title: AIM29 KO, Ribo-seq

city: Cambridge

first: Vladimir

last: Denic

state: MA

address: 52 Oxford St, Room 442

department: Molecular and Cellular Biology

institute: Harvard University

data_processing:
Raw reads from Illumina NextSeq were checked for read quality using FastQC (v. 0.11.5)
Four random nucleotides generated during library prep were trimmed using seqtk (parameter trimfq -b 4) and 3' adapters were trimmed using cutadapt
Fastq files were converted to collapsed fasta files and analyzed using RiboToolkit
Assembly: S288c (v. R64-3-1)
Supplementary files format and content: bigWig file with log-ratio of AIM29 KO vs WT generated using bamCompare tool from the deepTools suite (binWidth = 1)
Library strategy: Ribo-seq

organism: Saccharomyces cerevisiae W303

source_name: yeast cell

growth_protocol: Wild-type and AIM29 KO cells were grown to mid-log phase in YPD.

extract_protocol:
Lysates were clarified and monosomes were isolated by sucrose gradient centrifugation after RNaseI treatment. RNA was extracted using SDS/hot phenol/chloroform.
Fragments ranging from 15-34 nt were gel purified and rRNA was depleted from this pool through Ribo-Zero Gold (Yeast) treatment. Upon dephosphorylation of sample RNA, a preadenylated linker was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing.

treatment_protocol: Cells were harvested by vacuum filtration and flash frozen. Samples were homogenized and lysed with lysis buffer using a freezer mill.

value: AIM29 KO

tag: cell type

value: yeast cell


title: resident eosinophils (3)

status: Public on Apr 17 2023

type: SRA

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

library_source: transcriptomic

data_processing:
Library quality control: FASTQC version 0.11.5
Quality and adapter trimming: trim_galore (uses cutadapt version 1.10)
Mapping: Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
Gene counting: HTseq-count version 0.6.1
Normalization and differential expression analysis: DESeq2 R package version 1.28.0

molecule: total RNA

organism: Mus musculus

source_name: eosinophils

extract_protocol: The CEL-Seq library was ran on an Illumina NextiSeq550 instrument

tag: strain


title: Caudate putamen Female 18mo 55ID

city: South San Francisco

first: Oliver

last: Hahn

state: CA

address: 1170 Veterans Blvd

country: USA

institute: Calico Life Sciences, LLC

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_55

data_processing:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v0.3.7, parameters: --paired --length 25). Trimmed sequences were aligned using STAR (v2.5.3a). Multi-mapped reads were filtered. Data visualization and analysis was performed using SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), custom RStudio (https://www.rstudio.com/) scripts and the following Bioconductor packages: Deseq2 (Love et al., 2014), topGO (Alexa and Rahnenfuhrer, 2010) and org.Mm.eg.db.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Caudate putamen

extract_protocol:
RNeasy Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT. Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.

tag: tissue

value: Caudate putamen

tag: Sex

value: Female

tag: age (months)

tag: mouse id number


title: usite3_S6_L002_R1_001_identifiedOfftargets

city: Wuhan

first: chen

last: peng

address: College of Life Sciences, Wuhan University

department: College of Life Sciences

country: China

institute: Wuhan University

library_source: genomic

data_processing:
Thecleandatawasgeneratedbytrimminglowqualitybasesatbothendsofreadandremoveshortfragments,thisworkwascompletedbysequencingcompany
Forguide-seq,thesequencingdatawasprocessedbycorrespondingsoftwarenamedguideseq,the human genome version used in the analysis is hg19;
Assembly: hg19
Supplementary files format and content: svg files include DNA sequences for each sample

molecule: genomic DNA

organism: Homo sapiens

source_name: embryonic kidney

extract_protocol:
Cells were collected after 48h post-transfection for genomic DNA extraction using FastPure Cell/Tissue DNA Isolation Mini Kit(Vazyme)
Libraries were prepared according to VAHTS Universal DNA Library Prep Kit for Illumina V2 (Vazyme)

