G4481-90010 Agilent Mammalian ChIP-on-chip Protocol Version 10.11). Purification of labeled DNA was performed using the Amicon Ultra-0.5, Ultracel-30, 30kDa (Millipore). Quantity and dye incorporation of labeled DNA were checked using the NanoDrop ND-1000 Spectrophotometer (Thermo) and the 2100 Bioanalyzer (Agilent).

growth_protocol: ES cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 15% fetal calf serum (FCS), 0.1 mM nonessential amino acids (Invitrogen), 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, and 2000 U/ml leukemia inhibitory factor (LIF) on gelatinized culture dishes without feeder cells.

extract_protocol: Approximately 3-5 x 10^6 cells were collected and washed twice with ice-cold PBS. The cells were suspended in 50 ul of 0.3 M sucrose containing buffer 1 (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.5mM dithiothreitol, 0.5 % Protease Inhibitor Cocktail (SIGMA P8340) , 15 mM Tris-HCl pH7.5). The cells were lysed by adding 50 ul of 0.8 % NP-40 and 0.3 M sucrose containing buffer 1 and put on ice for 10 min. The lysate was layered over 0.8 ml of 1.2 M sucrose containing buffer 1. The nuclear pellets were collected by centrifuge 8.5 k rpm 10 min, and resuspended in 250 ul of micrococcal nuclease (MNase) digestion buffer (4 mM MgCl2, 1 mM CaCl2, 0.32 M sucrose, 0.5 % Protease Inhibitor Cocktail (SIGMA P8340) , 50 mM Tris-HCl pH7.5). MNase digestion was performed at 37 degrees C for 20 min with 0.8 U MNase (Takara), then stopped by addition of EDTA to final 20 mM. The chromatin extract was obtained as the supernatant of centrifugation at 13 k rpm 10 min. 60 x 2 (duplicate), 30 and 80 ul of the chromatin extracts were used for immunoprecipitation for H3K4me2, H3K9me2 and H3K27me3, respectively, and remained extract was served for the input sample (MNase digested input DNA). 60 x 2 (duplicate), 30, 80 ul of Dynabeads M-280 Sheep anti-Mouse IgG (Invitorogen), pre-equilibrated with incubation buffer (50 mM NaCl, 5 mM EDTA, 0.1 % NP-40, 0.1 mM PMSF, 20 mM Tris-HCl pH 7.5), were incubated overnight with 3, 1.5 and 4 ug of mouse monoclonal antibodies against H3K4me2 (Monoclonal antibody institute, MABI0303), H3K9me2 (Monoclonal antibody institute, MABI0307) and H3K27me3 (Abcam, ab6002), respectively, in 200 ul of incubation buffer. Beads-antibody complexes were collected and resuspend in 540 x 2 (duplicate), 270 and 720 ul, for H3K4me2, H3K9me2 and H3K27me3, respectively, of incubation buffer and incubated 4 hours with the chromatin extract. The immune complexes were sequentially washed with 75, 125 and 175 mM NaCl containing buffer A (10 mM EDTA, 0.1 % NP-40, 50 mM Tris-HCl pH 7.5). Both input and immunoprecipitated samples were treated with RNase and proteinase K, and purified with MinElute Reaction Cleanup kit (Qiagen).

treatment_protocol: The cells were recovered by trypsinization and used for RNA preparation.

tag: cell line

value: Line 19-1

tag: genotype/variation

value: embryonic stem (ES) cells

tag: chip antibody

tag: chip antibody vendor

value: Monoclonal antibody institute

tag: chip antibody catalog #

tag: chip antibody lot #

source_name: MNase digested input DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells for H3K9me2 ChIP, replicate 1

treatment_protocol: The cells were recovered by trypsinization and used for chromatin IP.

value: none, MNase digested input DNA


title: NT_1


title: Mtb_1


title: S5 smallRNAs

city: Poznan

first: Andrzej

last: Pacak

address: Uniwersytetu Poznanskiego 6

country: Poland

institute: Adam Mickiewicz University, Poznan

data_processing:
Raw reads where trimmed using CLC Genomics Workbech (Qiagen)
Trim settings: removal - low quality sequence (limit = 0.02), ambiguous nucleotides: maximal 2 nucleotides allowed, adapter sequences, removal of sequences on length: minimum length 18 nucleotides and maximum length 25 nucleotides.
Extract and count was performed using CLC Genomics Workbench.
Empirical analysis of (EDGE) was used to find significant fold changes in small RNA expression levels between samples derived from different treated barley. Moreover we performed EDGE Bonferroni and EDGE FDR p-value correction calculation.
Unique sequences were annotated in a two-step process: firstly were mapped to miRBase to extract data about known microRNAs.
Secondly, unannotated to miRBase reads were maped to the Ensembl Plants database v.40 to annotate other small RNAs to different types of barley cDNAs.
Genome_build: miRBase release 22 and Hordeum vulgare, Ensembl Plants database v.40
Supplementary_files_format_and_content: Small RNA which are annotated to miRBase, small RNA which expression is changed significantly (Bonferroni p-value correction < 0.05).

organism: Hordeum vulgare

source_name: shoot

growth_protocol: Barley seeds were germinated on wet, sterile Whatman filter paper for 3 days in a growth chamber under long-day (16 h) conditions at 23 °C until white hypocotyls were visible. Three seedlings were then transferred to a single pot that contained a mixture of sterile low-Pi soil (8 mg P/kg) and sand (7:2 ratio). The plants were subsequently grown under controlled conditions, which included a 16 h day/8 h night photoperiod at a temperature of 22 °C. Plant material was obtained from two different Pi regimes: low-Pi and Pi-sufficient (control).

extract_protocol:
Shoots and roots of 23 old barley were harvested and frozen in liquid nitrogen. Total RNA was extracted from 100 mg of grinded organ using RNA extraction buffer: 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate pH 5.0, 5% v/v glycerol, 38% v/v saturated acidic phenol, 5 mM EDTA, 0.5% sodium lauroylsarcosine, in diethylpyrocarbonate-treated water (DEPC) (Smoczynska et al., 2019) and protocol that allow for enrichment of small RNAs (Kruszka et al., 2013). Quality of the isolated RNA was analyzed using Plant RNA Nano assay and 2100 Bioanalyzer (Agilent Technologies). Reference: Smoczynska A, Sega P, Stepien A, Knop K, Jarmolowski A, Pacak A, Szweykowska-Kulinska Z. (2019) miRNA Detection by Stem-Loop RT-qPCR in Studying microRNA Biogenesis and microRNA Responsiveness to Abiotic Stresses. Methods Mol Biol. 1932:131-150.  Kruszka K, Pacak A, Swida-Barteczka A, Stefaniak AK, Kaja E, Sierocka I,  Karlowski W, Jarmolowski A, Szweykowska-Kulinska Z. (2013) Developmentally regulated expression and complex processing of barley pri-microRNAs. BMC Genomics. 14:34.
Total RNA was separated on 15 % 8M urea polyacrylamide gel and small RNA fraction 15 nt -30 nt was excised from the gel, purified and was used for libraries construction. Libraries were prepared using TruSeq Small RNA Library Preparation Kit (Illumina). Quantity of the purified libraries were performed using Qubit® dsDNA HS Assay kit (Invitrogen, Thermo Fisher Scientific) and Qubit 3.0 Fluorometer (Invitrogen, Thermo Fisher Scientific). Finally, the quality of the libraries was analyzed using High Sensitivity D1000 ScreenTape Assay (Agilent Technologies) and 2200 TapeStation (Agilent Technologies).

treatment_protocol: Stressed plants and control plants were growing on same soil (low-Pi contaning 8 mg of P/kg). To control plants additional 60 mg of P/kg (using KH2PO4) was added to provide Pi-sufficient conditions.

tag: tag

value: Rolap

tag: tissue

value: shoot

tag: condition

value: low Pi condition


title: Sample_3_U2OS50_KBr_1h_hoGG1 [damage]

city: Tel Aviv

first: Yuval

last: Ebenstein

state: HaMerkaz (Central)

