title: STIM_C

city: San Francisco

first: Alex

last: Lee

address: 1550 Fourth St.

institute: UCSF

data_processing:
Raw reads ( bcl files ) were demultiplex into FASTQs using Illumina’s bcl2fastq software
Samples were trimmed for adaptor sequence and remove for low-quality sequence  then mapped to hg38 genome using  STAR 2.5.1b and counts were computed using the parameter --quantMode and gtf from genecode
Sequences were imported into R , scaled, filter for low counts and  TMM normalized using the edgeR package.
log2 cpm, prior.count=2
Genome_build: hg38
Supplementary_files_format_and_content: single tab delimited file containing   log2 cpm: genes as rows and one sample per column

source_name: Human neural progenitor cells

growth_protocol: hNPCs, passages 6-9, were used in these experiments and kept in AB2TM Basal Neural Medium supplemented with ANSTM Neural supplement (Aruna Biomedical), bFGF (50 µg/ml, Croning), L-Glutamine (200 mM, Invitrogen), and LIF (10 µg/ml, Millipore).

extract_protocol:
obtained from ArunA Biomedical
Libraries  created with TruSeq Stranded mRNA kit (Illumina, RS-122-2101) following manufacturer's instructions and sequenced on an Illumina 4000

treatment_protocol: Stimulated cells received 1 hour of electrical stimulation via the conductive polymer implant (800mV at 100Hz)

value: electrical stimulation (800mV, 100Hz for 1 hour)

tag: lineage

value: neuroepithelial cell lineage of WA09 human embryonic stem


title: HLE-B3 Atg7KO_0h_rep3

status: Public on Jan 19 2022

type: SRA

city: Hangzhou

first: Wei

last: Han

state: Zhejiang

address: 88 Jiefang Road

department: Eye Center

country: China

institute: Second Affiliated Hospital, School of Medicine, Zhejiang University

library_source: transcriptomic

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
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
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
Genome_build: GRCh38(hg38)
Supplementary_files_format_and_content: Matrix table with FPKM for every gene in all samples
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene in all samples

molecule: total RNA

organism: Homo sapiens

source_name: human lens epithelial cells,HLE-B3

growth_protocol: HLE-B3 cells were cultured in DMEM/F12 supplemented with 10% FBS. All cells were incubated at 37°C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Cells were treated with or without 200 μM H2O2 for 12 hrs.

tag: cell line

tag: genotype

tag: cell type

value: human lens epithelial cells

tag: treatment

value: untreated


title: STIM_B

state: CA

country: USA


title: HLE-B3 Atg7KO_0h_rep2


title: Acriflavine_HUVEC_3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Trimmomatic was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (nt) (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads between 30 and 150 nt were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (ensemble release 101) using STAR 2.7.7a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%
For mLECs, Ensembl mouse genome version mm10 (GRCm38.p5) and STAR 2.6.0c was used.
The number of reads aligning to genes was counted with featureCounts tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes in HUVEC were identified using DESeq2 version 1.30.0 (for mLEC version 1.18.1 was used).
The Ensembl annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt))
Genome_build: hg38 / mm10
Supplementary_files_format_and_content: library size normalized counts

source_name: human umbilical vein endothelial cells

growth_protocol: Culturing of pooled human umbilical vein endothelial cells (HUVEC) purchased from PromoCell (C-12203, Lot No. 405Z013, 408Z014, 416Z042, Heidelberg, Germany) was performed at 37°C with 5% CO2. Dishes were coated with gelatin (Sigma-Aldrich, G1890-500G) prior to culturing. Endothelial growth medium (EGM) was prepared by supplementing endothelial basal medium (EBM) with human recombinant epidermal growth factor (EGF), EndoCGS-Heparin (PeloBiotech, Germany), 8% fetal calf serum (FCS) (S0113, Biochrom, Germany), penicillin (50 U/ml) and streptomycin (50 µg/ml) (15140-122, Gibco/ Lifetechnologies, USA). Biological replicates comprised at least three different batches from passage 3. Murine lung endothelial cells (mLEC) were isolated as described previously (DOI: 10.1242/jcs.02541). Briefly, the tissue was minced and digested with dispase at 37°C for 60 min. After washing and filtering, mLEC separation was done with CD144 coated Dynabeads. mLECs were cultured in DMEM/F12 supplemented with 20% FCS, penicillin (50 U/ml) and streptomycin (50 µg/ml) and ECGF Bovine + Heparin (PeloBiotech) at 37°C with 5% CO2.

extract_protocol:
Total RNA Isolation was performed using the RNA Mini Kit (Bio&Sell).
). 1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech).

treatment_protocol: Acriflavine (10µM) or DMSO for 16h.

value: HUVEC


title: STIM_D


title: RNAseq of NK-92 cell line infected with empty vector, rep3

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

data_processing:
Illumina Casava2.20 software used for basecalling.
Paired-end reads were mapped to hg19 whole genome using bowtie STAR
Read counts were generated using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample.

growth_protocol: The NK-92 cell line was cultured in Minimum Essential Medium Eagle - alpha modification (STEMCELL TECHNOLOGIES, #36463) supplemented with 12.5% heat-inactivated FBS, 12.5% heat-inactivated horse serum (Gibco, #16050122), and 100 U/mL penicillin-streptomycin in the presence of 100 U/ml recombinant human IL-2 (Protech, #200-2) at 37°C and 5% carbon dioxide.

extract_protocol:
RNA was extracted from isolated human engrafted cells by AllPrep DNA/RNA Mini kit (Qiagen, #80204) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using total-standard Illumina protocols

treatment_protocol: The NK-92 cells were infected on RetroNectin (Takara, #T100B)-coated plates preloaded with viral supernatants of empty vector, wild-type CCL22, and Pro79Arg-CCL22 cloned CL20-MSCV-IRES-GFP vector and cultured in the presence of cytokines for 48 hours.

value: NK

tag: age

value: empty vector

value: infected with empty vector


title: Lung adenocarcinoma sample4

city: Shenyang

first: Le-Tian

last: Huang

state: Liaoning

address: NO.39 Huaxiang Road, Tiexi District

department: Department of Oncology

institute: Shengjing Hospital of China Medical University

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequencing quality were examined by FastQC and trimmed reads (pass Illumina quality filter, trimmed 5,3-adaptor bases by cutadapt) were aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that did not map were aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software. The remaining reads were aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
The abundance of tRF and tiRNA were evaluated using their sequencing counts and was normalized as counts per million of total aligned reads (CPM).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

growth_protocol: The samples were frozen freshly in liquid nitrogen and stored in -80 degrees Celsius until the specimens were used.

extract_protocol:
Total RNA was first pretreated to remove some RNA modifications that interfere with small RNA-seq library construction by Agilent DNA 1000 chip kit (Agilent, part # 5067-1504).
Diluted libraries were loaded onto reagent cartridge and forwarded to sequencing run on Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (#FC-4042005, Illumina), according to the manufacturer’s instructions.

tag: tissue

value: lung

tag: pathology

value: adenocarcinoma

tag: state of organism

value: Initial diagnosis with no treatment


title: RNAseq of NK-92 cell line with P75R mutation, rep3

value: CCL22 P79R

value: infected with CCL22 P79R


title: kd_vitro_sgScr_RNAseq_2

city: Xi’an, China

first: lei

last: zhao

state: Shaanxi

address: Youyixi Road 21

department: School of Ecology and Environment

institute: Northwestern Polytechnical University

description:
vitro_sgKdm5d_counts.csv
vitro_sgkdm5d_deseq_normalize.csv

data_processing:
Sequenced reads were mapped to GRCm38 reference using STAR
Counts were normalized by deseq2
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files with gene counts
Supplementary_files_format_and_content: csv files with gene deseq2 normalized

molecule: polyA RNA

organism: Mus musculus

source_name: ckit

growth_protocol: The AML was developed on recipient mice after transplantation through tail vein injection.

extract_protocol:
RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mLOY(sgSsty1/sgSsty2) or control(sgScr) with AE in Trp53-/- ckit+ cells or BM harvested from AML mice. sgKdm5d or control(sgScr) in Trp53-/- cas9 ckit+ cells or BM harvested from AML mice.

tag: strain

tag: sample type

value: Trp53-/- c-kit+ HSPCs in vitro

value: control(sgScr)

tag: replicates


title: kd_vitro_sgScr_RNAseq_1


title: STIM_A


title: Adjacent normal sample3

value: normal


title: UNSTIM_C

value: No stimulation


title: HLE-B3 WT_12h_rep3

value: wild type

value: 200 μM H2O2 for 12 hrs


title: kd_vitro_sgKdm5d_RNAseq_3


title: kd_vitro_sgKdm5d_RNAseq_2


title: kd_vivo_sgScr_RNAseq_1

description:
vivo_sgKdm5d_counts.csv
vivo_sgKdm5d_deseq_normalize.csv

source_name: Bone Marrow

value: sgKdm5d/sgScramble;Trp53-/- Bone marrow in vivo


title: Lung adenocarcinoma sample3


title: HLE-B3 WT_12h_rep2

value: human lens epithelial cells


title: UNSTIM_B

value: neuroepithelial cell lineage of WA09 human embryonic stem


title: kd_vitro_sgKdm5d_RNAseq_1


title: UNSTIM_A


title: HLE-B3 WT_12h_rep1


title: HLE-B3 WT_0h_rep3

value: untreated


title: Adjacent normal sample2


title: LOY_vitro_sgScr_RNAseq_3

description:
ssty1_ssty2_all_sample_counts.csv
ssty1_ssty2_all_sample_deseq_normalize.csv


title: Lung adenocarcinoma sample2


title: LOY_vitro_sgScr_RNAseq_2


title: HLE-B3 WT_0h_rep2


title: LOY_vitro_sgSsty2_RNAseq_3


title: HLE-B3 WT_0h_rep1


title: IR_60d

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

data_processing:
The Cell Ranger software pipeline (version 5.0.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner.
the unique molecular identifier (UMI) count matrix using the R package Seurat(version 3.1.1)
Library size normalization was performed with NormalizeData function in Seurat to obtain the normalized count. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and the results were logtransformed.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

organism: Rattus norvegicus

source_name: skin

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). cDNA was then amplified by PCR with appropriate cycles which depend on the recovery cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated and library amplification. Then these libraries were sequenced on the Illumina sequencing platform and 150 bp paired-end reads were generated.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: irradiated 60 days


title: Adjacent normal sample1


title: Lung adenocarcinoma sample1


title: HLE-B3 Atg7KO_0h_rep1


title: LOY_vitro_sgScr_RNAseq_1


title: IR_28d

value: irradiated 28 days


title: IR_7d

value: irradiated 7 days


title: BoxB-MS2 adRNA + ADAR2-DDC(E488Q)-λN-P2A-MCP-ADAR2-DDN (93)

