title: MDAMB468_Hypo_1


title: HCC1806_Hypo_1

status: Public on Sep 27 2023

type: SRA

city: Bethesda

first: Stefan

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

country: USA

institute: NCI

library_source: genomic

data_processing:
ATAC-seq samples were pooled and sequenced on NextSeq using OMNI ATAC-seq protocol adapted from M.R. Corces, et al., 2017 and paired-end sequencing. All the samples have percent of Q30 bases above 95%. Samples were trimmed for adapters using Cutadapt before the alignment. The trimmed reads were aligned with Human - hg38 reference using Bowtie2 alignment.
Assembly: hg38
Supplementary files format and content: excel files include Z-scores for motifs for each Sample

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: For normoxic (21% O2) condition, cells were cultured at 37 °C in a 5% CO2 humidified environment as an adherent monolayer. Hypoxia experiments were performed in a hypoxia chamber (BioSpherix) at 1% O2 at 37 °C in a 5% CO2 humidified environment.

extract_protocol:
Cell revival, cell lysis, transposition, and DNA extraction were done using a published method by Corces et al., 2017 (PMID: 28846090) with some modifications for cryopreserved cell processing (Caravaca et al., 2022) and sequencing was performed on an Illumina NextSeq 2000 machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
Library complexity was measured by uniquely aligned reads using Picard’s MarkDuplicate utility. All the samples had library complexity with percent non-duplicated reads ranging from 38 to 69%. The peaks were called using Genrich and total number of peaks ranged between 54,835 and 83,046. The number of reads falling in peaks (FRiP score), ranges between 20.1 to 34.3%.

tag: tissue

value: breast cancer cell line

tag: condition

value: hypoxia

tag: ethnicity

value: AA

tag: er status

value: Neg

tag: cell lines


title: MDAMB157_Hypo_1


title: bsi_KO_far-red, rep 2

city: Ames

first: Gwyn

middle: A

last: Beattie

state: IOWA

address: 2213 Pammel Dr

department: Plant Pathology, Entomology, & Microbiology

institute: Iowa State University

description: total RNA

library_source: transcriptomic

data_processing:
The raw reads were filtered by BGI Genomics using SOAPnuke (v1.5.2) to remove reads containing sequencing adapters and low-quality reads (reads containing >20% of bases having quality scores ≤15 or an ambiguous sequence content of >1%). FASTQ files of the resulting “clean” reads were used for further quality assessment using FastQC v0.11.4 and analysis.
The clean reads from each sample were mapped to the B728a reference genome GCF_000012245.1 (2005 version) using Bowtie2 (v2.2.6) and TopHat2 (v2.1.0).
The number of reads that mapped to each gene in the genome were counted using HTSeq-count (v0.6.0) with parameters -i locus_tag -t gene -s reverse -r pos -m intersection-nonempty -a 10 -f bam. Genes with average read counts of <1 across all samples were excluded from subsequent analyses.
Counts were normalized for library size using upper-quartile normatilzation.
Normalized gene counts for all 66 samples were used to assess differential expression between specified strain x treatment combinations using the R package QuasiSeq (negative binomial model, strain x treatment interaction and replicate used as fixed effects, and the QLSpline method for FDR estimates), with q-value ≤ 0.00105 used to define statistical significance.
Assembly: Pseudomonas syringae B278a, GCF_000012245.1 assembly was downloaded from NCBI in October 2016; the original RefSeq annotation (submitted in 2005 by the Joint Genome Institute) was replaced replaced by a PGAP annotation in 2023 without changing the accession number, but the original annotation used here is still available under NCBI accession GCA_000012245.1
Supplementary files format and content: raw_counts.csv is is a matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: norm_counts.csv is a matrix table with natural log-transformed normalized gene counts for all genes with average raw read counts of ≥1 across all samples
Supplementary files format and content: B728aLight_QuasiSeq_results.xlsx is an Excel file with the results of the QuasiSeq differential analysis results (Ln[fold change], Log2[fold change], fold change, q-value) for all genes along with transcript metadata including gene name, product description, and functional classification.

molecule: total RNA

organism: Pseudomonas syringae pv. syringae B728a

source_name: bacteria

growth_protocol: Two independent cultures of each strain were grown on each of six separate days. For each culture, an initial culture was grown from a single colony in KB medium containing Rif (50 μg/mL) to a density of approx. 10^9 cells/mL, at which point 10 μL was sub-cultured into 5 mL KB medium and grown again to a density of approx. 10^9 cells/mL. A 0.2-mL aliquot was sub-cultured into 20 mL KB in a 125-mL flask and grown for 4–6 h with shaking in the dark at 20–22°C until an optical density at 600 nm (OD600) of approx. 0.5.

extract_protocol:
Immediately after treatment, 0.5 mL of each culture sample was added to 1 mL of RNAprotect (Qiagen) and vortexed for 5 sec. Following a 5-min incubation at room temperature, the cells from the two independent cultures for a single strain x treatment combination were combined and centrifuged at 5,000 x g for 10 min. The supernatant was decanted, and the cell pellet was stored at -70°C. For each strain, this process was repeated on six separate days. The cell pellets for a given strain x treatment combination collected on two separate days were thawed on ice and combined, and this pool was considered one biological replicate. In this manner, each strain x treatment combination was represented by three biological replicates, each of which contained cells derived from four independently exposed cultures. Total RNA was extracted using a RNeasy Mini Kit (Qiagen) with on-column Dnase I treatment, with one biological replicate for each strain x treatment combination extracted at the same time.
Library construction and sequencing were performed by BGI Genomics (China). For each sample, total RNA was depleted for ribosomal RNA using an Epicentre Ribo-Zero Magnetic Kit (Bacteria), fragmented, and then used for RNA-seq library construction using a TruSeq RNA Sample Prep Kit v2 (Illumina). Libraries were assessed for quality using a 2100 Bioanalyzer, quantified using real-time quantitative PCR, and sequenced on an Illumina HiSeq 4000 with 100-bp paired-end reads.

treatment_protocol: Two-milliliter culture aliquots were transferred into individual wells of replicate 6-well cell culture plates and plates were immediately exposed to blue light (20 μmol/m^2/s), red light (30 μmol/m^2/s), far-red light (188 μmol/m^2/s), or white light (34 μmol/m^2/s), or maintained in the dark for 15 min at 20–22°C without shaking. As a follow-up to prior microarray studies, the Δlov mutant was subject to two additional treatments in which cells cultivated in defined HMM medium were exposed for 15 min to blue light in the presence or absence of 0.23 M NaCl.

tag: strain

tag: cell type

value: bacteria

tag: genotype

tag: treatment

value: far-red


title: CON-D19

type: genomic

city: Shenyang

first: Chen

middle: yu

last: lan

address: Nan Jing Bei Street

country: China

institute: Department of Clinical Epidemiology and Evidence-based Medicine, the First Affiliated Hospital, China Medical University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylationEPIC BeadChip (Illumina, Inc., CA, USA) (850K array) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data was processed with the the Chip Analysis Methylation Pipeline (ChAMP) package in R. Probes were removed if they did not pass the detection cut-off (p < 0.01), were associated with known SNPs, were associated with the X and Y chromosomes, or were non-CpG probes. Following normalization, a single value decomposition (SVD) analysis was used to identify batch effects which were removed using ComBat with the SVA package using gene-wise linear models. DMPs with a P < 0.05 and a |Δβ| > 0.1 were selected for subsequent analysis. LEF-related differentially methylated genes (DMGs) were then identified, including genes associated with both hypo- and hypermethylation.

label: Cy3, Cy5

source_name: Whole Blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from RA samples using QIAamp DNA Blood Mini Kit (QIAGEN)  according to standard instructions

value: Whole Blood

tag: gender

value: male

tag: age

tag: age at diagnosis

tag: group

value: control


title: CON-D27

value: female


title: CON-E3


title: CON-D30


title: MDAMB231_Norm_1

value: normoxia

value: CC


title: bsi_KO_far-red, rep 1

description: total RNA


title: bphOP1_KO_bphP2R_KO_far-red, rep 3

description: total RNA

value: delta_bphOP1 delta_bphP2R


title: CON-D11


title: bphOP1_KO_bphP2R_KO_far-red, rep 2

description: total RNA


title: HS578T_Norm_1


title: HCC70_Norm_1


title: MDAMB157_Norm_1


title: HCC1806_Norm_1


title: MDAMB436_Norm_1


title: bphOP1_KO_bphP2R_KO_far-red, rep 1

description: total RNA


title: 15_Dorsey

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed using STAR/RSEM tools. Differential expression analysis was done using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

extract_protocol:
RNA isolation was done using TRIzol method . Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina NextSeq 2000 machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line


title: lov_KO_pN-lov_dark, rep 3

description: total RNA

value: delta_lov (pN-lov)

value: dark-mantained


title: NIH22B3571431

city: daejeon

first: Jonglyul

last: Park

address: 52, Eoeun-dong, Yuseong-gu

department: Medical genomics

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: normal blood samples

hyb_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Minfi

label: Cy5 and Cy3

source_name: gDNA from Blood

extract_protocol: genomic DNA was extracted and purified from blood samples using Qiagen DNeasy Kit according to standard instructions

value: Blood

value: Male


title: 14_Dorsey

value: breast cancer cell line


title: lov_KO_pN-lov_dark, rep 2

description: total RNA


title: CON-T31


title: 13_Dorsey

value: hypoxia


title: 11_Dorsey

value: AA


title: 10_Dorsey

value: Neg


title: lov_KO_pN-lov_blue, rep 3

description: total RNA

value: bacteria

value: blue


title: lov_KO_pN-lov_dark, rep 1

description: total RNA


title: NIH22B3764610

description: normal blood samples

value: Female


title: NIH22B3777003

description: normal blood samples


title: MDAMB468_Norm_1


title: 8_Dorsey


title: 16_Dorsey


title: NIH22B3836301

description: normal blood samples


title: CON-T35

value: Whole Blood

value: male


title: 9_Dorsey


title: 7_Dorsey


title: CON-T183

value: female

value: control


title: 6_Dorsey

value: normoxia

value: CC


title: lov_KO_pN-lov_blue, rep 2

description: total RNA

value: delta_lov (pN-lov)


title: 3_Dorsey


title: CON-T22


title: NIH22B3220052

description: normal blood samples


title: NIH22B3356275

description: normal blood samples


title: lov_KO_dark, rep 3

description: total RNA

value: dark-mantained


title: lov_KO_dark, rep 2

description: total RNA


title: 12_Dorsey


title: CON-D95


title: CON-T202


title: 5_Dorsey


title: NIH22B3960374

description: normal blood samples

value: Blood


title: lov_KO_pN-lov_blue, rep 1

description: total RNA


title: OA_FLS3_UT

city: Atlanta

first: Sergio

last: Ramirez-Perez

state: Georgia

address: 615 Michael St NE

department: Orthopaedics

institute: Emory University

description: FLS_OA 3 - log2 total RPKM

data_processing:
NovaSeq 6000 Paired-end sequencing was used, PE150, Q30≥85%.
Sequenced reads were mapped to the homo sapiens GRCh37 genome assembly using DNASTAR software, normalization was performed by RPKM on ArrayStar software . We obtained xxx genes.
Assembly: GRCh37
Supplementary files format and content: Matrix table - delimited text files include normalized expression levels for each sample

source_name: FLS

extract_protocol:
Synovial fibriblats from RA and OA patients were cultured and RNA was harvested using Trizol reagent.
Human mRNA Sequencing (WOBI) was used to perform RNA sample QC. Poly A enrichment was implemented for mRNA library preparation. NovaSeq PE150 was used to generate 6 G raw data per sample.

