title: blastocyst - HC4 - Rep4

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809 enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on an Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 2 per group from at least one experimental group. At this step, 29699 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 27101 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: blastocyst

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 2 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions adapted to improve cRNA yields, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: We used the Arcturus PicoPure™ RNA isolation kit (LifeTechnologies, Courtaboeuf, France) for RNA extraction. Briefly, 100μl of extraction buffer was added to each pool of embryos. The samples were then incubated at 42°C for 30 minutes and then 100μl of ethanol (70%) were added to each sample. The samples were then deposited on columns previously incubated with 250µl of conditioning buffer. After two centrifugations, the columns were washed once with 100 μl of washing buffer. The samples were then incubated with 40μl of DNase (Qiagen, Courtaboeuf, France) for 15 minutes at 25°C. The samples were then washed three times, finally 11 μl of elution buffer were added to the samples. After incubation (1 minute) and two centrifugations, the RNA of each sample was isolated and frozen at -80°C until analyses. RNAs quantities and qualities were checked using the Agilent 5200 Fragment Analyzer System. Mean total RNA concentration was 1.44 ± 0.46 ng/ml and RNA quality was good (RNA Quality Numbers and 28S/18S ratios respective means ± SD: 9.37 ± 1.36 and 2.38 ± 0.77).

value: Blastocysts

tag: condition


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G5_ad001

status: Public on Oct 01 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: ACA,PL,ILA

tag: Sex

value: male

tag: age

tag: strain


title: Sildenafil_Dose3_Rep2

city: Chicago

first: Sonia

last: Brockway

state: IL

address: 303 E Superior St, SQBRC 7-500

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Library strategy: QMAP-Seq
Individual samples were demultiplexed based on i5 and i7 index sequences by running bcl2fastq Conversion Software (Illumina).
Data was processed using QMAP-Seq bioinformatic analysis pipeline (https://github.com/mendillolab/QMAP-Seq). Briefly, sgRNA and cell line barcode sequences were extracted from Read 1 sequences as follows: [ACACCG][sgRNA:20][Interval:102][CellLineBarcode:8]. The number of reads for each cell line-sgRNA pair was counted, allowing up to one nucleotide mismatch per barcode. Cell number was interpolated from sequencing reads using sample-specific standard curves. The number of cells for a compound-treated sample was normalized to the median number of cells for the DMSO-treated samples.
Data was filtered using the following exclusion criteria. First, samples with low read counts were excluded. Second, cell line-sgRNA pairs with high variation (standard deviation of log2(cell number) > 0.7) were excluded. Third, compounds with an AUC > 550 for any cell line-sgRNA pair were excluded. Fourth, noncytotoxic cell line-compound pairs (relative cell number of sgNT with highest dose ≥ 90%) were excluded. Fifth, cell line-compound pairs without a dose-dependent reduction in cell viability (difference in relative cell number of sgNT between lowest and highest dose < 25%) were excluded.
Genome_build: N/A (sgRNA library sequencing)
Supplementary_files_format_and_content: Plain text document (.txt) files with read counts for each cell line-sgRNA pair. Individual files for each sample.
Supplementary_files_format_and_content: Comma-separated values (.csv) file with relative cell numbers (i.e., cell number (%DMSO)) for each cell line-sgRNA-compound-dose-replicate combination. Matrix table with data for all samples.

organism: Homo sapiens

source_name: Pool of 5 breast cancer cell lines

growth_protocol: Cell line pools were cultured in RPMI-1640, 10% Tet System Approved FBS, 1% Penicillin/Streptomycin, 100 ng/mL doxycycline for 7 days prior to compound treatment.

extract_protocol:
Cell line pools were lysed with lysis buffer (10% 10x Taq DNA Polymerase Buffer, 0.45% IGEPAL CA-630, 0.45% TWEEN 20, 10% Proteinase K, 79.1% Nuclease-Free Water) containing cell spike-in standards. Cells were incubated at 60°C for 1 hour. Proteinase K from lysis buffer was inactivated at 95°C for 15 minutes.
Barcoded region was PCR amplified with a unique set of indexed primers for each sample. PCR products were pooled and purified twice. Sequencing library was diluted, combined with PhiX, denatured, and sequenced on a NovaSeq 6000 (Illumina).

treatment_protocol: Cell line pools were treated with compound or DMSO over a four-point concentration range (10-fold dilutions) in duplicate using either a standard dose range (10 nM to 10 μM) or a low dose range (1 nM to 1 μM). Dose1=lowest dose. Dose4=highest dose. Cells were treated for 72 hours.

tag: cell lines

tag: sgrnas

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2

tag: compound treatment


title: blastocyst - HC3 - Rep4

type: RNA

country: France

molecule: total RNA

tag: tissue


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G5_ad010


title: blastocyst - HC2 - Rep4


title: Tivozanib_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G4_ad012


title: blastocyst - HC1 - Rep4


title: Everolimus_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G4_ad001


title: Dasatinib_Dose3_Rep2


title: blastocyst - HC5 - Rep3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G4_ad007


title: blastocyst - HC4 - Rep3


title: Pazopanib_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G4_ad006


title: Topotecan_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G6_ad012


title: PYR41_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G4_ad004


title: blastocyst - HC3 - Rep3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G4_ad010


title: Saracatinib_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G4_ad002


title: blastocyst - HC5 - Rep2


title: blastocyst - HC6 - Rep2


title: blastocyst - HC3 - Rep2


title: Rigosertib_Dose3_Rep2


title: blastocyst - HC2 - Rep3


title: Ornidazole_Dose3_Rep2


title: blastocyst - HC1 - Rep3


title: blastocyst - HC6 - Rep4


title: blastocyst - HC4 - Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G4_ad008


title: Chlorambucil_Dose3_Rep2


title: blastocyst - HC6 - Rep3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G3_ad007


title: Gemcitabine_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G3_ad001


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G3_ad012


title: Ciclopirox_Dose3_Rep2


title: Lovastatin_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G3_ad010


title: blastocyst - HC5 - Rep4


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G3_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G2_ad012


title: blastocyst - HC1 - Rep2


title: Hearts, Inhibitor_2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

library_source: transcriptomic

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC
Reaper version 13-100 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides (Davis et al., 2013).  Only reads between 30 and 150 nucleotides were used in subsequent analyses.
Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 (GRCz11.92) using STAR 2.4.0a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package (Liao et al., 2014).  Only reads mapping at least partially inside exons were admitted and aggregated per gene, while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses.
Differentially expressed genes were identified using DESeq2 version 1.18.1(Love et al., 2014).  To remove a batch effect from the comparison, the replicates were presented to DESeq2 as covariates (DMSO_1/Inhib_1 = 1, DMSO_2/Inhib_2 = 2).
The raw count matrix was batch corrected using CountClust (Dey et al., 2017) and then normalized with DESeq2.
Genome_build: DanRer11
Supplementary_files_format_and_content: library size normalized counts

organism: Danio rerio

source_name: Hearts

extract_protocol:
Hearts from 56 hpf Tg(kdrl:EGFP) control and Alk5 inhibitor treated embryos were manually dissected using forceps.  Approximately 20 hearts per replicate were pooled, and total RNA was isolated using the miRNeasy micro kit (Qiagen), combined with on-column DNase digestion
100 ng of total RNA was used as input for VAHTS Stranded mRNA-seq Library (Vazyme) preparation, following manufacture’s protocol (Vazyme).

value: 56 hpf

tag: genotype

tag: treatment

value: Alk5 inhibitor

value: Hearts


title: Paclitaxel_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G3_ad004


title: blastocyst - HC5 - Rep1


title: blastocyst - HC2 - Rep1


title: KU55933_Dose3_Rep2


title: Hearts, Inhibitor_1


title: blastocyst - HC3 - Rep1


title: DMSOPlate6WellF10_Dose3_Rep2


title: RG108_Dose3_Rep2


title: Hearts, DMSO_2

value: DMSO


title: blastocyst - HC4 - Rep1


title: Nitroxoline_Dose3_Rep2


title: DMSOPlate6WellC10_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G3_ad008


title: Hearts, DMSO_1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G2_ad001


title: DimethylFumarate_Dose3_Rep2


title: Lapatinib_Dose3_Rep2


title: BjiPS_P3

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Data of RNA-seq (fastq file format) were quality-checked, and low-quality reads (score < 30), adapter sequences, and overrepresented sequences such as poly-A chain were trimmed using the Trim Galore! (ver.0.4.0).
The remaining reads were mapped to the Homo sapiens genome (hg19) using the STAR (ver.2.5.3a), and the output file (BAM file format) were summarized using the featureCounts (1.5.2).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Induced pluripotent stem cells

growth_protocol: See the citation

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: See the citation

tag: cell type

value: Induced pluripotent stem cells


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G2_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G6_ad001


title: BjFibro_EPB_NSM_P1

source_name: Induced neural stem cell-like cells

value: Induced neural stem cell-like cells


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G2_ad006


title: BjFibro_EPB_NSM_d5


title: blastocyst - HC1 - Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G2_ad004


title: Selumetinib_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G2_ad002


title: Tivantinib_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G2_ad008


title: BardoxoloneMethyl_Dose3_Rep2


title: ATAC-seq_3591T

city: Kunming

first: Ming

last: Li

state: Yunnan

address: NO 32 Jiao-Chang Donglu

country: China

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

data_processing:
For RNA-Seq, trimmomatic v0.32 were used to examine the sequencing quality and trim reads. Clean paired-end reads were aligned to the reference genome using Hisat2.We quantified gene-level reads counts using htseq-count. DESeq2 was used to analyze the expression differences between experimental groups.
For ATAC-Seq, the raw 150-bp paired-end reads of the ATAC-Seq libraries from HiSeq X Ten sequencer underwent quality control processes using FastQC and trimmomatic-0.36.Bowtie2 (-X 2000 --sensitive-local --dovetail) was used to align trimmed reads to the GRCh37.p13 build of the human genome. Potential PCR duplicate reads were marked using MarkDuplicates program from the Picard tool. Reads from mitochondrial DNA and the Y chromosome were filtered using SAMtools. Peaks were called in the each sample using MACS2 with parameters: --nomodel --shift -100 --extsize 200. Narrow peaks mapped to the blacklisted regions were excluded using bedtools. Peaks called from different samples were then merged using the mergePeaks program (-d 2000) in the HOMER tool. The reads counts of each peak were quantified using featureCounts based on the chromosome position of merged peaks. The Wald test in DESeq2 was used to identify differently accessible peaks between groups.
Genome_build: For RNA-Seq, GRCh38. For ATAC-Seq, hg19.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of each gene in RNA-Seq analysis and reads counts of each peak in ATAC-Seq analysis for each sample

source_name: Monocolony HEK293T cell carrying [A/A] genotype at rs4420550.