city: La Jolla

first: Dario

last: Meluzzi

address: 9500 Gilman Drive #0648

department: School of Medicine

institute: UC San Diego

data_processing:
Basecalls were performed using Illumina RTA3, and fastq files were then generated using Illumina bcl2fastq2 v2.20. Both tasks were carried out by the UCSD IGM Genomics Center.
RNA-seq read pairs with 100 bases per read mate were aligned to the GRCh38 reference genome using STAR aligner version 2.7.1a or 2.7.3a (Dobin A et al 2013). The genome index was built using primary assembly annotations from GENCODE release 32. Default parameters were used to run STAR, except for the following relevant settings: --clip3pAdapterSeq AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, --outSAMtype BAM Unsorted, --outBAMcompression 0, --quantMode GeneCounts, --outReadsUnmapped Fastx, --genomeLoad LoadAndRemove, --alignSJDBoverhangMin 1, --peOverlapNbasesMin=10, --peOverlapMMp=0.05, --outSAMmultNmax 1, --alignEndsType EndToEnd, --outFilterMismatchNmax -1, --outFilterMismatchNoverReadLmax 0.2, --outFilterMultimapNmax 1.
The reads of the resulting uniquely aligned pairs were sorted by genomic coordinate using samtools sort (Li H. et al 2009). Duplicated read pairs were marked using samtools markdup and were removed from subsequent RNA-editing analysis.
The uniquely aligned reads for each sample were down-sampled using samtools view with option -s. Down-sampling fractions were calculated by dividing the smallest number of uniquely aligned reads among all samples by the number of uniquely aligned reads available for the sample being down-sampled. Down-sampling was not performed on the reads of the control samples. The down-sampled reads where then fed to samtools mpileup, whose output was parsed to extract the counts of each base found at each A-site and T-site in the GRCh38 reference genome. Insertions and deletions were ignored. Reference sites with read coverage of less than 10 were discarded. From the remaining reference A- and T-sites a final list was selected by choosing sites common to all samples and with at least one G or C at a reference A- or T-site, respectively, in at least one sample.
For each pair of compared control and treatment samples, and for each reference A- or T- site selected as described above, a Fisher exact test was carried out to calculate the p-value for the change in proportion of G or C bases, respectively, at that site. The p-values for all selected reference sites were adjusted for multiple testing using the Benjamini-Hochberg method. The measured base proportions for each site (row) and sample (column) are reported in processed data file pm_adar_rned_008-mcplns_seq_rna_ed_bfscr_0_res-bpr-0.tsv.gz. The adjusted p-values for the comparison (column) of base proportion between each sample and the control sample at each site (row) are reported in processed data file pm_adar_rned_008-mcplns_seq_rna_ed_bfscr_0_res-pad-0.tsv.gz.
Genome_build: GRCh38
Supplementary_files_format_and_content: pm_adar_rned_008-mcplns_seq_rna_ed_bfscr_0_res-bpr-0.tsv.gz: measured proportions of G or C bases at each A or T site (row) for each sample (column)
Supplementary_files_format_and_content: pm_adar_rned_008-mcplns_seq_rna_ed_bfscr_0_res-pad-0.tsv.gz: adjusted p-values for each comparison (column) of base proportions between a sample and the untreated sample at each site (row)

source_name: Cell line

growth_protocol: All experiments were carried out in HEK293FT cells which were  grown in DMEM supplemented with 10% FBS and 1% Antibiotic-Antimycotic (Thermo Fisher) in an incubator at 37 °C and 5% CO2 atmosphere.

extract_protocol:
RNA was extracted using the RNeasy mini kit.
RNA-seq libraries were prepared from 250ng RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: Plasmid transfection for the split-ADAR2 samples according to standard protocols.

value: Plasmid transfection


title: ATAC-seq in DMSO-treated SEM cells

city: Warsaw

first: Malgorzata

last: Firczuk

state: masovian

address: Nielubowicza 5 Street

department: Department of Immunology

country: Poland

institute: Medical University of Warsaw

library_source: genomic

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling using Homer

molecule: genomic DNA

source_name: Leukemia cell line (SEM)

growth_protocol: Cells were continuously grown in RPMI with 10% FBS with 1% penicillin/streptomycin solution, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
cells were washed with PBS and lysed with 0.1% IGEPAL CA-630, followed by Tn5 transposase treatment
Libraries were made using the Nextera DNA library prep kit (Illumina)

treatment_protocol: Cells were seeded at 1.0 x 106/ml density in RPMI with 10% FBS and 1% penicillin/streptomycin solution and treated with DMSO (control) or with 1.5 µM of auranofin (AUR) for 4h

value: DMSO-treated cells for 4h

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: con

value: control


title: LOY_vitro_sgSsty2_RNAseq_2

value: Trp53-/- c-kit+ HSPCs in vitro


title: LOY_vitro_sgSsty2_RNAseq_1


title: WPMY-1 shCAVIN1 Rep_3

city: Baltimore

first: Jin-Yih

last: Low

state: MD

address: 1550 Orleans St

department: Radiation Oncology and Molecular Radiation Sciences

institute: Johns Hopkins School of Medicine

data_processing:
Illumina CASAVA performed base-calling of Illumina NextSeq 500 76bp paired-end data producing FASTQ files.
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq 2.17.1.14
Using Tophat version 2.2.5 with default parameters, raw data were aligned to the NCBI human reference genome and Fragments Per Kilobase Of Exon Per Million (FPKM) values were obtained.
Genome_build: NCBI GRCh38
Supplementary_files_format_and_content: Processed data NLaw041818-Gene_FPKM.txt is tab-delimited text file of the Tophat-derived gene symbol and FPKM values in linear notation.

source_name: WPMY-1 immortalized human normal prostate stromal cells

growth_protocol: Cells were maintained in DMEM media (ATCC-3002) supplemented with 5% FBS.

extract_protocol:
RNA was harvested using TRIzol (Life Technologies, Carlsbad, CA) as per manufacturer's instructions
Illumina stranded totalRNA sample prep kit

treatment_protocol: Lentiviral shRNA plasmid was purchased from Johns Hopkins High Throughput Biology core facility (shCAVIN1  5’-GTGGAGGTTGAGGAGGTTATT-3’. Control plasmid, pLKO1 was used as shCtrl. Following transfection in HEK293T cells for production of lentiviral particles, the viruses were transduced into WPMY-1 cells, and selected for puromycin resistance to generate stable CAVIN1 knock-down clones.

value: shRNA CAVIN1 knockdown

value: Normal prostate stromal cells


title: BoxB-MS2 adRNA + ADAR2-DDC-λN-P2A-MCP-ADAR2-DDN (92)


title: Brain, Control_TilingArray_M04

type: RNA

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

hyb_protocol: Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.

data_processing:
We used the TileShuffle algorithm (Otto C, Reiche K, Hackermuller J. Detection of differentially expressed segments in tiling array data. Bioinformatics 2012; 28: 1471–1479) to determine expressed and differentially expressed genomic intervals. Affymetrix Human Whole Genome Tiling Array 1.0 Set raw signal intensities were mapped to human genome version NCBI36 using Affymetrix BPMAP files. Expressed segments were detected with the TileShuffle parameter settings: window size = 200, the window score was defined as the arithmetic mean trimmed by the maximal and minimal values over signal intensities of all probes in a window, number of permutations = 10 000 and number of GC classes = 4. All windows with an adjusted p < 0.05 according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995) were defined to be significantly expressed. DE-TARs are differentially expressed TileShuffle intervals with adjusted p < 0.05 (window size = 200, the window score was defined as the logfold-change discarding all probes with converse behavior as observed for the relevant significantly expressed windows, number of permutations = 100 000 and number of GC classes = 1). Finally, the genome coordinates of all significantly expressed and all significantly differentially expressed segments were lifted over to GRCh37 (hg19) using liftOver (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver).
[additional results files] Ueberham_AD_K_highdiff3.bed:  significantly differentially expressed segments (adjusted p<0.05)

label: biotin

source_name: human brain tissue

label_protocol: The Affymetrix Human Whole Genome Tiling Array 1.0 Set consisting of 14 arrays was used according to the manufacturer’s instructions, except that separate labeling reactions were used for each array starting from 10 μg pooled total RNA.

extract_protocol: RNA was isolated by Trizol™ method (Invitrogen, Karlsruhe, Germany). 100mg deeply frozen human brain tissue (temporal cortex) was homogenized in the presence of 1ml Trizol in a glass-Teflon™ homogenizer. The homogenate was transferred to a microtube and after adding chloroform, samples were centrifuged at 15 000 g (4 °C) for 15min and the supernatant transferred to a fresh tube. Samples were mixed with equal amounts of isopropanol and centrifuged at 12 000 g (4 °C) for 15min to precipitate the RNA. After washing, the pellet was air-dried and dissolved in water. RNA quality was assessed by denaturing formaldehyde agarose gel electrophoresis, by spectrophotometry (scanning at 220−320 nm) and by analysis using Agilent 2100 bioanalyzer. Only samples with RIN > 5 were further processed. The RNA concentration was estimated spectrophotometrically by absorbance at 260 nm, concentration was adjusted to 1mg/ml and RNA was stored at −80 °C until use.

tag: disease state

value: Control

value: brain


title: WPMY-1 shCAVIN1 Rep_2


title: ADAR2-DDC-λN-P2A-MCP-ADAR2-DDN (94)


title: Brain, AD_TilingArray_M04

scan_protocol: Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.

value: Alzheimer's disease (AD)


title: Brain, Control_TilingArray_M06


title: 293FT (125)


title: LOY_vitro_sgSsty1_RNAseq_2


title: WPMY-1 shCtrl Rep_3

value: shRNA vector control


title: LOY_vitro_sgSsty1_RNAseq_1


title: IR_14d

value: irradiated 14 days


title: Brain, Control_TilingArray_M13


title: WPMY-1 shCtrl Rep_2


title: LOY_vivo_sgScr_RNAseq_1

description:
BM_vivo_sgSsty2_counts.csv
BM_vivo_sgSsty2_deseq_normalize.csv

value: sgKdm5d/sgScramble;Trp53-/- Bone marrow in vivo

value: control(sgScr)


title: WPMY-1 shCtrl Rep_1


title: LOY_vivo_sgScr_RNAseq_2


title: ATAC-seq in auranofin-treated cells

value: 1.5 µM auranofin (AUR)-treated cells for 4h


title: Brain, AD_TilingArray_M13


title: Brain, AD_TilingArray_M06


title: MCP-ADAR2-DD (123)


title: MCP-ADAR2-DD (89)


title: LOY_vivo_sgSsty2_RNAseq_2


title: ADAR2-DDC(E488Q)-λN-P2A-MCP-ADAR2-DDN (126)


title: S. maltophilia D457 bacterial culture collected after 1-hour induction with 16 μg/mL fosfomycin - Rep 3

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

data_processing:
Quality check of paired-end short reads (in FASTQ format) was evaluated with FASTQC. Traces of illumina adapters were detected at 3' end so reads were 50 nt cropped in the alignment process
Reads were aligned against S. maltophilia genome (NC_017671) using RNA-STAR (--alignIntronMax 1 --clip3pNbases 50)
Optical and PCR duplicates were identified with 'markduplicates' function of GATK suite
S. maltophilia genes were quantified using featureCounts function from Bioconductor's package Rsubread  (strandSpecific=2,isPairedEnd=TRUE,requireBothEndsMapped=TRUE,primaryOnly=TRUE, ignoreDup=TRUE)
Genome_build: NC_017671.1
Supplementary_files_format_and_content: Gene IDs, genome coordinates and raw counts in text-tabulated format

organism: Stenotrophomonas maltophilia

source_name: Bacterial culture

growth_protocol: S. maltophilia were grown overnight in LB broth at 37°C and 250 rpm. This culture was used to inoculate new flasks to reach an optical density at 600 nm (OD600) of 0.01, and the cultures were grown at 37°C until an OD600 of 0.6 was reached. When bacteria grew in the exponential phase (OD600 ≈ 0.6) the transcriptional response of S. maltophilia to a treatment with 16 μg / ml fosfomycin, 2.5 mM PEP or 0.5 GA-3P was evaluated by adding the compounds to the bacterial cultures for 1 hour at 37°C. A culture without treatment was used as the expression control.