tag: cell line

value: HEK 293 cells

value: embryonic kidney

tag: read length

tag: genotype

value: wild type


title: Usite6_S1_L001_R1_001_identifiedOfftargets


title: usite2_S2_L001_R1_001_identifiedOfftargets


title: 10x scATAC-seq on mix of MM031, MM074, MM047 and MM029

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

data_processing:
scATAC-seq runs reads were mapped to GRCh38 and fragments files generated using cellranger-atac count command (v2.0.0) using default parameters. Fragment files  for both libraries can be found under the names: CRM__34940b_fragments.tsv.gz and NML__a56c4b_fragments.tsv.gz. A merged fragment count matrix can be found under the name: "mm_lines_fragment_counts.tsv.gz".
Cell barcodes were demultiplexed based on their cell line identity using demuxlet using cell line specific mutations obtained from bulk ATAC-seq data on individual cell lines. For this, Genotypes of the individual cell lines were called using the bcftools mpileup command (v.1.11; options, --max-depth 8000 and --skip-indels) and bcftools call command (v1.11; options, --multiallelic-caller, -variants-only, --skip-variants indels and --output-type b). Only variants which were SNPs and not homozygous across samples were kept. To run demuxlet the scATAC-seq bam files were filtered to only contains reads covering SNPs and having a cell barcode (based on CB tag), reads were piledup using the popscle dsc-pileup command using default parameters and demuxlet was run using the popscle demuxlet command (using the option –field GT).
Based on the cell barcode to cell line annotation pseudobulk consensus peaks were called and a binary count matrix of chromatin accessibility of cells over consensus peaks was generated using pycisTopic.
Only high quality barcodes corresponding to cells were kept by filtering out cells with less than 3.25 and 3.8 log number of unique fragements per cell, FRIP below 0.5 and TSS enrichment below 4 and 5, respectively for data from NML__a56c4b and CRM__34940b using pycisTopic. Doublets based on Scrublet calls with a threshold of 0.25 were removed.
Using the high quality barcodes and the binary accessibility matrix an imputed accessibility matrix, resolving drop outs, was generated using topic modeling. For this Latent Dirichlet allocation with a collapsed Gibbs samples was used and a model of 30 topics using pycisTopic.
Pseudo multi ome data was generated by bootstrapping 5 cells of the same cell line into multiple meta cells containing both imputed chromatin accessibility data and gene expression data( from GSE134432 ) for the cell lines present in both assays. This data is available in the mm_lines_gene_expression_matrix.tsv and mm_lines_region_accessibility_matrix.tsv.gz file together with meta cell to cell line annotations in mm_lines_cell_metadata.tsv.
hg38
Supplementary files format and content: mm_lines_gene_expression_matrix.tsv:  tab seperated flat text file containing gene expression counts for the pseudo multi ome data (rows are meta cells and columns are genes).
Supplementary files format and content: mm_lines_region_accessibility_matrix.tsv.gz: tab seperated flat text file, compressed using gzip, containing imputed chromatin accessibility data for the pseudo multi ome data (columns are meta cells and rows are genomic region coordinates).
Supplementary files format and content: mm_lines_cell_metadata.tsv.: tab seperated flat text file containing meta cell to cell line annotations.
Supplementary files format and content: mm_lines_fragment_counts.tsv.gz: tab seperated flat text file, compressed using gzip, containing raw fragment counts (columns are cell barcodes and rows are genomic coordinates).
Supplementary files format and content: CRM__34940b_fragments.tsv.gz: tab seperated flat text file, compressed using gzip, containig Tn5 fragments from scATAC-seq library CRM__34940b (first three columns describe genomic region coordinates (chrom, start, end), column four contains the cell barcode identifier, column five contains the total number of read pairs associated with this fragment).
Supplementary files format and content: CRM__34940b_fragments.tsv.gz: tab seperated flat text file, compressed using gzip, containig Tn5 fragments from scATAC-seq library NML__a56c4b (first three columns describe genomic region coordinates (chrom, start, end), column four contains the cell barcode identifier, column five contains the total number of read pairs associated with this fragment).

source_name: melanoma cell lines

growth_protocol: Cells were cultured in Ham’s F10 nutrient mux (Thermo Fisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific) and 100  µg ml−1 penicillin–streptomycin. Cell cultures were kept at 37°C and 5% CO2. The identity of each line has been determined using RNA-seq and ATAC-seq and cell cultures used for experiments providing data to this study were tested for myoplasm contamination and were found to be negative.