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

description: processed data file: Damage.bedgraph

library_source: genomic

data_processing:
library strategy: Repair Assisted Damage Detection sequencing (RADD-seq)
Sequencing reads were aligned to the hg38 human reference using Bowtie 2 (version 2.3.4.2) with default parameters
Following alignment, reads with MAPQ less than 30 were filtered with SAMtools, and the remaining reads were de-duplicated with MateCigar (version 2.18.2.1) to eliminate PCR duplication bias
Genomic coverage damaged DNA was calculated using BEDTools genomecov (version 2.27.1)
Each of the data sets, damage, repaired and input data, were generated using an in house sliding window script with 200 bp window size and 1bp length step size
Correlation of biological replicates was assessed using Pearson correlation in 1 kb bins
The two biological replicates for damage and repair data sets were combined by averaging the number of reads in each region
The data in both sample types (“damage” and “repaired”) was normalized to the input DNA, to eliminate any bias resulting from the pull-down assay and mis-alignment to repetitive areas in the genome. In the first step, we divided the input DNA into 200 bp sized-windows, and the read count in each window falling in the range of (mean+1Stdv - mean+2Stdv) was divided by mean+1Stdv (values were ranging between 1-1.14). In the second step, values lower than mean+1Stdv was set to 1, and all regions higher than mean+2Stdv were discarded from the data since they represent areas with high background level. Next, the read count for damage and repaired data in each 200 bp window was divided by the normalized input DNA respective windows
The regions discarded from the input data were discarded from these data sets as well. Finally, reads mapping to the ENCODE-defined blacklist regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were discarded
Genome_build: hg38
Supplementary_files_format_and_content: Bedgraph, Bed

organism: Homo sapiens

source_name: damaged

growth_protocol: U2OS (human osteosarcoma) cells were cultured in Dulbecco's modified Eagle's medium (DMEM), supplemented with 10% fetal bovine serum (Gibco), L-glutamine (2 mM) and 1% Penicillin-Streptomycin (10,000 U/mL, Gibco). Cells were incubated at 37 °C with 5% CO2.

extract_protocol: DNA was extracted from approximately 106 cells using the “GenElute-Mammalian Genomic DNA Miniprep Kit” (Sigma) according to manufacturer's instructions.

treatment_protocol: Final concentration of 50 mM KBrO3 was added to culture medium for one hour. Cells were washed with PBS twice, and genomic DNA was immediately extracted (for damage samples). Alternatively,  cell medium was replaced, and cells were allowed to repair for one hour at 37 °C with 5% CO2 before DNA extraction (for repaired samples). Cells were allowed to grow up to a week post KBrO3 treatment, to validate their viability.

value: human osteosarcoma cell line

tag: treatment group

value: damaged


title: Sample_5_U2OS50_KBr_0h_hoGG1 [repair]

description: processed data file: Repaired.begraph

source_name: repaired

value: repaired


title: S4 smallRNAs


title: S16 smallRNAs

value: Pi sufficient condition


title: TKO_ES_K4_rep1

description: H3K4me2 ChIP-chip data from Dnmt1-/-Dnmt3a-/-Dnmt3b-/- ES cells

source_name: H3K4me2 ChIP DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 1

source_name: MNase digested input DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells for H3K4me2 ChIP, replicate 1


title: Sample_1_U2OS50_KBr_0h_hoGG1 [damage]

description: processed data file: Damage.bedgraph


title: Sample_7_U2OS50_KBr_1h_hoGG1 [repair]

description: processed data file: Repaired.begraph


title: Proof-of-concept-raw-BspqPreCRbiotin_ACAGTG_all

source_name: Proof-of-concept-raw-BspqPreCRbiotin


title: WT_ES_K27_rep2

description: H3K27me3 ChIP-chip data from wild-type ES cells

source_name: H3K27me3 ChIP DNA from mouse wild-type (WT) ES cells, replicate 2

growth_protocol: ES cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 10% KNOCKOUT Serum Replacement (Invitrogen), 10 micro-M human adrenocorticotrophic hormone (Kurabo), 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, and 2000 U/ml leukemia inhibitory factor, on gelatinized culture dishes without feeder cells.

value: Line J1

value: wild-type

value: Abcam

source_name: MNase digested input DNA from mouse wild-type (WT) ES cells for H3K27me3 ChIP, repalicate 2


title: TKO_ES_K4_rep2

source_name: H3K4me2 ChIP DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells, replicate 2

source_name: MNase digested input DNA from mouse Dnmt1-/-Dnmt3a-/-Dnmt3b-/- (TKO) ES cells for H3K4me2 ChIP, replicate 2


title: Cwr22rv1-6

city: Xinxiang

first: Bing

last: Su

address: East Hualan Avenue

institute: The Third Affiliated Hospital Of Xinxiang Medical University

data_processing:
illumina xten fastp-0.20.0 software used for basecalling.
First, reads and reference genome of each sample were respectively compared with TopHat to obtain the comparison result of each sample.Then cufflinks is used to assemble the transcript and get the assembly result of each sample.Secondly, several samples were grouped and merged by Cuffmerge according to different treatments, and the results of different groups were also combined by Cuffmerge, and finally the expression level of genes in different groups was obtained.Finally, the predicted genes were analyzed by edgeR, and then the different genes were annotated functionally, and the new genes were annotated.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

source_name: prostate cancer cell lines

extract_protocol:
Collect the cells from the petri dish,Total RNA from each sample was isolated using the TRIzol Reagent kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: wild type


title: Sirt6_sample1

city: Beijing

first: Jiayu

last: Zhang

address: Beichen West Road 1-5

department: Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.1.0 with parameters -p 8 --dta -x
Transcripts per million of library size (TPM) were calculated using Stringtie v1.3.3. 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 normolized to the abundances of the other transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mTEC

extract_protocol:
total RNA was extracted using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Thymus

tag: age

value: 4 weeks


title: WT_sample2


title: Glioblastoma E100 10x

city: Cambridge

first: Orr

last: Ashenberg

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

country: USA

institute: Broad Institute

data_processing:
5' RNAseq (10x kit V3 chemistry)
Demultiplexing is run using Cell Ranger mkfastq v3.1.
Count matrices are generated using Cell Ranger count v3.1.
Full-length RNAseq (Smart-Seq2)
Demultiplexing is run using bcl2fastq.
Reads are aligned using Bowtie v0.12.7.
Gene expression values are quantified using RSEM v1.2.19.
Genome build: hg19 (Smart-Seq2) or GRCh38 (10x)
Supplementary_files_format_and_content:  [E*_raw_feature_bc_matrix.h5.gz]  Single-cell RNA-Seq (10X). The count matrix is stored as an HDF5 file.
[metadata_10x.csv]  For each cell (row): cell name, sampleid (name of patient sample), number of UMIs detected per cell, number of genes detected per cell, clonotype_id (unique id assigned to set of T cells in the same clonotype), clonotype_size (number of T cells in the clonotype), cdr3s_aa (CDR3 sequence from alpha and/or beta chain), clonotype_category (no reconstruction = no TCR reconstructed, not recurrent = TCR reconstructed but TCR not shared with other T cells, recurrent = TCR reconstructed and TCR is shared with other T cells in a clonotype), annotate_Tcelltype (T cell type annotation), annotate_clonotype (consensus T cell type for all T cells in the clonotype).

source_name: glioblastoma

extract_protocol:
Dissociated individual cells from fresh tumor samples. Live T cells were isolated by flow sorting for CD45 and CD3.
5' RNAseq (10x kit V3 chemistry and Single Cell V(D)J TCR kit) or Full length RNAseq (SMART-Seq2)

tag: disease state

value: glioblastoma

value: fresh tumor sample


title: WT_ES_K9_rep2

description: H3K9me2 ChIP-chip data from wild-type ES cells

source_name: H3K9me2 ChIP DNA from mouse wild-type (WT) ES cells, replicate 2

value: embryonic stem (ES) cells

value: Monoclonal antibody institute

source_name: MNase digested input DNA from mouse wild-type (WT) ES cells for H3K9me2 ChIP, repalicate 2


title: Glioblastoma E99 10x


title: WT_sample1


title: Cwr22rv1-5

value: Akt1/2 knockout


title: Sirt6_sample2


title: Glioblastoma E37 10x


title: WT_ES_K9_rep1

source_name: H3K9me2 ChIP DNA from mouse wild-type (WT) ES cells, replicate 1

source_name: MNase digested input DNA from mouse wild-type (WT) ES cells for H3K9me2 ChIP, repalicate 1

value: none, MNase digested input DNA


title: Glioblastoma E10 10x


title: Glioblastoma E39 10x


title: Glioblastoma and IDH-mut glioma Smart-Seq2

data_processing:
5' RNAseq (10x kit V3 chemistry)
Demultiplexing is run using Cell Ranger mkfastq v3.1.
Count matrices are generated using Cell Ranger count v3.1.
Full-length RNAseq (Smart-Seq2)
Demultiplexing is run using bcl2fastq.
Reads are aligned using Bowtie v0.12.7.
Gene expression values are quantified using RSEM v1.2.19.
Genome build: hg19 (Smart-Seq2) or GRCh38 (10x)
Supplementary_files_format_and_content:  [tpm.csv.gz]  Full-length RNAseq (SMART-Seq2). The expression levels for each gene (rows) in each single cell (column) in transcripts per million (TPM) as calculated using RSEM.
[metadata_Smart-Seq2.csv]  For each cell (row): cell name, experiment (name of patient sample), TPM per cell, number of genes detected per cell, case status, therapy received, steroid treatment, tumor class (IDH-G, GBM), clonal (whether T cell is member of a clonotype), clonal_group (unique number assigned to set of T cells in the same clonotype), group_size (number of T cells in the clonotype), T cell type annotation.