value: FLS

value: Untreated

tag: diagnosis

value: Osteoarthritis


title: 2_Dorsey

value: breast cancer cell line

value: AA


title: CON-T12


title: CON-E69


title: lov_KO_dark, rep 1

description: total RNA

value: bacteria


title: 1_Dorsey

value: Neg


title: 4_Dorsey


title: NIH22B3421252

description: normal blood samples

value: Male


title: CON-E63

value: Whole Blood


title: lov_KO_blue, rep 3

description: total RNA

value: blue


title: NIH22B3034692

description: normal blood samples

value: Female


title: OA_FLS2_UT

description: FLS_OA 2 - log2 total RPKM


title: CON-T19

value: female

value: control


title: CON-E20


title: CON-D31


title: lov_KO_blue, rep 2

description: total RNA


title: CON-T292


title: NIH22B3757093

description: normal blood samples


title: NIH22B3272420

description: normal blood samples


title: NIH22B3520851

description: normal blood samples


title: KO2_rep2

city: Shanghai

first: Zhonghua

last: Tao

address: No. 270, Dong’an Road

institute: Fudan University Shanghai Cancer Center

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were mapped to human genome hg38 using bowtie2. Detailed parameters include local, keeping alignments with MAPQ >= 10.
Reads Per Gene were calculated by FeatureCount.
Assembly: hg38
Supplementary files format and content: RNAseq_transcript_expression.txt: Tab-delimited text file including counts, FPKM values, and TPM values.

extract_protocol:
RNA was extracted with Trizol reagent.
RNA libraries were prepared using TruSeq Stranded Total RNA Library Preparation protocol for sequencing.

value: triple negative breast cancer cells

value: ARID1A knockout


title: KO2_rep1


title: KO1_rep2


title: bphOP1_KO_pN-bphOP1_dark, rep 3

description: total RNA

value: delta_bphOP1 (pN-bphOP1)

value: dark-mantained


title: RA8

type: RNA

city: Guangzhou

first: Shibai

last: Xiao

address: guangzhou avenue, NO.1023

institute: Nanfang Hospital, Southern Medical University

description: Fibroblast-like synoviocytes in vitro

hyb_protocol: We did according to the guildline of kits below:Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242);10X Blocking Agent;25X Fragmentation Buffer;2x GEx Hybridization Buffer HI-RPM;Hybridization Chamber, stainless (Agilent p/n G2534A);Hybridization Chamber gasket slides (Agilent p/n G2534-60003);Hybridization oven (Agilent p/n G2545A);Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029)

scan_protocol: 1.Assemble the slides into an slide holder. 2.Place assembled slide holders into scanner carousel.3.Verify scan settings for one-color scans.4.Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent)

source_name: Fibroblast-like synoviocytes

label_protocol: Agilent Microarray Scanner (Agilent p/n G2565BA)

extract_protocol: TRIzol® reagent was used to obtain total RNA

treatment_protocol: Fibroblast-like synoviocytes isolated from synovial tissue and cultivated in vitro  at 37 ºC in a humidified incubator with 5% CO2.

tag: subject status

value: rheumatoid arthritis patient

tag: Sex

value: Fibroblast-like synoviocytes


title: OA-9

description: Fibroblast-like synoviocytes in vitro

value: osteoarthritis patient


title: NIH22B3014281

description: normal blood samples

tag: tissue

value: Blood


title: RA1

description: Fibroblast-like synoviocytes in vitro


title: lov_KO_blue, rep 1

description: total RNA


title: RA4

description: Fibroblast-like synoviocytes in vitro


title: KO1_rep1


title: OA-7

description: Fibroblast-like synoviocytes in vitro


title: NC_rep2


title: bphOP1_KO_pN-bphOP1_dark, rep 1

description: total RNA


title: MDA-MB-231 cells, Gefitinib 1µM + THZ531 200nM, Rep3

city: Durham

first: Charles

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

data_processing:
Trimmomatic v0.32
Reads that were 20nt or longer after trimming were filtered for further analysis. Reads were aligned using the alignment tool STAR v2.4.1a following the proposed 2-pass strategy to first identify a splice junction database to improve the overall mapping quality.
Alignment was performed to GRCh38/hg38 of the human genome and transcriptome with ERCC synthetic spike-in RNA sequences (Annotations from product webpage manuals, https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_095 047.txt) appended for mapping. The TPM (transcripts per million) was computed for each mapped gene and synthetic spike-in RNA using RSEM v1.2.25.
Differential expression analysis was performed using DESeq2 v1.22.0 (88) running on R (v3.5.1).
Briefly, raw counts were imported and filtered to remove genes with low or no expression, that is, keeping genes having two or more counts per million (CPMs) in two or more samples. Filtered counts were then normalized with the DESeq function, using the counts for the ERCC spike-in probes to estimate the size factors. In order to find significant differentially expressed genes, the nbinomWaldTest was used to test the coefficients in the fitted Negative Binomial GLM using the previously calculated size factors and dispersion estimates. Genes having a Benjamini-Hochberg false discovery rate (FDR) less than 0.05 were considered significant (unless otherwise indicated). Differential gene expression was tested for all possible drug pairwise comparisons within each cell line, for example, single drug versus DMSO control, combination versus DMSO control, combination versus single drug and so on.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: CAL51 cells were maintained in MEM supplemented with 20% fetal bovine serum (FBS) and antibiotics (penicillin/streptomycin) in humidified atmosphere with 5% CO2 at 37C. MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics (penicillin/streptomycin) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cell counts were determined using C-Chip disposable hemocytometers (Bulldog bio, DHC-N01) and equalized across all samples before lysis and RNA extraction. Total RNA from 1E6 cells per replicate was isolated using RNeasy96 kit (Qiagen). External RNA Controls Consortium (ERCC) ExFoldRNA Spike-in Control Mixes (Invitrogen #4456740) (4 µL/sample, diluted at 1:100, ERCC User Guide, Table 4) were added after cell lysis step. The extraction was then continued according to manufacturer’s instructions and eluted in 50 µL nuclease-free water.
Total RNA was quantified using QubitTM RNA Broad Range Assay kit (Invitrogen) and analyzed on Agilent 4200 TapeStation for integrity. Samples with the RNA Integrity Number (RIN) above 9.0 and normalized to 500 ng total RNA for library preparation using TruSeq® stranded mRNA sample prep kit (Illumina, #20020595) following manufacturer's protocols. After library preparation, samples were quantified using QubitTM assay, checked fragment sizes on Agilent 4200 TapeStation, normalized and pooled for sequencing.

treatment_protocol: Cells were seeded in 10-cm plates and incubated in media with DMSO or indicated drugs for 12h, in triplicates

value: Breast adenocarcinoma, epithelial cell from mammary gland

value: WT

value: Gefitinib 1microM + THZ531 200nM

tag: time


title: bphOP1_KO_pN-bphOP1_far-red, rep 3

description: total RNA

value: bacteria

value: far-red


title: bphOP1_KO_pN-bphOP1_dark, rep 2

description: total RNA


title: NIH22B3645061

description: normal blood samples

value: Male


title: NC_rep1


title: MDA-MB-231 cells, Gefitinib 1µM + THZ531 200nM, Rep1


title: MDA-MB-231 cells, THZ531 200nM, Rep3


title: MDA-MB-231 cells, THZ531 200nM, Rep2


title: NIH22B3782022

description: normal blood samples

value: Female


title: NIH22B3637078

description: normal blood samples


title: NIH22B3080955

description: normal blood samples


title: MDA-MB-231 cells, Gefitinib 1µM + THZ531 200nM, Rep2


title: OA-5

description: Fibroblast-like synoviocytes in vitro

value: female


title: NIH22B3403454

description: normal blood samples


title: MDA-MB-231 cells, Gefitinib 1µM, Rep2

value: Gefitinib 1microM


title: bphOP1_KO_pN-bphOP1_far-red, rep 2

description: total RNA


title: NIH22B3314955

description: normal blood samples


title: MDA-MB-231 cells, THZ531 200nM, Rep1


title: bphOP1_KO_pN-bphOP1_blue, rep 2

description: total RNA

value: blue


title: MDA-MB-231 cells, Gefitinib 1µM, Rep3


title: bphOP1_KO_pN-bphOP1_blue, rep 3

description: total RNA


title: MDA-MB-231 cells, Gefitinib 1µM, Rep1


title: MDA-MB-231 cells, DMSO, Rep3

value: DMSO


title: NIH22B3380510

description: normal blood samples


title: NIH22B3207104

description: normal blood samples


title: MDA-MB-231 cells, DMSO, Rep2


title: CAL51 cells, THZ531 200nM, Rep3

value: Breast carcinoma, derived from metastatic site:Pleural effusion.


title: NIH22B3040941

description: normal blood samples


title: bphOP1_KO_pN-bphOP1_red, rep 1

description: total RNA

value: delta_bphOP1 (pN-bphOP1)

value: red


title: bphOP1_KO_pN-bphOP1_red, rep 2

description: total RNA


title: NIH22B3225949

description: normal blood samples


title: CAL51 cells, Gefitinib 1µM + THZ531 200nM, Rep2


title: CAL51 cells, Gefitinib 1µM + THZ531 200nM, Rep3


title: bphOP1_KO_pN-bphOP1_blue, rep 1

description: total RNA


title: CAL51 cells, Gefitinib 1µM + THZ531 200nM, Rep1


title: bphOP1_KO_pN-bphOP1_red, rep 3

description: total RNA


title: bphOP1_KO_dark, rep 3

description: total RNA

value: dark-mantained


title: CAL51 cells, DMSO, Rep3


title: CAL51 cells, THZ531 200nM, Rep2


title: CAL51 cells, Gefitinib 1µM, Rep1


title: CAL51 cells, DMSO, Rep1


title: bphOP1_KO_dark, rep 2

description: total RNA


title: CAL51 cells, Gefitinib 1µM, Rep3


title: bphOP1_KO_dark, rep 1

description: total RNA


title: NIH22B3739072

description: normal blood samples


title: bphOP1_KO_pN-bphOP1_far-red, rep 1

description: total RNA


title: NIH22B3690144

description: normal blood samples


title: CAL51 cells, THZ531 200nM, Rep1


title: NIH22B3004387

description: normal blood samples


title: CAL51 cells, DMSO, Rep2


title: NIH22B3239967

description: normal blood samples


title: BR24 INPP5D(OE) veh 6

city: Boston

first: Richard

middle: VanDyke

last: Pearse

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Womens Hospital

description:
co-treated with VSV-G virus-like Particles  (required for iMGL transduction)
NA09

data_processing:
read trimming using trimmomatic
pseudo-alignment to GRCh38 transcriptome (cDNA+ncRNA) using kallisto v0.43.1
import to sleuth
normalize counts and control for batch
export as normalized matrix
Assembly: CRCh38
Supplementary files format and content: VC101-116_XpresMatrix_CBdiff.csv, gene-level normalized TPM counts with ENSG IDs
Supplementary files format and content: full.NA1-12.XM.filt.csv, gene-level normalized TPM counts with ENSG IDs

molecule: polyA RNA

growth_protocol: Differentiation of iMGLs from iPSC according to protocol in (doi.org/10.1016/j.neuron.2017.03.042)

extract_protocol:
Invitrogen PureLink RNA extract kit followed by pA selection
Azenta RNAseq library pipeline

value: iPSC-derived Microglia

value: INPP5D retrovirus


title: BR24 INPP5D(KD) veh 3

description:
vehicle was VSV-G virus-like Particles alone (without actual INPP5D OE virus)
NA12