extract_protocol:
Nuclei were extracted from the mm lines as follows; Cells were washed with phosphate buffered saline (1x PBS; Thermo Fisher Scienific), detached using trypsin (Thermo Fisher Scientific) and centrifuged at 1,000 r.p.m. for 5 min to remove the medium after this protocol CG000169 (10x Genomics) was followed. Briefly, cells were washed with PBS + 0.04% BSA and cell concentration was determined with the LUNA-FL Dual Fluorescence Cell Counter. For each cell line, 500k cells were resuspended in 100 µl nuclei lysis buffer (10 mM Tris-HCl pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% Tween-20; 0.1% NP40; 0.01% Digitonin and 1% BSA in nuclease-free water). After 5 min incubation on ice, 1 ml chilled wash buffer was added to the lysed cells (10 mM Tris-HCl pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% Tween-20 and 1% BSA in nuclease-free water). The lysed cell suspension was centrifuged at 500 rcf for 5 min at 4°C and the pellet was resuspended in 1x nuclei buffer.
Single-cell libraries were generated using the GemCode Single-Cell Instrument and Single Cell ATAC Library & Gel Bead Kit v1-v1.1 and ChIP Kit (10x Genomics). Briefly, single nuclei suspended in 1x nuclei buffer were incubated for 60 min at 37°C with a transposase that fragments the DNA in open regions of the chromatin and adds adapter sequences to the ends of the DNA fragments. After generation of nanoliter-scale gel-bead-in-emulsions (GEMs), GEMs were incubated in a C1000 Touch Thermal Cycler (Bio-Rad) under the following program: 72°C for 5 min; 98°C for 30 s; 12 cycles of 98°C for 10 s, 59°C for 30 s, 72°C for 1 min; and hold at 15°C. After incubation, single-cell droplets were broken, and the single-strand DNA was isolated and cleaned using Cleanup Mix containing Silane Dynabeads. Illumina P7 sequence and a sample index were added to the single-strand DNA during library construction via PCR: 98°C for 45s; 9-13 cycles of 98°C for 20 s, 67°C for 30 s, 72°C for 20 s; 72°C for 1 min; and hold at 15°C. The sequencing-ready library was cleaned up with SPRIselect beads.

value: melanoma cell lines

tag: treatment


title: Caudate putamen Female 15mo 54ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_54


title: Caudate putamen Female 21mo 52ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_52


title: Caudate putamen Female 18mo 51ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_51


title: Caudate putamen Female 15mo 50ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_50


title: Wild-type, Ribo-seq

value: wild-type


title: uPPP1R13L_S5_L004_R1_001_identifiedOfftargets


title: Caudate putamen Female 3mo 53ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_53


title: Spsite6_S1_L004_R1_001_identifiedOfftargets


title: Caudate putamen Male 26mo 5ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_5

value: Male


title: Caudate putamen Female 21mo 48ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_48


title: Caudate putamen Female 18mo 47ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_47


title: Caudate putamen Female 15mo 46ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_46


title: spsite3_S5_L001_R1_001_identifiedOfftargets


title: Caudate putamen Female 3mo 49ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_49


title: sfsite6_S1_L001_R1_001_identifiedOfftargets


title: sfsite3_S2_L001_R1_001_identifiedOfftargets


title: Caudate putamen Female 21mo 44ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_44


title: RVRP2_S1_L002_R1_001_identifiedOfftargets


title: Caudate putamen Female 18mo 43ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_43


title: spsite2_S3_L002_R1_001_identifiedOfftargets


title: Caudate putamen Female 15mo 42ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_42


title: RVRP1_S4_L004_R1_001_identifiedOfftargets


title: Caudate putamen Female 21mo 40ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_40


title: R4mP2_S1_L003_R1_001_identifiedOfftargets


title: QRP_S8_L003_R1_001_identifiedOfftargets


title: R4mP1_S5_L002_R1_001_identifiedOfftargets


title: Caudate putamen Female 3mo 37ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_37


title: Caudate putamen Female 3mo 41ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_41


title: RVR5_S2_L002_R1_001_identifiedOfftargets


title: Caudate putamen Female 18mo 39ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_39


title: R4m5_S2_L003_R1_001_identifiedOfftargets


title: Caudate putamen Male 21mo 36ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_36


title: Caudate putamen Female 12mo 4ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_4


title: Psite6_S1_L003_R1_001_identifiedOfftargets


title: psite3_S4_L001_R1_001_identifiedOfftargets


title: Caudate putamen Male 18mo 35ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_35


title: psite2_S1_L002_R1_001_identifiedOfftargets


title: Caudate putamen Male 15mo 34ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_34