source_name: glioblastoma and IDH-mut glioma

value: glioblastoma and IDH-mut glioma


title: MCF7_0.5_rep2 [B4_S8_L001]

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR (version 2.7.3a; Dobin et al. 2013, Bioinformatics) with default parameters.
The abundance of transcripts was quantified using StringTie (version 2.0.6; Pertea et al. 2015, Nat Biotechnol.) by means of transcripts per million (TPM). Then, differentially expressed genes (DEGs) were identified using DESeq2 (version 1.24.0; Love et al. 2014, Genome Biol.) with an adjusted p-value cutoff of 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM (or raw readcount) values for each Sample.

source_name: MCF7_Arsenic hexoxide 0.5 μM

growth_protocol: The cells were cultured at 37℃ in a 5% CO2 incubator. HUMEC were maintained in HuMEC Ready Medium containing HuMEC Basal Serum Free Medium, HuMEC Supplement, and bovine pituitary extract (Cat # 12752-010, Thermo Fisher Scientific, USA). MCF7 cells were cultured in DMEM (Cat # 10013CV, Corining, USA) containing 10% fetal bovine serum (FBS, Gibco, USA) and 1% penicillin/streptomycin (P/S, Thermo Fisher, USA).

extract_protocol:
After 50 h incubation, the cells were washed with cold PBS once and scraped. The cells were washed again with cold PBS twice before extracting total RNA molecules using Qiagen RNeasy Kit (Qiagen, Germany).
The RNA sequencing was performed by Omega Bioservices  (https://omegabioservices.com, USA). The RNA concentration was measured with Nanodrop 2000c  spectrophotometer (Thermo Fisher Scientific, USA) and integrity was assessed using Agilent 2200  Tapestation instrument (Agilent Technologies, USA). One microgram of total RNA was used to prepare  Ribo-Zero RNA-Sequencing (RNA-Seq) libraries. Briefly, ribosomal RNA (rRNA) is removed using  biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads following Illumina  Reference Guide (Illumina, USA). After purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. First-strand cDNA syntheses were performed at 25°C for 10 minutes, 42°C for 15 minutes and 70°C for 15 minutes, using random hexamers and ProtoScript II Reverse Transcriptase (New England BioLabs, USA). In a second strand cDNA synthesis the RNA  templates were removed, and a second replacement strand was generated by incorporation dUTP (in place of dTTP, to keep strand information) to generate ds cDNA. The blunt-ended cDNA was cleaned up from the second strand reaction mix with beads. The 3`ends of the cDNA were then adenylated and followed by the ligation of indexing adaptors. PCR (15 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds) were used to selectively enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. The libraries were quantified and qualified using the Agilent D1000 ScreenTape on a 2200 TapeStation instrument.

treatment_protocol: HUMEC and MCF7 cells were grown to 60-70% confluence in 6-well plates and the media were exchanged with the fresh complete media including AS6 at final concentration of 0.5 µM or H2O only as an untreated control.

tag: treatment

value: Arsenic hexoxide 0.5 μM


title: WT_TS_K9_rep2

description: H3K9me2 ChIP-chip data from trophoblastic stem cells derived from nuclear transferred embryos with a wild-type ES cell as the nuclear donor

source_name: H3K9me2 ChIP DNA mouse wild-type (WT) ntTS cells, replicate 2

growth_protocol: ntTS cells were maintained in RPMI 1640 GlutaMax (Invitrogen) supplemented with 20% fetal bovine serum, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 25 ng/ml FGF4, and 1 micro-g/ml heparin with mouse embryonic fibroblast feeder cells.

treatment_protocol: The cells were recovered by trypsinization. To remove feeder cells, the ntTS cells were purified by sorting GFP positive cells with FACS-Aria (BD Biosciences).

value: Line 9.2

value: wild-type, carrying the CAG-GFP transgene

value: nuclear transfer trophoblastic stem (ntTS) cells, derived from nuclear transferred blastocyst

source_name: MNase digested input DNA from mouse wild-type (WT) ntTS cells for H3K9me2 ChIP, replicate 2


title: MCF7_0_rep3 [C3_S11_L001]


title: WT_ES_K27_rep1

source_name: H3K27me3 ChIP DNA from mouse wild-type (WT) ES cells, replicate 1

value: Line J1

source_name: MNase digested input DNA from mouse wild-type (WT) ES cells for H3K27me3 ChIP, repalicate 1


title: P7_3% Sevoflurane_6h_4

type: RNA

city: Milwaukee

first: Thiago

last: Arzua

state: WI

address: 8701 W Watertown Plank Rd

institute: Medical College f Wisconsin

description: Postnatal day 7 C57/Bl6 mouse

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).
The raw microarray intensity values are normalized across the arrays as normalized intensities for the comparison of expression levels. Normalized values are reported

source_name: P7 mouse, sevoflurane (3%, 6 hours)

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 mixture of oligo(dT) and random primers (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.

growth_protocol: C57BL/6 mice were derived from Jackson Laboratories (Bar Harbor, USA) and housed in the specific pathogen free animal facility in Medical College of Wisconsin (MCW).

extract_protocol: Total RNA was extracted with the QIAzol lysis reagent kit (Qiagen Inc., Valencia, CA).Before performing the microarray assay, RNA underwent quality control analysis of RNA integrity, quantity, and purity, in addition to the detection of genomic DNA contamination and the efficacy of probe labeling

treatment_protocol: P7 mice were exposed to either sevoflurane (3%) in a chamber with 40% O2 or 40% O2 alone as an air control. After 6 hours of exposure, the mice were euthanized and their hippocampus was harvested.


title: OA5, chondrocytes untreated rep5

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description:
Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and cultured for 24h in starvation medium.
OA5 Control

hyb_protocol: Affymetrix GeneChip® Human PrimeView arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Express Labeling Assay User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

label: biotin

source_name: chondrocytes, untreated

label_protocol: 250ng of total RNA were amplified and labeled using the Affymetrix 3` IVT Express Kit (Catalog Number 901229, Affymetrix, Santa Clara, CA)

growth_protocol: Osteoarthritic chondrocytes were isolated from femoral condyles and tibial plateaus of articular cartilage. Isolated chondrocytes were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) containing 10% fetal calf serum (Biochrom) and 100 µg/ml gentamicin (Gibco) in a humidified atmosphere of 5% CO2/95% air at 37°C. To preserve the chondrocyte phenotype, only freshly isolated and seeded cells without subculturing were used for all assays.

extract_protocol: Total RNA was extracted using the innuPREP RNA Mini Kit (Analytik Jena, Jena, Germany). For quality control and quantification of total RNA, each sample was run on the Agilent 2100 Bioanalyzer Nano LabChip (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Upon 90% confluency, chondrocyte cultures were starved overnight using DMEM supplemented with gentamicin and treated with 10 µg/ml recombinant Galectin-8 in starvation medium for 24 h.