growth_protocol: HEK293T cells were cultured in a humidified 5% CO2 incubator at 37 °C in Dulbecco’s Modified Eagle’s Medium (DMEM) basic (Gibco) supplemented with 10% fetal bovine serum (FBS) (Biological Industries), 1% non-essential amino acids, 1% Sodium pyruvate and 1% penicillin-streptomycin (Life Technologies). PCR detection was regularly performed to ensure there were no mycoplasma contamination.

extract_protocol:
For RNA-Seq, total RNAs were extracted from cultured cells using the TRIzol Reagent (Life Technologies) according to standard protocol. For ATAC-Seq, 3×104 HEK293T cells were lysed in lysis buffer [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.1% (v/v) Igepal CA-630] on ice for 10 minutes to release the nuclei. The mixture was centrifuged at 4 °C at 500× g for 5 minutes and the supernatant was discarded as much as possible. The nuclei pellet was then incubated with a reaction mix containing Tn5 transposome at 37 °C for 30 minutes. DNA was purified immediately after transposition by using a Qiagen MinElute
For RNA-Seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. For ATAC-Seq, the transposed DNA fragments were PCR-amplified using the following conditions: 72 °C for 3 minutes, 98 °C for 30 seconds, and thermocycling for 15 cycles at 98 °C for 15 seconds, 60 °C for 30 seconds and 72 °C for 30 seconds, followed by 72 °C for 5 minutes. The PCR products were immediately purified with 1.2×AMPure (Beckman) beads to obtain ATAC-Seq libraries.

treatment_protocol: The [A/A] genotype at rs4420550 in wild-type HEK293T cells were precisely edited by CRISPR/cas9 to [G/G] genotype. Briefly, the pL-CRISPR-E.EFS.GFP construct targeting rs4420550 and the ssODN carrying C allele at rs4420550 were transiently co-transfected into wild-type HEK293T cells and cells positive for GFP fluorescence were sorted with a flow cytometer, and cultured for 5-7 days to form distinct colonies derived from single cells. Genomic DNA was then extracted from each colony for amplifying the target region containing rs4420550, and Sanger sequencing was performed to confirm the genomic editing. Overall, eight single cell colonies were selected after flow cytometry for subsequent analysis. Four colonies carried the [A/A] genotype at rs4420550, and the other four carried the [G/G] genotype.

tag: cell line

tag: snp

value: A/A


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G2_ad010


title: Vincristine_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G12_ad010


title: RacRotigotine_Dose3_Rep2


title: ATAC-seq_3589T


title: ATAC-seq_3010T


title: BjFibro_P4

source_name: Fibroblasts

value: Fibroblasts


title: Trifluoperazine_Dose3_Rep2


title: ATAC-seq_3612C

source_name: Monocolony HEK293T cell edited by CRISPR/cas9 carrying [G/G] genotype at rs4420550.

value: G/G


title: Carfilzomib_Dose3_Rep2


title: ATAC-seq_3531C


title: ATAC-seq_3546C


title: Cyclophosphamide_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G12_ad004


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G12_ad001


title: WP1130_Dose3_Rep2


title: STF31_Dose3_Rep2


title: Crizotinib_Dose3_Rep2


title: Simvastatin_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G11_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G12_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G11_ad012


title: Etoposide_Dose3_Rep2


title: FiveFluorouracil_Dose3_Rep2


title: Tcells_RP_index2

city: Hangzhou

first: Xue

state: Zhejiang

address: yuhangtang road

institute: zhejiang University

data_processing:
Each scRNA-seq sample data was separately demultiplexed, aligned to the human genome (version GRCh38), and calculated unique molecular identifier (UMI) were estimated using the Cellranger toolkit (Version 3.0.0, 10X Genomics), with default parameters. Cells with fewer than 200 detected genes, or 20,000 detected transcripts, or total mitochondrial gene expression exceeding 5% were excluded from the analysis. Genes expressed in less than 3 cells were also removed. Across five samples, the average number of cells sequenced was 5,115 with an average number of 86,580 reads per cell.
Five UMI matrices from three phases were considered as three batches, and data integration were performed into a single Seurat objects using the R package Seurat (v3.0.0)36. The data was then normalized as expression level using the NormalizeData function in Seurat by the LogNormalize method with a scale factor of 10000. Anchors were identified using FindIntegrationAnchors with 1-60 dimensions and 5000 anchor features. On average, 55,488 cells × 18501 genes were obtained for further analysis.
Downstream analysis after integration included data feature scaling (ScaleData), principal component analysis (PCA, RunPCA), and SNN graph building (FindNeighbors). The first 60 dimensions were used for UMAP reduction by the RunUMAP function.
Genome_build: GRCh38 - 10x reference
Supplementary_files_format_and_content: csv-delimited table of the aggregated UMI count matrix

source_name: endogenous T cells

extract_protocol:
After obtaining the PBMCs for each phase, CD3+CAR+ (CAR-T) and CD3+CAR- (endogenous T) cells were collected by fluorescence-activated cell sorting (FACS, BD FACS Aria II) with anti-Mouse IgG Biotin (Jackson), FITC Streptavidin (Biolegend), and anti-human CD3 APC (clone UCHT1, Biolegend). Single-cell suspensions of all samples were resuspended in DPBS-0.04% BSA at 1x106 cells/mL.
ScRNA-seq libraries were generated from the 10X Chromium Single Cell 3` Reagent Kits v2 (PN-120237) according to the manufacturer’s protocol (10x Genomics). Libraries were sequenced on the Illumina Hiseq X10 platform according to the manufacturer’s instructions (Illumina). Read 1 and Read 2 (paired end) were 150 bp, and the index primer was 8 bp. All samples were sequenced to an average depth of 236 million paired-end reads per sample, with 150 bp on the Read 1 and Read 2.

treatment_protocol: Single-cell RNA sequencing samples were collected at three phases: CAR-T products before infusion, CAR-T on day 8 after infusion, and CAR-T on day 15 after infusion.

tag: phase

value: Remission phase

tag: time point

value: PBMCs


title: Tcells_RP_index3


title: Tcells_RP_index1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G12_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G11_ad008


title: Letrozole_Dose3_Rep2


title: Tcells_PP_index4

value: Peak phase


title: Mebendazole_Dose3_Rep2


title: Tcells_PP_index3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G12_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G12_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G12_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G11_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G11_ad004


title: Tcells_PP_index2


title: PD318088_Dose3_Rep2


title: Trametinib_Dose3_Rep2


title: blastocyst - HC2 - Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G11_ad002


title: KX2391_Dose3_Rep2


title: Doxorubicin_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G10_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G11_ad001


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G10_ad010


title: CART_RP_index1

source_name: CAR-T cells


title: Sitagliptin_Dose3_Rep2


title: CART_RP_index2


title: CART_RP_index3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G11_ad007


title: Nilotinib_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G10_ad006


title: Ruxolitinib_Dose3_Rep2


title: CART_PP_index4

value: day 8


title: CART_RP_index4


title: Cisplatin_Dose3_Rep2


title: Tcells_PP_index1


title: SR1001_Dose3_Rep2


title: CART_PP_index3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G1_ad001


title: ATAC-seq_3015T


title: Zebularine_Dose3_Rep2


title: CART_PP_index1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G1_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G1_ad010


title: CART_IP_index3

value: Infusion product

value: day 0


title: ATAC-seq_3602C


title: CART_IP_index4


title: Bexarotene_Dose3_Rep2


title: DMSOPlate6WellF6_Dose3_Rep2


title: Tigecycline_Dose3_Rep2


title: CART_IP_index2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G1_ad002

value: ACA,PL,ILA

value: male


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F9_ad012


title: DMSOPlate6WellC6_Dose3_Rep2

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G1_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G10_ad004


title: CART_IP_index1


title: Input-ad-ube3b-p-RNAPII(ser2)_ChIPSeq

city: bei jing

first: wang

last: feng

address: nan wei road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College,

data_processing:
Illumina bcl2fq software was used for basecalling.
Low-quality reads (Q≤19 bases over 50%), Ns reads (N%>5%) and adapter polluted reads (adapter bases>5 bp) are filtered out.
ChIP-seq reads were aligned to the human genome assembly using Bowtie2.
Peaks were called using MACS2.
Genome_build: mm9

source_name: Raji cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~150 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X following the manufacturer's protocols.

value: B lymphocyte

value: peripheral blood

tag: morphology

value: lymphoblast

tag: chip antibody


title: Input-ad-con-p-RNAPII(ser2)_ChIPSeq


title: Tcells_RP_index4


title: Dacarbazine_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F9_ad007

tag: brain region


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F9_ad006

tag: Sex


title: Ip-ad-ube3b-p-RNAPII(ser2)_ChIPSeq

value: Phospho-Rpb1 CTD (ser2)(E1Z3G)(Cell Signaling Technology, #13500)


title: Lenvatinib_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_G1_ad006

tag: age


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F9_ad004

tag: strain


title: CART_PP_index2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F9_ad002


title: Ip-ad-con-p-RNAPII(ser2)_ChIPSeq

value: Phospho-Rpb1 CTD (ser2)(E1Z3G)(Cell Signaling Technology, #13499)


title: 28185: HP-15085-01T2D

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

data_processing:
Illumina basecalling with bcl2fastq, various versions
Read alignment and expression calculation; using RUM (Grant et al. Bioinformatics  doi: 10.1093/bioinformatics/btr427)
Conversion from reads to trimmed normalized CPMs.  Briefly CPMs for genes between 25 to 75% quantiles were used to compute a normalization factor which was then applied to all CPMs.
Manual and semi-automated cell type calling. Marker genes and differentially expressed genes used to rate cell type and purity which was subsequently curated.
Genome_build: hg19
Supplementary_files_format_and_content: TSV files with raw rea counts or normalized CPMs.  Donor annotation and called cell types included as well.