title: pPPP1R13L_S4_L003_R1_001_identifiedOfftargets


title: Caudate putamen Female 3mo 45ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_45


title: Caudate putamen Male 18mo 31ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_31


title: Caudate putamen Male 21mo 32ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_32


title: Hipersite2_S2_L002_R1_001_identifiedOfftargets


title: sfsite2_S4_L002_R1_001_identifiedOfftargets


title: Hipersite3_S1_L001_R1_001_identifiedOfftargets


title: Caudate putamen Male 3mo 33ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_33


title: Caudate putamen Male 15mo 30ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_30


title: HiperSI_S7_L003_R1_001_identifiedOfftargets


title: HF15_S2_L003_R1_001_identifiedOfftargets


title: Caudate putamen Male 12mo 3ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_3


title: Caudate putamen Male 3mo 29ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_29


title: HF14mP2_S1_L004_R1_001_identifiedOfftargets


title: HF14mP1_S4_L003_R1_001_identifiedOfftargets


title: Caudate putamen Male 21mo 28ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_28


title: HF14m5_S2_L004_R1_001_identifiedOfftargets


title: Caudate putamen Male 21mo 24ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_24


title: Caudate putamen Female 15mo 38ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_38


title: Caudate putamen Male 15mo 26ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_26


title: Hipersite6_S1_L003_R1_001_identifiedOfftargets


title: HF1P2_S1_L003_R1_001_identifiedOfftargets


title: CePD1_S9_L002_R1_001_identifiedOfftargets


title: HF1P1_S5_L002_R1_001_identifiedOfftargets


title: Caudate putamen Male 15mo 22ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_22


title: Caudate putamen Male 18mo 27ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_27


title: CeNL_S4_L004_R1_001_identifiedOfftargets


title: CeCL_S5_L004_R1_001_identifiedOfftargets


title: Caudate putamen Male 21mo 20ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_20


title: HiperPPP1R13L_S4_L004_R1_001_identifiedOfftargets


title: CeB2_S7_L002_R1_001_identifiedOfftargets


title: Caudate putamen Male 26mo 2ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_2


title: Assite6_S4_L003_R1_001_identifiedOfftargets


title: Assite3_S3_L001_R1_001_identifiedOfftargets


title: Assite2_S1_L002_R1_001_identifiedOfftargets


title: Caudate putamen Male 3mo 17ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_17


title: AsSI_S1_L001_R1_001_identifiedOfftargets


title: AsRP_S1_L002_R1_001_identifiedOfftargets


title: Caudate putamen Male 12mo 15ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_15


title: Caudate putamen Male 21mo 16ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_16


title: Caudate putamen Male 18mo 23ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_23


title: Caudate putamen Male 26mo 14ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_14


title: AsH2_S3_L004_R1_001_identifiedOfftargets


title: Caudate putamen Female 12mo 13ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_13


title: Caudate putamen Male 3mo 21ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_21


title: Caudate putamen Male 26mo 11ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_11


title: AsCL4_S1_L002_R1_001_identifiedOfftargets


title: AsD4_S1_L002_R1_001_identifiedOfftargets


title: AsNL4_S1_L004_R1_001_identifiedOfftargets


title: Caudate putamen Male 12mo 12ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_12


title: Caudate putamen Female 12mo 10ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_10


title: Caudate putamen Female 12mo 1ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_1


title: Motor cortex Male 12mo 9ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_9

source_name: Motor cortex

value: Motor cortex


title: As4_S2_L001_R1_001_identifiedOfftargets


title: Entorhinal cortex Male 15mo 34ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_ent_34

source_name: Entorhinal cortex

value: Entorhinal cortex


title: Caudate putamen Male 18mo 19ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_19


title: Caudate putamen Male 15mo 18ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cp_18


title: A4mNL4_S2_L003_R1_001_identifiedOfftargets


title: Motor cortex Male 26mo 8ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_8


title: A4mCL4_S1_L002_R1_001_identifiedOfftargets


title: 4mSI_S2_L002_R1_001_identifiedOfftargets


title: AsPPP1R13L_S2_L004_R1_001_identifiedOfftargets


title: Motor cortex Male 12mo 6ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_6


title: Motor cortex Male 28mo 59ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_59


title: 4mP2_S1_L002_R1_001_identifiedOfftargets


title: Motor cortex Male 28mo 58ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_58


title: Motor cortex Male 28mo 57ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_57