tag: individual

value: patient 5

tag: gender

value: female

value: Osteoarthritis

value: Osteoarthritic knee chondrocytes

tag: agent

value: control


title: MCF7_0.5_rep3 [C4_S12_L001]

tag: cell line


title: MCF7_0.5_rep1 [A4_S4_L001]


title: P7_3% Sevoflurane_6h_1

description: Postnatal day 7 C57/Bl6 mouse

tag: strain


title: P7_3% Sevoflurane_6h_3

description: Postnatal day 7 C57/Bl6 mouse


title: P7_3% Sevoflurane_6h_2

description: Postnatal day 7 C57/Bl6 mouse


title: P7_Control_6h_4

description: Postnatal day 7 C57/Bl6 mouse

source_name: P7 mouse, control (6 hours)


title: OA4, chondrocytes untreated rep4

description:
Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and cultured for 24h in starvation medium.
OA4 Control

value: patient 4

tag: cell type


title: P7_Control_6h_3

description: Postnatal day 7 C57/Bl6 mouse


title: OA5, chondrocytes Gal-8 rep5

description:
Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and treated with 10 µg/ml Galectin-8 for 24h in starvation medium.
OA5 Gal-8

source_name: chondrocytes, Gal-8, 10 µg/ml


title: OA4, chondrocytes Gal-8 rep4

description:
Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and treated with 10 µg/ml Galectin-8 for 24h in starvation medium.
OA4 Gal-8


title: WT_ES_K4_rep2

description: H3K4me2 ChIP-chip data from wild-type ES cells

source_name: H3K4me2 ChIP DNA from mouse wild-type (WT) ES cells, replicate 2

tag: genotype/variation

value: wild-type

tag: chip antibody

tag: chip antibody vendor

source_name: MNase digested input DNA from mouse wild-type (WT) ES cells for H3K4me2 ChIP, repalicate 2


title: WT_ES_K4_rep1

source_name: H3K4me2 ChIP DNA from mouse wild-type (WT) ES cells, replicate 1

value: embryonic stem (ES) cells

tag: chip antibody catalog #

tag: chip antibody lot #

source_name: MNase digested input DNA from mouse wild-type (WT) ES cells for H3K4me2 ChIP, repalicate 1


title: MCF7_0_rep2 [B3_S7_L001]


title: MCF7_0_rep1 [A3_S3_L001]


title: HUMEC_0.5_rep2 [B2_S6_L001]

source_name: HUMEC_Arsenic hexoxide 0.5 μM

value: HUMEC


title: HUMEC_0.5_rep3 [C2_S10_L001]


title: OA3, chondrocytes untreated rep3

description:
Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and cultured for 24h in starvation medium.
OA3 Control

value: patient 3


title: submandibular glands, C2

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

data_processing:
Raw reads were filtered with FastQC: Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides(N); removing reads without 3’adapters; removing reads containing 5’adapters; removing reads containing 3’ and 5’ adapters but no small RNA fragment between them; removing reads containing ployA in small RNA fragment; removing reads shorter than 18nt
Applied with Bowtie, we aligned our clean reads with small RNAs in GeneBank database (Release 209.0) and Rfam database (11.0) to identify and remove rRNA, scRNA, snoRNA, snRNA and tRNA. We also mapped our clean reads with goat reference genome (Capra hircus ARS1), and those reads mapped to exons, introns and repeat sequences were removed. To identify known miRNAs, we mapped clean reads with miRBase database (Release 22)
All of the unmapped reads were applied for novel miRNA identification according to their genome positions and hairpin structures predicted by software Mireap_v0.2. The parameters of Mireap_v0.2 were settled as follows: Minimal miRNA sequence length is 18nt, maximal miRNA sequence length is 26nt, minimal miRNA reference sequence length is 20nt, maximal miRNA reference sequence length is 24nt, minimal depth of Drosha/Dicer cutting site is 3, maximal copy number of miRNAs on reference is 20, maximal free energy allowed for a miRNA precursor is 18 kcal/mol, maximal space between miRNA and miRNA* is 35nt, minimal space between miRNA and miRNA* is 14nt, maximal bulge between miRNA and miRNA* is 4nt, maximal asymmetry of miRNA/miRNA* duplex is 5nt, flank sequence length of miRNA precursor is 10nt.
Genome_build: Capra hircus ARS1
Supplementary_files_format_and_content: Matrix table with raw miRNA counts for every miRNA and every sample

organism: Capra hircus

source_name: submandibular gland

extract_protocol:
Total RNA was extracted from the submandibular salivary gland tissues using TRIzol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina miRNA protocols

treatment_protocol: All goats were raised under the same conditions, including natural lighting and free access to food.

tag: tissue

value: submandibular gland

value: 24 month


title: P7_Control_6h_2

description: Postnatal day 7 C57/Bl6 mouse


title: RAP3_input

city: Chicago

first: Issam

last: BEN-SAHRA

state: IL

address: 512 North McClurg Ct

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: text files include FPKM values and annotation for each Sample
Supplementary_files_format_and_content: text files include peak  information for each group

source_name: Lacks's cancerous cervical tumor

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average  size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: HeLa cells

value: Rapamycin 20 nM (24h)


title: OA3, chondrocytes Gal-8 rep3

description:
Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and treated with 10 µg/ml Galectin-8 for 24h in starvation medium.
OA3 Gal-8


title: OA2, chondrocytes untreated rep2

description:
Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and cultured for 24h in starvation medium.
OA2 Control

value: patient 2


title: OA1, chondrocytes untreated rep1

description:
Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and cultured for 24h in starvation medium.
OA1 Control

value: patient 1


title: HUMEC_0.5_rep1 [A2_S2_L001]

value: Arsenic hexoxide 0.5 μM


title: OA2, chondrocytes Gal-8 rep2

description:
Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and treated with 10 µg/ml Galectin-8 for 24h in starvation medium.
OA2 Gal-8


title: submandibular glands, C5


title: Umbilical cord blood-PE3

city: Nanjing

first: Juan

last: Wen

address: Tianfei Xiang 123#

institute: Women’s Hospital of Nanjing Medical University

description: RNA expression profiles in umbilical cord blood exosomes from preeclampsia patients

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, USA) in Hybridization Oven (Agilent technologies, USA), according to the manufacturer’s instructions.

scan_protocol: After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, USA) with Gene Expression Wash Buffer Kit (Agilent technologies, USA), followed the manufacturer’s instructions. Slides were scanned by Agilent Microarray Scanner (Agilent technologies, USA) with default settings.

data_processing:
Data were extracted with Feature Extraction software 12.0 (Agilent technologies, USA).
Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Umbilical cord blood

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit (Agilent technologies, USA), following the manufacturer’s instructions. Labeled cRNA was purified by RNeasy mini kit (QIAGEN, Germany).

extract_protocol: Total exosomal RNA was extracted using Serum/Plasma Kit (QIAGEN, Germany) according to the manufacturer’s instructions and checked for RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, USA).

value: Umbilical cord blood

tag: condition

value: preeclampsia


title: P7_Control_6h_1

description: Postnatal day 7 C57/Bl6 mouse


title: RAP1_input

tag: genotype


title: OA1, chondrocytes Gal-8 rep1

description:
Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and treated with 10 µg/ml Galectin-8 for 24h in starvation medium.
OA1 Gal-8

value: female

value: Osteoarthritis


title: submandibular glands, C3

tag: age


title: Umbilical cord blood-PE2


title: submandibular glands, B5

value: 12 month


title: HUMEC_0_rep2 [B1_S5_L001]


title: submandibular glands, A3

value: 1 month


title: submandibular glands, B4


title: NT2_input

value: Vehicle (DMSO, 24h)


title: RAP2_input


title: Umbilical cord blood-NC3

description: RNA expression profiles in umbilical cord blood exosomes from normal controls

value: normal


title: Umbilical cord blood-NC1


title: NT1_input


title: Umbilical cord blood-PE1


title: HUMEC_0_rep3 [C1_S9_L001]

value: HUMEC


title: submandibular glands, A2


title: Umbilical cord blood-NC2


title: NT3_input


title: submandibular glands, B3


title: SBF_23

city: Utrecht

first: Jeroen

last: den Hertog

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Not all cells were used, see plate layour for which cells were used

data_processing:
Well numbers (X001-X384) in *.TranscriptCounts.tsv refer to well numbers of the 384-well plate in the following order: A1 to A24 - B1 to B24 - until P24.
The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded.
During sequencing, Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode, cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA (Anders and Huber, 2010). Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo
Tabular-separated file indicating number of transcripts per section obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads, *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI-corrected transcripts per gene per cell
The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases. Read 1 was not used for quantification.
cell specific barcodes are specified in the file “cel-seq2_barcodes.csv”
Genome_build: zV9 Danio Rerio

organism: Danio rerio

source_name: Caudal Hematopoietic Tissue

extract_protocol:
Cells were sorted into 384 well plates. All wells underwent Cel-Seq2 protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

tag: sort day (see plate layout)

tag: genotype or treatment (see plate layout)


title: K15SKO2, quadriceps muscle

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to mouse genome release mm10 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: TSV text file containing FPKM for all samples and genes

source_name: quadriceps muscle

extract_protocol:
Cell lysates were isolated using the Roche HighPure RNA isolation kit. 1ug of RNA was used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 2 months

value: quadriceps muscle


title: SBF_24

source_name: Aorta-Gonad Mesonephros


title: RAP3_IP

tag: treatment


title: RAP2_IP


title: SBF_25


title: SBF_22


title: SBF_21

value: wildtype


title: SBF_20


title: submandibular glands, A1

value: submandibular gland


title: NT3_IP

value: HeLa cells


title: HUMEC_0_rep1 [A1_S1_L001]