molecule: polyA RNA

extract_protocol: Fluidigm C1 single-cell RNA-Seq using 96-well chip

value: pancreas

tag: celltype

value: pancreatic islets

tag: agecategory

value: adult

tag: healthcategory

tag: combinedcategory

value: beta


title: 28184: HP-15085-01T2D

tag: tissue

value: alpha


title: VER155008_Dose3_Rep2

tag: cell lines

tag: sgrnas

tag: compound treatment


title: 28183: HP-15085-01T2D


title: PIK93_Dose3_Rep2


title: Input-con-2-RNAPII

tag: cell type


title: Sorafenib_Dose3_Rep2


title: 28182: HP-15085-01T2D

value: acinar


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F9_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F8_ad001


title: Decitabine_Dose3_Rep2


title: Input-cm4-RNAPII


title: 28181: HP-15085-01T2D

value: dropped


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F8_ad012


title: Input-con-RNAPII


title: Fingolimod_Dose3_Rep2


title: 28180: HP-15085-01T2D

value: pp


title: Ip-cm4-RNAPII_ChIPSeq

value: Rpb1 CTD (4H8) (Cell Signaling Technology, #2629)


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F8_ad007

value: ACA,PL,ILA


title: 28179: HP-15085-01T2D


title: Ip-con-2-RNAPII_ChIPSeq


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F8_ad006

value: male


title: Ip-con-RNAPII_ChIPSeq


title: Ip-ad-ube3b-RNAPII_ChIPSeq


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F8_ad002


title: CHIR99021_Dose3_Rep2

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: Linsitinib_Dose3_Rep2


title: Clofarabine_Dose3_Rep2


title: Input-ad-ube3b-RNAPII

value: B lymphocyte


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F8_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F7_ad012


title: Input-con-c-myc_ChIPSeq

value: peripheral blood


title: 28175: HP-15085-01T2D


title: blastocyst - HC6 - Rep1

value: Blastocysts

tag: condition


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F7_ad001


title: Valdecoxib_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F7_ad010


title: PLX4720_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F8_ad010


title: Input-ad-c-myc-k427r_ChIPSeq

value: lymphoblast


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F7_ad006


title: Input-TRIB3-cas9-RNAPII_ChIPSeq


title: Ip-con-c-myc_ChIPSeq

value: c-Myc antibody[9E11] (Abcam, Ab56)


title: Fluvastatin_Dose3_Rep2


title: Gefitinib_Dose3_Rep2


title: Cabozantinib_Dose3_Rep2


title: Niclosamide_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F7_ad004


title: Input-c-RNAPII_ChIPSeq


title: Fulvestrant_Dose3_Rep2


title: Ki8751_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F7_ad002


title: Ip-TRIB3-cas9-RNAPII_ChIPSeq

value: Rpb1 CTD (4H8) (Cell Signaling Technology, #2630)


title: Pacbio-SW837

city: Bethesda

first: Andre

last: Nussenzweig

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

data_processing: Data was aligned to hg19 human reference genome

growth_protocol: Cell lines containing doxycycline-inducible shWRN cassette (KM12, HCT116, SW837, RPE-1) were generated as previously described 3. Cell lines were grown in medium supplemented with 10% fetal bovine serum (FBS), penicillin (100 µg/mL) / streptomycin (100 µg/mL), and L- glutamine (Gibco, 292 µg/mL) unless stated otherwise.

extract_protocol: Pacbio CLR (Continuous Long Reads)

tag: cell line

tag: genotype/variation

value: DOX inducible shWRN


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F7_ad008


title: Parthenolide_Dose3_Rep2


title: Ip-ad-c-myc-k427r_ChIPSeq

tag: morphology

tag: chip antibody


title: Pacbio-SW620


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F6_ad001

tag: brain region

tag: Sex


title: Dabrafenib_Dose3_Rep2


title: DMSOPlate6WellF3_Dose3_Rep2


title: Ip-c-RNAPII_ChIPSeq


title: Pacbio-HCT116


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F6_ad010

tag: age

tag: strain


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F6_ad007


title: Pacbio-KM12


title: DMSOPlate6WellC3_Dose3_Rep2


title: 26118: ICRH76

value: pancreas

tag: celltype

value: pancreatic islets

tag: agecategory

value: toddler

value: control

value: Toddler


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F6_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F6_ad004


title: Anastrozole_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F6_ad002


title: P7 Liver Hmgcs2 KO4

city: Kumamoto-City

first: Yuichiro

last: Arima

address: 1-1-1 Honjo

institute: Kumamoto University

data_processing:
Resulting reads were aligned to the UCSC hg19 reference genome using TopHat.
Normalization, differential analysis, and gene ontology analysis was performed using Strand NGS (Strand Genomics).
Supplementary_files_format_and_content: summarized data of transcript expression

source_name: liver tissue

extract_protocol:
Total RNA from HEL cells was extracted using RNeasy Mini Kit (Qiagen). mRNA was purified using NEB Next Poly (A) mRNA Magnetic Isolation Module (NEB).
cDNA library for sequencing was synthesized using NEB Next Ultra DNA Library Prep Kit for Illumina (NEB) and was sequenced on NextSeq 500 sequencer (Illumina) with 75-bps single-end reads.

value: KO


title: P7 Liver Hmgcs2 KO3


title: Abiraterone_Dose3_Rep2


title: MK0752_Dose3_Rep2


title: P7 Liver Hmgcs2 KO2


title: P7 Liver Hmgcs2 KO1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F5_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F5_ad007


title: P7 Liver Hmgcs2 WT4

value: WT


title: Blebbistatin_Dose3_Rep2


title: NVPAUY922_Dose3_Rep2


title: Alisertib_Dose3_Rep2


title: Erlotinib_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F6_ad012

value: ACA,PL,ILA


title: P7 Liver Hmgcs2 WT3


title: Nelarabine_Dose3_Rep2


title: P7 Liver Hmgcs2 WT2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F5_ad010

value: male


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F5_ad006


title: Regorafenib_Dose3_Rep2

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: P7 Liver Hmgcs2 WT1


title: Mitoxantrone_Dose3_Rep2


title: TIL Tconv_3

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

data_processing:
Sequencing reads were trimmed for adapters using Cutadapt41 prior to being aligned to Mus musculus reference genome (mm10) using the RNA-seq aligner HISAT2.
Subread’s featureCounts function was used for gene level quantification and results were normalized to Transcripts Per Kilobase Million (TPM)
Using the raw quantification, differential genes were found with the R package DESeq2 and statistical cutoffs of q-value <0.05 and log2foldchange|>1.5.
Genome_build: mm10
Supplementary_files_format_and_content: TPMs, csv

source_name: Tconv cells (CD4+Foxp3-)

extract_protocol:
Immediately after sorting cDNA was generated using SMART-seq HT kit (Cat # 634456 Clontech) using 1000 cells. cDNA product was checked by Tape Station D5000 from Agilent technologies 2200 to make sure cDNA was successfully generated
Library construction was done using Nextrera XT kit # 15031942 from Illumina. 1ng cDNA was used in total volume 5ul. Sequencing was done using NextSeq 500 System. High Output 75 Cycles kit with run Parameter Paired Read 150 cycles (2X75).

treatment_protocol: Lymphocytes from a Foxp3 reporter mouse were pulsed with 2NBDG for 20 minutes at 37 C and stained with viablity dye and anti-CD4 antibody. 1000 low glucose and high glucose consuming Treg cells (CD4+ Foxp3+) were sorted directly into lysis buffer in a 96-well plate.

value: Treg cell

tag: 2nbdg subset

value: Bulk


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F5_ad002


title: TIL Tconv_2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F5_ad008


title: RITA_Dose3_Rep2


title: Cimetidine_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F6_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F4_ad012


title: TIL Glucose High_6

source_name: 2NBDG High Treg cells


title: Cediranib_Dose3_Rep2


title: Exemestane_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F4_ad006


title: Thalidomide_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F4_ad010


title: TIL Glucose High_3


title: PHA793887_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F5_ad004


title: TIL Glucose High_1


title: Temozolomide_Dose3_Rep2


title: Tacrolimus_Dose3_Rep2


title: TIL Glucose High_2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F4_ad008


title: TIL Glucose Low_6

source_name: 2NBDG low Treg cells


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F4_ad004


title: TIL Tconv_1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F4_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F3_ad012


title: TIL Glucose Low_4


title: Bendamustine_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F3_ad001


title: TIL Glucose Low_5


title: Tivozanib_Dose3_Rep1


title: TIL Glucose Low_3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F3_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F4_ad007


title: Brivanib_Dose3_Rep1


title: TIL Glucose Low_2


title: Dexamethasone_Dose3_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F3_ad010


title: Dasatinib_Dose3_Rep1


title: Sildenafil_Dose3_Rep1


title: TIL Glucose Low_1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F3_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F3_ad004


title: Everolimus_Dose3_Rep1


title: LN Tconv_3

value: Tconv cells (CD4+Foxp3-)


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F3_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F2_ad001


title: Pazopanib_Dose3_Rep1


title: LN Tconv_1


title: BrefeldinA_Dose3_Rep1


title: Topotecan_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F2_ad012


title: LN Glucose High_6


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F2_ad007


title: PYR41_Dose3_Rep1


title: LN Glucose High_4


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F2_ad010


title: TIL Glucose High_5


title: LN Glucose High_5


title: Rigosertib_Dose3_Rep1


title: LN Glucose High_3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F2_ad006


title: Ornidazole_Dose3_Rep1


title: Saracatinib_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F2_ad004


title: LN Glucose High_2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F2_ad002


title: Chlorambucil_Dose3_Rep1


title: LN Glucose High_1


title: LN Tconv_2


title: Gemcitabine_Dose3_Rep1


title: LN Glucose Low_6


title: Ciclopirox_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F2_ad008


title: Lovastatin_Dose3_Rep1


title: LN Glucose Low_5


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F12_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F12_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F12_ad008


title: RG108_Dose3_Rep1


title: TIL Glucose High_4


title: KU55933_Dose3_Rep1


title: DMSOPlate5WellF10_Dose3_Rep1


title: LN Glucose Low_2


title: LN Glucose Low_1


title: LN Glucose Low_3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F12_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F12_ad002


title: Striatum WT adult male rep3

city: Los Angeles

first: Xinzhu

last: Yu

address: 10833 Le Conte Ave, CHS 53-359

institute: University of California Los Angeles

description:
Striatal single cells from WT rep3
mRNA
scRNA-seq-Str_WT_2m.h5ad

data_processing:
Align to mouse genome (mm10) and count reads using CellRanger-3.0.
Count reads were filtered with Scanpy package.
PCA was performed using Arpack wrapper function.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: scRNA-seq-Str_WT_2m.h5ad: h5ad file with matrix of genes and read counts as well as parameters used for downstream analysis.