value: no virus


title: BR24 INPP5D(KD) veh 1

description:
vehicle was VSV-G virus-like Particles alone (without actual INPP5D OE virus)
NA10


title: BR24 INPP5D(OE) veh 5

description:
co-treated with VSV-G virus-like Particles  (required for iMGL transduction)
NA08


title: NIH22B3712694

description: normal blood samples

value: Blood


title: BR24 INPP5D(OE) veh 3

description:
co-treated with VSV-G virus-like Particles  (required for iMGL transduction)
NA06


title: bphOP1_KO_far-red, rep 2

description: total RNA


title: BR24 INPP5D(OE) veh 4

description:
co-treated with VSV-G virus-like Particles  (required for iMGL transduction)
NA07


title: bphOP1_KO_far-red, rep 1

description: total RNA


title: bphOP1_KO_far-red, rep 3

description: total RNA


title: MDA-MB-231 cells, DMSO, Rep1

value: Breast adenocarcinoma, epithelial cell from mammary gland

value: WT


title: BR24 INPP5D(OE) veh 2

description:
co-treated with VSV-G virus-like Particles  (required for iMGL transduction)
NA05


title: bphOP1_KO_blue, rep 3

description: total RNA

value: bacteria


title: NIH22B3813637

description: normal blood samples

value: Male


title: BR24 INPP5D(OE) veh 1

description:
co-treated with VSV-G virus-like Particles  (required for iMGL transduction)
NA04


title: NIH22B3355538

description: normal blood samples


title: BR24 INPP5D(WT) veh 2

description:
vehicle was VSV-G virus-like Particles alone (without actual INPP5D OE virus)
NA02


title: BR24 INPP5D(KD) veh 2

description:
vehicle was VSV-G virus-like Particles alone (without actual INPP5D OE virus)
NA11


title: BR24 INPP5D(WT) veh 1

description:
vehicle was VSV-G virus-like Particles alone (without actual INPP5D OE virus)
NA01


title: NIH22B3340822

description: normal blood samples


title: NIH22B3499241

description: normal blood samples

value: Female


title: NIH22B3717595

description: normal blood samples


title: bphOP1_KO_blue, rep 1

description: total RNA


title: BR33.7 INPP5D(HET) veh 1

value: untreated


title: bphOP1_KO_red, rep 3

description: total RNA


title: NIH22B3712236

description: normal blood samples


title: NIH22B3044871

description: normal blood samples


title: BR24 INPP5D(WT) veh 3

description:
vehicle was VSV-G virus-like Particles alone (without actual INPP5D OE virus)
NA03


title: BR33.7 INPP5D(WT) 3AC 4

description:
INPP5D inhibitor
VC112


title: BR33.7 INPP5D(HET) veh 2


title: BR33.7 INPP5D(WT) 3AC 1

description:
INPP5D inhibitor
VC109


title: BR33.7 INPP5D(WT) 3AC 2

description:
INPP5D inhibitor
VC110


title: BR33 INPP5D(WT) iMGL veh 4

value: Vehicle


title: bphOP1_KO_red, rep 2

description: total RNA


title: NIH22B3756247

description: normal blood samples


title: BR33.7 INPP5D(WT) 3AC 3

description:
INPP5D inhibitor
VC111


title: bphOP1_KO_blue, rep 2

description: total RNA

value: blue


title: BR33 INPP5D(WT) iMGL veh 3


title: BR33 INPP5D(WT) iMGL veh 1


title: NIH22B3145578

description: normal blood samples


title: bphOP1_KO_red, rep 1

description: total RNA


title: WT_white, rep 3

description: total RNA

value: white


title: BR33.47 INPP5D(WT) veh 2


title: BR01 INPP5D(WT) iMGL 3AC 2

description:
INPP5D inhibitor
VC104


title: NIH22B3906953

description: normal blood samples


title: BR33.47 INPP5D(WT) veh 1


title: WT_white, rep 1

description: total RNA


title: BR01 INPP5D(WT) iMGL veh 2


title: WT_dark, rep 3

description: total RNA


title: NIH22B3832091

description: normal blood samples


title: BR01 INPP5D(WT) iMGL veh 1


title: NIH22B3725825

description: normal blood samples


title: WT_dark, rep 1

description: total RNA


title: WT_dark, rep 2

description: total RNA


title: BR33 INPP5D(WT) iMGL veh 2


title: NIH22B3435908

description: normal blood samples


title: NIH22B3108028

description: normal blood samples


title: WT_blue, rep 3

description: total RNA


title: NIH22B3012108

description: normal blood samples


title: NIH22B3182297

description: normal blood samples


title: WT_white, rep 2

description: total RNA


title: NIH22B3715405

description: normal blood samples


title: NIH22B3361828

description: normal blood samples


title: WT_far-red, rep 1

description: total RNA

value: far-red


title: WT_blue, rep 1

description: total RNA


title: WT_red, rep 3

description: total RNA


title: WT_red, rep 2

description: total RNA


title: NIH22B3556193

description: normal blood samples


title: NIH22B3274952

description: normal blood samples


title: BR01 INPP5D(WT) iMGL 3AC 1

description:
INPP5D inhibitor
VC103


title: WT_red, rep 1

description: total RNA


title: NIH22B3473364

description: normal blood samples


title: NIH22B3740440

description: normal blood samples


title: NIH22B3204313

description: normal blood samples


title: NIH22B3798893

description: normal blood samples


title: h- siw14∆::HygMX, 3

city: New York

first: Ana

middle: M

last: Sanchez

state: NY

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description:
count_matrix_siw14.xlsx
siw14_DESeq.xlsx
siw14∆_biol_rep_3

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
Resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts

organism: Schizosaccharomyces pombe

source_name: fission yeast

growth_protocol: Log phase cultures grown at 30˚C in YES medium

extract_protocol:
Hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA seq

tag: lab strain number

tag: developmental stage

value: Vegetative growth

value: siw14 knockout

value: fission yeast


title: D88_S12_L002

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
FastQC (Version 0.72) was performed on the concatenated replicate raw sequencing paired-end reads from each library to ensure minimal PCR duplication and sequencing quality.
Reads were aligned to the mouse mm10 genome using HISAT2 (Version 2.1.0) and annotated against Ensembl v90.
After removal of multiple-aligned reads, remaining reads were counted using featurecounts (Version 2.0.1) with default parameters, and filtered to remove genes with low counts (<10 reads across samples).
For male 48-hr CSDS RNA-seq, RUVg was performed to normalize read counts based on empirically determined control genes that do not vary between control and susceptible groups (i.e. genes with p-val > 0.5 based on a first-pass differential expression analysis performed prior to RUVg normalization). For female RNA-seq experiments and the serotonylation manipulation experiments with the Q5A virus, RUVr was performed to normalized read counts based on the residuals from a first-pass GLM regression of the unnormalized counts on the covariates of interest.
DESEQ2 (Version 2.11.40.6) was used to perform pairwise differential expression analyses between indicated comparisons.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing raw counts

organism: Mus musculus

source_name: Susceptible

extract_protocol:
RNA-seq, RNA was harvested using Rneasy Micro kit (Qiagen). 300 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Truseq RNA Library Prep Kit V2 following manufacturer's protocols.

value: Susceptible


title: D65_S11_L002


title: D86_S10_L002

value: FLX


title: h- siw14∆::HygMX, 2

description:
count_matrix_siw14.xlsx
siw14_DESeq.xlsx
siw14∆_biol_rep_2


title: WT_far-red, rep 2

description: total RNA


title: WT_blue, rep 2

description: total RNA


title: D91_S2_L002


title: WT_far-red, rep 3

description: total RNA


title: h- siw14∆::HygMX, 1

description:
count_matrix_siw14.xlsx
siw14_DESeq.xlsx
siw14∆_biol_rep_1


title: NIH22B3393345

description: normal blood samples


title: h-, 2

description:
count_matrix_siw14.xlsx
WT_biol_rep_2


title: NIH22B3601526

description: normal blood samples


title: D64_S7_L002


title: D63_S1_L002


title: NIH22B3645642

description: normal blood samples


title: D43_S3_L002


title: NIH22B3970078

description: normal blood samples


title: h-, 1

description:
count_matrix_siw14.xlsx
WT_biol_rep_1


title: NIH22B3334979

description: normal blood samples


title: h-, 3

description:
count_matrix_siw14.xlsx
WT_biol_rep_3


title: C61_S6_L002

source_name: Control

value: Control


title: C64_S16_L002


title: D46_S9_L002


title: C59_S19_L002


title: iSLK-RGB-KO NAT10_rep3-IP

city: Nanjing

first: Liuxue

last: Sheng

state: Jiangsu

address: Tian Yuan East Road

institute: Nanjing Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then clean reads were aligned to the GRCh38 and NC_009333.1 genome assembly using HISAT2 version 2.1.0 with the following parameters:--rna-strandness RF
peaks were called using exomePeak version 2.13.2 with the following setting: PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200,and ac peaks were annotated.
Genome_build: GRCh38_Ensembl91_year_2017
Genome_build: NC_009333.1
Supplementary_files_format_and_content: tab-delimited text files with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table of ac peak annotation

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: iSLK-RGB

growth_protocol: Four iSLK cells were routinely cultured in 10% FBS DMEM

extract_protocol:
Standard RNA extraction protocol
The stranded RNA sequencing library was constructed by using EpiTM mini longRNA-seq kit
acRIP-seq

treatment_protocol: Doxycycline treatment for 72 h.

value: iSLK-RGB

value: treated with Doxycycline for 72 h

tag: acrip

value: EpiTM ac4C immunoprecipitation kit (Epibiotek, cat. no R1815)


title: NIH22B3399421

description: normal blood samples

value: Blood


title: C49_S17_L002


title: iSLK-RGB-KO NAT10_rep2-IP


title: iSLK-RGB-KO NAT10_rep1-IP


title: C46_S18_L002


title: NIH22B3702495

description: normal blood samples


title: D53_S8_L002


title: iSLK-RGB-KO NAT10_rep3-input

description: All.count.txt


title: C45_S13_L002


title: NIH22B3827049

description: normal blood samples


title: NIH22B3908916

description: normal blood samples


title: C48_S20_L002


title: NIH22B3131502

description: normal blood samples


title: C44_S15_L002


title: C41_S14_L002


title: C43_S5_L002


title: iSLK-RGB-KO NAT10_rep2-input

description: All.count.txt


title: TKO_batch4_Uninfected [Lu15]

city: Seattle

first: Kimberly

last: Dill-McFarland

state: WA

address: 750 Republican St

department: Allergy and Infectious Diseases

institute: University of Washington

data_processing:
Sequence quality was assessed by FastQC , and sequences were cleaning using AdapterRemoval (remove adapters, <1 ambiguous base, trim ends to a 30+ Phred score).
Sequences were aligned to the mouse genome mm10 using STAR, and alignments were assessed with Picard and samtools. Total reads in gene exons were quantified using featureCounts.
Assembly: mm10
Supplementary files format and content: CSV, rows are genes, columns are libraries, values are total counts per library

source_name: lung

growth_protocol: Tollip-/- mixed bone marrow chimera mice were generated from B6 mice that were lethally irradiated and then intravenously reconstituted with a 1:1 mixture of CD3-depleted Tollip-/- and C57BL/6J bone marrow.

extract_protocol:
Total RNA from sorted cells was isolated using the manufacturer’s instructions (TRIzol, Invitrogen)
RNAseq libraries were prepared from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit and Illumina TruSeq RNA Sample Preparation Kit. Samples were sequenced as 50 bp paired-end reads on a Illumina HiSeq 2500.