title: K15SKO3, quadriceps muscle


title: SBF_19

value: wildtype and LY294002-treated


title: NT2_IP


title: MyoCre3, quadriceps muscle

value: Myogenin-Cre/+


title: MyoCre2, quadriceps muscle


title: SBF_18


title: SBF_17


title: NT1_IP


title: MyoCre1, quadriceps muscle


title: K15SKO4, soleus muscle

source_name: soleus muscle

value: soleus muscle


title: SBF_16

value: pten mutant


title: K15SKO3, soleus muscle


title: K15SKO2, soleus muscle


title: MyoCre4, soleus muscle


title: MyoCre2, soleus muscle


title: SBF_6


title: SBF_4


title: SBF_5


title: K15SKO1, soleus muscle


title: MyoCre3, soleus muscle


title: SBF_3


title: SBF_15

value: 8 and 9

value: pten sibling


title: RAP1_IP

value: Rapamycin 20 nM (24h)


title: SBF_b


title: SBF_26


title: Liver, ML5, KO

city: Hangzhou

first: JinChao

last: Hou

address: Qingchun Road 79

institute: Zhejiang University

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using  the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for  determining differential expression in digital gene expression data using a model  based on the negative binomial distribution. The resulting P-values were adjusted  using the Benjamini and Hochberg’s approach for controlling the false discovery  rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as  differentially expressed.
GO and KEGG enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by  genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: GRCm (mm10)
Supplementary_files_format_and_content: Files include FPKM values or Raw gene counts for each Sample

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

tag: Sex

value: Male

value: Trem2 KO

value: High Fat Diet Model


title: K15SKO1, quadriceps muscle


title: Liver, ML6, KO


title: Liver, ML4, KO


title: SBF_a


title: Liver, ML3, WT

value: control


title: ZFPM2-5-2-p1-5B

city: New York

first: Ian

middle: A

last: Mellis

state: NY

institute: Columbia University

data_processing:
Base-calling performed by Illumina Basespace
Alignment to hg19 performed by STAR v2.5.2a
Gene-level counts quantified by HTSeq v0.6.1 with settings --mode=union \   --stranded=no \   --type=exon \   --order=name Genome_build: hg19
Supplementary_files_format_and_content: gene-level counts per sample were generated using HTSeq

molecule: polyA RNA

source_name: iPSC-derived cardiac myocytes

growth_protocol: Cardiac myocytes were obtained by differentiating human induced pluripotent stem cells (WTc cell line) as described previously (Miyaoka et al. 2014; Judge et al. 2017).

extract_protocol:
Cells lysed with buffer RLT on Day 10 after first transfection. RNA extraction by Qiagen RNeasy kit.
NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB E7770L), NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) oligos (NEB E7600S)

treatment_protocol: Oligos for siRNA knockdown were ordered from Horizon Discovery. A total of three oligos per target were pooled together. All knockdown experiments were performed in triplicate. Knockdown (day 0) was performed using the Lipofectamine RNAiMAX reagent (ThermoFisher) and pooled siRNA at a final concentration of 10uM. Media was changed to fresh media 48 hours later. Five days post knockdown, a second identical dose of lipofectamine+siRNA was added to the cells for another 48 hours

tag: celltype

value: iPSC-derived cardiac myocytes

tag: cell line

value: WTc

tag: sirna target

tag: replicate number

tag: treatment type

value: targeting siRNA


title: SBF_14


title: ZFPM2-5-3-p1-5C


title: Liver, ML2, WT


title: ZFPM2-5-1-p1-5A


title: SOX11-7-3-p2-1C


title: Liver, ML1_N, WT


title: Kupffer cells, WT_2

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using  the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for  determining differential expression in digital gene expression data using a model  based on the negative binomial distribution. The resulting P-values were adjusted  using the Benjamini and Hochberg’s approach for controlling the false discovery  rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as  differentially expressed.
GO and KEGG enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by  genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Files include FPKM values or Raw gene counts for each Sample

source_name: Kupffer cells

extract_protocol:
Kupffer cells were sorted, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Kupffer cells


title: SOX11-7-2-p2-1B


title: SOX11-7-1-p2-1A


title: MyoCre1, soleus muscle

value: 2 months


title: Kupffer cells, WT_3


title: SBF_13


title: Kupffer cells, KO_3


title: Kupffer cells, WT_1


title: SKIDA1-9-3-p2-3C


title: SKIDA1-9-2-p2-3B


title: SKIDA1-9-1-p2-3A


title: Kupffer cells, KO_2


title: SCR-10-3-p2-4C

value: SCR

value: scrambled non-targeting siRNA


title: Kupffer cells, KO_90

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: miRBase 22.0
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

extract_protocol:
Kupffer cells were sorted by flow cytometer cell sorters, and Small RNA was prepared by TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
Small RNA libraries were prepared for sequencing using standard Illumina protocols


title: SCR-10-1-p2-4A


title: Kupffer cells, KO_88


title: SCR-10-2-p2-4B


title: Kupffer cells, KO_40


title: Kupffer cells, KO_1


title: NOSI-C-1-p2-5A

value: NOSI

value: non-transfected no siRNA


title: NKX2-5-1-3-p1-1C


title: NOSI-C-2-p2-5B


title: Kupffer cells, WT_80


title: Kupffer cells, WT_37


title: NKX2-5-1-2-p1-1B


title: NKX2-5-1-1-p1-1A


title: Kupffer cells, KO_46


title: Kupffer cells, WT_35


title: NOSI-C-3-p2-5C


title: CPEB3_IP_2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analyzed the unique reads binding regions of CPEB3 on genome using “ABLIRC” strategy.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

growth_protocol: HT22 cells were first lysed in ice-cold lysis buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 10 mM DTT) with 200 U/ml RNase inhibitor (Promega) and a protease inhibitor (Roche) on ice for 5 min

extract_protocol:
The beads were washed 6 times with lysis buffer and then divided into two groups, one for RNA isolation from CPEB3-RNA complexes and another for the western blotting assay for CPEB3 immunoprecipitation.The CPEB3-bound RNAs were isolated from the immunoprecipitate of monoclonal Flag antibody (Sigma), followed by the preparation of the Illumina Truseq pair-end libraries.
The reverse transcription was performed with RT primers harboring 3′ adaptor sequence and random hexamer. The generated cDNAs were PCR-amplified and the 200–500 bp products were purified

treatment_protocol: The supernatant was pre-cleared with 100 μl of DynaBeads protein G (Life Technologies) at 4 °C for 30 min. The pre-cleared supernatant was incubated with DynaBeads protein G conjugated with monoclonal Flag antibody (Sigma) or Input at 4℃ for 30 min.

value: HT22 cell expressing vector with CPEB3-FLAG

tag: rip antibody

value: anti-FLAG (Sigma, F7425)


title: Liver, ZY24

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using  the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for  determining differential expression in digital gene expression data using a model  based on the negative binomial distribution. The resulting P-values were adjusted  using the Benjamini and Hochberg’s approach for controlling the false discovery  rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as  differentially expressed.
GO and KEGG enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by  genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Files include FPKM values or Raw gene counts for each Sample

tag: donor type

value: NAFLD


title: Liver, ZY10

tag: tissue

value: Liver


title: CPEB3_input_1


title: MEF2C-3-3-p1-3C


title: CPEB3_input_2


title: CPEB3_IP_1


title: Liver, D1_30

value: Male


title: IRX4-8-3-p2-2C


title: MEF2C-3-1-p1-3A


title: NC_3rd

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue < =0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene read andFPKM values for each Sample

source_name: HT22 cell

growth_protocol: The mouse HT22 cell line was purchased from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. Cells were seeded into a petridish (100 mm) at a density of 1 × 105 cells/mL per well, and cultured at 37 ℃with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (Hyclone), penicillin (100 U/ml) and streptomycin (100 g/ml). ZFP36 overexpression plasmid transfection of HT22 cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Transfected cells were harvested after 48 h.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: OE_RNA against mouse CPEB3 transfection of HT22 cells was performed using lipofectAMINE 2000

value: ht22 cell (control plasmid)