title: 4mP1_S1_L001_R1_001_identifiedOfftargets


title: Motor cortex Female 12mo 7ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_7


title: 4mH2_S1_L001_R1_001_identifiedOfftargets


title: Motor cortex Female 21mo 56ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_56


title: AsB_S1_L003_R1_001_identifiedOfftargets


title: 4mD4_S2_L002_R1_001_identifiedOfftargets


title: Motor cortex Female 18mo 55ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_55


title: Motor cortex Female 15mo 54ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_54


title: 4mB_S2_L003_R1_001_identifiedOfftargets


title: Motor cortex Female 3mo 53ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_53


title: 4m5_S2_L002_R1_001_identifiedOfftargets


title: 4m4_S3_L002_R1_001_identifiedOfftargets


title: Motor cortex Female 18mo 51ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_51


title: Motor cortex Female 21mo 52ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_52


title: Motor cortex Female 15mo 50ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_50


title: human Islets, EtOH, rep3

city: New Orleans

first: Franck

last: Mauvais-Jarvis

state: LA

address: 1430 Tulane Avenue Lab# 2301

department: Department of Medicine - Section of Endocrinology and Metabolism

institute: Tulane University

description: 59yo, Caucasian male, 155lbs, BMI=22.6, HbA1c = 5.2%

library_source: transcriptomic single cell

data_processing:
For all datasets, we utilized CellRanger v4.0.0 software using the [-mkfastq] command to de-multiplex FASTQ data. Reads were mapped and aligned to the human genome (10X genomics pre-built GRCh38-2020-A Homo sapiens reference transcriptome assembly) with STAR (95.83±0.54% of reads confidently mapped to the human genome) (Dobin et al., 2013). Subsequently, final digital gene expression matrices and c-loupe files were generated for downstream multimodal analysis. Cellranger identified 31,198 correctly allocated barcodes (cells) (98.18%±0.14% valid barcodes), having 20,625±5634 reads/cell (99.65±0.39% valid UMIs) and 3848±560 genes/cell.
We deployed Seurat v4 (https://github.com/satijalab/seurat/releases/tag/v4.1.0) scripts to perform merging, thresholding, normalization, principal component analysis (linear dimensionality reduction), clustering analysis (non-linear multidimensional reduction), visualization and differential gene expression analysis.
Assembly: GRCh38
Supplementary files format and content: Processed data as a gene expression matrix in csv format. Genes in rownmanes and Sample_cellbarcodes in column names.

source_name: Pancreas

growth_protocol: Human islets (750 IEQ per condition) were treated with either 10nM DHT or EtOH overnight in a humidified incubator containing 4% CO2 at 37°C.

extract_protocol:
Islet cells were dispersed using TrypLE (Thermofischer), and immediately evaluated for viability (89.88±1.77%) by Cellometer Automated Cell Counter (Nexcelom Bioscience) prior to single cell RNAseq library preparation.
For 10x single cell RNAseq library preparation, 5000 individual live cells per sample were targeted by using 10x Single Cell 3’ RNAseq technology provided by 10x Genomics (10X Genomics Inc). Briefly, viable single cell suspensions were partitioned into nanoliter-scale Gel Beads-In-EMulsion (GEMs). Full-length barcoded cDNAs were then generated and amplified by PCR to obtain sufficient mass for library construction. Following enzymatic fragmentation, end-repair, A-tailing, and adaptor ligation, single cell 3’ libraries comprising standard Illumina P5 and P7 paired-end constructs were generated. Library quality controls were performed by using Agilent High Sensitive DNA kit with Agilent 2100 Bioanalyzer (Agilent) and quantified by Qubit 2.0 fluorometer (ThermoFisher).
Pooled libraries at a final concentration of 750pM were sequenced with paired end single index configuration by Illumina NextSeq 2000 (Illumina).

treatment_protocol: Samples were treated with either 10nM DHT or vehicle.