extract_protocol:
Twenty milliliters of each bacterial culture was spun down at 6,000 × g for 3 min at 4°C and immediately frozen on dry ice and stored at −80°C. RNA was isolated from cell pellets using the RNeasy minikit (Qiagen) following the manufacturer’s instructions. To remove the remaining genomic DNA, total RNA samples were treated with DNase I (RNase-Free DNase Set [Qiagen]), and a second digestion was then performed following the Turbo DNA-free (Ambion) protocol. The RNA was purified and concentrated using RNeasy minikit columns. Finally, DNA contamination was checked by PCR with primers 27 and 48. Only RNAs containing no DNA contamination were used for further studies.
Libraries were constructed with Truseq stranded total RNA Library and rRNA depleted with NebNext rRNA depletion kit. Sequencing was conducted by Illumina NovaSeq 6000 sequencing technology using a 150-bp paired-end format and 20 million total reads/sample, using three independent biological replicates of each sample

value: 16 μg/mL fosfomycin


title: WPMY-1 shCAVIN1 Rep_1


title: S. maltophilia D457 bacterial culture collected after 1-hour induction with 16 μg/mL fosfomycin - Rep 2


title: MS2-MS2 adRNA (88)


title: LOY_vivo_sgSsty2_RNAseq_1


title: LOY_vitro_sgSsty1_RNAseq_3


title: MS2-MS2 adRNA + MCP-ADAR2-DD(E488Q) (87)


title: LMVECs, PTPRZko3

city: Patras

first: Evangelia

last: Papadimitriou

state: Achaia

address: Panepistimioupoli

department: Dept of Pharmacy

country: Greece

institute: University of Patras

description:
PTPZ_KOvsPTPZ_WT_DEG_all.txt
PTPZ_KOvsPTPZ_WT_DEG.txt
PTPZ_KOvsPTPZ_WT_DEG_down.txt
PTPZ_KOvsPTPZ_WT_DEG_up.txt

data_processing:
Downstream analysis was performed using combination of STAR, HTseq, Cufflink and Illumina wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR.
GO and KEGG enrichment was implemented by the ClusterProfiler.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR).
Gene Ontology (GO) enrichment analysis was implemented by the clusterProfiler R package
Genome_build: Mus Musculus (GRCm38/mm10)
Supplementary_files_format_and_content: files containing lists of readcounts, fpkms, differentially Expressed Genes

source_name: LMVEC

growth_protocol: For LMVEC isolation, 2-5 mice were humanely euthanized at an age between 3-8 weeks by exposure to CO2 levels greater than 70% for 5 min. The lungs were immediately harvested, cut in small pieces in 1 ml DMEM and treated with 0.2% collagenase for 2 h at 37oC. The cell-tissue suspension was filtered through a 140 μm and a 60 μm filters, the filtrate was centrifuged at 500 g for 5 min at RT and the cell pellet was resuspended and cultured in DMEM containing 10% fetal bovine serum, 150 μg/ml Endothelial Cell Growth Supplement, 5 U/ml heparin sodium and antibiotics. When the plate was confluent, endothelial cells were sorted off by using magnetic CD31-conjugated beads.

extract_protocol:
Total RNA from LMVEC was extracted using the NucleoSpin RNA Plus kit from Macherey-Nagel. The concentration and purity of RNA was measured by using a Thermo Scientific™ NanoDrop™ One Microvolume UV-Vis Spectrophotometer and visualized at an agarose 1% gel. RNA from 3 independent fresh cell isolations from the Ptprz1+/+ and the Ptprz1-/- LMVEC was extracted and sent for RNAseq analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated cells

value: lung

value: lung microvascular endothelial cell (LMVEC)

value: untreated


title: MS2-MS2 adRNA + MCP-ADAR2-DD (86)

value: Plasmid transfection


title: S. maltophilia D457 bacterial culture collected after 1-hour induction with 0.5 mM GA-3P - Rep 3

value: 0.5 mM GA-3P


title: S. maltophilia D457 bacterial culture collected after 1-hour induction with 16 μg/mL fosfomycin - Rep 1


title: LMVECs, PTPRZko2


title: S. maltophilia D457 bacterial culture collected after 1-hour induction with 0.5 mM GA-3P - Rep 2


title: S. maltophilia D457 bacterial culture collected after 1-hour induction with 0.5 mM GA-3P - Rep 1


title: LMVECs, PTPRZko1


title: MCP-ADAR2-DDN (83)


title: SVR Trametinib and Cediranib 3

city: Seattle

first: Michael

middle: J

last: Wagner

state: Washington

address: 825 Eastlake Ave E

institute: University of Washington

data_processing:
Image analysis and basecalling was performed using Illumina's Real Time Analysis v1.18 software, followed by demultiplexing of indexed reads and generation of FASTQ files with Illumina's bcl2fastq-1.8.4 software.
Sequenced reads were aligned to Ensembl's GRCm38 using STAR aligner v2.7.1a in the software's two-pass mode, where the software uses splice junctions detected in the first pass to identify spliced reads mapping to novel junctions in the second pass. Some of the parameters that were used --outFilterMultimapNmax 20 --alignIntronMax 500000 --alignMatesGapMax 1000000 --sjdbScore 2 --alignSJDBoverhangMin 1 --outFilterMatchNminOverLread 0.33 --outFilterScoreMinOverLread 0.33 --sjdbOverhang 100
Subread featureCounts software v1.6.0 was used for gene-level quantification in paired-end mode.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited file containing raw gene counts per-sample

source_name: SVR tumor xenograft

growth_protocol: SVR xenografts were grown in nude mice.

extract_protocol:
Total RNA extraction from flash frozen mouse tumor tissue was done using the RNEasy Mini kit (Qiagen, Valencia, CA).  The method involved using 5 mm stainless beads in conjunction with the TissueLyser LT (Qiagen, Valencia, CA) to achieve tissue lysis and homogenization. On-column DNase I digestion and RNA extraction was carried out following the manufacturer’s recommended protocol. Total RNA integrity was checked using an Agilent 4200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA).
Libraries were prepared from total RNA using the TruSeq RNA Exome library prep kits (Illumina, Inc., San Diego, CA, USA).

treatment_protocol: Tumors were allowed to establish for 3-7 days and then treatment began by oral gavage. Mice were treated with vehicle (10% cremaphor, 10% PEG 400, 1% tween), trametinib 1 mg/kg, cediranib 3 mg/kg, or trametinib and cediranib combined by oral gavage daily until tumors became ulcerated or greater than 1 cm.

value: SVR

value: Trametinib and Cediranib


title: ADAR2-DDC-λN (84)


title: LMVECs, PTPRZwt2


title: S. maltophilia D457 bacterial culture collected after 1-hour induction with 2.5 mM PEP - Rep 3

value: 2.5 mM PEP


title: LOY_vivo_sgSsty2_RNAseq_3


title: MCP-ADAR2-DDN + ADAR2-DDC(E488Q)-λN (82)


title: S. maltophilia D457 bacterial culture collected after 1-hour induction with 2.5 mM PEP - Rep 2


title: SVR Trametinib and Cediranib 1


title: SVR Cediranib 3

value: Cediranib


title: LMVECs, PTPRZwt1


title: Inflammatory B-3

city: Newark

first: Jason

last: Weinstein

state: NJ

address: New Jersey Medical School Cancer Center 205 South Orange Ave

department: Center for Immunity and Inflmmation

institute: Rutgers New Jersey Medical School

data_processing:
Base calling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and Alignment (Cutadapt v2.5, STAR vSTAR_2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Genome_build: Genome_build: GRCm38
Supplementary_files_format_and_content: Comma delimited file (csv) for differential gene expression counts via DESeq2.

source_name: Spleen

extract_protocol:
RNA was extracted using the RNAeasy plus mini kit (Qiagen)
Paired end strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols at Rutgers NJMS Genomics Core.

tag: infected with

value: LCMV Armsttrong

tag: timepoint

value: Day 12 post LCMV infection

value: Inflammatory B cell


title: MCP-ADAR2-DDN + ADAR2-DDC-λN (81)


title: S. maltophilia D457 bacterial culture collected after 1-hour induction with 2.5 mM PEP - Rep 1


title: BoxB-MS2 adRNA (96)


title: SVR Cediranib 2


title: Inflammatory B-2


title: BoxB-MS2 adRNA + ADAR2-DDC(E488Q)-λN (79)


title: Inflammatory B-1


title: SVR Trametinib 3

value: Trametinib


title: ADAR2-DDC(E488Q)-λN (85)


title: BoxB-MS2 adRNA + ADAR2-DDC-λN (78)


title: SVR Trametinib and Cediranib 2


title: S. maltophilia D457 bacterial culture collected at 0.6 OD600nm - Rep 2

description: S. maltophilia D457 bacterial culture collected at OD600nm = 0.6


title: LMVECs, PTPRZwt3


title: SVR Trametinib 2


title: GC-3

value: Naive B cell


title: S. maltophilia D457 bacterial culture collected at 0.6 OD600nm - Rep 1


title: BoxB-MS2 adRNA + MCP-ADAR2-DDN (77)


title: GC-2


title: SVR Trametinib 1


title: BoxB-MS2 adRNA + MCP-ADAR2-DDN + ADAR2-DDC(E488Q)-λN (76)


title: BoxB-MS2 adRNA + MCP-ADAR2-DDN + ADAR2-DDC-λN (75)


title: Naïve-3

description: diffexpr-results_geneIDCD11.csv, diffexpr-results_geneIDGCB.csv


title: SVR Control 3

value: Vehicle


title: GC-1

value: GC B cell


title: GFP (74)


title: S. maltophilia D457 bacterial culture collected at 0.6 OD600nm - Rep 4


title: 293FT (73)


title: SVR Cediranib 1


title: SVR Control 1


title: S. maltophilia D457 bacterial culture collected at 0.6 OD600nm - Rep 3


title: Naïve-1


title: SMAdel7_HomP2_R2

status: Public on Jan 18 2022

city: Boston

first: Amanda

middle: J.

last: Guise

state: MA

address: 3 Blackfan Circle

department: F.M. Kirby Center for Neurobiology

institute: Boston Children's Hospital & Harvard Medical School

description:
RNA from P2 spinal cord, SMA, Rep2
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking

data_processing:
Sequencing quality was evaluated with FastQC (Mean Phred Score > 30).
Raw fastq files were subsequently processed using the Tuxedo suite: reads were mapped to the mouse genome (v. GRCm38vM11, (GRCm38), version M11 (Ensembl 86), 2016-09-20) using Bowtie (v. 2.2.4) (Langmead et al., 2009) and Tophat (v. 2.1.1) (Kim et al., 2013) with the following options enabled: library type --fr-firststrand --coverage-search --no-mixed --no-discordant with the Gencode reference GTF supplied (-G option).
Following the initial Tophat search, read insert size parameters for each set of PE files were extracted using Picard for manual inclusion in a second Tophat refinement search specifying --mate-inner-dist and --mate-std-dev.
Resulting .bam files were assembled using Cufflinks (v. 2.2.1) (Trapnell et al., 2010), followed by additional analysis using Cuffmerge, Cuffcompare, and Cuffdiff (Trapnell et al., 2013) specifying six sample groups (SMA P2, P6, P10 and CTRL P2, P6, P10) for pairwise determination of differentially expressed genes and transcripts at individual developmental stages or stage-to-stage.
Genome_build: v. GRCm38vM11, (GRCm38), version M11 (Ensembl 86), 2016-09-20

source_name: P2 spinal cord

extract_protocol:
RNA was isolated from whole heterozygote control or homozygote SMN7 mouse spinal cords (P2, P6, or P10) by Trizol/chloroform extraction. Tissues were dissociated in 1mL Trizol using a bead beater homogenizer (Precellys) using 1.4 mm Zirconium oxide beads (5500–3x-20s-030). Homogenized samples were then incubated for 5 minutes at room temperature (RT) followed by addition of 200uL chloroform and vigorous agitation for 15 seconds. Samples were then incubated for an addition 3 minutes at RT then centrifuged at 12,000 rcf for 15 minutes at 4C, after which the aqueous layer was collected for subsequent clean-up using an RNeasy isolation kit (Qiagen) with DNase treatment according to manufacturer’s instructions with extraction in 50 μl RNAse-free water. RNA concentration was measured by nanodrop and submitted for sequencing.
RNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with RiboZero (Illumina)

tag: developmental stage

value: Spinal cord

tag: mouse strain

value: Homozygote (SMA)


title: SMAdel7_HetP2_R3

description:
RNA from P2 spinal cord, Control, Rep3
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking

value: Heterozygote (control)


title: SMAdel7_HomP10_R2

description:
RNA from P10 spinal cord, SMA, Rep2
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking

source_name: P10 spinal cord


title: SMAdel7_HetP6_R3

description:
RNA from P6 spinal cord, Control, Rep3
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking

source_name: P6 spinal cord


title: SW48, siControl

city: Chiba city

first: Nami

last: Sato

state: Chiba purefecture

address: Chuo-ku, Inohana 1-8-1

department: General Surgery

country: Japan

institute: Chiba university

description: description

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: SW48 cells were cultured in the RPMI 1640 medium (GIBCO, Grand Island, NY, USA) containing 10% FBS (Thermo Fisher Scientific, Inc., Massachusetts, USA) at 37 ℃ in a 5% CO2 incubator.