title: Liver, ZY12

value: non-NAFLD


title: NC_2nd


title: Kupffer cells, WT_82

value: control

value: High Fat Diet Model


title: Liver, D2_8

value: Female


title: IRX4-8-1-p2-2A

value: iPSC-derived cardiac myocytes

value: WTc

value: targeting siRNA


title: HMGB2-6-3-p1-6C


title: CPEB3_3rd

value: CPEB3 overexpression in ht22 cell


title: Liver, D2_26


title: Liver, D2_25


title: CPEB3_2nd


title: Liver, ZY6


title: HMGB2-6-1-p1-6A


title: Liver, D2_17


title: CPEB3_1st


title: Liver, D1_22


title: HAND1-2-3-p1-2C


title: Liver, D2_21


title: MEF2C-3-2-p1-3B


title: HMGB2-6-2-p1-6B


title: IRX4-8-2-p2-2B


title: Treated_2

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq was done by 10X Genomics
Raw data quality was checked using FastQC (v0.11.9), and adapter trimming on raw data was performed using Cutadapt (v2.9). The reference genome was downloaded from Ensembl mm10 release 99, and the reference genome index was built using Bowtie2 (v2.4.1) software. Paired-end trimmed reads alignment and raw read count calculation were performed using RSEM software (v1.3.1).  Statistical analysis were performed using the DESeq2 package (v1.26) in R (v3.6).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw reads for each Sample

source_name: Mammary gland fibrosis

growth_protocol: MMTV-NeuT/ATTAC mice were derived from MMTV-NeuT mice expressing a constitutively active rat ErbB2[V664E] gene, and FAT-ATTAC mice expressing an FKBPv-caspase-8 fusion protein under the control of the FABP4 promoter

extract_protocol:
Snap-frozen tissue was pulverized in a mortar and pestle and RNA extracted using an RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mammary gland fibrosis was induced in female six-week-old NeuT/ATTAC mice by i.p. injection of 0.4 mg/kg AP20187 (MedChemExpress) dissolved in a vehicle (4% ethanol, 10% PEG-400 and 1.75% Tween-20 in water) three times per week, and are hereafter referred to as ‘NeuT/ATTAC+AP’ mice. AP20187 is a dimer analog of FK506 and serves as a selective FKBPv-caspase 8 dimerizer resulting in partial ablation of mammary fat and its replacement by fibrotic tissue. At eight weeks of age, NeuT/ATTAC+AP mice were administered ad libitum a diet (LabDiet 5053) supplemented with 0.05% (w/w) DMHCA (WuXi App Tec, China), which is equivalent to a dose of ~100 mg/kg.  No weight loss or overt toxicity resulted from AP21087 or DMHCA treatment.

tag: strain

value: NeuT/ATTAC

value: DMHCA

value: Mammary gland fibrosis


title: Patient_2A_D200_untreated2

city: Bethesda

first: Zachary

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: Patient retinal organoid, untreated

data_processing:
Data was processed through cellranger suite v3.1.0.
Fastq files were generated from raw BCL files using "cellranger mkfastq" with default settings.
Expression matrix were generated using "cellranger count" with default settings.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: raw and filtered output in HSF format containing gene expression matrix in single-cell resolution.

source_name: Retinal Organoid

growth_protocol: Retinal organoids were derived using a combination of 2D and 3D culture. Embryoid bodies were formed from iPSCs by EDTA treatment, cultured for 7 days in neural induction medium followed by plating on Matrigel. Between 3-4 weeks neural retina domains were dissected from adherent cultures forming organoids, which were subsequently maintained as floating cultures in ultra-low attachment 96-well plate format until collection.

extract_protocol:
Organoids were dissociated using papain at the indicated day of differentiation.
Cell suspension was passed through 10x Genomics' protocol for "Chromium Single Cell 3' v2" following manufacturers instructions.
scRNA-seq

treatment_protocol: An AAV construct to drive human CRX expression was added to patient organoids at d120.

tag: genotype

value: Untreated


title: Treated_3


title: Mono-D3-Tm 25hr-1

first: Kwontae

last: You

state: MASSACHUSETTS

address: 415 main street

data_processing:
With cellranger: produced fastq, generated UMI counts separately for each of 6 conditions, then aggregated all conditions with “--normalize“.
Genome_build: mm10
Supplementary_files_format_and_content: UMI counts

source_name: differentiated monolayer from intestinal organoids

growth_protocol: Briefly, day3 colonic spheroids were dissociated into single cells using TrypLE and passed through a 70 mm filter into 50% L-WRN conditioned medium containing 10 mM Y27632. Cells were plated on a 24-well transwell insert coated with 1:40 Matrigel diluted in PBS. Medium was added to the upper and lower compartments. After 24 h, the media in both compartments was replaced with 50% L-WRN medium. After an additional 24 h, the media was replaced with 5% L-WRN medium to induce differentiation. Media was replaced daily, and day3 monolayers were used for the Tm treatment and scRNA-seq analysis.

extract_protocol:
Scraped out the monolayer using 200ul pipet tip and incubated in 5mM DTT and EDTA–PBS on ice for 30 min, shaking every 10 min. Centrifuged at 800g for 4min. Resuspended the cell with 400ul TrypLE and pipetting 7 times, incubated it for 3min at 37°C. Resuspended the single cells in MACS buffer and then passed through a 40-μm filter.  Count the number of cells after removing dead cells using EasySep Dead cell removal Kit (Stemcell Tech).
10X genomics 3' V2 library construction
10X genomics 3' V2 library construction

treatment_protocol: At differentiation day3 morning, treat 0.5ug/ml of Tm (for 25hr sample) or DMSO (for DMSO or 13hr set). 12hrs later, treat Tm on one of the DMSO set to make the 13hr set. Harvest the cells at differentiation day 4 morning.

tag: agent

value: Tm

tag: time point

value: small intestine

value: Rosa26-floxed STOP-Cas9 x cmv-cre B6


title: Patient_2A_D200_untreated1

description: Patient retinal organoid, untreated

tag: age


title: Mono-D3-Tm 13hr-2


title: COPS2-4-3-p1-4C


title: NC_1st


title: Patient_2A_D200_AAV2

description: Patient retinal organoid, AAV-treated CRX rescue

value: AAV


title: Mono-D3-Tm 13hr-1


title: Control_3

value: AP20187 Vehicle


title: Control_2


title: Mono-D3-DMSO-2

value: DMSO


title: Patient_2A_D200_AAV1


title: COPS2-4-1-p1-4A


title: Control_1


title: Control_2A_D200

description: Control retinal organoid, untreated

value: WT


title: Mono-D3-Tm 25hr-2


title: HAND1-2-2-p1-2B


title: Mono-D3-DMSO-1


title: HAND1-2-1-p1-2A


title: AP2-G2_GFP_Gam_Rep2

status: Public on Feb 16 2021

city: University Park

first: Manuel

last: Llinas

state: PA

address: Millennium Science Complex

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

data_processing:
Reads were trimmed using trimmomatic 0.36.3
Reads were mapped against P. falciparum genome using BWA-MEM tool 0.7.15.1
Reads that mapped to more than one locations were filiered
Peaks were called using MACS2 package version 2.1.1.20160309.0, q value 0.05
Genome_build: Pf 3D7 v28
Supplementary_files_format_and_content: Bigwig files were generated from BAM files using deeptools bamCoverage 2.5.0.0

organism: Plasmodium falciparum

growth_protocol: All the strains of Plasmodium falciparum parasites were cultured at 370C under standard conditions in the presence of 5% O2 and 7% CO2 in RPMI 1640 media. The media was supplemented with 2M HEPES, NaHCO3, hypoxanthine, albumax, and gentamycin (50 mg/ml).