treatment_protocol: After 10 weeks of recovery, chimeric mice were infected with mCherry Mtb H37Rv at 50-100 CFU. Mice were euthanized 28 days after infection, lungs were gently homogenized, and alveolar macrophages with and without intracellular Mtb were isolated by flow cytometry.

value: lung

value: aveolar macrophage

value: B6.Cg-Tollip(tm1Kbns)/Cnrm (Tollip-/-)

value: uninfected


title: iSLK-RGB-KO NAT10_rep1-input

description: All.count.txt


title: iSLK-RGB-WT_rep3-IP

value: wild type


title: NIH22B3885969

description: normal blood samples

value: Female


title: TKO_batch4_Infected [Lu16]

value: Mtb H37Rv infected


title: TKO_batch2_Infected [Lu12]


title: NIH22B3180229

description: normal blood samples


title: TKO_batch3_Uninfected [Lu13]


title: TKO_batch1_Infected [Lu10]


title: iSLK-RGB-WT_rep2-IP


title: NIH22B3006297

description: normal blood samples

value: Male


title: TKO_batch2_Uninfected [Lu11]


title: TKO_batch1_Uninfected [Lu09]


title: iSLK-RGB-WT_rep1-IP


title: WT_batch4_Infected [Lu08]

value: C57BL/6J (wild-type)


title: iSLK-RGB-WT_rep3-input

description: All.count.txt


title: NIH22B3406221

description: normal blood samples


title: WT_batch4_Uninfected [Lu07]


title: WT_batch3_Infected [Lu06]


title: NIH22B3463600

description: normal blood samples


title: WT_batch3_Uninfected [Lu05]


title: WT_batch2_Infected [Lu04]


title: NIH22B3492080

description: normal blood samples


title: iSLK-RGB-WT_rep1-input

description: All.count.txt


title: WT_batch1_Infected [Lu02]


title: iSLK-RGB-WT_rep2-input

description: All.count.txt


title: WT_batch2_Uninfected [Lu03]


title: TKO_batch3_Infected [Lu14]


title: iSLK-RGB_rep3-IP


title: WT_batch1_Uninfected [Lu01]


title: NIH22B3303306

description: normal blood samples


title: ClpX cKO spermatocytes, PD 35 [ClpX_cKO_ip]

city: Shenzhen

first: Chenxi

last: Guo

address: 1 Haiyuan 1st Rd

institute: The University of Hong Kong-Shenzhen Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary cell

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: primary cell

value: male germ cells

value: ClpX knockout

value: Day 35


title: ClpP cKO spermatocytes, PD 35 [ClpP_cKO_input]

value: ClpP knockout


title: NIH22B3535663

description: normal blood samples


title: iSLK-RGB_rep2-IP

value: iSLK-RGB

value: treated with Doxycycline for 72 h


title: ClpP cKO spermatocytes, PD 35 [ClpP_cKO_ip]


title: WT control spermatocytes, PD 35 [WT_ip]

value: WT


title: iSLK-RGB_rep1-IP

value: EpiTM ac4C immunoprecipitation kit (Epibiotek, cat. no R1815)


title: NIH22B3188784

description: normal blood samples

value: Blood


title: WT control spermatocytes, PD 35 [WT_input]


title: iSLK-RGB_rep3-input

description: All.count.txt


title: NIH22B3634765

description: normal blood samples


title: NIH22B3280011

description: normal blood samples


title: ClpX cKO spermatocytes 3

value: PD 35


title: ClpX cKO spermatocytes 2


title: ClpX cKO spermatocytes 1


title: iSLK-RGB_rep2-input

description: All.count.txt


title: NIH22B3126770

description: normal blood samples


title: ClpP cKO spermatocytes 3


title: iSLK-RGB_rep1-input

description: All.count.txt


title: ClpP cKO spermatocytes 2


title: NIH22B3697193

description: normal blood samples


title: NIH22B3025019

description: normal blood samples


title: NIH22B3548619

description: normal blood samples


title: iSLK-puro_rep3-IP

source_name: iSLK-puro

value: iSLK-puro


title: iSLK-puro_rep2-IP


title: ClpP cKO spermatocytes 1


title: Control spermatocytes  3


title: ClpX cKO spermatocytes, PD 35 [ClpX_cKO_input]


title: Control spermatocytes  2


title: smallRNA_Htt Q111 NPC replicate 2

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

data_processing:
Illumina Casava 1.8 software was used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence and low-quality nucleotides, then aligned against the mouse Gencode v23 transcriptome using STAR (genes) with default parameters and quantified with htseq-count
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample

source_name: NPC

growth_protocol: The allelic series of heterozygous Hdh CAG knock-in mouse embryonic stem cell (mESC) lines, consisting of 4 alleles of different Htt CAG size (20, 50, 89 and 111 CAG) were kindly given by Dr. Marcy E. MacDonald (Massachussets General Hospital and Harvard Medical School, Boston, US). They were cultured in KnockOut DMEM (Gibco), supplemented with 15% of ES cell FBS (Gibco), 2 mM L-glutamine (Gibco), 100 U/ml Penicillin/Streptomycin (Gibco), 1% Non-essential Amino Acids (Gibco), 0.1 mm 2-mercaptoethanol (Sigma) and 1000 U/ml of leukemia inhibitory factor (LIF) (Voden), on plates coated with 0.1% gelatin (Millipore) and with a feeder layer of CF-1 IRR MEF (TebuBio). Differentiation of mESC to mNPC was performed as described in Conti et al., PLoS Biology 2005.  Both mESCs and mNPCs were incubated at 37°C and 5% CO2.

extract_protocol:
RNA was extracted from cell lines by using TRIzol reagent (Invitrogen) following manufacturer's instructions.
The RNA samples were subjected to DNAse I treatment (Ambion) according to manufacturer instructions . RNA library preparation was obtained using the standard Illumina protocols, and sequenced on a Illumina HiSeq 2500 machine using single-end, 50bp reads, obtaining approx 15M reads/sample.

treatment_protocol: Self-renewing mES cells were dissociated and plated onto 0.1% gelatin-coated tissue culture plastic at a density of 0.5–1.5  104/cm2 in N2B27 medium. N2B27 is a 1:1 mixture of DMEM/F-12 (Thermo Fisher Scientific) supplemented with N-2 supplement (Gibco) and Neurobasal medium (Thermo Fisher Scientific) complemented with B27 supplement (Thermo Fisher Scientific).The medium was renewed every other day. After 7 days, cells were detached using Accutase (Thermo Fisher Scientific) and plated on 3 µg/ml laminin-coated tissue culture dishes in NS expansion medium. Mouse neural progenitor cells were routinely passaged 1:2-1:4 every 3-5 days using Accutase and maintained in NS medium, composed by Euromed-N (Euroclone) supplemented with 1:1000 FGF (R&D) and EGF (Sigma), 1% N-2 Supplement (Gibco), 2 mM L-glutamine (Gibco) and 100 U/ml Penicillin/Streptomycin (Gibco) on laminin-coated plates (Sigma, 3.5 µg/ml).

value: NPC

value: Q111 Htt


title: Control spermatocytes  1


title: iSLK-puro_rep1-IP


title: smallRNA_Htt Q92 NPC replicate 2

value: Q92 Htt


title: smallRNA_Htt Q92 NPC replicate 1


title: smallRNA_Htt Q111 NPC replicate 1


title: smallRNA_Htt Q50 NPC replicate 1

value: Q50 Htt


title: smallRNA_Htt Q50 NPC replicate 2


title: NIH22B3713254

description: normal blood samples

value: Female


title: iSLK-puro_rep2-input

description: All.count.txt


title: NIH22B3999915

description: normal blood samples


title: smallRNA_Htt Q20 NPC replicate 2

value: Q20 Htt


title: iSLK-puro_rep1-input

description: All.count.txt


title: NIH22B3477892

description: normal blood samples


title: smallRNA_Htt WT NPC replicate 2

description: HttWTNPCb

value: wild type


title: iSLK-RGB-NAT10_rep3-IP

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then clean reads were aligned to the GRCh38 and NC_009333.1 genome assembly using STAR version 2.5.3a with default parameters
Data were filtered using the following specifications:abs(log2FC>1),pvalue<0.05.We selected proteins up-regulated in IP relative to input as genes that NAT10 may combine with.
peaks were called using exomePeak version 3.8 and peaks were annotated using bedtools Version 2.25.0.
Genome_build: Homo_sapiens.GRCh38
Genome_build: NC_009333.1
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Standared RNA extraction protocol
The stranded RNA sequencing library was constructed by using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina®

tag: genotype/variation

tag: rip-antibody

value: DDDDK-tag (MBL,M185-3L)


title: NIH22B3726404

description: normal blood samples


title: smallRNA_Htt KO NPC replicate 2

description: HttKONPCb

tag: cell type

tag: genotype

value: Htt knockout


title: NIH22B3320725

description: normal blood samples

tag: gender

value: Male


title: NIH22B3481120

description: normal blood samples


title: smallRNA_Htt Q111 mESC replicate 1

source_name: mESC

value: mESC


title: iSLK-RGB-NAT10_rep1-IP

value: iSLK-RGB

tag: treatment

value: treated with Doxycycline for 72 h


title: smallRNA_Htt Q111 mESC replicate 2


title: smallRNA_Htt Q92 mESC replicate 2


title: iSLK-RGB-pCDH-RFP_rep3-IP

value: pCDH-RFP-flag


title: smallRNA_Htt KO NPC replicate 1

description: HttKONPCa


title: iSLK-puro_rep3-input

description: All.count.txt

value: EpiTM ac4C immunoprecipitation kit (Epibiotek, cat. no R1815)


title: NIH22B3710290

description: normal blood samples

value: Blood


title: NIH22B3604565

description: normal blood samples


title: smallRNA_Htt Q50 mESC replicate 2


title: NIH22B3507379

description: normal blood samples


title: smallRNA_Htt Q92 mESC replicate 1


title: iSLK-RGB-pCDH-RFP_rep2-IP


title: smallRNA_Htt Q50 mESC replicate 1


title: smallRNA_Htt Q20 mESC replicate 1


title: iSLK-RGB-pCDH-RFP_rep1-IP


title: smallRNA_Htt Q20 NPC replicate 1


title: NIH22B3713130

description: normal blood samples


title: iSLK-RGB-NAT10_rep3-input


title: smallRNA_Htt WT NPC replicate 1

description: HttWTNPCa


title: iSLK-RGB-NAT10_rep2-IP


title: Rpb1ChIP_dhh1D_Replicate_3

first: Alan

middle: G

last: Hinnebusch

state: Maryland

address: 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
For ribo-seq/RNA-Seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with tophat (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
The sequenced CAGE reads of each sample were aligned to the reference genome of S. cerevisiae S288c (Assembly version: sacCer3) using HISAT2. CAGE reads mapped to rRNA genes were identified using rRNAdust (http://fantom.gsc.riken.jp/5/sstar/Protocols:rRNAdust), and were excluded from subsequent TSS analyses. CAGE reads with a mapping quality score (MAPQ) > 20 were considered uniquely mapped reads and were used for subsequent analyses. CAGE signals of biological replicates were then merged as a single sample. The transcription abundance of each TSS was quantified as the numbers of CAGE tags/reads supporting the TSS per million mapped reads (TPM). For RNA-Seq samples in parallel with CAGE-Seq, Fastq files after passing the QC and the adapter content check they were mapped to yeast genome (sacCer3) with STAR aligner, then PCR duplicates were removed by samtools.
For ChIP-Seq: Sequence data were aligned to the SacCer3 version of the genome sequence using Bowtie2 with parameters -X 1000 -very-sensitive, to map sequences up to 1 kb with maximum accuracy. PCR duplicates from ChIP-seq data were removed using the samtools rmdup package.
Assembly: sacCer3
Supplementary files format and content: Processed data (csv) files contain raw reads for each file. For Ribo and parallel RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. For CAGE-sequencing and parallel RNA-Sequencing, each file contains two columns providing: systemmatic gene name (Gene_ID), total reads. For Rpb1 ChIP-Seq, average occupancy  file contains two columns providing: systemmatic gene name (ORF) and avg occupancy.