source_name: Striatum

extract_protocol:
Striatum was sectioned and dissected out in ice-cold ACSF. Tissue was digested with pronase and triturated into single cells. Dissociated cells were filtered and processed with debris removal kit from Miltenyi Biotec. 10X Genomics platform was used for scRNA-seq.
Libraries prepared using the Illumina Kit and sequenced on an Illumina NextSeq500 sequencer.

tag: genotype

value: Male

value: 8-9 weeks

tag: tissue

value: Striatum


title: Striatum WT adult male rep2

description:
Striatal single cells from WT rep2
mRNA
scRNA-seq-Str_WT_2m.h5ad


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F12_ad004


title: Striatum WT adult male rep1

description:
Striatal single cells from WT rep1
mRNA
scRNA-seq-Str_WT_2m.h5ad


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F12_ad001


title: DimethylFumarate_Dose3_Rep1

tag: cell lines

tag: sgrnas


title: Nitroxoline_Dose3_Rep1

tag: compound treatment


title: DMSOPlate5WellC10_Dose3_Rep1


title: Lapatinib_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F11_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F11_ad012


title: Selumetinib_Dose3_Rep1


title: LN Glucose Low_4

tag: cell type


title: Tivantinib_Dose3_Rep1


title: CD178

city: Birmingham

first: Jennifer

middle: L

last: Larson-Casey

state: AL

address: 1918 University Blvd 710 MCLM

institute: University of Alabama at Birmingham

data_processing:
Basecallig was performed using Illumina bcl2fastq version 2.18.0.12
Raw sequences were trimmed using Trim Galore version 0.6.2 with parameters --paired; --trim1; --nextseq 20; --trim-n
Trimmed sequences were aligned using STAR version 2.7.1a with parameters --outReadsUnmapped Fastx; --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using HTSeq-count version 0.11.2 with parameters -r pos; -t exon; -I gene_id; -a 10; -s no; -f bam
Genome_build: Gencode GRCm38 p4 Release M11
Supplementary_files_format_and_content: tab-delimited Excel file containing raw counts for each gene in each sample

source_name: BAL cells

extract_protocol:
BAL was performed. Fluid and cells were centrifuged. Cells were removed, frozen, and RNA was harvested using TriReagen. Qiagen Rneasy Plus Kit (Cat#74134) was used.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: 8-12 weeks


title: CD176


title: CD177


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F11_ad008

source_name: C57BL/6J Male P56 Mouse Brain


title: CD174


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F11_ad007


title: CD171


title: BardoxoloneMethyl_Dose3_Rep1

source_name: Pool of 5 breast cancer cell lines


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F11_ad006


title: RacRotigotine_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F11_ad004


title: CD170


title: Vincristine_Dose3_Rep1


title: mESCs_M5_KO_3_N2B27_D6

city: Guangzhou

first: shuibin

last: lin

state: Guangdong

address: Nonglin street

department: Center for Translational Medicine

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
SOAPnuke software used for filtering.
Sequenced reads mapped to mm10 whole genome using Bowtie2 to obtain the alignment results. Then RSEM was used to calculate gene and transcript expression levels.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each sample

source_name: Embryonic stem cells

growth_protocol: 105 cells were seeded in 100 mm tissue culture dishes of the Mettl5 knockout and wildtype mESCs

extract_protocol:
ESCs were collected and RNA was harvested using Trizol reagent.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces and then cDNA was generated using random hexamer-primed reverse transcription and amplified by PCR for construction of sequencing libraries.

treatment_protocol: For spontaneous differentiation of mESCs, the cell culture dishes were coated with Poly (2-hydroxyethyl methacrylate) to prevent cell attachment. Then 5 × 106 mESCs were cultured with LIF (-) medium in the Poly 2-pre-coated dishes to induce embryoid body formation for 6 days. To induce the neural lineage differentiation of mESCs, 5 × 105 mESCs were cultured in N2B27 medium for 6 days.

value: Embryonic stem cells

tag: treatment

value: cultured in N2B27 medium for 6 days


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F11_ad002


title: Crizotinib_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F11_ad001


title: Paclitaxel_Dose3_Rep1


title: Carfilzomib_Dose3_Rep1


title: Trifluoperazine_Dose3_Rep1


title: mESCs_WT_N2B27_D6

value: wild type


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F10_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F10_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F10_ad008


title: mESCs_Ctr_N2B27_D6


title: Cyclophosphamide_Dose3_Rep1


title: mESCs_M5_KO_3_EB_D6

value: cultured with LIF (-) medium in the Poly 2-hydroxyethyl methacrylate-pre-coated dishes for 6 days


title: STF31_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F10_ad007


title: Simvastatin_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F10_ad004


title: mESCs_M5_KO_2_EB_D6


title: mESCs_WT_EB_D6


title: mESCs_M5_KO_1_EB_D6


title: Etoposide_Dose3_Rep1


title: mESCs_Ctr_EB_D6


title: mESCs_M5_KO_2_N2B27_D6


title: mESCs_M5_KO_1_N2B27_D6


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F10_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F1_ad012


title: mESCs_M5_KO_3_D0

value: untreated


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F10_ad001


title: Mebendazole_Dose3_Rep1


title: PD318088_Dose3_Rep1


title: mESCs_M5_KO_2_D0


title: mESCs_M5_KO_1_D0


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F1_ad007


title: WP1130_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F1_ad010


title: mESCs_WT_D0


title: KX2391_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F10_ad006


title: FiveFluorouracil_Dose3_Rep1


title: Trametinib_Dose3_Rep1


title: mESCs_Ctr_D0


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F1_ad004


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F1_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F12_ad006


title: Doxorubicin_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_F1_ad006


title: Letrozole_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E9_ad006


title: Sitagliptin_Dose3_Rep1


title: Cisplatin_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E9_ad002


title: WT_RPF_2

city: Boston

first: Qi

last: Liu

state: MASSACHUSETTS

address: Boston, 02115.USA

institute: Boston Children's Hospital

description:
OE_RPF_2
MEF_Wt_METTL1_WDR4_TE_list.xlsx

data_processing:
Library strategy: Ribo-Seq
After adapter-trimming and quality-filtering, the sequences were further filtered to exclude rRNA and tRNA reads by aligning to mouse rRNA and tRNA sequence which were retrieved from Ensembl (Release 91) (https://useast.ensembl.org/Mus_musculus/Info/Index) and GtRNAdb databases , respectively. The cleaned ribosome-protected fragments (RPFs) were aligned to the mouse gene models (GENCODE, mm10) using Bowtie with a maximum one mismatch allowed .The translation efficiency (TE) was calculated by dividing RPF abundancy on CDS by its mRNA abundancy. We used 2 fold change of TE to define the differential translation genes.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx

source_name: MEF Wt

growth_protocol: MEF-WT cell line with SV40 T antigen stably transduced with either empty vector (EV) or wild type METTL1 and WDR4 were grown to 80-90% confluence in DMEM supplemented with 10% FBS in 15-cm dishes.

extract_protocol:
Cells were treated by cyclohexamide to pause translation and lyzed in Mammalian Polysome Buffer (Illumina). Input mRNAs and RPFs were isolated, ribosomal RNAs were depleted and cDNA libraries were prepared according to the TruSeq Ribo Profile pipeline (Illumina)
TruSeq Ribo Profile pipeline (Illumina)

treatment_protocol: We generated stable clones that overexpress METTL1 and WDR4, both components of the methyltransferase complex or empty vector control cells. pBabe vectors containing the wild-type METTL1 (METTL1-Wt) and WDR4 were used for transduction. MEF-WT cells overexpressing METTL1-Wt+WDR4 or empty vector were maintained in medium supplemented with puromycin (2.5ug/mL) and G418 (400 ug/mL). No antibiotic was used during cell expansion and cell lysate preparation.

value: MEF expressing SV40 T

tag: sample type

value: RPF


title: WT_RPF_1

description:
OE_RPF_1
MEF_Wt_METTL1_WDR4_TE_list.xlsx


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E9_ad008

value: ACA,PL,ILA


title: Zebularine_Dose3_Rep1


title: EV_RPF_1

description:
Control_RPF_1
MEF_Wt_METTL1_WDR4_TE_list.xlsx

value: empty vector


title: Ruxolitinib_Dose3_Rep1

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: DMSOPlate5WellF6_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E9_ad004

value: male


title: Tigecycline_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E8_ad012


title: WT_input_1

description:
OE_input_1
MEF_Wt_METTL1_WDR4_TE_list.xlsx

value: Input


title: Bexarotene_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E8_ad007


title: SR1001_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E8_ad006


title: Nilotinib_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E8_ad010


title: DMSOPlate5WellC6_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E9_ad012


title: Decitabine_Dose3_Rep1


title: EV_input_2

description:
Control_input_2
MEF_Wt_METTL1_WDR4_TE_list.xlsx


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E9_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E8_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E8_ad004


title: MEF Wt METTL1-Mut2 cleaved

description:
METTL1 Mutant +WDR4
MEF_Wt_METTL1_WDR4_Trac-Seq.xlsx

data_processing:
Library strategy: Trac-Seq
Adapter sequences were trimmed and low quality sequences (Q20) were discarded using trim_galore. For tRNA chemical sequencing data, clean reads were mapped to the mature tRNA sequences downloaded from GtRNAdb using Bowtie with a maximum of two mismatches allowed. The alignments were then processed to record the read depth of each site on tRNAs using Bedtools. Based on tRNA mapping bam files and read depth information, cleavage score and cleavage score ratio between input and chemically-treated sample using the program cleavage_score.R (https://github.com/rnabioinfor/TRAC-Seq). Based on 21 bp sequences around m7G sites, the enriched motifs were analyzed by MEME with a maximum 7bp width. To conduct tRNA expression analysis for Input samples, we used the programs ARM-Seq data analysis pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx

extract_protocol:
m7G TRAC-Seq, meRIP was performed as previously described (Lin et al., 2018). First, isolated small RNAs were first treated with recombinant wild-type and D135S AlkB proteins to remove the dominant methylations on RNA. Briefly, 10ug small RNAs were treated with 80 pmol wt AlkB and 160 pmol D135S AlkB mutant for 2 hours. AlkB treated RNA was precipitated with ethanol and resuspended. Input samples followed library preparation. For m7G cleaveage, AlkB treated RNA was then treated with 0.1M NaBH4 for 30 min on ice at dark in the presence of 1 mM free m7GTP as methylation carrier. After ethanol precipitation, the NaBH4-treated RNAs were subsequently treated with aniline-acetate solution (H2O: glacial acetate acid:aniline, 7:3:1) at room temperature at dark for 2 hours to induce the site specific cleavage. Purified RNA samples were then used for cDNA library construction using NEBNext Small RNA Library Prep Set (New England Biolabs) followed by sequencing with Illumina Nextseq 500.
NEBNext Small RNA Library Prep Set (New England Biolabs)

value: METTL1-Mut +WDR4

value: Cleaved AlK-B - NaBH4


title: Dacarbazine_Dose3_Rep1


title: VER155008_Dose3_Rep1


title: EV_input_1

description:
Control_input_1
MEF_Wt_METTL1_WDR4_TE_list.xlsx


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E8_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E7_ad012


title: PIK93_Dose3_Rep1


title: MEF Wt METTL1-WT1 cleaved

description:
METTL1 Wild type +WDR4
MEF_Wt_METTL1_WDR4_Trac-Seq.xlsx

value: METTL1-Wt +WDR4


title: Sorafenib_Dose3_Rep1


title: MEF Wt METTL1-WT2 cleaved

description:
METTL1 Wild type +WDR5
MEF_Wt_METTL1_WDR4_Trac-Seq.xlsx


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E7_ad001


title: MEF Wt Empty Vector 1 cleaved

description:
Empty vector control
MEF_Wt_METTL1_WDR4_Trac-Seq.xlsx

value: Empty vector Control


title: Fingolimod_Dose3_Rep1


title: Valdecoxib_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E7_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E7_ad006


title: Lenvatinib_Dose3_Rep1


title: MEF Wt METTL1-Mut1 cleaved


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E7_ad002


title: MEF Wt METTL1-WT1 input

value: Input AlKB - Only


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E7_ad008


title: CHIR99021_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E7_ad004


title: MEF Wt METTL1-WT2 input


title: MEF Wt Empty Vector 2 input


title: Linsitinib_Dose3_Rep1


title: Clofarabine_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E7_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E6_ad001


title: MNP Hand2 rep2

city: Cincinnati

first: Samantha

last: Brugmann

state: OH

address: Department of Developmental Biology, DK 1 BLDG R, 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

description: Hand2 MNP Shared Reps BED

data_processing:
1X75bp reads were generated on a NextSeq instrument (Illumina)
The resulting reads were mapped to mouse genome assembly mm10 (GRCm38/mm10) using bwa (Li and Durbin 2009).
Pooled replicates were used to identify potential regulatory regions
A final set of peak calls for each factor to use for motif enrichment was determined using bedtools (Quinlan and Hall 2010) to merge biological replicates and identify peaks shared between replicates
ChIP-seq peak overlap significance was calculated using the RELI software package (https://github.com/WeirauchLab/RELI) (Harley et al. 2018).
TF binding site motif enrichment analyses were performed using the HOMER software package (Heinz et al. 2010) modified to use a log 2-based scoring system and contain mouse motifs obtained from the Cis-BP database, build 1.94d (Weirauch et al. 2014).
Genome_build: mm10
Supplementary_files_format_and_content: BED files containing final peak calls

source_name: mandibular prominence

growth_protocol: Timed matings were recorded and embryonic day 0.5 was counted to be noon of the day on which a copulation plug was discovered.

extract_protocol:
Individual ChIP-seq experiments were carried out on pooled embryonic tissue collected in ice-cold PBS. Dissected tissues were immediately fixed in 1% formaldehyde/PBS for 20 minutes at room temp followed by glycine quench (125 mM). ChIP procedures were performed as previously described (Peterson et al. 2012 and Osterwalder et al. 2014).  All ChIP experiments were performed using mouse monoclonal anti-FLAG M2 antibody (Sigma-Aldrich).
RNA libraries were prepared for sequencing using standard Illumina sequencing protocols
ChIP-seq libraries were prepared according to manufacturers’ instructions and 1X75bp reads were generated on a NextSeq instrument (Illumina).

value: mandibular prominence

value: embryonic day 11.5

value: Hand2 3XFlagbio


title: MEF Wt METTL1-Mut2 input


title: Fluvastatin_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E6_ad010

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E6_ad012


title: MNP Hand2 rep1

description: Hand2 MNP Shared Reps BED


title: Ki8751_Dose3_Rep1

data_processing:
Library strategy: QMAP-Seq
Individual samples were demultiplexed based on i5 and i7 index sequences by running bcl2fastq Conversion Software (Illumina).
Data was processed using QMAP-Seq bioinformatic analysis pipeline (https://github.com/mendillolab/QMAP-Seq). Briefly, sgRNA and cell line barcode sequences were extracted from Read 1 sequences as follows: [ACACCG][sgRNA:20][Interval:102][CellLineBarcode:8]. The number of reads for each cell line-sgRNA pair was counted, allowing up to one nucleotide mismatch per barcode. Cell number was interpolated from sequencing reads using sample-specific standard curves. The number of cells for a compound-treated sample was normalized to the median number of cells for the DMSO-treated samples.
Data was filtered using the following exclusion criteria. First, samples with low read counts were excluded. Second, cell line-sgRNA pairs with high variation (standard deviation of log2(cell number) > 0.7) were excluded. Third, compounds with an AUC > 550 for any cell line-sgRNA pair were excluded. Fourth, noncytotoxic cell line-compound pairs (relative cell number of sgNT with highest dose ≥ 90%) were excluded. Fifth, cell line-compound pairs without a dose-dependent reduction in cell viability (difference in relative cell number of sgNT between lowest and highest dose < 25%) were excluded.
Genome_build: N/A (sgRNA library sequencing)
Supplementary_files_format_and_content: Plain text document (.txt) files with read counts for each cell line-sgRNA pair. Individual files for each sample.
Supplementary_files_format_and_content: Comma-separated values (.csv) file with relative cell numbers (i.e., cell number (%DMSO)) for each cell line-sgRNA-compound-dose-replicate combination. Matrix table with data for all samples.

extract_protocol:
Cell line pools were lysed with lysis buffer (10% 10x Taq DNA Polymerase Buffer, 0.45% IGEPAL CA-630, 0.45% TWEEN 20, 10% Proteinase K, 79.1% Nuclease-Free Water) containing cell spike-in standards. Cells were incubated at 60°C for 1 hour. Proteinase K from lysis buffer was inactivated at 95°C for 15 minutes.
Barcoded region was PCR amplified with a unique set of indexed primers for each sample. PCR products were pooled and purified twice. Sequencing library was diluted, combined with PhiX, denatured, and sequenced on a NovaSeq 6000 (Illumina).


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E6_ad004


title: MEF Wt METTL1-Mut1 input


title: PLX4720_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E6_ad002


title: MNP Gli3 rep2

description: Gli3 MNP Shared Reps BED

value: Gli3 3XFlagbio


title: Niclosamide_Dose3_Rep1


title: MNP Gli3 rep1

description: Gli3 MNP Shared Reps BED


title: Whole Face Gli3 rep2

description: Gli3 Whole Face Shared Reps BED

source_name: whole face

value: whole face


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E5_ad012


title: Fulvestrant_Dose3_Rep1


title: Cabozantinib_Dose3_Rep1


title: Gefitinib_Dose3_Rep1


title: Parthenolide_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E5_ad010


title: Dabrafenib_Dose3_Rep1


title: 26020: HP-15085-01T2D

value: pancreas

value: pancreatic islets

value: adult

tag: healthcategory

tag: combinedcategory

value: alpha


title: DMSOPlate5WellC3_Dose3_Rep1

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: EMC_chem_DZNep_3

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

data_processing:
Illumina Bcl2fastq v2.18
Reads were aligned to mm9 using STAR
For rpkm calculation cufflinks was used.
Genome_build: mm9
Supplementary_files_format_and_content: csv file of log2 RPKM table

source_name: Prostate

growth_protocol: All mouse prostate cancer organoids were cultured in standard organoid growth medium + 10nM R1881

extract_protocol:
Total RNA was extracted using standard TRiZOL methods
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol

treatment_protocol: Mouse prostate cancer organoids were treated with controls (DMSO or EtOH) or 1uM DZNep or 1uM Tamoxifen.

value: Prostate dorsal-lateral lobe

value: post natal 8 weeks


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E5_ad002

first: Joseph

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

tag: brain region

value: ACA,PL,ILA

value: male


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E5_ad004

tag: Sex


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E5_ad006

tag: age


title: Whole Face Gli3 rep1

description: Gli3 Whole Face Shared Reps BED

tag: strain


title: EMC_gen_Tam_1


title: EMC_chem_DZNep_2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E4_ad001


title: EMC_gen_EtOH_2


title: Blebbistatin_Dose3_Rep1

first: Sonia

address: 303 E Superior St, SQBRC 7-500

institute: Northwestern University


title: EMC_gen_EtOH_1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E4_ad010


title: WT_input_2

description:
OE_input_2
MEF_Wt_METTL1_WDR4_TE_list.xlsx

value: MEF expressing SV40 T

value: Input


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E4_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E5_ad007


title: Erlotinib_Dose3_Rep1


title: MK0752_Dose3_Rep1


title: EMC_chem_DZNep_1


title: Alisertib_Dose3_Rep1


title: EMC_chem_DMSO_1


title: Abiraterone_Dose3_Rep1


title: Exemestane_Dose3_Rep1


title: Anastrozole_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E4_ad007


title: tumor_ko_rep2

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

data_processing:
Fastq files were generated using Illuminas base calling software GenerateFASTQ v1.1.0.64 and overall sequencing quality was analyzed using the FastQC script.
For RNA-seq, reads were aligned to the mouse genome (mm10) using Tophat v2.1.1 (Kim et al., 2013) and Bowtie2 v2.3.2 (Langmead et al., 2012) using the parameters  –n 1 -- and samples were normalized to the number of mapped reads in the smallest sample.
For gene expression analysis, reads per gene (Ensembl gene database) were counted with the “summarizeOverlaps” function from the R package “GenomicAlignments” using the “union”-mode and non- or weakly expressed genes were removed (mean read count over all samples <1).
Genome_build: mm10
Supplementary_files_format_and_content: Differential Expression log2FC values matrix containing all samples.