extract_protocol: Total RNA was isolated using the QIAGEN RNeasy Mini Kit (Qiagen, Inc., Chatsworth, CA, USA).

treatment_protocol: The double-stranded small interfering RNA (Hs_YY1_1 Cat#SI00051912(Qiagen Inc.)) was used to knock down YY1. The control cells were treated with negative control siRNA (AllStars negative control siRNA; Qiagen Inc.). These siRNAs (final concentration, 5 nmol/L) were transfected into cells using Lipofectamine RNAiMAX (Invitrogen; Thermo Fisher Scientific).

value: colorectal cancer (CRC)

value: colorectal cancer cell line

value: control


title: SMAdel7_HetP10_R3

description:
RNA from P10 spinal cord, Control, Rep3
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: SMAdel7_HomP10_R3

description:
RNA from P10 spinal cord, SMA, Rep3
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: SMAdel7_HomP6_R3

description:
RNA from P6 spinal cord, SMA, Rep3
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: SMAdel7_HomP2_R3

description:
RNA from P2 spinal cord, SMA, Rep3
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: SW48, siYY1

description: description

value: YY1 knockdown


title: SMAdel7_HetP10_R2

description:
RNA from P10 spinal cord, Control, Rep2
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: SMAdel7_HetP2_R2

description:
RNA from P2 spinal cord, Control, Rep2
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: SMAdel7_HomP10_R1

description:
RNA from P10 spinal cord, SMA, Rep1
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: SMAdel7_HomP2_R1

description:
RNA from P2 spinal cord, SMA, Rep1
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: SMAdel7_HomP6_R1

description:
RNA from P6 spinal cord, SMA, Rep1
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: SVR Control 2

value: SVR


title: DLD1, siControl

growth_protocol: DLD-1 cells were cultured in the RPMI 1640 medium (GIBCO, Grand Island, NY, USA) containing 10% FBS (Thermo Fisher Scientific, Inc., Massachusetts, USA) at 37 ℃ in a 5% CO2 incubator.


title: SMAdel7_HetP10_R1

description:
RNA from P10 spinal cord, Control, Rep1
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: SMAdel7_HetP6_R1

description:
RNA from P6 spinal cord, Control, Rep1
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: SMAdel7_HetP2_R1

description:
RNA from P2 spinal cord, Control, Rep1
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: Human subcutaneous white adipose 13-1

first: NORC

last: Boston

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

description:
processed data file:
Hs10X.counts.mtx.gz
Hs10X.counts.barcodes.tsv.gz
Hs10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Hs_SAT_13-1

data_processing:
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0).
Digital expression matrices were generated from the FASTQ files using the Drop-Seq tools <https://github.com/broadinstitute/Drop-seq> pipeline (version 2.3.0). Adjustments were made to the cell-tagging functions of this pipeline to account for the structure of the 10X barcode read: “BASE_RANGE=1-16” and “BASE_RANGE=17-28”, for the cell and UMI barcodes, respectively. The 10X TSO was provided to the starting sequence trimmer (“SEQUENCE=AAGCAGTGGTATCAACGCAGAGTACATGGG”); this is a minor deviation from the assumed TSO. Reads from were aligned with STAR (version 2.7.3) against the GRCm38 and GRCh38 genome assemblies for mouse and human, respectively. Gene counts were obtained, per-droplet, by summarizing the unique read alignments across exons and introns (Drop-Seq tools “Digital Expression” option: “LOCUS_FUNCTION_LIST=INTRONIC”) in release 16 of the GENCODE mouse annotation or release 27 of the human annotation.
CellBender (Fleming, et. al 2019) version 0.2.0 was used to remove background/ambient signal from the mouse DGE matrices.
In 10X Chromium Single Cell 5’ Solution (v3.x) data, the cDNA read is single-ended (read 2); read 1 contains cell and UMI barcodes pertaining to the read
Genome_build: GRCh38 or GRCm38
Supplementary_files_format_and_content: Digital gene expression matrices (“dge.tsv.gz” files): gene-by-cell UMI counts. Species-wise gene expression matrices in matrix market format: “Hs10X.counts.mtx.gz” and “Mm10X.counts.mtx.gz”. Row (feature) and column (barcode) for the combined expression matrices.

source_name: subcutaneous adipose tissue

extract_protocol:
Nuclei were isolated from frozen mouse and human adipose tissue samples for 10x snRNA-seq using a slightly modified approach to what was previously described50–52. Samples were kept frozen on dry ice until immediately before nuclei isolation, and all sample handling steps were performed on ice. Each flash-frozen adipose tissue sample was placed into a gentleMACS C tube (Miltenyi Biotec) with 2 mL freshly prepared TST buffer (0.03% Tween 20 [Bio-Rad], 0.01% Molecular Grade BSA [New England Biolabs], 146 mM NaCl [ThermoFisher Scientific], 1 mM CaCl2 [VWR International], 21 mM MgCl2 [Sigma Aldrich], and 10 mM Tris-Hcl pH 7.5 [ThermoFisher Scientific] in Ultrapure water [ThermoFisher Scientific]) with or without 0.2 U/ µL of Protector RNase Inhibitor (Sigma Aldrich). gentleMACS C tubes were then placed on the gentleMACS Dissociator (Miltenyi Biotec) and tissue was dissociated by running the program “mr_adipose_01” twice, and then incubated on ice for 10 minutes. Lysate was passed through a 40 µm nylon filter (CellTreat) and collected into a 50 mL conical tube (Corning). Filter was rinsed with 3 mL of freshly prepared ST buffer buffer (146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2; 10 mM Tris-Hcl pH 7.5) with or without 0.2 U/µL RNase Inhibitor, and collected into the same tube. Flow-through was centrifuged at 500 x g for 5 minutes at 4ºC with brake set to low. Following centrifugation, supernatant was removed, and the nuclear pellet was resuspended in 50 - 200 µl PBS pH 7.4 (ThermoFisher Scientific) with 0.02% BSA, with or without 0.2U/µL RNase Inhibitor. In order to reduce ambient mRNA, the nuclear pellets of some samples were washed 1-3 times with 5 mL of PBS-0.02% BSA before final resuspension. An aliquot of nuclei from each sample was stained with NucBlue (Thermofisher Scientific), counted in a hemocytometer using fluorescence to identify intact nuclei, and then immediately loaded on the 10x Chromium controller (10x Genomics) according to the manufacturer’s protocol.
For each sample, 10,000-16,500 nuclei were loaded in one channel of a Chromium Chip (10x Genomics). The Single Cell 3’ v3.1 chemistry was used to process all samples. cDNA and gene expression libraries were generated according to the manufacturer's instructions (10x Genomics). cDNA and gene expression library fragment sizes were assessed with a DNA High Sensitivity Bioanalyzer Chip (Agilent).
cDNA and gene expression libraries were quantified using the Qubit dsDNA High Sensitivity assay kit (ThermoFisher Scientific). Gene expression libraries were multiplexed and sequenced on the Nextseq 500 (Illumina) with a 75-cycle kit and the following read structure: Read 1: 28 cycles, Read 2: 55 cycles, Index Read 1: 8 cycles.
10X Chromium Single-Cell 3’ (v3 Chemistry);

value: white adipose tissue

tag: Sex

value: male

tag: bmi

tag: surgery

value: VSG


title: Naïve-2

description: diffexpr-results_geneIDCD11.csv, diffexpr-results_geneIDGCB.csv

value: LCMV Armsttrong

value: Day 12 post LCMV infection

tag: cell type


title: Human subcutaneous white adipose 11-1

description:
processed data file:
Hs10X.counts.mtx.gz
Hs10X.counts.barcodes.tsv.gz
Hs10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Hs_SAT_11-1

value: female


title: Human subcutaneous white adipose 12-1

description:
processed data file:
Hs10X.counts.mtx.gz
Hs10X.counts.barcodes.tsv.gz
Hs10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Hs_SAT_12-1


title: Human subcutaneous white adipose 266-1

description:
processed data file:
Hs10X.counts.mtx.gz
Hs10X.counts.barcodes.tsv.gz
Hs10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Hs_SAT_266-1

value: Colon polyp


title: DLD1, siYY1

tag: cell line

tag: genotype


title: Human subcutaneous white adipose 09-1

description:
processed data file:
Hs10X.counts.mtx.gz
Hs10X.counts.barcodes.tsv.gz
Hs10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Hs_SAT_09-1

tag: tissue

tag: age


title: Human visceral white adipose 12-1

description:
processed data file:
Hs10X.counts.mtx.gz
Hs10X.counts.barcodes.tsv.gz
Hs10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Hs_OAT_12-1

source_name: omental adipose tissue


title: Human subcutaneous white adipose 10-1

description:
processed data file:
Hs10X.counts.mtx.gz
Hs10X.counts.barcodes.tsv.gz
Hs10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Hs_SAT_10-1

value: RYGB


title: SMAdel7_HomP6_R2

description:
RNA from P6 spinal cord, SMA, Rep2
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: Human visceral white adipose 266-1

description:
processed data file:
Hs10X.counts.mtx.gz
Hs10X.counts.barcodes.tsv.gz
Hs10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Hs_OAT_266-1


title: SMAdel7_HetP6_R2

description:
RNA from P6 spinal cord, Control, Rep2
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking


title: Human visceral white adipose 13-1

description:
processed data file:
Hs10X.counts.mtx.gz
Hs10X.counts.barcodes.tsv.gz
Hs10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Hs_OAT_13-1


title: Human visceral white adipose 09-1

description:
processed data file:
Hs10X.counts.mtx.gz
Hs10X.counts.barcodes.tsv.gz
Hs10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Hs_OAT_09-1


title: Human visceral white adipose 10-1

description:
processed data file:
Hs10X.counts.mtx.gz
Hs10X.counts.barcodes.tsv.gz
Hs10X.counts.features.tsv.gz
cell_metadata.tsv.gz
Hs_OAT_10-1


title: 10584-5-T-RNA

city: Pamplona

first: Pablo

last: Sarobe

address: Avda. Pio XII, 55

institute: CIMA

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 genome using align function of Rsubread
Calculate raw counts with featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts from featureCounts

source_name: Hepamut

extract_protocol: RNA-seq library preparation was performed using NEBNext Ultra II Directional RNA Library Prep Kit and NebNext rRNA Depletion kit (NEB).