extract_protocol:
Crosslinked nuclei of PfA2-G2 GFP parasite was sheared in SDS lysis buffer (0.1% SDS, 10 mM Tris pH 8.1, 1 mM EDTA) to obtain chromatin of fragment size of 100-150bp using an M220 focused-ultrasonicator (Covaris Inc.) using the following settings: peak power 75W, 2% duty factor, 200 cycles per burst and total treatment time of 600 s. To immunoprecipitate sheared chromatin is diluted 1:10 with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 150 mM NaCl). To reduce the non-specific background chromatin solution is pre-cleared using 20ul/ml of magnetic beads A/G (Millipore 16-663) for 2 hours at 4oC with gentle agitation. Supernatant is collected and 50ul of the aliquot is removed as input. Input is control without the actual IP to get rid of the background noise. Rest of the chromatin was incubated overnight at 4oC with 1 μg of polyclonal anti-GFP antibody (Abcam ChIP grade, abcam 290) or, as control, the same amount of IgG. The immunoprecipitated antibody/chromatin complex was collected using A+G magnetic beads and is washed extensively with wash buffers for 5 min under agitation at 4oC. Finally the complex is eluted using 100 µL of fresh elution buffer (10µl 20% SDS, 20µl 1M NaHCO3, 170µl H2O). The input and ChIP samples were reverse cross-linked overnight at 45oC using 0.2M final concentration of NaCl. The sample is treated with RNAase (30min at 37oC) and proteinase K (3 µL of 20 mg/mL with 2 hours incubation at 45oC) and purified by using the QIAGEN MinElute PCR purification kit.
5-10 ng of ChIP enriched DNA was used as the starting material for preparing the Illumina TruSeq libraries. For accurate quantification of the ChIP DNA Qubit dsDNA HS assay was used. Barcoded TruSeq libraries for NextSeq (high output 150x150) single-end sequencing were constructed using NEBNext DNA library Prep reagents (New England Biolabs) by following the standard Illumina library preparation protocol. First ChIP DNA was end repaired for 30 minutes at 20oC and was cleaned using Ampure XP beads.  Then 3’ends are adenylated for 30 minutes at 37oC to prevent them ligating from one another and was cleaned again on beads. NEXTflex illumina DNA barcodes (diluted 1/10) were ligated to DNA fragments using NEB quick ligase incubating at 20oC for 10 minutes followed by the bead clean up steps. The resulting DNA is then size selected for 250bp inserts, PCR amplified and purified. The final library was quantified using Qubit fluorometer HD DNA kit and was analyzed using Agilent DNA 1000 Bioanalyzer to asses the quality, size distribution and detection of any artifacts.

treatment_protocol: (This is only for gametocytes) The early gametocyte rings were treated with media with heparin (20 U/ml) to prevent the reinvasion of asexual parasites in the next round for four days.

tag: developmental stage

value: Stage III gametocytes

tag: antibody


title: AP2-G2_In_Troph_Rep3

value: Trophozoite

value: polyclonal anti-GFP antibody (Abcam ChIP grade, abcam 290)


title: AP2-G2_In_Gam_Rep1


title: AP2-G2_GFP_Gam_Rep1


title: Treated_1

tag: treatment


title: AP2-G2_In_Gam_Rep2


title: AP2-G2_In_Troph_Rep1


title: AP2-G2_In_Troph_Rep2


title: AP2-G2_GFP_Troph_Rep3


title: COPS2-4-2-p1-4B

tag: celltype

value: iPSC-derived cardiac myocytes

value: WTc


title: AP2-G2_GFP_Troph_Rep1


title: AP2-G2_GFP_Troph_Rep2


title: Alm_A37_rep3

first: Yu

last: Wei

address: No.12 Zhongguancun South St.,Haidian District   Beijing  P.R.China

institute: Chinese academy of agricultural sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
The RNA-seq reads that containing adaptors, with 5% sequencing errors and/or q-value less were removed
De novo assembly was performed using Trinity with parameters: --seqType fq --left  Alm_R1.fq --right  Alm_R2.fq --CPU 50 --SS_lib_type RF --min_contig_length 200 --max_memory 1000G --normalize_by_read_set --bflyCalculateCPU --normalize_reads
The longest sequences of the redundant transcripts were considered as representative unigenes and subjected to downstream functional annotation and coding sequence (CDS) prediction
The CDS were predicted using Trinotate v3.1.1
Clean reads were aligned back to the representative unigenes using Bowtie2
The read count number for each gene was calculated using RNA-Seq by Expectation-Maximization (RSEM)
Gene expression levels were normalized and estimated to Fragments Per Kilobase of transcript per Million fragments mapped (FPKM)
Average normalized FPKM value of each gene was calculated based on the FPKM value of three replicates
Genome_build: none
Supplementary_files_format_and_content: tab-delimited .txt files include FPKM values for each Sample

organism: Prunus dulcis

source_name: Plant sample

extract_protocol:
Total RNA was extracted from each fruit sample using RNAiso Plus (Takara). cDNA was generated in 25-μl reaction mixtures containing 2 μg DNAse I-treated RNA, 200 U M-MLV reverse transcriptase (Takara), 40 U Recombinant RNase Inhibitor (Takara) and 0.1 μΜ oligo (dT)18 primer. Library construction and quality detection were completed by the Biomarker company (Beijing, China)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: ZhiPi

value: fruitlets

tag: tissue condition

value: abnormal


title: Alm_A37_rep2


title: Alm_A37_rep1


title: Alm_A32_rep1


title: Alm_A32_rep2


title: Alm_A27_rep2


title: Alm_A27_rep3


title: Alm_A22_rep3


title: Alm_A27_rep1


title: Alm_A22_rep2


title: Alm_A22_rep1


title: RAW-WT-LPS treatment

city: Sendai

first: Hiroyuki

last: Inuzuka

address: 4-1 Seiryo, Aoba-ku

institute: Tohoku University

description: RMA expression value derived from Expression Console software; exon-level analysis

hyb_protocol: Following fragmentation, 5.5 ug of ssDNA were hybridized for 17 hr at 45C on Clariom S Array, Mouse. Clariom S Arrays were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: Clariom S Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Raw data were processed with the Guanine Cytosine Count Normalization (GCCN) and Signal Space Transformation (SST) algorithms prior to Robust Multiarray Average (RMA) using Expresson Console Software (ThermoFisher Scientific) according to the default analysis settings (Gene Level-SST-RMA).

source_name: Murine macrophage RAW-D cells treated with LPS

label_protocol: Biotinylated ssDNA were prepared using GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) according to the standard manufacturer's protocol from 100 ng total RNA.

growth_protocol: The RAW cells were cultured in α-MEM supplemented with 10% (v/v) fetal bovine serum, 100 U penicillin, and 100 μg/mL streptomycin.

extract_protocol: Total RNA was extracted from the cells with QIAshredder and RNeasy mini kit (Qiagen) according to the standard manufacturer's protocol.

treatment_protocol: WT and Lpin2 KO RAW cells were left untreated (-) (control) or treated with 200 ng/mL LPS for 4 h (+).

tag: cell line

value: RAW-D

value: LPS


title: RAW-Lpin2 KO #1-LPS treatment

value: Lpin2 KO


title: RAW-WT

description: RMA expression value derived from Expression Console software; gene-level analysis

source_name: Murine macrophage RAW-D cells


title: RAW-Lpin2 KO #1


title: RAW-Lpin2 KO #2-LPS treatment


title: RAW-Lpin2 KO #2


title: Alm_A17_rep1

city: Beijing


title: Alm_A17_rep2


title: Alm_A17_rep3


title: Alm_A12_rep2


title: Alm_A12_rep3


title: Alm_N37_rep2

value: normal


title: Alm_A32_rep3


title: Alm_N37_rep1


title: Alm_N37_rep3


title: Alm_A12_rep1


title: Alm_N32_rep2


title: Alm_N32_rep1


title: V3-9-a-1 BSseq

city: Los Angeles

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

data_processing:
For BS-PCR samples (V1-1, V1-2, V1-5, V1-9), reads were first compared to the primer sequences used to amplify the desired regions and only reads containing these primer sequences were kept. Reads were then truncated to exclude the primer sequences. Pre-processed reads were mapped to TAIR10 using Bismark and processed into per-position methylation count data.
For BS-seq samples (V2 and V3 samples), reads were aligned to TAIR10 using Bismark and processed into per-position methylation count data. Whole genome metaplots and overall genome-wide methylation were generated using ViewBS.
Genome_build: TAIR10
Supplementary_files_format_and_content: For BS-seq (V2, V3 samples), text files containing all per-position methylation data are provided for each sample (*cxfile), with 7 fields: chromosome, position (1-based), strand of C, number of methylated reads, number unmethylated reads, sequence context, and specific 3 bp sequence context. Separate bigWig tracks of methylation levels for CG, CHG and CHH methylation are also provided; only positions with 5+ coverage were used to generate the bigWig files. In .bw files, values of -10 indicate positions where there was 5+ coverage, but the methylation level was zero (to distinguish from positions with less than 5 coverage). For BSPCR, processed files are BED-like files containing per-position DNA methylation data over the primer-amplified regions. These files have 6 fields: chromosome, start (0-based index), end, number of unmethylated reads, number of methylated reads, and percent methylated reads.

organism: Arabidopsis thaliana

source_name: rosette leaf

growth_protocol: Plants were grown under long-day conditions (16h light/8h dark) at 23°C in controlled growth chambers.

extract_protocol:
Libraries were prepared from approximately 75-150 ng genomic DNA using the Ovation Ultralow Methyl-seq kit (NuGEN) and sequenced on NovaSeq.
DNA was extracted using the CTAB-based method.