source_name: melanoma

growth_protocol: 781 cells were grown in DMEM (PAN). All media were supplemented with 10% FBS (PAN) and 1% penicillin/streptomycin (Sigma).

extract_protocol:
Tumors were resected and RNA extraction was performed with the RNeasy Mini Kit (Qiagen) according to manufacturer’s instruction and using in-column DNase digestion. The NEBNextPoly(A) mRNA Magnetic Isolation Module (NEB) was used according to manufacturer's protocol to purify Poly-A+ RNA from total RNA.
RNA extraction was performed with the RNeasy Mini Kit (Qiagen) according to manufacturer’s instruction and using in-column DNase digestion. The NEBNextPoly(A) mRNA Magnetic Isolation Module (NEB) was used according to manufacturer's protocol to purify Poly-A+ RNA from total RNA.
RNA quality was assessed employing a Fragment Analyzer (Agilent) and cDNA libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions.

tag: cell line

value: tumor of 781

tag: genotype/variation

value: Nfe2l2 knockout


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E4_ad008

city: La Jolla

last: Ecker


title: EMC_chem_DMSO_3


title: Nelarabine_Dose3_Rep1

city: Chicago

last: Brockway


title: EMC_chem_DMSO_2


title: EMC_gen_Tam_2


title: tumor_ko_rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E5_ad008


title: Regorafenib_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E3_ad012


title: tumor_wt_rep3

value: Nfe2l2 wildtype


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E3_ad001


title: Mitoxantrone_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E4_ad004


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E4_ad006


title: NVPAUY922_Dose3_Rep1


title: Cimetidine_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E3_ad010


title: tumor_ko_rep3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E3_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E3_ad007


title: RITA_Dose3_Rep1


title: MEF Wt Empty Vector 1 input

value: Empty vector Control

value: Input AlKB - Only


title: tumor_wt_rep1


title: PHA793887_Dose3_Rep1


title: Temozolomide_Dose3_Rep1


title: Thalidomide_Dose3_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E3_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E4_ad002


title: invitro_ko_rep3

extract_protocol:
Cell pellets were harvested and RNA extraction was performed with the RNeasy Mini Kit (Qiagen) according to manufacturer’s instruction and using in-column DNase digestion. The NEBNextPoly(A) mRNA Magnetic Isolation Module (NEB) was used according to manufacturer's protocol to purify Poly-A+ RNA from total RNA.
RNA extraction was performed with the RNeasy Mini Kit (Qiagen) according to manufacturer’s instruction and using in-column DNase digestion. The NEBNextPoly(A) mRNA Magnetic Isolation Module (NEB) was used according to manufacturer's protocol to purify Poly-A+ RNA from total RNA.
RNA quality was assessed employing a Fragment Analyzer (Agilent) and cDNA libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions.


title: invitro_wt_rep1


title: invitro_wt_rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E2_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E2_ad001


title: Tacrolimus_Dose3_Rep1


title: Cediranib_Dose3_Rep1


title: invitro_ko_rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E2_ad007


title: invitro_wt_rep3


title: tumor_wt_rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E3_ad004


title: Dexamethasone_Dose3_Rep1


title: Bendamustine_Dose3_Rep1


title: BrefeldinA_Dose2_Rep2


title: invitro_ko_rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E3_ad008


title: Tivozanib_Dose2_Rep2


title: Donor5_6_TRA_Th2

city: Moscow

first: Sofya

middle: A.

last: Kasatskaya

address: Bolshoy Boulevard 30, bld. 1

department: Life Sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
Illumina software was used for barcode identification and sample demultiplexing.
Sequenced reads were processed with MiGEC software v.1.2.9 for Unique Molecular Identifiers (UMI) extraction with MiGEC Checkout and Assemble utilities.
Reads assembled in UMI groups were aligned and errors were corrected with MIXCR software v.2.1.1 using built-in reference library.
VDJtools v.1.2.1 Convert utility was used to convert processed txt files to widey used vdjtools format of cloneset tables.
Supplementary_files_format_and_content: tab-delimited text files for each Sample present cloneset tables in standart VDJtools format

source_name: memory Th subsets sorted from PBMC

extract_protocol:
T cell subsets were FACS sorted from fresh PBMC samples from 5 healthy donors. Effector/memory functional subsets were sorted at >98% purity into RLT  537 buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich).  after exclusion of naive CCR7+CD45RA+ were sorted in lysis buffer
TCRα and TCRβ cDNA libraries were 569 prepared using a Human TCR Kit (MiLaboratory LLC)  with template switch-based incorporation of UMIs.
OTHER: target RNA-seq (RACE)

tag: subset

tag: tcr chain

value: TCR alpha

tag: donor

value: Donor 5


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E2_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E2_ad006


title: Donor5_4_TRA_Th2a


title: Donor5_8_TRA_Th1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E2_ad002


title: Donor5_3_TRA_Th1-17


title: Donor5_1_TRA_Tfh

value: Tfh


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E2_ad004


title: Donor5_5_TRA_Th17


title: Brivanib_Dose2_Rep2

tag: cell lines


title: Donor5_7_TRA_Th22


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E12_ad012


title: Dasatinib_Dose2_Rep2

tag: sgrnas


title: Sildenafil_Dose2_Rep2

tag: compound treatment


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E2_ad008


title: DMSOPlate5WellF3_Dose3_Rep1


title: Topotecan_Dose2_Rep2


title: Donor5_2_TRA_TREG

value: Treg


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E12_ad010


title: Everolimus_Dose2_Rep2


title: Donor4_6_TRA_Th2

value: Donor 4


title: Donor4_7_TRA_Th22


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E12_ad007


title: Donor4_5_TRA_Th17


title: Rigosertib_Dose2_Rep2

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: Donor4_5_2_TRA_Th17


title: Donor4_8_TRA_Th1


title: Pazopanib_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E11_ad010


title: Donor4_2_TRA_TREG


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E11_ad007


title: RG108_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E12_ad008


title: Saracatinib_Dose2_Rep2


title: Donor4_1_TRA_Tfh


title: EV_RPF_2

description:
Control_RPF_2
MEF_Wt_METTL1_WDR4_TE_list.xlsx

tag: cell type

tag: genotype

value: empty vector

value: RPF


title: PYR41_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E10_ad012

value: ACA,PL,ILA


title: Donor3_8_TRA_Th1

value: Donor 3


title: DMSOPlate4WellF10_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E12_ad006

value: male


title: Ciclopirox_Dose2_Rep2


title: Gemcitabine_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E12_ad002


title: Ornidazole_Dose2_Rep2


title: Donor4_4_TRA_Th2a


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E10_ad010


title: Chlorambucil_Dose2_Rep2


title: Donor3_6_TRA_Th2


title: Donor4_3_TRA_Th1-17


title: Donor4_3_2_TRA_Th1-17


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E11_ad008


title: Lovastatin_Dose2_Rep2


title: Donor3_5_TRA_Th17


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E11_ad006


title: Donor4_2_2_TRA_TREG


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E11_ad004


title: DimethylFumarate_Dose2_Rep2


title: KU55933_Dose2_Rep2


title: Donor3_2_TRA_TREG


title: Selumetinib_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E11_ad002


title: Donor3_7_TRA_Th22


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E11_ad012


title: Paclitaxel_Dose2_Rep2


title: Nitroxoline_Dose2_Rep2


title: Donor2_8_TRA_Th1

value: Donor 2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E10_ad008


title: DMSOPlate4WellC10_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E1_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E10_ad007


title: RacRotigotine_Dose2_Rep2


title: Donor3_4_TRA_Th2a


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E10_ad006


title: Donor3_3_TRA_Th1-17


title: Lapatinib_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E10_ad002


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E10_ad004


title: Donor3_1_TRA_Tfh


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E1_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E1_ad012


title: BardoxoloneMethyl_Dose2_Rep2


title: Donor2_3_TRA_Th1-17


title: Carfilzomib_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E1_ad002


title: Donor2_7_TRA_Th22


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E1_ad008


title: Donor2_6_TRA_Th2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D9_ad012


title: STF31_Dose2_Rep2


title: Vincristine_Dose2_Rep2


title: Donor2_5_TRA_Th17


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E1_ad010


title: Crizotinib_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D9_ad001


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D9_ad010


title: Donor1_6_TRA_Th2

value: Donor 1


title: Donor2_4_TRA_Th2a


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D9_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E1_ad004


title: Trifluoperazine_Dose2_Rep2


title: Cyclophosphamide_Dose2_Rep2


title: Donor2_2_TRA_TREG


title: Donor1_7_TRA_Th22


title: Donor2_1_TRA_Tfh


title: Simvastatin_Dose2_Rep2


title: FiveFluorouracil_Dose2_Rep2


title: Donor1_8_TRA_Th1


title: WP1130_Dose2_Rep2


title: Donor1_3_TRA_Th1-17


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D8_ad012


title: Mebendazole_Dose2_Rep2


title: Donor1_5_TRA_Th17


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D8_ad001


title: PD318088_Dose2_Rep2


title: Etoposide_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D8_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D9_ad002


title: Letrozole_Dose2_Rep2


title: Donor1_1_TRA_Tfh


title: Trametinib_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D9_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D8_ad010


title: Doxorubicin_Dose2_Rep2


title: Donor1_2_TRA_TREG


title: KX2391_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D8_ad006


title: Sitagliptin_Dose2_Rep2


title: RNA seq of human ki3

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

data_processing:
Sequenced reads were mapped to the human reference genome sequences (hg19) using STAR.
The aligned reads were quantitated by Htseq
The normalization and differentially expressed genes test were implemented by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene normalized counts for every gene and every sample

source_name: hPSCs with inducible exogenous SMARCB1

extract_protocol:
Total RNA was extracted using a RiboEx Total RNA purification solution (GeneAll)
For library preparation NEBNext RNA ultra II RNA library preparation kit (NEB) was used. All RNA samples underwent PolyA selection following the manufacturers' protocols.