value: Pancreas

value: cadaveric human tissue

value: Islets

value: EtOH


title: human Islets, DHT[10nM], rep2

description: 44yo, Asian male, 210lbs, BMI=28.7, HbA1c = 5%

value: DHT (10nM)


title: Motor cortex Female 3mo 49ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_49


title: human Islets, DHT[10nM], rep1

description: 39yo, Caucasian male, 162lbs, BMI=22.7, HbA1c = 5.1%


title: 4mRP_S3_L002_R1_001_identifiedOfftargets


title: human Islets, EtOH, rep2


title: Motor cortex Male 26mo 5ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_5


title: Motor cortex Female 21mo 48ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_48


title: human Islets, DHT[10nM], rep3


title: human Islets, EtOH, rep1


title: Motor cortex Female 18mo 47ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_47


title: Motor cortex Female 21mo 44ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_44


title: Motor cortex Female 15mo 42ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_42


title: Motor cortex Female 15mo 46ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_46


title: Motor cortex Female 3mo 45ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_45


title: Motor cortex Female 21mo 40ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_40


title: Motor cortex Female 18mo 39ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_39


title: Motor cortex Female 3mo 41ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_41


title: Motor cortex Female 12mo 4ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_4


title: Motor cortex Female 18mo 43ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_43


title: Motor cortex Female 3mo 37ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_37


title: SLAMseq_THP1_REP3_DMSO

city: Melbourne

first: Izabela

last: Todorovski

state: VIC

address: 305 Grattan Street

department: Cancer Research Division

country: Australia

institute: Peter MacCallum Centre

data_processing:
Single-end reads were demultiplexed using bcl2fastq (v2.17.1.14) and resulting FASTQ files were trimmed for adapter sequences using Trim_galore (v0.6.5) with a stringency overlap of 3bp.
Trimmed FASTQ files were processed with SLAM-dunk (v0.4.3), enabling multi-mapper reconciliation.
Differential gene testing was performed on counts normalized to library sizes scaled to external S2 spike-ins and filtered for lowly expressed genes using edgeR (v3.32.1) on Rstudio (v4.0.2).
Assembly: hg38 and dm6
Supplementary files format and content: SLAMseq_THP1_ReadCounts_Total.tsv (raw total RNA counts)
Library strategy: SLAM-seq

source_name: THP-1 cell line

growth_protocol: THP-1 cells were cultured in Roswell Park Memorial Institute (RPMI) medium containing 10% (v/v) heat-inactivated fetal bovine serum (HI-FBS), penicillin (100 U/ml), streptomycin (100 μg/ml) and 2 mM GlutaMAX at 37°C and 5% carbon dioxide.

extract_protocol:
Cells were washed in ice-cold PBS and resuspended in 300μL TRIzol. To extract RNA, one-fifth volume of chloroform was added to TRIzol lysates, followed by shaking, incubation at room temperature for 2 minutes and centrifugation (16000g at 4°C for 15 minutes). The aqueous phase was isolated and RNA was precipitated using DTT (10mM), 100% isopropanol (1 volume) and GlycolBlue co-precipitant, incubated at room temperature for 10 minutes and centrifuged (16000g at 4°C for 20 minutes). Supernatant was removed, RNA pellets were washed in 75% (v/v) ethanol and DTT (100μM) and centrifuged (7500g at room temperature for 5 minutes). Supernatant was removed and RNA pellets dried for 10 minutes prior to reconstitution in Ultrapure DNAse/RNAse-free distilled water supplemented with DTT (1mM) and incubation at 55°C for 10 minutes. Thiol-containing bases were reduced by incubating RNA (10μg) with IAA (10mM, 50 mM NaPO4 pH 8.05 and 50% (v/v) DMSO) in a final volume of 50μL for 15 minutes at 55°C. Reaction was stopped by quenching IAA with DTT (20μM). RNA was precipitated using 3M NaOAc pH 5.2 (5μL), 100% ethanol (125μL) and GlycolBlue co-precipitant, incubated at -80°C for 30 minutes and centrifuged (16000g at 4°C for 30 minutes). Supernatant was removed and RNA pellet was washed in 75% (v/v) ethanol and centrifuged (16000g at 4°C for 10 minutes) twice, dried at room temperature for 10 minutes and reconstituted in Ultrapure DNAse/RNAse-free distilled water. RNA clean-up was performed by incubating RNA solution in 2 volumes of AMPure XP Beads, for 2 minutes at room temperature. Beads were washed in 80% (v/v) ethanol twice, dried at room temperature for 3 minutes and resuspended in Ultrapure DNAse/RNAse-free distilled water. Eluate was collected and S2 spike-in material (5%) was added to RNA.
QuantSeq 3′mRNA-seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria)
3'mRNA-seq

treatment_protocol: Treated with transcriptional inhibitors for 2 hours, with 1mM 4-thiouridine in the final 10 minutes of treatment.