organism: Saccharomyces cerevisiae

source_name: Whole cells

extract_protocol: Briefly, for ChIP assays, chromatin was prepared from formaldehyde-crosslinked cells, immunoprecipitated with Rpb1 antibodies, and the DNA was extracted . DNA libraries for Illumina paired-end sequencing were prepared using DNA Library Prep Kit for Illumina from New England Biolabs

value: yeast cells

tag: chip antibody

tag: fraction

value: DNA


title: NIH22B3959715

description: normal blood samples


title: Rpb1ChIP_dhh1D_Replicate_2


title: smallRNA_Htt WT mESC replicate 1

description: HttWTESCa


title: Rpb1ChIP_dhh1D_Replicate_1


title: NIH22B3667649

description: normal blood samples


title: Rpb1ChIP_pat1D_Replicate_3


title: iSLK-RGB-pCDH-RFP_rep3-input


title: NIH22B3354654

description: normal blood samples


title: smallRNA_Htt KO mESC replicate 1

description: HttKOESCa


title: smallRNA_Htt Q20 mESC replicate 2


title: iSLK-RGB-NAT10_rep1-input


title: Rpb1ChIP_pat1D_Replicate_2


title: NIH22B3479410

description: normal blood samples


title: smallRNA_Htt KO mESC replicate 2

description: HttKOESCb


title: NIH22B3137067

description: normal blood samples


title: iSLK-RGB-pCDH-RFP_rep1-input


title: Rpb1ChIP_pat1D_Replicate_1


title: NIH22B3581771

description: normal blood samples


title: T_RNA_dhh1D_Replicate_2

extract_protocol: RNA sequencing libraries were produced in parallel from the same total RNA samples subjected to CAGE sequencing by the NHLBI DNA sequencing Core at NIH (Bethesda, MD) using the TruSeq Stranded mRNA Library Prep Kit (Illumina, Paired-end 50 bp reads).

value: total RNA


title: smallRNA_Htt WT mESC replicate 2

description: HttWTESCb


title: 4_20_3_b, eccD1, M63 + NH4Cl

city: San Francisco

first: Nadia

last: Herrera

state: CA

address: 600 16th Street, GH S416 BOX 2240

department: Medicine

institute: University of California San Francisco

data_processing:
Transcript quantification: Transcript abundances were quantified based on version GCF_000015005.1_ASM1500v1_cds_from_genomic.fna
Relative abundances (reported as TPM values) and estimated counts (est_counts) of each transcript in each sample were estimated by alignment free comparison of k-mers between the reads and assembled transcripts using KALLISTO version 0.43.0.
Further analysis was restricted to transcripts with TPM ≥ 10 in at least one sample.
KALLISTO was invoked for each SAMPLE as:
for i in *.fastq.gz; do kallisto quant -i CDS_MC2155.idx -o "${i%fastq.gz}kallisto" --single -l 250 -s 50 "${i}"; done
Differentially expressed genes were identified by linear regression on four independent factors using LIMMA version 3.26.1.
Specifically, KALLISTO est_counts were rounded to the nearest integer and imported as counts per million (CPM) in a DGEList in R. Samples were TMM normalized with calcNormFactors and VOOM was used to estimate the mean/variance trend.
Samples were classified on four factors: batch (1 or 3), genotype (WT or msb2), media (GlcNAc or glucose), and time (0, 2d, 6d, or 8d). For each transcript, the observed counts were fit to a model assuming a mean transcript abundance plus independent corrections for each factor using lmFit. Shrinkage of the individual gene variances over the full data was applied with eBayes, and significantly differential genes were identified by extracting genes with a significantly non-zero genotype coefficient (at 5% FDR) with an effect size of at least 2x (absolute log2 fold change ≥ 1) using topTable.
The key processing steps in R were:
dge <- DGEList(counts)
dge <- calcNormFactors(dge)
time <- as.factor(time)
genotype <- as.factor(genotype)
media <- as.factor(media)
batch <- as.factor(batch)
d <- model.matrix(~time+genotype+media+batch)
v <- voom(dge, d)
fit <- lmFit(v, d)
fit <- eBayes(fit)
topTable(fit, coef="genotypeMSB2", n = 20000, lfc=1, p.value = .05)
The fit parameters and adjusted p-values from the LIMMA analysis are given, along with gene annotations and the input estimated counts from KALLISTO, in supplementary file Table_profiles.cdt (Excel and JavaTreeView compatible tab-delimited text).
Genome_build: GCF_000015005.1_ASM1500v1_cds_from_genomic.fna
Supplementary_files_format_and_content: All processed data files are tab-delimited text (generated as abundance.tsv by kallisto)

organism: Mycolicibacterium smegmatis MC2 155

source_name: liquid culture

growth_protocol: Starter cultures were inoculated from a single colony grown in 7H9 agar plates in either M63 medium or M63 medium with 20 mM NH4Cl added. They were passaged a second time 1:50 into 50mL of medium and grown to OD600 = 0.7-0.8. Samples were grown in biological triplicates.

extract_protocol:
Cultures were harvested by centrifugation,  pellets were re-suspended in RNA Protect buffer from the Monarch Total RNA Miniprep Kit. Re-suspended pellets were flash frozen in liquid nitrogen and stored at -80°C. Extraction was done by  re-suspending frozen pellets in kit lysis buffer and 0.1 mm zirconia beads were used to lyse samples with a vortex adapter bead beater, the kit protocol was followed as per the manufacturer's protocol. RNA was DnaseI digested after extraction and rRNA was depleted using the  NEBNext rRNA Depletion Kit (Bacteria).
Libraries for RNAseq were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina and multiplexing was done with custom multiplex oligos. Average fragment sizes were determined using the High Sensitity DNA bioanalyzer chip from Aligent Technologies. Libraries had an average length of 200 - 400 bp. The concentration of the individual libraries was determined by Quibit dsDna High Sensitivity Assay (Invitrogen). 10ng of each livrary was pooled into a final library and ran on a High Sensitivity DNA bioanalyzer chip to determine average fragment size. Final library was submitted to the Chan Zuckerberg Biohub Sequencing platform.

tag: medium

value: M63 + 20mM Ammonium Chloride

tag: batch


title: NIH22B3377305

description: normal blood samples


title: T_RNA_dhh1D_Replicate_1


title: 4_20_2_b, eccD1, M63 + NH4Cl


title: SAMPLE 5 amniotic fluid fetal cells

city: Fuzhou

first: Yanting

last: Que

address: No. 88, Jiaotong Road, Taijiang District, Fuzhou City, Fujian Province

institute: Fujian Medical University

description: Hybridized to CytoScan 750K

hyb_protocol: DNA was processed as follows. Restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer`s instructions.

scan_protocol: The arrays were then washed using Affymetrix Fluidics Stations, and scanned using the GeneChip Scanner 750K

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console (AGCC version 4.0.0.1567). Data processing and analysis (CEL file generation, smoothing and segmentation) were used Chromosome Analysis Suite (version 3.3).
Copy number variation status (CNV)

label: Biotin

source_name: amniotic fluid fetal cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA of fetal cells in amniotic fluid or cord blood sampling was extracted with using the QIAamp DNA extraction kit (Qiagen, Dusseldorf, Germany)

tag: cell

value: amniotic fluid fetal cells

tag: diagnosis

value: Fetal omphalocele (a mass of 1.5 cm × 0.8 cm × 0.9 cm bulging into the umbilical cord on the right side of the umbilicus, with echogenic bowel, well-defined borders of the mass, and echogenic umbilical cord on the surface of the mass.)


title: iSLK-RGB-NAT10_rep2-input


title: T_RNA_pat1D_Replicate_2


title: 4_20_1_b, eccD1, M63 + NH4Cl


title: SAMPLE 4 amniotic fluid fetal cells 14

description: Hybridized to CytoScan 750K

value: Fetal omphalocele, nasal bones absence, ductus venosus a-wave reversed


title: iSLK-RGB-pCDH-RFP_rep2-input


title: 4_19_1_b, eccCa1, M63 + NH4Cl


title: 4_19_2_b, eccCa1, M63 + NH4Cl


title: 4_19_3_b, eccCa1, M63 + NH4Cl


title: 4_16_3_b, esxB, M63 + NH4Cl

value: esxB


title: 4_16_2_b, esxB, M63 + NH4Cl


title: 4_16_1_b, esxB, M63 + NH4Cl


title: 4cell embryos FLI3

city: Libechov

first: Alexandra

middle: Rosenbaum

last: Bartkova

address: Rumburska 89

country: Czech Republic

institute: IAPG CAS

data_processing:
Reads with lengths less than 15 nt were discarded.
Expression analysis was done using the Differential Expression in Two Groups tool in CLC Genomics Workbench v. 22.0 according to anegative binomial Generalized Linear Model function.
Data were normalized (counts per million mapped reads) and filtered (cpm > 0.5, at least two samples from each group of replicates) and expression values of read count and CPM were calculated for all of the genes.
For the normalization of data, the trimmed mean of M-values normalization method was used.
Assembly: SScrofa11.1
Supplementary files format and content: Expression Browser processed data DESeq2.xlsx; Complete list of genes after data processing and comparison of different cultivation times among themselves.

organism: Sus scrofa

source_name: embryo

extract_protocol:
Total RNA was isolated from 2,4,8 cell embryos DMEM /FLI experimented group (each of three replicates) using a Micro kit (Thermo Fisher, AM1931) according to the manufacturer’s instructions.
The amount of RNA was measured by a Qubit 2.0 Fluorometer with Qubit™ RNA High Sensitivity kit. SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian Kit (Takara, France) was used for RNA library construction. Libraries quality and quantity were assessed using Bioanalyzer 2100 with a High Sensitivity DNA assays kit and a Qubit dsDNA High Sensitivity kit. Libraries were sequenced on NovaSeq 6000 according to the manufacturer’s protocol using NovaSeq 6000 SP Reagent kit (200 cycles) using a mode for reading at the end of pairs with a length of reading 2 x 100 base pairs (bp).

value: embryo

value: 4 cell

tag: group

value: FLI


title: 4cell embryos FLI2


title: 8cell embryos FLI3

value: 8 cell


title: 8cell embryos FLI1


title: 8cell embryos FLI2


title: 4cell embryos FLI1


title: SAMPLE 3 amniotic fluid fetal cells

description: Hybridized to CytoScan 750K

value: Fetal omphalocele, alobar holoprosencephaly, skull defect with meningoencephalocele, cleft lip and palate, narrow eye distance, microtia, cardiac dysplasia (ventricular septal defect, double outlet right ventricle), hooked hand, rocking chair foot.