value: human pluripotnet stem cells


title: Donor1_4_TRA_Th2a


title: RNA seq of human ki_dox2

source_name: hPSCs with inducible exogenous SMARCB1treated with (SMARCB1 GOF)


title: RNA seq of human ki2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D8_ad004


title: Ruxolitinib_Dose2_Rep2


title: RNA seq of human ki_dox1


title: RNA seq of human ki1


title: Nilotinib_Dose2_Rep2


title: RNA seq of human ki_dox3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D8_ad002


title: Cisplatin_Dose2_Rep2


title: RNA seq of human kiko_wo_dox3

source_name: SMARCB1 targetd hPSCs  without Doxycycline (SMARCB1 LOF)


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D7_ad012


title: SR1001_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D7_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D7_ad001


title: RNA seq of human kiko_wo_dox2


title: RNA seq of human kiko_wo_dox1


title: DMSOPlate4WellF6_Dose2_Rep2


title: RNA seq of human kiko3

source_name: SMARCB1 targetd hPSCs treated with Doxycycline


title: Bexarotene_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D7_ad006


title: RNA seq of human kiko2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D8_ad008


title: RNA seq of human kiko1


title: Tigecycline_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D7_ad004


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D7_ad002


title: RNA seq of human WT_dox3

source_name: WT hPSCs treated with Doxycycline


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D7_ad008


title: Dacarbazine_Dose2_Rep2


title: Zebularine_Dose2_Rep2


title: Lenvatinib_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D6_ad012


title: RNA seq of human WT_dox2


title: RNA seq of human WT_dox1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D6_ad001


title: RNA seq of human WT2

source_name: WT hPSCs


title: VER155008_Dose2_Rep2


title: PIK93_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D7_ad010


title: RNA seq of human WT3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D6_ad007


title: RNA seq of human WT1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D6_ad010


title: DMSOPlate4WellC6_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D6_ad006


title: Decitabine_Dose2_Rep2


title: Buffy coat cells COVID+ Rep7

city: London

first: David

middle: E

last: Carter

state: ON

address: 1151 Richmond Street North

department: London Regional Genomics Centre

country: Canada

institute: Robarts Research Institute

data_processing:
Base-calling: Illumina BaseSpace: FASTQ generation version 1.0.0
Alignment: Partek Flow: STAR 2.7.3a
Quantify to annotation model: Partek Flow (Partek E/M): hg19 - RefSeq Transcripts 93 - 2020-02-03
Filtering: Partek Flow: Exclude features where maximum (reads) <= 18.0
Normalization: Partek Flow: TMM and Add: 1.0E-4
Remove batch effect: Partek Flow: Status + Date(Remove) + Status*Date(Remove)
GSA: Partek Flow: Model AICc
Genome_build: hg19 - RefSeq Transcripts 93 - 2020-02-03

source_name: Buffy coat cells

extract_protocol:
Trizol LS and RNeasy Micro Plus Kit
Vazyme VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina

value: Leukocytes

tag: disease state

value: COVID19 Positive


title: Buffy coat cells COVID+ Rep6


title: Valdecoxib_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D6_ad004


title: Buffy coat cells COVID- Rep7

value: COVID19 Negative


title: Fingolimod_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D5_ad012


title: Buffy coat cells COVID- Rep6


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D5_ad001


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D5_ad008


title: Linsitinib_Dose2_Rep2


title: Buffy coat cells COVID- Rep5


title: Buffy coat cells COVID+ Rep4


title: Sorafenib_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D4_ad012


title: Buffy coat cells COVID+ Rep5


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D4_ad001


title: Clofarabine_Dose2_Rep2


title: Ki8751_Dose2_Rep2


title: CHIR99021_Dose2_Rep2


title: Buffy coat cells COVID+ Rep3


title: Fluvastatin_Dose2_Rep2


title: PLX4720_Dose2_Rep2


title: Buffy coat cells COVID- Rep3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D4_ad007


title: Buffy coat cells COVID- Rep4


title: Niclosamide_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D6_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D4_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_E1_ad001


title: Fulvestrant_Dose2_Rep2


title: Buffy coat cells COVID+ Rep2


title: Cabozantinib_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D4_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D4_ad002


title: Buffy coat cells COVID+ Rep1


title: ENZ replicate4

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

data_processing:
The quality and number of reads for each sample were assessed with FastQC v0.11.3 (18).
Adaptors were trimmed from reads, and low-quality bases, with Phred scores < 28, were trimmed from ends of reads, using Trimgalore v0.4.4 (19). Trimmed reads of <20 nucleotides were discarded.
Reads passing all quality control steps were aligned to the hg38 assembly of the human genome using TopHat v2.1.1 (20) allowing for up to two mismatches. Reads not uniquely aligned to the genome were discarded.
HTSeq-count v0.6.1 (21) was used with the union model to assign uniquely aligned reads to Ensembl Hg38.86-annotated genes.
Data were normalized across libraries by the trimmed mean of M-values (TMM) normalization method, implemented in the R v3.5.0, using Bioconductor v3.6 EdgeR v3.20.9 package (22). Only genes expressed at count-per-million value greater than 10 in at least 2 samples per group were retained for further analysis. Differential expressed genes were selected based on the robust version of the quasi-likelihood negative binomial generalized log-linear model (23), with false discovery rate (FDR) set at 0.05.
Genome_build: Hg38
Supplementary_files_format_and_content: Text tab delimited filed counting counts per million (cpm) data

source_name: LNCaP

extract_protocol:
Total RNA was extracted using Trizol and miRNAeasy Kit (Qiagen), according to the manufacturer's instructions.
Libraries were generated using 800 ng of RNA and NEXTflex Rapid Illumina Directional RNA-Seq Library Prep Kits
RNA-Seq; Illumina NextSeq 500 (High Output v2) single-end 75 bp reads.

treatment_protocol: LNCaP cells were grown in baseline conditions (media supplemented with 10% FBS). Cells were transfected with siRNAs for 48h or treated with DMSO/Enzalutamide for 24h.

value: LNCaP

tag: agent

value: 1uM Enzalutamide


title: Buffy coat cells COVID- Rep1


title: DMSOPlate4WellF3_Dose2_Rep2


title: Parthenolide_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D3_ad012

source_name: C57BL/6J Male P56 Mouse Brain


title: Gefitinib_Dose2_Rep2

source_name: Pool of 5 breast cancer cell lines


title: ENZ replicate3

growth_protocol: LNCaP cells were grown in baseline conditions (media supplemented with 10% FBS).


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D4_ad004


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D3_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D3_ad001


title: Dabrafenib_Dose2_Rep2


title: Erlotinib_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D3_ad004


title: Buffy coat cells COVID- Rep2


title: ENZ replicate1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D3_ad002


title: DMSO replicate4

value: 0.1percent Vehicle_DMSO


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D3_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D2_ad012


title: DMSO replicate3


title: MK0752_Dose2_Rep2


title: DMSO replicate2


title: Anastrozole_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D2_ad001


title: Tivantinib_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D4_ad008


title: Blebbistatin_Dose2_Rep2


title: DMSO replicate1


title: siAR replicate4

tag: transfection

value: transient transfection (12.5nM Ambion Silencer Select siAR, Cat#:4390825, siRNA ID s1539)


title: siAR replicate3


title: ENZ replicate2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D2_ad007

tag: brain region


title: Exemestane_Dose2_Rep2


title: Alisertib_Dose2_Rep2


title: NVPAUY922_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D2_ad006

tag: Sex


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D2_ad010

tag: age


title: DMSOPlate4WellC3_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D2_ad002

tag: strain


title: siAR replicate1

tag: cell line


title: siAR replicate2


title: Nelarabine_Dose2_Rep2


title: Regorafenib_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D2_ad008


title: siCon_replicate4

value: transient transfection (12.5nM Ambion Silencer Neg Control siRNA#2, Cat#:AM4637)


title: Abiraterone_Dose2_Rep2

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: siCon_replicate3


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D12_ad012


title: siCon_replicate2


title: Mitoxantrone_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D12_ad008


title: Cimetidine_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D12_ad007


title: siCon_replicate1


title: Cediranib_Dose2_Rep2


title: LNZ308_shMETTL1_1_cleaved

description:
shMETTL1 AlkB NaBH4 Cleaved
LNZ308_METTL1_KD_Trac-seq.xlsx

data_processing:
Library strategy: Trac-Seq
Adapter sequences were trimmed and low quality sequences (Q20) were discarded using trim_galore. For tRNA chemical sequencing data, clean reads were mapped to the mature tRNA sequences downloaded from GtRNAdb using Bowtie with a maximum of two mismatches allowed. The alignments were then processed to record the read depth of each site on tRNAs using Bedtools. Based on tRNA mapping bam files and read depth information, cleavage score and cleavage score ratio between input and chemically-treated sample using the program cleavage_score.R (https://github.com/rnabioinfor/TRAC-Seq). Based on 21 bp sequences around m7G sites, the enriched motifs were analyzed by MEME with a maximum 7bp width. To conduct tRNA expression analysis for Input samples, we used the programs ARM-Seq data analysis pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx

growth_protocol: LNZ308 human GBM cells stably transduced with shGFP control or shRNA targeting METTL1 were grown to 80-90% confluence in DMEM supplemented with 10% FBS in 15-cm dishes.

treatment_protocol: We generated METTL1 KD or shGFP stable clones control using RNAi. pLKO.1-shMETTL1 vectors  were used for transduction. LNZ308 METTL1 KD or shGFP control cells were maintained in medium supplemented with puromycin (2.5ug/mL). No antibiotic was used during cell expansion and cell lysate preparation.