value: Acute Myeloid Leukemia

value: THP-1 cell line

tag: pre-treatment

value: DMSO


title: Motor cortex Male 21mo 36ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_36


title: Motor cortex Female 15mo 38ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_38

value: Female


title: SLAMseq_THP1_REP1_YKL5124

value: 1mM 4-thiouridine in the final 10 minutes of treatment


title: SLAMseq_THP1_REP2_DMSO


title: SLAMseq_THP1_REP2_YKL5124


title: SLAMseq_THP1_REP3_YKL5124


title: Motor cortex Male 18mo 35ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_35


title: SLAMseq_THP1_REP1_DMSO


title: Motor cortex Male 15mo 34ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_34


title: SLAMseq_THP1_REP3_THZ531


title: SLAMseq_THP1_REP2_THZ531


title: Motor cortex Male 21mo 32ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_32


title: Motor cortex Male 3mo 33ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_33


title: SLAMseq_THP1_REP1_THZ531


title: Motor cortex Male 18mo 31ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_31


title: Motor cortex Male 15mo 30ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_30


title: SLAMseq_THP1_REP2_AZ5576


title: Motor cortex Male 12mo 3ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_3


title: SLAMseq_THP1_REP3_AZ5576


title: Motor cortex Male 15mo 26ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_26


title: SLAMseq_THP1_REP1_AZ5576


title: Motor cortex Male 18mo 27ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_27


title: Motor cortex Male 3mo 25ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_25


title: Motor cortex Male 21mo 28ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_28


title: THP1-SCR_DMSO-3

description:
THP1_SCR_ELAVL1-KO_ReadCounts_Exons.txt
THP1_SCR_ELAVL1_KO_ReadCounts_Spike-in.txt

data_processing:
Single-end reads were demultiplexed using bcl2fastq (v2.17.1.14) and resulting FASTQ files were quality checked using fastqc (v0.11.6), trimmed 12 bp from the 5’ end to remove primer bias, trimmed for polyA stretches, and filtered for quality and length using cutadapt (v2.1; -u 12 -q 10 -m 20 -a AAAAAAAAAA).
Trimmed reads were mapped to GRCh37/hg19 and BDGP R5/dm3 genomes using hisat2 (v2.1.0) using standard single-end settings and resulting SAM files were converted to BAM files using samtools (v1.9; view), which were then sorted (sort) and indexed (index).
Reads mapping to exonic genomic intervals were counted using a combined hg19/dm3 GTF file with FeatureCounts from the subread package (v2.0.0; featureCounts -O -M -F GTF -T 16 -s 0).
Differential gene testing was performed on counts normalized to library sizes scaled to external S2 spike-ins and filtered for lowly expressed genes using edgeR (v3.32.1) on Rstudio (v4.0.2).
Assembly: hg19 and dm3
Supplementary files format and content: THP1_SCR_ELAVL1-KO_ReadCounts_Exons.txt (exon raw counts)
Supplementary files format and content: THP1_SCR_ELAVL1_KO_ReadCounts_Spike-in.txt (spike-in raw counts)

source_name: THP1 cells expressing Cas9 and non-targeting control sgRNA (SCR)

growth_protocol: THP1 Cas9 cells expressing non-targeting control sgRNA (SCR) or sgRNA targeting ELAVL1 (ELAVL1 KO) were cultured in Roswell Park Memorial Institute (RPMI) medium containing 10% (v/v) heat-inactivated fetal bovine serum (HI-FBS), penicillin (100 U/ml), streptomycin (100 μg/ml) and 2 mM GlutaMAX at 37°C and 5% carbon dioxide.

extract_protocol:
THP1 Cas9 cells expressing non-targeting control sgRNA (SCR) or sgRNA targeting ELAVL1 (ELAVL1 KO) were harvested, centrifuged (500g at 4°C for 4 minutes), washed in ice-cold PBS and resuspended in 600μL TRIzol. RNA was extracted using the Directzol RNA Miniprep Kit, where an additional DNase I digestion step was performed.
QuantSeq 3′mRNA-seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria)
3'mRNA-seq

treatment_protocol: THP1 Cas9 cells expressing non-targeting control sgRNA (SCR) or sgRNA targeting ELAVL1 (ELAVL1 KO) were treated with DMSO or 100nM AZ-5576 for 6 hours at 37°C and 5% carbon dioxide.