value: hepatocellular carcinoma

tag: individual

value: patient 10584

value: tumor


title: 10584-5-NT-RNA

value: non-tumor


title: 10615-5-NT-RNA

value: patient 10615


title: 10635-8-NT-RNA

value: patient 10635


title: 92_org + 72h PF4014

city: SEATTLE

first: THOMAS

middle: A

last: REH

state: WA

address: 1959 NE PACIFIC STREET

department: BIOLOGICAL STRUCTURE

institute: UNIVERSITY OF WASHINGTON

description: 92_org + 72h PF4014

data_processing:
Reads were demultiplexed and fastqs were created using cellranger-atac mkfastq (1.2.0)
Reads were alligned, peaks were called, and fragment files and peak x cell matricies were created using cellranger-atac count (1.2.0)
Peaks were re-called using Macs2 (through Signac) and new peak x cell matricies were created using Signac::FeatureMatrix()
TFIDF was run on the peak x cell matricies using Signac::RunTFIDF()
Downstream processing was preformed in R using Signac, Seurat, ChromVar, and Monocle 3
Genome_build: GRCH38
Supplementary_files_format_and_content: filtered_peak_bc_matrix.tar.gz files 10x filtered_peak_bc_matrix files (peak x cell matricies), fragments.tsv.gz (10x Tn5 fragment files), Macs2_TFIDF.mtx files (cells x Macs2 peaks), metadata.csv.gz (metadata for samples)

source_name: retinal organoid

extract_protocol:
Fresh tissue, from both fetal retina or cultured organoids and retinospheres, was dissociated in papain and DNAse (#LK003170 and #LK00316, Worthington) for 20 to 30 minutes on a nutator at 37Â°C until a single cell suspension was achieved.
10x Single Cell ATAC v1.1

tag: treatment

tag: culture

value: retinal organoid


title: 10635-4-T-RNA


title: 92_org

value: control


title: 92_org + 48h PF4014

description: 92_org + 48h PF4014


title: 92_org + 24h PF4014

description: 92_org + 24h PF4014


title: 10632-3-T-RNA

value: patient 10632


title: 10632-3-NT-RNA


title: 10628-8-T-RNA

value: patient 10628


title: 10628-8-NT-RNA


title: 10627-2-T-RNA

value: patient 10627


title: 10627-2-NT-RNA


title: 10622-4-NT-RNA

value: patient 10622


title: 10619-13-NT-RNA

value: patient 10619


title: 10622-2-T-RNA


title: MCP-ADAR2-DD(E488Q) (124)

value: Plasmid transfection


title: 10594-4-NT-RNA

value: patient 10594


title: 10615-11-T-RNA


title: 10594-10-T-RNA


title: GB539_INPUT_SHEPMYCNT58A_MLN

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
ChIPseq reads were aligned with Bowtie1 to hg19
human reads were normalized to the same number of reads
metagenes were established with ngs.plot.r v2.63
chromosome ideagrams were drawn with RIdeogram v0.2.2
Genome_build: hg19
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

source_name: neuroblastoma cell line

growth_protocol: cells where synchronized uing double thymidine block

extract_protocol:
crosslink (5 min), harvest, spike-in with 10 % NIH-3T3, lysis of cells, fragment with covaris
libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: after second release cells where treated with 1 µM MLN8237

value: neuroblastoma cell line

tag: genotype/variation

value: pooled input from the all cell lines

tag: chip antibody


title: GB539_INPUT_SHEP_MLN


title: GB539_INPUT_SHEPMYCNT58A_DMSO


title: GB539_INPUT_SHEPMYCNWT_MLN


title: GB539_INPUT_SHEPMYCNWT_DMSO


title: H3_SHEP_DMSO

value: SH_EP parental cells

tag: input file


title: GB539_INPUT_SHEP_DMSO


title: H3_SHEP_MLN


title: C1 at R+3

city: Yerevan

first: Arsen

last: Arakelyan

state: Yerevan

address: 7 Hasratyan St.

department: Bioinformatics

country: Armenia

institute: Institute of Molecular Biology NAS RA

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for demultiplexing and basecalling.
Adaptor sequences and low quality bases were removed using Cutadapt v2.7. Read quality control was performed with FastQC v0.11.9 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
lncRNA analysis:  Trimmed and filtered reads were mapped with bowtie1 to the reference genome (GRCh38.p12). GENCODE release 38 was used for gene and transcript annotations. Read counts were obtained with featureCounts, then normalized using Ruvseq (4 latent variables) and EdgeR (TMM library normalization). Differential expression of lncRNAs at R+3 vs L-10 was calculated using edgeR.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: comma-separated matrix table with Ruvseq and edgeR normalized CPM counts for every lncRNA gene and every sample.

source_name: peripheral blood sEVs

extract_protocol:
sEVs were isolated from peripheral blood (PB) samples of 3 astronauts at L-10 and R+3 using the ExoQuick Plasma preparation and sEV precipitation kit (Cat # EXOQ5TM, System Biosciences, CA, USA). 400 μl of plasma was mixed with thrombin and kept at room temperature (RT) for 5 minutes. Subsequently, samples were centrifuged at 10,000 rpm for 5 minutes. Samples were then incubated with the exosome precipitation solution and refrigerated at 4ºC for 30 minutes. After centrifugation at 1,500 x g for 30 minutes at 4ºC, a beige-colored pellet was observed and dissolved in 100 μl of sterile 1xPBS. NS-300 Nanosight instrument (Malvern Instruments Ltd., Malvern, UK) equipped with an sCMOS camera (Hamamatsu Photonics, Hamamatsu, Japan) and a 405 nm laser was used. Data acquisition and processing were performed using NTA software version 2.3 build 0025. Background extraction was applied, and automatic settings were employed to determine the minimum expected particle size, minimum track length, and blur settings. Data were obtained at camera level 12 (shutter: 600, gain: 350). Three movies of 30 seconds at 25 frames per second were recorded and assigned a single measurement in triplicates.
Total RNA from sEVs was isolated from PB samples using miRNeasy kit following manufacturer's protocol (Cat#217084, Qiagen). RNA quality was assessed using an Agilent TapeStation (Agilent, Palo Alto, CA, USA), and RNA concentration was quantified by Qubit 4.0 spectrophotometer. The library for small RNA-sequencing (RNA-Seq) was prepared using the Smarter smRNAseq kit for Illumina (Takara Bio Inc., USA). The quantity and quality of amplified libraries were evaluated using Qubit (Invitrogen, Carlsbad, CA, USA) and Agilent TapeStation high sensitivity D1000 Screen Tape. Small RNA-seq libraries were sequenced using single-end 75 base pairs (SE75) sequencing chemistry on NextSeq 500 instruments following the manufacturer's protocols (Illumina).

value: peripheral blood sEVs

tag: time point


title: C3 at L-10


title: C2 at L-10


title: C2 at R+3


title: H3_SHEPMYCNWT_DMSO

value: SH-EP transfected with MYCN construct


title: H3_3_SHEP_MLN


title: H3_SHEPMYCNWT_MLN


title: H3_3_SHEP_DMSO


title: H3_3_SHEPMYCNWT_MLN


title: H3_3_SHEPMYCNWT_DMSO


title: C1 at L-10


title: H3S10_SHEP_DMSO


title: MCP-ADAR2-DD(E488Q) (90)

source_name: Cell line


title: H3S10_SHEP_MLN


title: C3 at R+3


title: H3S10_SHEPMYCNWT_DMSO


title: 10619-13-T-RNA

tag: disease state

value: hepatocellular carcinoma

value: tumor


title: SKNDZ input DNA

city: Heidelberg

first: Carl

last: Herrmann

address: INF 267

department: Medical Faculty

institute: University Heidelberg

data_processing:
Reads were trimmed using the Trimgalore
Genome alignment was done using Bowtie2 with standard parameter
Duplicates were removed as well as reads mapping multiple times
Input and corresponding IP datasets were scaled using the SES method and converted into a bigwig track using the bamCompare tool of the deepTools2 suite
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files containing histone mark signal intensity

source_name: Neuroblastoma cell lines

growth_protocol: The neuroblastoma cell lines were cultured in RPMI 1640 medium (Thermo Fisher Scientific) at 37 °C with 5% CO2 and supplemented with 1% penicillin/streptomycin (AppliChem) and 10% fetal calf serum (Gibco)

extract_protocol:
Chromatin immunoprecipitation, formaldehyde cross-linking of cells, cell lysis, sonication and library preparation were performed as described previously (Blecher-Gonen, R. et al. High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states. Nature protocols 8, 539-554, doi:10.1038/nprot.2013.023 (2013)). Approximately 4 × 106 cells (1 × 106 cells per individual immunoprecipitation) were used and cell lysis for each sample was achieved by 30 min incubation on ice in 950 µl RIPA I (10 mM Tris-HCl (pH 8.0), 1 mM ethylenediaminetetraacetic acid (pH 8.0), 140 mM NaCl, 0.2% sodium dodecyl sulfate and 0.1% sodium deoxycholate (DOC)).
Library preparation was performed using the NEBNext Ultra DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s protocol. Samples were mixed in equal molar ratios and sequenced on an Illumina sequencing platform.

value: Neuroblastoma

value: SKNDZ

value: untreated


title: SKNDZ H3K4me3

value: H3K4me3; rabbit polyclonal; Abcam; ab8580


title: SKNDZ H3K9me3

value: H3K9me3; rabbit polyclonal; Abcam; ab8898


title: SKNDZ H3K4me1

value: K3K4me1; rabbit polyclonal; Abcam; ab 8895


title: SK-N-FI input DNA

value: SK-N-FI


title: SKNDZ H3K27me3

value: H3K27me3; rabbit polyclonal; Active Motif 39155


title: SKNDZ H3K36me3

value: H3K36me3; rabbit polyclonal; Abcam ab9050


title: SK-N-FI H3K9me3


title: SK-N-FI H3K27me3


title: SK-N-FI H3K4me1


title: SK-N-FI H3K36me3


title: SH-EP H3K9me3

value: SH-EP


title: SH-EP input DNA


title: SK-N-FI H3K4me3


title: SK-N-FI H3K27ac

value: H3K27ac; rabbit polyclonal; Abcam; ab4729


title: SH-EP H3K36me3


title: SH-EP H3K27ac


title: SH-EP H3K27me3


title: SH-EP H3K4me3


title: NBL-S H3K4me3

value: NBL-S


title: NBL-S H3K9me3


title: NBL-S input DNA


title: NBL-S H3K4me1


title: NBL-S H3K36me3


title: NBL-S H3K27me3


title: H3S10_SHEPMYCNWT_MLN

value: neuroblastoma cell line


title: NBL-S H3K27ac


title: Hepa1-6 cells, 50T_50a_5_16

city: Shanghai

first: Xingyu

last: Rong

address: Dongan Road 130

institute: Fudan university

data_processing:
Illumina Hiseq used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
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: Hepa1-6 cells

growth_protocol: Hepa1-6 were maintained in Dulbecco's modiﬁed Eagle's medium (DMEM) with 10% fetal bovine serum (FBS)

extract_protocol:
Trizols Regent methods
Total RNA was extracted, and mRNA was isolated using Oligo Magnetic Beads and fragmented for cDNA synthesis. RNA-seq cDNA libraries were prepared and sequenced on an Illumina sequencing platform in 2*150 sequencing mode.