title: SAMPLE 1 amniotic fluid fetal cells

description: Hybridized to CytoScan 750K

value: Fetal omphalocele, mild separation of fetal left renal pelvis 3.1 cm × 1.7 cm × 3.0 cm


title: SAMPLE 2 amniotic fluid fetal cells

description: Hybridized to CytoScan 750K

value: Fetal omphalocele (contents are liver, most intestinal canal and part of gastric bubble) abdominal wall defect about 2.6 cm, where a mass 4.6 cm × 4.3 cm × 3.8 cm bulging, containing liver, most intestinal canal and part of gastric bubble echoes, the mass boundary is clear, and umbilical cord echoes are observed on the surface of the mass.


title: 2 cell embryos FLI3

value: 2 cell


title: 4_10_3_b, WT, M63 + NH4Cl

value: WT


title: 4_10_2_b, WT, M63 + NH4Cl


title: 2 cell embryos FLI2


title: 4_10_1_b, WT, M63 + NH4Cl


title: 2 cell embryos FLI1


title: 1_20_3_b, eccD1, M63


title: 8cell embryos DMEM3

value: DMEM


title: 1_20_2_b, eccD1, M63


title: 1_20_1_b, eccD1, M63


title: T_RNA_pat1D_Replicate_1

city: Bethesda

value: yeast cells


title: 8cell embryos DMEM2


title: RNA_ WT_Replicate_1

extract_protocol: For RNA-seq library preparation, total RNA was extracted and purified from aliquots of the same snapped-frozen cells described above using hot phenol-chloroform extraction. Five µg of total RNA was randomly fragmented by mixing with 2× alkaline fragmentation solution (2 mM EDTA, 10 mM Na2CO3, 90 mM NaHCO3, pH ≈ 9.3). After incubation for 20 min at 95ºC, fragmentation reactions were mixed with ice-cold stop solution (300 mM NaOAc pH 5.5, 30 µg GlycoBlue (Invitrogen; AM9516)). RNA was precipitated by adding one part of isopropanol followed by the standard protocol of precipitation. Fragment size selection, library generation, and sequencing were carried out using the same protocol described above for RPF library preparation, except the Ribo-Zero Gold rRNA Removal Kit (Illumina; MRZ11124C), was employed to remove rRNA after linker-ligation.

value: RNA


title: Ribo_pat1Ddhh1D_Replicate_1

data_processing:
For ribo-seq/RNA-Seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with tophat (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
The sequenced CAGE reads of each sample were aligned to the reference genome of S. cerevisiae S288c (Assembly version: sacCer3) using HISAT2. CAGE reads mapped to rRNA genes were identified using rRNAdust (http://fantom.gsc.riken.jp/5/sstar/Protocols:rRNAdust), and were excluded from subsequent TSS analyses. CAGE reads with a mapping quality score (MAPQ) > 20 were considered uniquely mapped reads and were used for subsequent analyses. CAGE signals of biological replicates were then merged as a single sample. The transcription abundance of each TSS was quantified as the numbers of CAGE tags/reads supporting the TSS per million mapped reads (TPM). For RNA-Seq samples in parallel with CAGE-Seq, Fastq files after passing the QC and the adapter content check they were mapped to yeast genome (sacCer3) with STAR aligner, then PCR duplicates were removed by samtools.
For ChIP-Seq: Sequence data were aligned to the SacCer3 version of the genome sequence using Bowtie2 with parameters -X 1000 -very-sensitive, to map sequences up to 1 kb with maximum accuracy. PCR duplicates from ChIP-seq data were removed using the samtools rmdup package.
Assembly: sacCer3
Supplementary files format and content: Processed data (csv) files contain raw reads for each file. For Ribo and parallel RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. For CAGE-sequencing and parallel RNA-Sequencing, each file contains two columns providing: systemmatic gene name (Gene_ID), total reads. For Rpb1 ChIP-Seq, average occupancy  file contains two columns providing: systemmatic gene name (ORF) and avg occupancy.
Library strategy: Ribo-seq

extract_protocol: Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in "Conserved mRNA-granule component Scd6  targets Dhh1 to repress translation initiation  and activates Dcp2-mediated mRNA decay in  vivo" Zeidan et al., 2018 Plos Genetics 15(7): e1008299

value: W303 F2182 (MATa ura3-1 trp1-1 ade2-1 leu2-3,112 his3-11,15 {delta}pat1::HIS3 {delta}dhh1::KanR)

value: Ribosome protected RNA 25-34 nt


title: Ribo_pat1Ddhh1D_Replicate_2


title: Ribo_ pat1D _Replicate_2


title: Ribo_pat1Ddhh1D_Replicate_3


title: RNA_ WT_Replicate_3


title: RNA_ WT_Replicate_2


title: CD28, replicate 1, scRNAseq

city: Utrecht

first: Peter

last: Brazda

address: Heidelberglaan 100

department: Center for Translational Immunology

country: Netherlands

institute: University Medical Center Utrecht

description: SORTseq

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the STAR package
Data were pre-processed (excluding low-quality cells (number of genes detected<200 or mitochondrial UMIs>30% or ERCC reads>50%) were excluded, next removing ERCC-reads) in base R. Cells we names based on their position on the 384w plates, using the 'cell ID table for 384w plate'.
Data were normalized, scaled to 10000 counts, and log-transformed using the NormalizeData function of the Seurat package.
Principal component analysis was performed on the scaled data with the 4000 most variable genes. The number of principal components used was determined using the ElbowPlot function.
We calculated a UMAP representation of the data for visualization and calculated clusters, using the FindNeighbors and FindClusters functions with the resolution parameter set to 0.3. Marker genes that differentiated between clusters were identified using the FindAllMarkers function.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: T cells

extract_protocol:
TEGs were co-cultured together with RPMI 8226 cells in the presence of 10 µM PAM during 48h. After incubation, cells were sorted by expression of γδTCR+CD4+ or γδTCR+CD8+ (pan-γδTCR-PE, clone IMMU510; CD4-PB, clone RPA-T4; CD8-PerCP Cy5.5, RPA-T8) into 384-well PCR plates using ARIA II.
Cells were sequenced according to the SORT-seq method based on CEL-Seq2, and libraries were sequenced with paired end sequencing on Nexseq500.
SORT-seq

value: T cells


title: CD28, replicate 2, scRNAseq

description: SORTseq


title: 103_41BB_t, replicate 1, scRNAseq

description: SORTseq


title: 41BB, replicate 1, scRNAseq

description: SORTseq


title: 103_41BB_t, replicate 3, scRNAseq

description: SORTseq


title: TEG, replicate 2, scRNAseq

description: SORTseq

value: TEG


title: 41BB, replicate 2, scRNAseq

description: SORTseq


title: CD28, replicate 3, scRNAseq

description: SORTseq


title: TEG, replicate 3, scRNAseq

description: SORTseq


title: TEG, replicate 1, scRNAseq

description: SORTseq


title: TEG_t, replicate 2, scRNAseq

description: SORTseq


title: 103_41BB_t, replicate 2, scRNAseq

description: SORTseq


title: 41BB, replicate 3, scRNAseq

description: SORTseq


title: TEG_t, replicate 1, scRNAseq

description: SORTseq


title: TEG_t, replicate 3, scRNAseq

description: SORTseq


title: 8cell embryos DMEM1


title: 1_19_3_b, eccCa1, M63


title: Ribo_ WT_Replicate_3


title: MPAL Patient 3, Diagnosis

first: Hope

last: Mumme

address: 1760 Haygood Dr NE

description: 10X Genomics

data_processing:
Raw scRNA-seq data was demultiplexed, aligned to human reference genome, and processed for single cell gene counting using the Cell Ranger Software from 10x Genomics (v7.0.0).
Assembly: hg38
Supplementary files format and content: Tab separated values files and matrix files

source_name: bone marrow

extract_protocol:
Frozen bone marrow samples were obtained from Aflac Cancer and Blood disorder center from Children’s Healthcare of Atlanta Pediatric Biorepository.The frozen BM were thawed viably using standardized protocol. Briefly the cells were thawed quickly (37C for ~2 minutes till a small ice crystal remains), and warm complete medium (RPMI1640, 5% heat inactivated FBS, 1x Penicillin. Streptomycin) was added gradually. The cells were pelleted (380g, RT, 5min), and washed one more time with complete medium, which was followed by one more wash with PBS containing BSA (0.04 to 1.0%). For cell multiplexing, cells were labelled with specific anti-human TotalSeq-B Hashtag antibodies (Biolegend) according to manufacturer’s protocol. The cells were resuspended in cell staining buffer (Biolegend) or PBS with1% BSA to get an optimal cell concentration of 700-1200 cells/µl. The single cell suspensions were then proceeded using 10x Genomics single cell assay protocols.
The single cell RNA-seq libraries were prepared using the Chromium single cell 3’v3 and 3’ v3.1 reagent kits (10x Genomics). The libraries were quantified using Qubit (Thermo Fisher Scientific) and quality was checked using Bioanalyzer HS DNA chips (Agilent). Sequencing was performed using the massively parallel sequencing NextSeq 500 and Novaseq S4 platforms (Illumina).

tag: individual

value: patient 3

tag: tissue

value: bone marrow

tag: sample type

value: diagnosis

value: Bone marrow blast and immune cells

tag: disease state

value: MPAL

tag: diagnosis subtype

value: B/My MPAL


title: 1_19_2_b, eccCa1, M63


title: MPAL Patient 1, Diagnosis

description: 10X Genomics

value: patient 1


title: MPAL Patient 6, Diagnosis

description: 10X Genomics

value: patient 6

value: T/My MPAL


title: MPAL Patient 4, Diagnosis

description: 10X Genomics

value: patient 4


title: MPAL Patient 5, Diagnosis

description: 10X Genomics

value: patient 5


title: 1_19_1_b, eccCa1, M63


title: Ribo_ WT_Replicate_1

extract_protocol: Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in "Conserved mRNA-granule component Scd6 targets Dhh1 to repress translation initiation and activates Dcp2-mediated mRNA decay in vivo" Zeidan et al., 2018 Plos Genetics 15(7): e1008299

value: yeast cells


title: Ribo_ WT_Replicate_2


title: 4cell embryos DMEM3

value: embryo

tag: developmental stage

value: 4 cell

value: DMEM


title: Ribo_ pat1D _Replicate_1

tag: cell type

value: Ribosome protected RNA 25-34 nt


title: 4cell embryos DMEM2


title: 2 cell embryos DMEM1

value: 2 cell


title: 4cell embryos DMEM1


title: 2 cell embryos DMEM3


title: 2 cell embryos DMEM2


title: 1_16_1_b, esxB, M63

tag: genotype

value: esxB


title: 1_16_2_b, esxB, M63


title: 1_10_3_b, WT, M63

value: WT


title: 1_16_3_b, esxB, M63


title: ES-E14 cells, shLncenc1_1, 72h

city: Milan

first: Emanuele

last: Monteleone

state: Italy

address: Via Olgettina 60

institute: Università Vita Salute San Raffaele

data_processing:
Sequencing reads were trimmed using cutadapt with options set to :  -e 0.1 -q 16 -O 3 --trim-n --minimum-length 25 -a AGATCGGAAGAGC.
Reads were mapped against the mm10 genome assemby using STAR with default parameters.
Differential expression (DE) analysis was performed using the R package DESeq2 . Genes with an adjusted p-value (FDR) of <0.05 and with a log2 fold change major of the absolute value of 1, were considered as differentially expressed.
Coverage tracks were created using the BamCoverage tool (deepTool)  using default parameters,
Assembly: mm10/GRCm38
Supplementary files format and content: bigWig coverage files

growth_protocol: E14 mouse ESCs were cultured without feeders on plastic coated with 0.1% gelatin (Sigma, cat. G1890) and replated every 2/3 days at a split ratio of 1 in 10. Cells were cultured in high-glucose DMEM (Invitrogen) supplemented with 15% FBS (Hyclone), 0.1 mM nonessential amino acids (Invitrogen), 1 mM sodium pyruvate (Invitrogen), 0.1 mM 2-mercaptoethanol, 1500 U/ml LIF (Millipore), 25 U/ml penicillin, and 25 μg/ml streptomycin,

extract_protocol:
Total RNA was extracted by using TRIzol reagent (Invitrogen), according to the manufacturer's protocol. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq RNA Library Prep kit (unstranded) following manufacturer's instructions.