treatment_protocol: For agroinoculation of Arabidopsis plants, the protocol from Burch-Smith et al. 2006 (Plant Physiol.) was followed. Briefly, GV3101 strains containing either TRV RNA1 and RNA2(no guide RNA)/g4/g4.g10.g18 were mixed in 1:1 proportion at an OD 600 =1.5 and was agro-inoculated onto the lowest two leaves of 12-14 days old Arabidopsis plants.

value: SunTag-TET1, no guide

tag: v1 parent

tag: v2 parent

value: rosette stage


title: Alm_N27_rep3


title: V3-5-a-1 BSseq


title: V3-2-d-1 BSseq


title: Alm_N27_rep2


title: V3-1-a-1 BSseq


title: Alm_N27_rep1


title: Alm_N22_rep3


title: Mouse mature sperm head PANDORA-seq rep 2

city: Riverside

first: Junchao

last: Shi

state: CA

address: 900 University Ave

department: Division of Biomedical Sciences, School of Medicine

institute: University of California, Riverside

description: RNAs were treated with T4PNK, then AlkB before cDNA library construction.

data_processing:
Sequence reads that fit any of the following parameters were removed with following standard quality control criteria: 1) the reads containing “N”; 2) the reads containing more than four bases with quality score <10; 3) the reads containing more than six bases with quality score is <13; 4) the reads with 5’ primer contaminants or without 3’ primer; 5) The reads without the insert tag; 6) the reads with ploy A.; and 7) the reads shorter than 15 nt and longer than 44 nt. The sequencing data analyses were performed upon the clean reads after data filtration.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: Mature sperm head

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

value: Mature sperm head

value: T4PNK, then AlkB


title: Mouse mature sperm head PANDORA-seq rep 3


title: Mouse mature sperm head PANDORA-seq rep 1


title: Alm_N22_rep2


title: Alm_N22_rep1


title: Mouse mature sperm head traditional rep 3

description: RNAs were sequenced with standard protocols.


title: Mouse mature sperm head traditional rep 2


title: Alm_N17_rep3


title: PyMT mice_1_with chemotherapy

city: Guangzhou

first: Jiang

last: Liu

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: This sample is isolated from breast tumor of PyMT mice with chemotherapy

hyb_protocol: Labeled cRNA were purified by RNeasy mini kit ( QIAGEN). Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies) in Hybridization Oven (Agilent technologies), according to the manufacturer’s instructions for 17 hours

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies).

source_name: TAMs isolated from PyMT mice with chemotherapy

label_protocol: RNA amplified and labeled by Low Input Quick Amp WT Labeling Kit (Agilent technologies), following the manufacturer’s instructions.

extract_protocol: RNA was extracted using TRIzol Reagent (Invitrogen) according to manufacturer’s instructions, RNA quantity and quality were measured by Qubit 4 (Invitrogen). RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: TAMs isolationed from fresh tumor samples collected from PyMT mice by magnetic-activated cell sorting using mouse monocyte isolation kit for TAMs.

tag: diagnosis

value: breast cancer

value: tumor-associated macrophages (TAMs)


title: PyMT mice_3_without chemotherapy

description: This sample is isolated from breast tumor of PyMT mice without chemotherapy

source_name: TAMs isolated from PyMT mice without chemotherapy


title: PyMT mice_3_with chemotherapy


title: PyMT mice_2_with chemotherapy


title: PyMT mice_2_without chemotherapy


title: PyMT mice_1_without chemotherapy


title: Mouse mature sperm head traditional rep 1


title: Alm_N32_rep3


title: Alm_N17_rep2


title: Alm_N17_rep1


title: Alm_N12_rep3


title: Alm_N12_rep1


title: Alm_N12_rep2


title: mESC_WT_Pol II Ser2P_ChIPseq

city: Illkirch

first: Fang

last: WANG

address: Parc d'Innovation 1, Rue Laurent Fries Illkirch, 67404

country: France

institute: INSTITUT DE GENETIQUE DE BIOLOGIE MOLECULAIRE ET CELLURAIRE (IGBMC)

description: Chromatin IP against RNA Pol II Ser2P

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peak calling was performed using MACS2 v2.1.1.20160309 with default parameters, except ‘narrow’ for pol II peaks and ‘broad’ for H2Bub peaks.
Genome_build: mm10
Supplementary_files_format_and_content: .narrowPeak or .broadPeak generated by MACS2

source_name: mESC_WT_Pol II Ser2P_ChIPseq

growth_protocol: mESCs were firstly cultured with feeders for two passages, then removed feeders and continued culturing in the presence of leukaemia inhibitory factor (LIF) in medium containing 15% foetal calf serum (FCS) containing PD0325901 (1uM) and CH99021 (3uM); MEF cells were generated from E10.5 mice embryos and cultured in MEF medium (DMEM with 10% FCS plus penicillin and streptomycin).

extract_protocol:
Chromatin was fixed in 1% Paraformaldehyde (PFA), sheared to 200-700bp using the Covaris E220 sonicator, then immunoprecipitated using the indicated antibody.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 7 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: No specific treatments

tag: cell type

value: Mouse embryonic stem cell (mESC)

value: Pol II Ser2P ChIP-seq

value: DBA/2 x C57BL/6


title: SAP rep1

city: Chengdu

first: bing

last: wang

state: Sichuan

address: No. 270, Tianhuan Road, Rongdu Avenue, Jinniu District, Chengdu City, Sichuan Province

department: General Surgery

institute: The General Hospital of Western Theater Command

data_processing:
Basecalls performed using CASAVA version 1.8
The high quality reads of circRNA were aligned to the reference genome/transcriptome with STAR software and circRNAs were detected and identified with DCC software.
Use the circBase database and Circ2Traits to annotate the identified circRNA.
The high quality reads of lncRNA and mRNA were aligned to the mouse reference genome (UCSC MM10) with hisat2 software.
Guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the FPKM as the expression profiles of lncRNA and mRNA
Genome_build: MM10
Supplementary_files_format_and_content: excel
Supplementary_files_format_and_content: The lncRNA expression profile file include FPKM Values, Counts and Annotations. The circRNA expression profile file include junction reads, Normalized Intensity and Annotations.

source_name: pancreatic tissues

extract_protocol:
According to the manufacturer's instructions, total RNA was extracted from frozen samples using Trizol reagent (Ambion), and the RNA concentration of each sample was measured using a NanoDrop ND-1000 instrument (Thermo Fisher Scientific, Waltham, MA, USA), with OD260/OD280 values as an indicator of RNA purity.
Ribo-Zero rRNA Removal Kits (Illumina, USA) was used to remove rRNAs from total RNA. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, USA).

treatment_protocol: The mice were randomly divided into control group and SAP group (3 mice per group). Before the operation, 5% isoflurane was given for inhalation anesthesia, and then 4% sodium taurocholate salt was slowly retrogradely injected into the biliopancreatic duct with a micro infusion pump to induce SAP.

tag: tissue

value: Pancreas


title: mESC_KO_Pol II Ser2P_ChIPseq

description: Chromatin IP against RNA Pol II Ser2P

source_name: mESC_KO_Pol II Ser2P_ChIPseq

tag: strain


title: mESC_KO_input_Pol II Ser2P_ChIPseq

description: Chromatin IP against RNA Pol II Ser2P

source_name: mESC_KO_input_Pol II Ser2P_ChIPseq

tag: genotype

value: input


title: mESC_WT_input_Pol II Ser2P_ChIPseq

description: Chromatin IP against RNA Pol II Ser2P

source_name: mESC_WT_input_Pol II Ser2P_ChIPseq


title: SAP rep2


title: Live CD45+CD11b-TCRβ+ cells sorted from LLC-OVA tumors subcutaneously injected in WT C57BL/6 mice.

city: Brussels

first: Daliya

last: Kancheva

address: Pleinlaan 2

country: Belgium

institute: Vrije Universiteit Brussel

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger 2.1.1  mkfastq
Demultiplexed data was then processed using the Cell Ranger 2.1.1 count pipeline
Genome_build: mm10
Supplementary_files_format_and_content: text file including raw counts (output CellRanger count) for one sample

source_name: Tumor

extract_protocol: All Methods listed in Van Damme et al.  Therapeutic depletion of CCR8+ tumor-infiltrating regulatory T cells elicits antitumor immunity and synergizes with anti-PD-1 therapy. Journal for ImmunoTherapy of Cancer. 2020.

tag: platform

value: 10x Genomics v2

tag: number of cells


title: control rep3


title: control rep1


title: control rep2