treatment_protocol: Two replicate was 50 μM TMAO treated for 24 hours;two replicate was 50 ng/ml TNF-α treated for 24 hours;Two replicate was 50 μM TMAO and 50 ng/ml TNF-α treated for 24 hours

value: Hepa1-6 cells

value: hepatoma carcinoma cells

tag: strain

value: treated with 50 μM TMAO and 50 ng/ml TMAO for 24 hours


title: Hepa1-6 cells, 50a_5_16

value: treated with 50 ng/ml TNF-α for 24 hours


title: NB69 input DNA

value: Neuroblastoma


title: Hepa1-6 cells, 50T_50a_5_14


title: NB69 H3K9me3


title: Hepa1-6 cells, 50a_5_14


title: SKNDZ H3K27ac

value: SKNDZ


title: NB69 H3K4me3

value: untreated


title: NB69 H3K4me1


title: Hepa1-6 cells, Control_5_16


title: Hepa1-6 cells, 50T_5_14

value: treated with 50 μM TMAO for 24 hours


title: Hepa1-6 cells, 50T_5_16


title: NB69 H3K36me3


title: NB69 H3K27me3


title: SH-EP H3K4me1


title: Kelly input DNA

value: Kelly


title: Kelly H3K9me3

value: H3K9me3; rabbit polyclonal; Abcam; ab8898


title: Hepa1-6 cells, Control_5_14


title: Kelly H3K4me3

value: H3K4me3; rabbit polyclonal; Abcam; ab8580


title: NB69 H3K27ac


title: Kelly H3K4me1

value: K3K4me1; rabbit polyclonal; Abcam; ab 8895


title: Kelly H3K27me3

value: H3K27me3; rabbit polyclonal; Active Motif 39155


title: Kelly H3K36me3

value: H3K36me3; rabbit polyclonal; Abcam ab9050


title: Kelly H3K27ac

value: H3K27ac; rabbit polyclonal; Abcam; ab4729


title: IMR575 input DNA


title: NOD LKs Combo replicate 2

city: San Diego

first: Dave

last: Robbins

address: 3535 General Atomics Court Ste. 200

institute: Fate Therapeutics

description: Gene expression data from dmPGE2 and dexamethasone (10uM for 4hr) ex vivo modulated NOD murine Lin- c-Kit+ (LKs) HSPCs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Exon 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the 3000 7G Scanner.

data_processing: Probe intensities were normalized according to signal space transformation robust multi-array analysis (SST-RMA) method in Transcriptome Analysis Console (TAC) 4.0.

source_name: LKs isolated from NOD mice

label_protocol: Biotinylated cRNA were prepared using Affymetrix GeneChip WT Pico reagent kit and the standard protocols using 10 ng total RNA.

growth_protocol: NOD murine Lin- c-Kit+ (LKs) HSPCs were ex vivo modulated in StemSpan media for 4 hours at 37 deg C.

extract_protocol: Total RNA was isolated from cells with the PicoPure RNA Isolation kit.

treatment_protocol: NOD murine Lin- c-Kit+ (LKs) HSPCs were ex vivo modulated with both dmPGE2 (10uM) and Dexamethasone (10 uM) and compared to vehicle (DMSO).

value: Lin- c-Kit+


title: IMR575 H3K4me3


title: IMR575 H3K9me3


title: NOD LKs Combo replicate 1


title: NOD LKs Vehicle replicate 1

description: Gene expression data from vehicle (DMSO for 4hr) ex vivo modulated NOD murine Lin- c-Kit+ (LKs) HSPCs


title: IMR575 H3K4me1


title: IMR575 H3K27me3


title: IMR575 H3K36me3


title: GI-ME-N input DNA

value: GI-ME-N


title: IMR575 H3K27ac


title: GI-ME-N H3K9me3


title: GI-ME-N H3K4me3


title: GI-ME-N H3K4me1


title: Telencephalon_skull_injury_7dpl_rep2

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from zebrafish telencephalon 7 days after skull injury

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

scan_protocol: According to the Affymetrix expression protocol (GeneChip Scanner 3000 7G)

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.3) including median polish and Sketch-Quantile normalisation

organism: Danio rerio

source_name: Telencephalon, skull injury, 7 days post lesion

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (Nugen)

growth_protocol: Fish were kept under standard husbandry conditions

extract_protocol: RNeasy Kit (Qiagen) including on-column DNAse digestion

treatment_protocol: As described in the paper. We carried out different stab wound injury paradigms: nostril and skull injury. Fish were anesthetized with 0.02% MS222 (Sigma-Aldrich) and injuries were performed in both telencephalic hemispheres. Nostril injury was performed as described previously (Baumgart et al., 2012). For the skull injury, a micro-knife (Fine Science Tools) was inserted vertically through the skull into the medial region of the telencephalon.

value: 3-5 months

value: wild-type


title: Telencephalon_skull_injury_7dpl_rep3


title: Telencephalon_skull_injury_3dpl_rep2

description: Gene expression data from zebrafish telencephalon 3 days after skull injury

source_name: Telencephalon, skull injury, 3 days post lesion


title: Telencephalon_skull_injury_7dpl_rep1


title: Telencephalon_skull_injury_3dpl_rep1


title: Telencephalon_skull_injury_3dpl_rep3


title: GI-ME-N H3K36me3


title: Telencephalon_skull_injury_3dpl_rep4


title: Telencephalon_skull_injury_2dpl_rep1

description: Gene expression data from zebrafish telencephalon 2 days after skull injury

source_name: Telencephalon, skull injury, 2 days post lesion


title: Telencephalon_skull_injury_1dpl_rep1

description: Gene expression data from zebrafish telencephalon 1 day after skull injury

source_name: Telencephalon, skull injury, 1 day post lesion


title: Telencephalon_skull_injury_1dpl_rep2


title: Telencephalon_skull_injury_2dpl_rep3


title: Telencephalon_skull_injury_2dpl_rep2


title: GI-ME-N H3K27me3


title: Telencephalon_nostril_injury_7dpl_rep2

description: Gene expression data from zebrafish telencephalon 7 days after nostril injury

source_name: Telencephalon, nostril injury, 7 days post lesion


title: NOD LKs Vehicle replicate 2


title: Telencephalon_nostril_injury_7dpl_rep3


title: GI-ME-N H3K27ac


title: OVCA432_4C_rep2

city: Tianjin

first: Guoli

last: Li

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

data_processing:
Library strategy: 4C-seq
The reduced genome was generated by extracting the sequences flanking the HindIII restriction sites (30 bp on each strand from the HindIII restriction sites to downstream) using the hg38 reference human genome, called 4C frag-ends. Non-unique frag-ends are discarded in subsequent analysis.
Subsequently, the highest covered frag-end was removed from the dataset in the normalization process and data are read-depth normalized to 1 million aligned intrachromosomal reads.
A Bioconductor package ‘r3Cseq’ with 2.5 kb sliding window was used to determine significant interactions and calculate interaction difference.
Genome_build: hg38
Supplementary_files_format_and_content: wig, bedGraph

source_name: heterozygous cell line OVCA432 (A/C)

growth_protocol: OVCA432 cell line was cultured in RPMI1640 medium containg 10%FBS.

extract_protocol:
4C-seq was performed by using Hind III for the first digestion, and Dpn II for the second digestion. In brief, cells were cross inked in 2% formaldehyde for 10 min at room temperature and quenched with 0.2M glycine (V900144, Sigma). Cells were rinsed for 2 times with ice PBS at room temperature. Then, cells were harvested and incubated in lysis buffer (50 mM Tris-Cl, 150 mM NaCl, 5 mM EDTA, 0.5% CA630, 0.5% Triton X-100 and protease inhibitor cocktail (04693132001, Roche)) while tumbling for 1 h at 4 °C. Cells were pelleted, washed, and resuspended in Hind III buffer. SDS was added to a concentration of 0.3% for an hour incubation in a thermomixer at 37 °C and 400 rpm. Triton X-100 was then added to a concentration of 1.8% and cells were incubated in a thermomixer at 37 °C and 400 rpm for 3 h. 200 units of Hind III enzyme (New England BioLabs Inc., R3104M) were added for 4 h incubation in a thermomixer at 37 °C and 900 rpm; another 200 units of Hind III enzyme were added for overnight incubation. Cells were then incubated for 20 min at 65 °C to heat inactivate Hind III enzyme, suspended with ligation buffer and 4,000 units of T4 ligase (New England BioLabs Inc., M0202M) and then incubated overnight at 16 °C. 300 μg Proteinase K was added for overnight incubation at 65 °C. The ligated DNA was purified, digested with 90 units Dpn II enzyme (New England BioLabs Inc., R0543S) in Dpn II buffer for overnight in a thermomixer at 37 °C and 500 rpm, followed by heat inactivation of Dpn II enzyme (65 °C for 25 min). Sample was diluted with ligation buffer. And 100 units of ligase were then added for overnight incubation at 16 °C. The circularized DNA was amplified with bait-specific inverse primers (one primer located 95 bp upstream of rs1192691 to identify allele at rs1192691 locus (CCTGACTCTGCCAAGAAATTTACC) and the other primer close to the Hind III restriction site to capture unknown DNA sequences that interact with bait locus (CCAACAGTGTGCTTTGTTTTCCAT)), pooled and purified.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an  Illumina sequencer following the manufacturer's protocols.

treatment_protocol: no treatment

value: heterozygous cell line OVCA432 (A/C)

value: ovarian cancer

value: AC


title: HC-24-CD19 RNA-Seq

city: San Francisco

first: Qin

last: Ma

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

data_processing:
The low quality reads were filtered by Trimmomatic, the sequencing reads were then aligned to the human reference (hg38) using hisat2.
The htseq-count tool and human gtf file from Ensembl were used to count aligned reads for each gene.
The raw counts were then normalized to counts per million (CPM) using cpm function in edgeR package.
Genome_build: hg38
Supplementary_files_format_and_content: The normalized CPM values for each sample.

source_name: peripheral blood

extract_protocol:
Total RNA was extracted using Quick-RNA Microprep Kit (Zymo Research).
The poly(A) selected paired-end sequencing libraries were constructed using the mRNA Hyper Prep Kit (KAPA), following the manufacturer’s instructions.

tag: disease status

value: Healthy control

value: peripheral blood

value: CD19+ B cells


title: HC-23-CD19 RNA-Seq


title: HC-22-CD19 RNA-Seq


title: HC-20-CD19 RNA-Seq


title: HC-19-CD19 RNA-Seq


title: OVCA432_4C_rep1


title: HC-21-CD19 RNA-Seq


title: Telencephalon_skull_injury_1dpl_rep3


title: Telencephalon_nostril_injury_2dpl_rep2

description: Gene expression data from zebrafish telencephalon 2 days after nostril injury

source_name: Telencephalon, nostril injury, 2 days post lesion


title: Telencephalon_nostril_injury_3dpl_rep2

description: Gene expression data from zebrafish telencephalon 3 days after nostril injury

source_name: Telencephalon, nostril injury, 3 days post lesion


title: HC-17-CD19 RNA-Seq


title: Telencephalon_nostril_injury_3dpl_rep1


title: Telencephalon_nostril_injury_1dpl_rep2

description: Gene expression data from zebrafish telencephalon 1 day after nostril injury

source_name: Telencephalon, nostril injury, 1 day post lesion


title: Telencephalon_nostril_injury_7dpl_rep1


title: Telencephalon_nostril_injury_2dpl_rep3


title: HC-14-CD19 RNA-Seq


title: Telencephalon_nostril_injury_3dpl_rep3


title: OMM2.3-S-rep1

first: gu

last: xiang

address: No.833 Zhizaoju Road

institute: Shanghai Jiao Tong University school of medicine

data_processing:
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 qualityreads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All thedownstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene wascalculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number ofFragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect ofsequencing depth and gene length for the reads count at the same time, and is currently the most commonlyused method for estimating gene expression levels.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05
GO and KEGG enrichment analysis of differentially expressed genes
Genome_build: hg38
Supplementary_files_format_and_content: bw

source_name: Uveal melanoma cell

growth_protocol: Uveal melanoma cells were extracted from uveal melanoma and cultured in a 6 cm culture dish with 1640.

extract_protocol:
Retinas were removed, flash frozen on dry ice, 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: Uveal melanoma

value: treated with SGC0946


title: OMM2.3-S-rep2


title: HC-16-CD19 RNA-Seq


title: HC-13-CD19 RNA-Seq


title: SKOV3(CC)-iEZH2_H3K27ac_IP_rep2

data_processing:
Basecalls performed using CASAVA version 1.4
Data were filtered using Trimmomatic
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2-2.3.5
Determination of the normalized factor using deeptools
peaks were called using MACS2
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig

source_name: SKOV3 possessing homozygous mutation (C/C) at rs1192691

growth_protocol: SKOV3(AA) and SKOV3(CC)  cell line were cultred in RPMI1640 medium containg 10%FBS.