treatment_protocol: Lncenc1 was silenced using two different strategies, one based on the treatment with Antisense Oligonucleotides (ASO) for 36 hours and the other on the transfection of shRNAs for 72 hours. Transfection of mES-E14 cells was performed using LipofectamineTM 2000 Transfection Reagent. For one well of a 6-well plate, we used 10 μl of transfection reagent, 4 μg of shRNA plasmid DNA and 800,000 cells in 800 μl of OPTIMEM. After 6 hours, cells were rinsed with 1.2 ml of complete ESCs medium. After overnight incubation, cells were detached and plated into a 10 cm2 plate. ShRNAs treated cells were selected with 1 μg of puromycin for 2 days and lysed the next day whereas ASOs treated cells were analyzed 36 hours after the transfection medium was removed

tag: cell line

value: mouse embryonic stem cells

value: Lncenc1 Knockdown

tag: time

value: 72 hours

value: sh Lncenc1


title: 1_10_2_b, WT, M63


title: SEM_PINO_RES_DOT1Li_Input

first: Ronald

middle: W.

last: Stam

address: Heidelberglaan 25

institute: Prinses Maxima Centrum

description: ChIPseq

data_processing:
QC was performed with fastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
reads were trimmed using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Reads were then aligned to the human genome, hg19, with bowtie2
Duplicate reads were removed using DeepTools alignmentSieve, with the flag –ignore duplicates
BigWigs were generated using the DeepTools bamCoverage command, with the flags –extendReads –normalize using RPKM
Assembly: hg19
Supplementary files format and content: bigWig

source_name: cell line

growth_protocol: SEM  and SEMPINORES  cells were continuously grown in in RPMI-1640 medium containing GlutaMAXTM supplemented with 10% fetal calf serum, 100 IU/ml Penicillin and Streptomycin, and 0.125µg/ml Amphotericin B (Life Technologies), at 37°C under a 5% CO2 containing atmosphere. Cell lines passed every 3-4 days and routinely tested for the absence of mycoplasma and DNA fingerprinted to assure cell line authenticity.

extract_protocol:
Up to 20 million leukemic cells were crosslinked and lysed using the SimpleChIP kit (Cell Signaling Technology®, #9003) according to the manufacturer’s recommendations and subsequently sonicated using a Bioruptor sonicator (Diagenode) to generate 150-300 bp fragment size. Next, immunoprecipitation and antibody-protein-DNA precipitation were performed according to the guidelines of the manufacturer.   Antibodies against KMT2A (Bethyl labs; cat.nr. A300-086-A), AFF1 (Abcam; cat.nr. ab31812), H3K4Me3, H3K27Ac and H3K79Me2 (Diagenode; cat. nrs. pAB-003-050, C15410196 and C15410051) were used. ChIP-seq DNA libraries were generated using the NEB Next Ultra DNA library preparation kit for Illumina (New England Biolabs) according to the manufacturer’s recommendations
ChIP-seq DNA libraries were generated using the NEB Next Ultra DNA library preparation kit for Illumina (New England Biolabs, E7645) according to the manufacturer’s recommendations

treatment_protocol: SEM  and SEMPINORES cells were cultured in the presence of 50 µM of the DOT1L inhibitor pinometostat (EPZ5676, Selleckchem) for 1 week, with passage of the cells after 3 days with fresh inhibitor

value: cell line

value: Acute Lymphoblastic Leukemia cell line SEM

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

value: t(4;11)(q21;q23) translocation

tag: treatment

value: 50uM pinometostat for 7 days

tag: chip antibody

value: 2% input DNA


title: SEM_PINO_RES_DOT1Li_H3K4me3

description: ChIPseq

value: H3K4Me3 (Diagenode pAB-003-050  lot. A1052D)


title: SEM_PINO_RES_DOT1Li_H3K79me2

description: ChIPseq

value: H3K79Me2 (Diagenode C15410051, lot. Lot:A1193)


title: microglia_6-3

first: Zhexing

last: Wen

address: 100 Woodruff Circle

department: Department of Psychiatry and Behavioral Sciences

institute: Emory University

description: Sample 40

data_processing:
raw fastq files were trimmed by fastp (v0.23.0)
trimmed fastq files were mapped to hg39 genome using STAR (2.7.10b)
raw read counts were extracted by subread (v2.0.6)
Assembly: hg38
Supplementary files format and content: csv text file includes raw read counts for reac sample

source_name: hiPSC-microglia

extract_protocol:
RNA was isolated using the Direct-zol™ RNA Miniprep Kit (Zymo, R2052). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq is a standard protocol widely utilized in our laboratory at Emory. RNA-seq libraries were generated using the NEB Next Ultra II Directional with Poly A Selection Kit. A qPCR-based KAPA library quantification kit was applied to accurately quantify library concentration.

value: hiPSC-microglia

value: TSC2, c.G4514C (Homozygous)


title: microglia_6-1

description: Sample 38


title: microglia_6-2

description: Sample 39


title: microglia_4-2

description: Sample 36


title: SEM_PINO_RES_DOT1Li_biol_rep_2_AFF1

description: ChIPseq


title: microglia_4-1

description: Sample 35


title: SEM_PINO_RES_DOT1Li_H3K27ac

description: ChIPseq


title: ES-E14 cells, shControl, 72h, replicate 2

value: sh scramble


title: microglia_2-3

description: Sample 34


title: SEM_PINO_RES_DOT1Li_biol_rep_1_AFF1

description: ChIPseq


title: ES-E14 cells, AsoLncenc1, 36h, replicate 2

value: 36 hours

value: Aso Lncenc1


title: ES-E14 cells, shControl, 72h, replicate 1

value: mouse embryonic stem cells

value: WT


title: ES-E14 cells, shLncenc1_2, 72h

value: Lncenc1 Knockdown

value: 72 hours


title: 1_10_1_b, WT, M63

tag: medium


title: 4_20_2, eccD1, M63 + NH4Cl

value: M63 + 20mM Ammonium Chloride

tag: batch


title: 4_20_1, eccD1, M63 + NH4Cl


title: microglia_2-2

description: Sample 33


title: microglia_2-1

description: Sample 32


title: ES-E14 cells, AsoLncenc1, 36h, replicate 1


title: SEM_PINO_RES_DOT1Li_biol_rep_1_KMT2A

description: ChIPseq

value: cell line

value: Acute Lymphoblastic Leukemia cell line SEM

value: KMT2A ( Bethyl labs A300-086-A   lot. 6)


title: 4_20_3, eccD1, M63 + NH4Cl


title: microglia_4-3

description: Sample 37


title: microglia_1-3

description: Sample 31

value: healthy control


title: SEM_DOT1Li_H3K27ac

description: ChIPseq

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

value: t(4;11)(q21;q23) translocation

value: 50uM pinometostat for 7 days


title: ES-E14 cells, AsoControl, 36h, replicate 2

value: Aso scramble


title: ES-E14 cells, AsoControl, 36h, replicate 1


title: 4_16_3, esxB, M63 + NH4Cl

value: esxB


title: microglia_1-2

description: Sample 30

value: hiPSC-microglia


title: 4_19_2, eccCa1, M63 + NH4Cl


title: 4_19_1, eccCa1, M63 + NH4Cl


title: neuron_TSC10HO_B

description: Sample 28

source_name: hiPSC-neuron

value: hiPSC-neuron

value: treated with TSC2 mutated microglia conditioned medium


title: SEM_DOT1Li_H3K79me2

description: ChIPseq

value: H3K79Me2 (Diagenode C15410051, lot. Lot:A1193)


title: SEM_DOT1Li_H3K4me3

description: ChIPseq

value: H3K4Me3 (Diagenode pAB-003-050  lot. A1052D)


title: SEM_DOT1Li_biol_rep_1_AFF1

description: ChIPseq


title: neuron_TSC10HO_A

description: Sample 27


title: 4_19_3, eccCa1, M63 + NH4Cl


title: SEM_DOT1Li_biol_rep_2_AFF1

description: ChIPseq


title: neuron_TSC010_B

description: Sample 26


title: 4_16_1, esxB, M63 + NH4Cl


title: neuron_TSC007_B

description: Sample 24


title: SEM_DOT1Li_Input

description: ChIPseq

value: 2% input DNA


title: neuron_TSC010_A

description: Sample 25


title: SEM_PINO_RES_DOT1Li_biol_rep_2_KMT2A

description: ChIPseq


title: 4_10_1, WT, M63 + NH4Cl

value: WT


title: 4_10_2, WT, M63 + NH4Cl

value: M63 + 20mM Ammonium Chloride


title: microglia_1-1

description: Sample 29


title: SEM_PINO_RES_H3K27ac

description: ChIPseq

value: cell line


title: SEM_DOT1Li_biol_rep_1_KMT2A

description: ChIPseq

value: Acute Lymphoblastic Leukemia cell line SEM


title: SEM_PINO_RES_Input

description: ChIPseq


title: 4_16_2, esxB, M63 + NH4Cl


title: 1_20_3, eccD1, M63


title: 4_10_3, WT, M63 + NH4Cl


title: SEM_DOT1Li_biol_rep_2_KMT2A

description: ChIPseq

value: KMT2A ( Bethyl labs A300-086-A   lot. 6)


title: As.si.PGR

first: yanzhi

last: Gai

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong university

description: cDNA expression data from AsPC-1 cells small interference PGR.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software12.6.1 (Agilent technologies, Santa Clara, CA, US).

data_processing:
The raw data (.cel files) were normalized using Gene Spring Software 12.6.1, and then the differential gene analysis between samples was performed. According to the sample conditions, Fold-change(Fold change in expression) was used to screen differential genes, and the selection conditions were as follows:
1) 2-fold difference: Fold Change (linear) =< 0.5 or Fold Change (linear) >= 2.
2) T-test p-value < 0.05 and p-value < 0.01

label: biotin

source_name: AsPC-1 cells, si-PGR

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: PGR interference cells were cultured in DMEM medium supplemented with 10% fetal bovine serum.   The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

value: pancreatic tumor cell

value: PGR-interference


title: neuron_PGP1_B

description: Sample 22

value: treated with healthy control microglia conditioned medium


title: neuron_PGP1_A

description: Sample 21


title: SEM_PINO_RES_H3K79me2

description: ChIPseq

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

value: t(4;11)(q21;q23) translocation


title: neuron_426_B

description: Sample 20


title: 1_20_2, eccD1, M63


title: 1_19_3, eccCa1, M63


title: 1_20_1, eccD1, M63


title: neuron_426_A

description: Sample 19


title: neuron_C1_2_B

description: Sample 18


title: As.Ctrl

description: cDNA expression data from AsPC-1 cells small interference Ctrl.