tag: sample type

value: Chemical treated


title: PHA793887_Dose2_Rep2


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D11_ad008


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D11_ad010


title: LNZ308_shMETTL1_2_input

description:
shMETTL1 AlkB - Input
LNZ308_METTL1_KD_Trac-seq.xlsx

value: Input


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D12_ad001

value: ACA,PL,ILA


title: Thalidomide_Dose2_Rep2


title: LNZ308_shGFP-2_cleaved

value: shGFP


title: Dexamethasone_Dose2_Rep2


title: Temozolomide_Dose2_Rep2


title: Tacrolimus_Dose2_Rep2


title: LNZ308_shMETTL1_1_input


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D11_ad007

value: male


title: LNZ308_shGFP-2_input

description:
shGFP AlkB - Input
LNZ308_METTL1_KD_Trac-seq.xlsx


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D11_ad002


title: BrefeldinA_Dose2_Rep1


title: LNZ308_shGFP-1_input


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D10_ad012


title: RITA_Dose2_Rep2


title: Calu1 TS Low_rep2

city: PHILADELPHIA

first: Irfan

last: Asangani

state: PA

address: 421 Curie Bld.

department: Cancer Biology

institute: University of Pennsylvania

description: TS Low_rep2

data_processing:
Illumina Nextseq500 reads were trimmed and clipped for quality control in …
Read quality was checked for each sample usign FastQC.
Alignment of reads were performed using STAR aligner with the default setting in Illumina Basespace (https:// basespace.illumina.com/home/indexIllumina)
Aligned reads were assembled using CUFFQUANT and normalized  using CUFFNORM
Differential expression analysis was performed using DESeq2 with DMSO samples for each cellline as the respective control
Genome_build: hg19
Supplementary_files_format_and_content: FPKM and count values for each sample

growth_protocol: A549 (NCI) and Calu1 (ATCC) cells were maintained in RPMI-1640 media (Sigma) supplemented with 10% FBS (Sigma), 1%Pen/Strep (Sigma) and 1%L-Glutamine (Sigma).  Cells were grown at 37°C in a 5% CO 2 incubator.

extract_protocol:
Total RNA was isolated using miRNeasy Kit (Invitrogen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 were transduced with lentivirus to generate shTS (TS knock down) and pLKO (control). Calu-1 cells  were transduced with lentivirus to generate Cells expressing mCherry gene under the control of TYMS promoter. (TS knock down) and pLKO (control). Cells were selected in 3µg/ml puromycin and culture was maintained in 1µg/ml Puromycin. No other treatment was done on the cells. Selected Calu1 cells were  sorted in TS High and TS Low.

tag: tissue

value: Non Small Cell Lung Cancer

tag: treatment

value: Sorted TS Low


title: Tivozanib_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D12_ad004


title: Calu1 TS Low_rep1

description: TS Low_rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D10_ad010


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D10_ad007


title: LNZ308_shGFP-1_cleaved

description:
shGFP AlkB NaBH4 Cleaved
LNZ308_METTL1_KD_Trac-seq.xlsx


title: Brivanib_Dose2_Rep1


title: Calu1 TS High_rep2

description: TS High_rep2

value: Sorted TS High


title: Dasatinib_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D10_ad004


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D10_ad001


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D1_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D1_ad001


title: Pazopanib_Dose2_Rep1


title: A549 shTS_rep1

value: Lung Adenocarcinoma

value: TS knock down


title: Sildenafil_Dose2_Rep1


title: Topotecan_Dose2_Rep1


title: A549 PLKO_rep2

value: pLKO control


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D1_ad010


title: Bendamustine_Dose2_Rep2


title: A549 shTS_rep2


title: A549 PLKO_rep1


title: Saracatinib_Dose2_Rep1


title: 22929: HP-15041

city: Philadelphia

first: Jonathan

last: Schug

address: 12-156 Smilow Ctr Trans Research

data_processing:
Illumina basecalling with bcl2fastq, various versions
Read alignment and expression calculation; using RUM (Grant et al. Bioinformatics  doi: 10.1093/bioinformatics/btr427)
Conversion from reads to trimmed normalized CPMs.  Briefly CPMs for genes between 25 to 75% quantiles were used to compute a normalization factor which was then applied to all CPMs.
Manual and semi-automated cell type calling. Marker genes and differentially expressed genes used to rate cell type and purity which was subsequently curated.
Genome_build: hg19
Supplementary_files_format_and_content: TSV files with raw rea counts or normalized CPMs.  Donor annotation and called cell types included as well.

extract_protocol: Fluidigm C1 single-cell RNA-Seq using 96-well chip

value: pancreas

tag: celltype

value: pancreatic islets

tag: agecategory

value: adult

tag: healthcategory

tag: combinedcategory

value: beta


title: PYR41_Dose2_Rep1

tag: cell lines

tag: sgrnas

tag: compound treatment


title: DF_ATAC_2480-8_T

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

source_name: Patient localized prostate tissue

extract_protocol:
One (histone ChIP) or three (transcription factor ChIP) 2 mm2 frozen cores were pulverized using the Covaris CryoPrep system. Tissue was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.

value: localized prostate tissue

tag: chip antibody

value: ATAC

tag: chip antibody vendor

tag: chip antibody cat.#

tag: chip antibody lot/batch#


title: 22928: HP-15041

value: dropped


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D1_ad004

tag: brain region

tag: Sex

tag: age


title: DF_ATAC_2114-8_T


title: Calu1 TS High_rep1

description: TS High_rep1

tag: cell line


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D1_ad006

tag: strain


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D1_ad008


title: Chlorambucil_Dose2_Rep1

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: Everolimus_Dose2_Rep1


title: Ornidazole_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_D1_ad002

value: ACA,PL,ILA


title: Rigosertib_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C9_ad012


title: DF_ATAC_2038-6_T

tag: tissue


title: DF_ATAC_2025-2_T


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C9_ad001


title: DF_H3K27me3_2208_T

value: Cell Signaling Technology


title: Ciclopirox_Dose2_Rep1


title: DF_H3K27me3_1944_T


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C9_ad008

value: male


title: DF_ATAC_2137-1_T


title: Lovastatin_Dose2_Rep1


title: Gemcitabine_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C9_ad010


title: DF_H3K27me3_1820_T


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C9_ad006


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C8_ad012


title: DF_H3K27me3_1752_T_A


title: KU55933_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C8_ad001


title: 22917: HP-15041

tag: celltype


title: DF_H3K27ac_2478_T

value: Diagenode


title: DF_H3K27me3_1726_T_A


title: 22911: HP-15041

tag: agecategory


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C8_ad002


title: DF_H3K27ac_2477_T


title: DMSOPlate3WellC10_Dose2_Rep1


title: RG108_Dose2_Rep1


title: DMSOPlate3WellF10_Dose2_Rep1


title: Nitroxoline_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C8_ad004


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C8_ad008


title: Paclitaxel_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C8_ad007


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C7_ad001


title: Selumetinib_Dose2_Rep1


title: DF_H3K27ac_2076_T


title: DF_H3K27ac_2228_T


title: Tivantinib_Dose2_Rep1


title: Osteoblasts

city: Innsbruck

first: Can

last: Gollmann-Tepeköylü

address: Anichstraße 35

department: Department for Cardiac Surgery

country: Austria

institute: Medical University of Innsbruck

data_processing:
Sequence reads were trimmed for adaptor sequence removal and quality controlled using CLCBIO Genomics Workbench
Reads were mapped to the human reference genome (GRCh38.p7) using the mapping protocol in the CLC Genomics Workbench (v7.0) (mismatch cost 2, insertion/deletion cost 3, length fraction 0.8, similarity fraction 0.8, global alignment no, strand specific bozh, max no of hits per read 5)
Transcript per million (TPM) and Reads Per Kilobase of exon per Million reads (RPKM) were calculated for each gene based on the NCBI gene models using the CLCBIO Genomics Workbench
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Raw counts and TPMs for all samples are summarized as two separated tab delimited txt file

source_name: bone

growth_protocol: Valvular interstitial cells from patients undergoing aortic valve replacement or cardiac transplantation were isolated via collagen digestion as described previously. Valves were rinsed in EBSS and subsequently subjected to collagenase digestion (Sigma, St. Louis, MO; 2.5 mg/mL in M199) for 30 minutes at 37°C. Thereafter, tissue samples were vortexed and supernatant containing endothelial cells was removed. Again, collagenase was added to the remaining valve tissue (1 mg/mL) for 3h at 37°C. For mechanical disintegration of the tissue, vortexing and repeated aspiration via pipette was performed. The supernatant was transferred into a new tube and subjected to centrifugation (1100 g for 8 minutes at 4°C). Subsequently, cells were resuspended in M199 medium containing 10% fetal calve serum, penicillin, streptomycin, glutamate and amphotericin B (2.5 mg/L). Human osteoblasts were purchased (Promocell, Heidelberg, Germany) and cultivated in in DMEM with 4.5 g/L glucose (Lonza, Basel, Switzerland), 10% FCS (Sigma, St. Louis, MO), penicillin, streptomycin, glutamate and amphotericin B (2.5 mg/L).

extract_protocol:
Total RNA was isolated using  RNeasy Mini Kit 50 (Qiagen) according to the manufacturer’s protocol.
Library preparation was performed with the TruSeq® Stranded mRNA HT technology, according to the manufacturer´s protocol . Quality was checked by DNA 1000 LabChip kits on the 2100 Bioanalyzer (Agilent Technologies) and quantified using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Invitrogen)

treatment_protocol: Polyinosinic:polycytidylic acid (Poly (I:C); Invivogen, San Diego, CA) was used to stimulate cells at a concentration of 20 µg/mL for 72h

tag: cell type

value: Osteoblasts

tag: treatment

value: Medium

tag: time

value: bone


title: DimethylFumarate_Dose2_Rep1

tag: cell lines

tag: sgrnas


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C7_ad007


title: Lapatinib_Dose2_Rep1

tag: compound treatment


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C7_ad012


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C7_ad006


title: Valvular interstitial cells cultured in medium for72h

source_name: cardiac valves

value: Valvular interstitial cells

value: cardiac valves


title: RacRotigotine_Dose2_Rep1


title: CEMBA190205_5A_1_CEMBA190205_5A_2_C7_ad002


title: DF_H3K27ac_2208_T

tag: chip antibody

tag: chip antibody vendor


title: BardoxoloneMethyl_Dose2_Rep1


title: Valvular interstitial cells cultured in medium + Poly(I:C) for72h

value: Medium+Poly (I:C)