extract_protocol:
1 × 10e7cells were washed with PBS and fixed with 37 °C pre-heated 10% FBS MEDIA/1% formaldehyde at room temperature for 10 min, and quenched with 0.125 M glycine (V900144, Sigma) for 5 min, and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Cells were maintained in the presence of DMSO or 5 μM EPZ005687 for 10 days with media and inhibitor replacement every other day before being harvested for ChIP assay.

value: CC

value: H3K27ac (ab4729, Abcam)


title: Telencephalon_nostril_injury_2dpl_rep1


title: SKOV3(CC)-iEZH2_H3K27ac_IP_rep1


title: Telencephalon_nostril_injury_1dpl_rep1


title: Telencephalon_Control_rep4

description: Gene expression data from zebrafish telencephalon control tissue

source_name: Telencephalon, no injury


title: Telencephalon_Control_rep3


title: Telencephalon_Control_technical_replicate1_rep1


title: Telencephalon_Control_technical_replicate2_rep1


title: Telencephalon_nostril_injury_1dpl_rep3


title: Telencephalon_Control_rep2


title: SKOV3(CC)-iEZH2_H3K27ac_input_rep2


title: SKOV3(CC)-iEZH2_H3K27ac_input_rep1


title: HC-11-CD19 RNA-Seq


title: SKOV3(CC)-WT_H3K27ac_IP_rep1

value: DMSO


title: HC-12-CD19 RNA-Seq


title: SKOV3(CC)-WT_H3K27ac_input_rep1


title: SKOV3(CC)-WT_H3K27ac_input_rep2


title: SKOV3(AA)-iEZH2_H3K27ac_IP_rep2

value: AA


title: MS-29-CD19 RNA-Seq

value: Multiple sclerosis


title: MS-28-CD19 RNA-Seq


title: mPB CD34+ Combo donor 1

description: Gene expression data from dmPGE2 and dexamethasone (10uM for 4hr) ex vivo modulated human HSPCs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133A 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Probe intensities were normalized according to robust multi-array analysis (RMA) method in Transcriptome Analysis Console (TAC) 4.0.

source_name: mPB isolated HSPCs

growth_protocol: Human mPB CD34+ HSPCs were ex vivo modulated in StemSpan media for 4 hours at 37 deg C.

treatment_protocol: Human mPB CD34+ HSPCs were ex vivo modulated with either dmPGE2 (10uM) or Dexamethasone (10 uM) or the Combination of both and compared to vehicle (DMSO).

tag: agent

value: dmPGE2 and dexamethasone (10uM)


title: SKOV3(AA)-iEZH2_H3K27ac_input_rep1


title: MS-27-CD19 RNA-Seq


title: SKOV3(AA)-WT_H3K27ac_IP_rep2


title: SKOV3(CC)-WT_H3K27ac_IP_rep2


title: SKOV3(AA)-iEZH2_H3K27ac_input_rep2


title: mPB CD34+ dmPGE2 donor 3

description: Gene expression data from dmPGE2 (10uM for 4hr) ex vivo modulated human HSPCs

value: dmPGE2 (10uM)


title: SKOV3(AA)-WT_H3K27ac_IP_rep1


title: MS-26-CD19 RNA-Seq


title: mPB CD34+ dmPGE2 donor 1


title: SKOV3(AA)-WT_H3K27ac_input_rep2


title: SKOV3(AA)-WT_H3K27ac_input_rep1


title: MS-25-CD19 RNA-Seq


title: mPB CD34+ Dex donor 3

description: Gene expression data from dexamethasone (10uM for 4hr) ex vivo modulated human HSPCs

value: dexamethasone (10uM)


title: mPB CD34+ Dex donor 2


title: MS-24-CD19 RNA-Seq


title: SKOV3(CC)_EZH2_IP_rep1

value: untreated


title: SKOV3(CC)_EZH2_IP_rep2


title: MS-23-CD19 RNA-Seq


title: SKOV3(CC)_EZH2_input_rep2


title: SKOV3(AA)-iEZH2_H3K27ac_IP_rep1


title: SKOV3(CC)_EZH2_input_rep1


title: mPB CD34+ Dex donor 1


title: mPB CD34+ dmPGE2 donor 2


title: SKOV3(AA)_EZH2_IP_rep2


title: SKOV3(AA)_EZH2_input_rep2


title: SKOV3(AA)_EZH2_input_rep1


title: MS-21-CD19 RNA-Seq


title: 9_Mutant_SF1

first: Pauline

middle: Anne Catherine

last: Marangoni

address: 513 Parnassus Avenue, HSE15

department: OFS

institute: UCSF

data_processing:
all reads trimmed at 3' end to 75x75bp
paired-end map to mouse RepeatMasker elements with bowtie. Use remaining (not mapped to repeat elements) reads in next steps
paired-end map (repeat-filtered reads) mapped to mm9 with tophat
duplicate mappings removed with samtools rmdup
differential expression analysis with DESeq on per-gene, per-sample read counts, 3 replicates per condition
use DESeq sizeFactors to report per-sample normalized read counts for significant genes
Genome_build: mm9
Supplementary_files_format_and_content: for each gene, the read counts, normalized by DESeq sizeFactors, are shown for all replicates.
Supplementary_files_format_and_content: call alternative splicing events: ran juncBASE v1.2-beta steps 1-6
Supplementary_files_format_and_content: statistical testing of alternative splicing events: ran DRIMSeq to obtain p-values associated with alternative splicing events between conditions

source_name: epithelial tissue

extract_protocol: Illumina TruSeq RNA sample preparation protocol

value: 8-10 weeks

value: incisor cervical loop

value: induced with TAM


title: 7_Control_SF1

value: not induced with TAM


title: mPB CD34+ Vehicle donor 2

description: Gene expression data from vehicle (DMSO) ex vivo modulated human HSPCs

value: vehicle (DMSO)


title: SKOV3(CC)_H3K9me3_IP_rep2

growth_protocol: SKOV3(AA) and SKOV3(CC)  cell lines were cultred in RPMI1640 medium containg 10%FBS.

extract_protocol:
1 × 10^7cells were washed with PBS and fixed with 37 °C pre-heated 10% FBS MEDIA/1% formaldehyde at room temperature for 10 min, and quenched with 0.125 M glycine (V900144, Sigma) for 5 min, and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an  Illumina sequencer following the manufacturer's protocols.

value: SKOV3 possessing homozygous mutation (C/C) at rs1192691

value: ovarian cancer

value: H3K9me3 (ab8898, Abcam)


title: MS-20-CD19 RNA-Seq

value: peripheral blood

value: CD19+ B cells


title: SKOV3(CC)_H3K9me3_IP_rep1

value: CC


title: 5_Mutant_SF1


title: MS-19-CD19 RNA-Seq


title: SKOV3(CC)_H3K9me3_input_rep1

source_name: SKOV3 possessing homozygous mutation (C/C) at rs1192692


title: SKOV3(CC)_H3K9me3_input_rep2

source_name: SKOV3 possessing homozygous mutation (C/C) at rs1192693


title: 4_Mutant_SF1


title: mPB CD34+ Vehicle donor 1


title: 3_Mutant_SF1


title: mPB CD34+ Vehicle donor 3


title: SKOV3(AA)_H3K9me3_IP_rep2

value: AA


title: SKOV3(AA)_H3K9me3_input_rep2


title: MS-17-CD19 RNA-Seq

value: Multiple sclerosis


title: HC-18-CD19 RNA-Seq

value: Healthy control


title: SKOV3(AA)_H3K9me3_input_rep1


title: SKOV3(AA)_EZH2_IP_rep1


title: 2_Control_SF1


title: MS-16-CD19 RNA-Seq


title: 1_Control_SF1


title: SKOV3(CC)_H3K27me3_IP_rep1

value: H3K27me3 (#9733, Cell signaling technology)


title: SKOV3(CC)_H3K27me3_IP_rep2


title: MS-15-CD19 RNA-Seq


title: SKOV3(CC)_H3K27me3_input_rep1

value: SKOV3 possessing homozygous mutation (C/C) at rs1192692


title: SKOV3(CC)_H3K27me3_input_rep2

value: SKOV3 possessing homozygous mutation (C/C) at rs1192693


title: SKOV3(AA)_H3K27me3_IP_rep2


title: SKOV3(AA)_H3K27me3_IP_rep1


title: MS-13-CD19 RNA-Seq


title: SKOV3(AA)_H3K27me3_input_rep2


title: SKOV3(AA)_H3K27me3_input_rep1


title: MS-18-CD19 RNA-Seq


title: Patient 4 CD8+ T cells day 60 V(D)J

last: Prlic

address: 1100 Fairview Ave, Mail stop E5-110

institute: Fred Hutch

description: 5' V(D)J

data_processing:
Samples were processed using CellRanger pipline version 2.1.1 or 3.0.2
FASTQ files were processed with CellRanger software v2.1.1 or v3.0.2 and corresponding sample sheet
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values with abundance measurements for each target.

source_name: PBMCs

extract_protocol:
RNA was extracted using 10x genomics protocols
RNA was extracted using 10x genomics protocols

treatment_protocol: 10^6 PBMCs  cells were stimulated for 18 hours at 37C with either DMSO control, pp65 peptide pool, or IE-1 peptide pool

tag: phenotype

tag: donors

value: Patient 4


title: SKOV3(AA)_H3K9me3_IP_rep1

tag: cell line

tag: cell type


title: Patient 4 CD8+ T cells day 30 V(D)J

description: 5' V(D)J


title: SKOV3(CC)_H3K4me3_IP_rep2

tag: genotype

value: H3K4me3 (ab8580, Abcam)


title: MS-11-CD19 RNA-Seq

tag: tissue


title: SKOV3(CC)_H3K4me3_IP_rep1


title: Patient 3 CD8+ T cells day 90 V(D)J

description: 5' V(D)J

value: Patient 3


title: SKOV3(CC)_H3K4me3_input_rep2


title: SKOV3(AA)_H3K4me3_IP_rep2


title: Patient 3 CD8+ T cells day 60 V(D)J

description: 5' V(D)J


title: MS-10-CD19 RNA-Seq


title: MS-9-CD19 RNA-Seq


title: SKOV3(CC)_H3K27ac_IP_rep2

value: H3K27ac (ab4729, Abcam)


title: Patient 4 CD8+ T cells day 90 V(D)J

description: 5' V(D)J


title: SKOV3(AA)_H3K4me3_input_rep2


title: SKOV3(AA)_H3K4me3_IP_rep1


title: MS-8-CD19 RNA-Seq


title: SKOV3(CC)_H3K27ac_IP_rep1


title: MS-14-CD19 RNA-Seq


title: SKOV3(AA)_H3K27ac_IP_rep2


title: Patient 2 CD8+ T cells day 60 V(D)J

description: 5' V(D)J

value: Patient 2


title: MS-6-CD19 RNA-Seq


title: SKOV3(CC)_H3K27ac or H3K4me3_input_rep1

description: SKOV3(CC)_H3K27ac or H3K4me3_input_rep1


title: MS-4-CD19 RNA-Seq


title: SKOV3(AA)_H3K27ac_IP_rep1


title: Patient 2 CD8+ T cells day 30 V(D)J

description: 5' V(D)J


title: SKOV3(CC)_H3K27ac_input_rep2


title: Patient 1 CD8+ T cells day 90 V(D)J

description: 5' V(D)J

value: Patient 1


title: SKOV3(AA)_H3K27ac_input_rep2

value: ovarian cancer


title: 225d Heart Mutant rep 5

city: New York

first: Nicole

last: Sayles

address: 407 East 61st Street

institute: Weill Cornell

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequence reads were processed using the BBDuk program in the BBMap package
Trimmed readsd were aligned to the mouse genome assembly GRCm38.p6 using the STAR aligner (version2.5.0a).
SAM files were converted to BAM to read overlapping reads per gene using HTseq-count (version 0.6.1)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: raw counts

source_name: Heart

extract_protocol:
Hearts were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent and Qiagen RNeasy Mini Kit (Cat# 74104). The Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

tag: age

value: post natal day 225


title: SKOV3(CC)_3

description: SKOV3(CC) rep 3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie2.
HTseq was used to quantify gene count.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA sequencing libraries were prepared using NovaSeq™ 6000 v1.5.