source_name: AsPC-1 cells, ctrl

value: control


title: SEM_PINO_RES_biol_rep_1_AFF1

description: ChIPseq


title: SEM_PINO_RES_H3K4me3

description: ChIPseq


title: SEM_PINO_RES_biol_rep_2_KMT2A

description: ChIPseq


title: SEM_PINO_RES_biol_rep_1_KMT2A

description: ChIPseq


title: 1_19_2, eccCa1, M63


title: SEM_Input

description: ChIPseq

value: 2% input DNA IgG (negative control kit ChIP Cell Signaling #2729P lot7)


title: 1_19_1, eccCa1, M63


title: neuron_C1_2_A

description: Sample 17

value: hiPSC-neuron


title: neuron_TSC007_A

description: Sample 23

value: treated with TSC2 mutated microglia conditioned medium


title: microglia_TSC010HO_2

description: Sample 16

value: hiPSC-microglia

value: TSC2 mutation


title: 1_16_3, esxB, M63

value: esxB


title: microglia_TSC010HO_1

description: Sample 15


title: 1_16_2, esxB, M63


title: SEM_H3K27ac

description: ChIPseq


title: 1_16_1, esxB, M63


title: SEM_PINO_RES_biol_rep_2_AFF1

description: ChIPseq


title: microglia_TSC010_2

description: Sample 14


title: microglia_TSC010_1

description: Sample 13


title: 1_10_3, WT, M63

value: WT


title: 1_10_2, WT, M63


title: microglia_TSC007_2

description: Sample 12


title: microglia_TSC007_1

description: Sample 11


title: 1_10_1, WT, M63


title: microglia_TSC002_2

description: Sample 10


title: SEM_biol_rep_1_AFF1

description: ChIPseq


title: microglia_TSC002_1

description: Sample 9


title: SEM_PINO_RES_biol rep 2 [ATAC]

description:
ATACseq
ATAC_SEM_vs_PINO_RES_diffpeaks.txt

data_processing:
QC was performed with fastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
reads were trimmed using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Reads were then aligned to the human genome, hg19, with bowtie2
Duplicate reads were removed using DeepTools alignmentSieve, with the flag –ignore duplicates and ATAC shift flag to correct for adapter insertion
BigWigs were generated using the DeepTools bamCoverage command, with the flags –extendReads –normalize using RPKM
Peaks were called with MACS2 and statistical analysis was conducted using DiffBind
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cells were lysed, pelleted and tagmented using the Nextera Library Prep Kit (Illumina, FC-131-1096).
Libraries were generated using the Nextera Library Prep Kit (Illumina, FC-131-1096)


title: SEM_biol_rep_2_KMT2A

description: ChIPseq


title: SEM_biol_rep_1_KMT2A

description: ChIPseq


title: SEM_PINO_RES_biol rep 1 [ATAC]


title: microglia_PGP1_2

description: Sample 8

value: healthy control


title: microglia_PGP1_1

description: Sample 7


title: SEM_biol rep 2 [ATAC]

value: cell line


title: SEM_biol rep 1 [ATAC]

value: Acute Lymphoblastic Leukemia cell line SEM


title: SEM_H3K79me2

description: ChIPseq

value: H3K79Me2 (Diagenode C15410051, lot. Lot:A1193)


title: microglia_426_1

description: Sample 5


title: SEM_PINO_RES_DOT1Li_biol rep 4 RNA

description:
SEM_vs_PINO_RES_DEGs_CPM.txt
SEM_vs_PINO_RES_featureCounts.txt

data_processing:
QC was performed with fastQC
reads were trimmed with trim_galore, then aligned against the human genome assembly (hg19) with STAR
read counts were used to identify differential gene expression using DESeq2 (v3.12)
Gene expression levels were quantified using the featureCounts function of the Subread package
Differential gene expression analysis was conducted using DEseq2
Assembly: hg19
Supplementary files format and content: logFC and CPM
Supplementary files format and content: featureCounts output

extract_protocol:
RNA was isolated from leukemic cells using the RNeasy Mini Kit (Qiagen)
Libraries were generated using the TruSeq Stranded mRNA library preparation kit (Illumina, RS-122-2103)

value: 50uM pinometostat for 7 days


title: SEM_H3K4me3

description: ChIPseq

value: H3K4Me3 (Diagenode pAB-003-050  lot. A1052D)


title: SEM_biol_rep_2_AFF1

description: ChIPseq


title: microglia_12C1_2

description: Sample 4


title: the plasma of DKD patients_rep5

city: Chongqing

first: Ziyue

last: Lin

state: Chongqing

address: Medical College Road

institute: Chongqing Medical University

description: circRNA expression in human plasma

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

scan_protocol: The Agilent Scanner G2505C was used to scan the slides

data_processing: Agilent Feature Extraction software was applied to asses the array images. Quantile normalization and subsequent data processing were performed with the GeneSpring GX v11.5.1 software package (Agilent Technologies).After quantile normalization of the raw data, circRNAs that at least 6 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.Differentially expressed circRNAs with statistical significance were identified through Volcano Plot filtering

source_name: patients with diabetic kidney disease

label_protocol: Rnase R (Epicentre, Madison, WI) was used to remove linear RNAs. The enriched circRNAs were amplified and transcribed into fluorescent cRNA by using a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: plasma

tag: gender

value: female

tag: age


title: SEM_PINO_RES_DOT1Li_biol rep 3 RNA

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

value: t(4;11)(q21;q23) translocation


title: the plasma of DKD patients_rep2

description: circRNA expression in human plasma


title: the plasma of DKD patients_rep3

description: circRNA expression in human plasma

value: male


title: microglia_C1_2_2

city: Atlanta

description: Sample 2


title: the plasma of DKD patients_rep1

description: circRNA expression in human plasma


title: microglia_426_2

description: Sample 6


title: microglia_12C1_1

description: Sample 3


title: SEM_PINO_RES_DOT1Li_biol rep 2 RNA


title: the plasma of DKD patients_rep6

description: circRNA expression in human plasma


title: SEM_PINO_RES_DOT1Li_biol rep 1 RNA


title: SEM_PINO_RES_biol rep 4 RNA


title: the plasma of DKD patients_rep4

description: circRNA expression in human plasma


title: the plasma of DM patients_rep6

description: circRNA expression in human plasma

source_name: patients with diabetes


title: the plasma of DM patients_rep5

description: circRNA expression in human plasma


title: microglia_C1_2_1

description: Sample 1


title: SEM_PINO_RES_biol rep 3 RNA


title: SEM_PINO_RES_biol rep 2 RNA


title: the plasma of DM patients_rep4

description: circRNA expression in human plasma


title: SEM_DOT1Li_biol rep 4 RNA


title: S1609_synovium_ATAC

city: Cambridge

first: Anika

last: Gupta

state: Massachusetts

address: 95 Dunster St, 110 Kirkland Mail Center

institute: Harvard University

description:
10x Genomics
peaksXcells_ALL_raw.h5ad
ATAC_ALL_CT_processed.h5ad

library_source: genomic single cell

data_processing:
Samples were initially processed using 10x Genomics Cell Ranger ARC 2.0.0, which includes barcode processing and read alignment, for both ATAC and RNA information.
Assembly: hg38
Supplementary files format and content: Comma-separated metadata files and h5ad (Hierarchical Data Formats) matrix files

source_name: Synovial tissue

extract_protocol:
Synovial tissue samples were collected and cryopreserved, then thawed and disaggregated, and the resulting single-cell suspensions were stained with anti-CD235a antibodies (clone 11E4B-7-6 (KC16), Beckman Coulter) and Fixable Viability Dye (FVD) eFlour 780 (eBioscience/ThermoFisher). Live non-erythrocyte (i.e., FVD- CD235-) cells were collected by fluorescence-activated cell sorting (BD FACSAria Fusion). The sorted live cells were then re-frozen in Cryostor and stored in liquid nitrogen.
Each sample was processed separately in the cell capture step. Nuclei were isolated using an adaptation of the manufacturer’s protocol (10X Genomics). Approximately ten thousand nuclei transposed nuclei were loaded on Chromium Next GEM Chip J followed by GEM generation. 10x Barcoded DNA from the transposed DNA (for ATAC) and 10x Barcoded, full-length cDNA from poly-adenylated mRNA (for Gene Expression) were produced during GEM incubation. The ATAC libraries and Gene Expression libraries were then generated separately. Both library types were sequenced to an average of 30,000 reads per cell on different flow cells with recommended sequencing cycles according to the manufacturer’s protocol (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, 10X Genomics) using Illumina Novaseq.

value: Synovial tissue

tag: disease

value: RA

tag: synovial lymphocytic_inflammation

value: Moderate (>1 perivascular aggregate + focal interstitial infiltration) (2)

tag: synovial lining_hyperplasia

value: 3-4 cells Thick (2)


title: S1611_synovium_ATAC

tag: tissue

value: Marked (both perivascular and widespread interstitial aggregates) (3)


title: S1607_synovium_ATAC

value: Band-like (4)

value: 1-3 cells Thick (1)


title: S1594_synovium_ATAC

value: Moderate (>1 perivascular aggregate + focal interstitial infiltration)


title: the plasma of DM patients_rep3

description: circRNA expression in human plasma


title: SEM_PINO_RES_biol rep 1 RNA

value: cell line

value: Acute Lymphoblastic Leukemia cell line SEM


title: S1592_synovium_ATAC


title: the plasma of DM patients_rep2

description: circRNA expression in human plasma


title: the plasma of healthy people_rep6

description: circRNA expression in human plasma

source_name: healthy people


title: the plasma of DM patients_rep1

description: circRNA expression in human plasma


title: the plasma of healthy people_rep4

description: circRNA expression in human plasma


title: S1590_synovium_ATAC

value: > 4 cells Thick (3)


title: the plasma of healthy people_rep5

description: circRNA expression in human plasma


title: SEM_DOT1Li_biol rep 3 RNA

value: 50uM pinometostat for 7 days


title: SEM_DOT1Li_biol rep 2 RNA


title: SEM_DOT1Li_biol rep 1 RNA


title: SEM_biol rep 4 RNA


title: S1389_synovium_ATAC


title: S1588_synovium_ATAC


title: SM3

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: biopsy of periapical tissues

extract_protocol:
Tissues were homogenized using pre-chilled Omni Bead Ruptor 24 Cryo Cooling Unit in 2.8mm ceramic tubes and pre-chilled 700 µl QIAzol Lysis reagent. Total RNA was extracted using the Qiagen RNAeasy PLUS Universal Mini Kit per the manufacturer's instructions.
Total RNA samples about 500ng were used for sequencing library preparation according to Illumina TruSeq Stradned mRNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Tissue of 3-8 mm^3 biopsies were collected patients who underwent endodontic microsurgery procedures, and snap-frozen in liquid nitrogen. Samples were then transferred to -80C before RNA extraction.

value: Male

value: periapical tissues

tag: pain status

value: Symptomatic Apical Periodontitis

tag: race/ethnicity

value: Hispanic


title: SM2


title: S1586_synovium_ATAC


title: SEM_biol rep 3 RNA

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

value: t(4;11)(q21;q23) translocation


title: the plasma of healthy people_rep3

description: circRNA expression in human plasma

value: plasma

value: male


title: S1387_synovium_ATAC

value: Synovial tissue

value: RA

value: Moderate (>1 perivascular aggregate + focal interstitial infiltration) (2)

value: 3-4 cells Thick (2)


title: the plasma of healthy people_rep2

description: circRNA expression in human plasma


title: SEM_biol rep 2 RNA


title: S1385_synovium_ATAC

value: Moderate (>1 perivascular aggregate + focal interstitial infiltration)

value: 1-3 cells Thick (1)


title: AM2

value: Asymptomatic Apical Periodontitis

value: White


title: SM1


title: SEM_biol rep 1 RNA

value: cell line

value: Acute Lymphoblastic Leukemia cell line SEM