title: 225d Heart Mutant rep 4


title: Patient 1 CD8+ T cells day 60 V(D)J

description: 5' V(D)J


title: SKOV3(AA)_2

description: SKOV3(AA) rep 2


title: mPB CD34+ Combo donor 2

value: dmPGE2 and dexamethasone (10uM)


title: SKOV3(AA)_3

description: SKOV3(AA) rep 3


title: Patient 3 CD8+ T cells day 30 V(D)J

description: 5' V(D)J


title: SKOV3(CC)_1

description: SKOV3(CC) rep 1

value: CC


title: 225d Heart Mutant rep 2


title: SKOV3(AA)_1

description: SKOV3(AA) rep 1

value: AA


title: Patient 4 CMV-tet+ CD8+ T and NK cells day 90 transcriptome

description: 3' Transcriptome


title: Patient 2 CD8+ T cells day 90 V(D)J

description: 5' V(D)J


title: HC-15-CD19 RNA-Seq

value: peripheral blood

value: CD19+ B cells


title: 225d Heart Mutant rep 1


title: 225d Heart WT rep7

value: wild type


title: HeLaS3_100K_NicE-C_rep2

city: HeFei

first: Zhengyu

last: Luo

state: AnHui

address: Huangshan street

institute: USTC

description:
HeLaS3_NicE-C_100K.hic
HeLaS3_NicE-C_100K.bw

data_processing:
Library strategy: NicE-C
For HiC and NicE-C, raw HiC data were processed through the HiC-Pro (2.10.0) pipeline (PMID: 26619908). *.hic files were generated using HiC-Pro (2.10.0) script: hicpro2juicebox.sh.
For RNA-seq, reads were aligned to the hg19 or mm9 genome assembly using hisat2 version 2.1.0. Data were sorted using Samtools v1.7. BedGraph files were generated using  homer version 4.9. Counts were getting using featureCounts v1.5.0-p1.
For NicE-seq and NicE-C, reads were aligned to the hg19 or mm9 genome assembly using Bowtie2 version 2.2.5 with the following configurations: -3 120. Data were filtered using the following specifications: Samtools v1.7 was used to remove duplicate reads and chromosome M. Peaks were called using Macs2 version 2.1.0. BedGraph files were generated using  homer version 4.9.
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: bigwig files were generated using  bedGraphToBigWig
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution

source_name: HeLaS3 cells

growth_protocol: HeLa cells, HeLa-S3 cells and IMR90 cells were grown in DMEM medium containing 10% fetal bovine serum (FBS) at 37°C and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Cells were croseelinked with 1% formaldehyde for 10 minutes at room temperature. For Hi-C, we followed in-situ Hi-C protocol, the cells were lysed. Then the lysed cells were digested by MboI overnight at 37℃. DNA fragment ends were filled and labeled with dCTP, dGTP, dTTP and biotin-dATP. Proximity ligation was performed at room temperature for 4 hours. Then the DNA were de-crosslinked at 65°C overnight with Proteinase K and DNA were purified. For NicE-seq, the cells were lysed and then digested by Nt.CviPII and DNA polemerase I (Ecoli)  with dGTP, dTTP, biotin-dATP, biotin-dCTP and 5-methyl-dCTP for 20 min at 37℃. Then the DNA were de-crosslinked at 65°C overnight with Proteinase K and DNA were purified. For NicE-C,  the cells were lysed and then digested by Nt.CviPII and DNA polemerase I (Ecoli)  with dGTP, dTTP, dATP and 5-methyl-dCTP for 20 min at 37℃. DNA fragment ends were filled with dNTP and dA-tailing was performed. Proximity ligation by bridge-linker was performed at room temperature for 4 hours. Then the DNA were de-crosslinked at 65°C overnight with Proteinase K and DNA were purified.
Hi-C, NicE-C and NicE-seq DNA were sonicated and binding to M280 beads, then end-repair, dA-tailing and adapter ligation on beads. After PCR amplification and DNA purification, the libraries were sequenced on Illumina NovaSeq 6000 using 150bp paired-end reads. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cultured HeLa-S3 cells were washed once with 1X PBS, then add fresh DMEM medium supplemented with final 10 ng/ml TNFα or water.

tag: sequence of bridge linker

value: ATGCAAGCTTGCAT


title: Patient 4 CMV-tet+ CD8+ T and NK cells day 60 transcriptome

description: 3' Transcriptome


title: HeLaS3_100K_NicE-C_rep1


title: 981-RR-1

city: Ann Abor

first: Maureen

last: Sartor

address: 100 Washtenaw Ave.

institute: University of Michigan

description: U251-ATRX_WT scRNA-seq

data_processing:
Data processing including quality control, read alignment using hg38 genome and gene quantification were conducted using the 10X Cell Ranger software.
R package Seurat (Stuart et al., 2019) was used for normalization, data integration, and clustering analysis .
Cells with mitochondrial expression > 25% or the number of expressed gene outside the 1.5´IQR (i.e. outliers) were filtered out.  The optimal number of PCs were selected when its decrease in standard deviation < 0.5%, and used for cell visualization by UMAP.
MAST approach (Finak et al., 2015) implemented in R Seurat package was applied to identify cluster markers and differential genes for each cluster between U251-ATRXKO and U251-ATRXEVcells.
The genes that expressed in > 25% cells at both comparative conditions and showed FDR < 0.05 and fold change (FC) > 1.5 were defined as cluster markers or differentially expressed genes by ATRX status.
Genome_build: hg38
Supplementary_files_format_and_content: 10X read count files

source_name: human U251 cell line with wild type ATRX

growth_protocol: U251 cells were cultured in RPMI (#SH3025502, ThermoFisher) supplemented with 10% FBS.

extract_protocol:
Cells were prepared as a single cell suspension of 1000 cells/ ul in 100 ul volume. The target was specified at 10,000 cells at a 50,000 read depth.
Libraries were sequenced on the Illumina NovaSeq 6000 sequencer to generate 28x98 bp paired end reads for the sequencing parameters.

value: ATRX wild type


title: SKOV3(AA)_H3K27ac or H3K4me3_input_rep1

description: SKOV3(AA)_H3K27ac or H3K4me3_input_rep1


title: 225d Heart WT rep6


title: HeLaS3_1M_NicE-C_rep1

description:
HeLaS3_NicE-C_1M.hic
HeLaS3_NicE-C_1M.bw


title: Patient 4 CMV-tet+ CD8+ T and NK cells day 30 transcriptome

city: Seattle

description: 3' Transcriptome

value: Patient 4


title: HeLaS3_1M_NicE-C_rep2


title: Patient 3 CMV-tet+ CD8+ T and NK cells day 90 transcriptome

description: 3' Transcriptome


title: 981-RR-2

description: U251-ATRX_KO scRNA-seq

source_name: human U251 cell line with ATRX knockout

value: ATRX knockout


title: SKOV3(CC)_2

description: SKOV3(CC) rep 2


title: IMR90_NicE-C_rep2

description:
IMR90_NicE-C.hic
IMR90_NicE-C.bw

source_name: IMR90 cells

value: ATGCGGATCCGCAT


title: 225d Heart Mutant rep 3


title: 225d Heart WT rep5


title: mPB CD34+ Combo donor 3


title: IMR90_NicE-C_rep1

description:
IMR90_NicE-C.hic
IMR90_NicE-C.bw


title: Patient 3 CMV-tet+ CD8+ T and NK cells day 60 transcriptome

description: 3' Transcriptome

value: Patient 3


title: 225d Heart WT rep4


title: Patient 1 CD8+ T cells day 30 V(D)J

description: 5' V(D)J


title: Patient 3 CMV-tet+ CD8+ T and NK cells day 30 transcriptome

description: 3' Transcriptome


title: 225d Heart WT rep3


title: HeLaS3_control_RNA_seq_rep2

data_processing:
For HiC and NicE-C, raw HiC data were processed through the HiC-Pro (2.10.0) pipeline (PMID: 26619908). *.hic files were generated using HiC-Pro (2.10.0) script: hicpro2juicebox.sh.
For RNA-seq, reads were aligned to the hg19 or mm9 genome assembly using hisat2 version 2.1.0. Data were sorted using Samtools v1.7. BedGraph files were generated using  homer version 4.9. Counts were getting using featureCounts v1.5.0-p1.
For NicE-seq and NicE-C, reads were aligned to the hg19 or mm9 genome assembly using Bowtie2 version 2.2.5 with the following configurations: -3 120. Data were filtered using the following specifications: Samtools v1.7 was used to remove duplicate reads and chromosome M. Peaks were called using Macs2 version 2.1.0. BedGraph files were generated using  homer version 4.9.
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: bigwig files were generated using  bedGraphToBigWig
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution

tag: treatment

value: treat with equivalent water for 1h as control


title: HeLaS3_TNFa_RNA_seq_rep1

value: treat with final 10 ng/ml TNFalpha for 1h


title: HeLaS3_control_RNA_seq_rep1


title: HeLaS3_TNFa_RNA_seq_rep2


title: HeLaS3_control_NicE-C_rep2

description:
HeLaS3_control_NicE-C.hic
HeLaS3_control_NicE-C.bw


title: 225d Heart WT rep2


title: HeLaS3_control_NicE-C_rep1


title: HeLaS3_TNFa_NicE-C_rep2

description:
HeLaS3_TNFa_NicE-C.hic
HeLaS3_TNFa_NicE-C.bw


title: HeLaS3_TNFa_NicE-C_rep1


title: Patient 2 CMV-tet+ CD8+ T and NK cells day 30 transcriptome

description: 3' Transcriptome

value: Patient 2


title: HeLa_NicE-seq_rep2

description:
After decrosslink, DNA purification and fragmentation, end-repair, dA-tailing, adapter ligation were used to generated the HeLa NicE-seq library similar to the Hi-C or NicE-C library generation in the project. However, for this NicE-seq library, we add additional sequence between insert DNA and sequencing adapter, the length of the additional linker is 65 bp at both ends.
HeLa_NicE-seq.bw

data_processing:
Library strategy: NicE-seq
For HiC and NicE-C, raw HiC data were processed through the HiC-Pro (2.10.0) pipeline (PMID: 26619908). *.hic files were generated using HiC-Pro (2.10.0) script: hicpro2juicebox.sh.
For RNA-seq, reads were aligned to the hg19 or mm9 genome assembly using hisat2 version 2.1.0. Data were sorted using Samtools v1.7. BedGraph files were generated using  homer version 4.9. Counts were getting using featureCounts v1.5.0-p1.
For NicE-seq and NicE-C, reads were aligned to the hg19 or mm9 genome assembly using Bowtie2 version 2.2.5 with the following configurations: -3 120. Data were filtered using the following specifications: Samtools v1.7 was used to remove duplicate reads and chromosome M. Peaks were called using Macs2 version 2.1.0. BedGraph files were generated using  homer version 4.9.
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: bigwig files were generated using  bedGraphToBigWig
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution

source_name: HeLa cells

value: HeLa


title: HeLa_NicE-seq_rep1


title: 125d Heart Mutant rep5

value: Heart

value: post natal day 125


title: Patient 1 CMV-tet+ CD8+ T and NK cells day 90 transcriptome

description: 3' Transcriptome

value: Patient 1


title: HeLa_RNA_seq_rep2


title: 125d Heart Mutant rep4