value: SCR

value: DMSO for 6 hours


title: THP1-SCR_AZ5576-3

value: 100nM AZ-5576 for 6 hours


title: THP1-SCR_DMSO-1


title: THP1-ELAVL1-KO-2_DMSO-2

source_name: THP1 cells expressing Cas9 and sgRNA #2 targeting ELAVL1


title: THP1-ELAVL1-KO-2_DMSO-1


title: THP1-SCR_AZ5576-2


title: Motor cortex Male 15mo 22ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_22


title: Motor cortex Male 21mo 20ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_20


title: THP1-SCR_AZ5576-1


title: Motor cortex Male 21mo 24ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_24


title: Motor cortex Male 18mo 19ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_19


title: Motor cortex Male 18mo 23ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_23


title: Motor cortex Male 3mo 21ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_21


title: Motor cortex Male 3mo 29ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_29


title: THP1-ELAVL1-KO-1_DMSO-3

source_name: THP1 cells expressing Cas9 and sgRNA #1 targeting ELAVL1


title: Motor cortex Male 3mo 17ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_17


title: THP1-ELAVL1-KO-2_AZ5576-3


title: THP1-ELAVL1-KO-2_DMSO-3


title: Motor cortex Male 26mo 2ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_2


title: THP1-ELAVL1-KO-2_AZ5576-2


title: THP1-ELAVL1-KO-1_AZ5576-3


title: THP1-ELAVL1-KO-1_AZ5576-2


title: Motor cortex Male 15mo 18ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_18


title: THP1-ELAVL1-KO-1_AZ5576-1


title: THP1-SCR_DMSO-2


title: THP1-ELAVL1-KO-2_AZ5576-1


title: Motor cortex Female 12mo 13ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_13


title: Motor cortex Male 12mo 12ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_12


title: TotalRNA_K562_cMYC_3UTRmut_REP1_DMSO_6hr

description:
K562_MYC_clones_TotalRNAseq_ReadCounts_Exons.txt
K562_MYC_clones_TotalRNAseq_ReadCounts_Introns.txt

data_processing:
Paired-end reads were demultiplexed using bcl2fastq (v2.17.1.14) and resulting FASTQ files were quality checked using fastqc (v0.11.6), trimmed 15 bp from the 5’ end to remove primer bias and filtered for quality and length using cutadapt (v2.1; -u 15 -U 15 -q 15 --pair-filter any --minimum-length 50).
Trimmed reads were mapped to GRCh38/hg38 and BDGP6/dm6 genomes using hisat2 (v2.1.0) with paired read settings and resulting SAM files were converted to BAM files using samtools (v1.9; view), which were then sorted (sort)and indexed (index).
Reads mapping to either exonic or intronic genomic intervals were counted using a combined hg38/dm6/GFP GTF file with FeatureCounts from the subread package (v2.0.0; featureCounts -O -M -T 32 -p -s 2).
Differential gene testing was performed on counts normalized to library sizes scaled to external S2 spike-ins and filtered for lowly expressed genes using edgeR (v3.32.1) on Rstudio (v4.0.2).
Assembly: hg38 and dm6
Supplementary files format and content: K562_MYC_clones_TotalRNAseq_ReadCounts_Exons.txt (exon raw read counts)\
Supplementary files format and content: K562_MYC_clones_TotalRNAseq_ReadCounts_Introns.txt (intron raw read counts)\

source_name: K562 c-MYC HPRT1 3'UTR cell line clone

growth_protocol: K562 HDR-edited cells were cultured in Roswell Park Memorial Institute (RPMI) medium containing 10% (v/v) heat-inactivated fetal bovine serum (HI-FBS), penicillin (100 U/ml), streptomycin (100 μg/ml) and 2 mM GlutaMAX at 37°C and 5% carbon dioxide.

extract_protocol:
K562 HDR-edited cells were centrifuged (500g at 4°C for 4 minutes), washed in ice-cold PBS and resuspended in 350μl of Buffer RLT Plus supplemented with 1% (v/v) β-mercaptoethanol from the RNeasy Plus Mini Kit. RNA was extracted using the same kit according to manufacturer’s instructions and quality was assessed using the Agilent 2200 TapeStation System  with RNA ScreenTape and Sample Buffer. S2 spike-in material (5%) was added to RNA.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with ribodepletion using the NEBNext rRNA Depletion Kit.
Total RNA-seq

treatment_protocol: K562 HDR-edited cells (1 x 10^6 per treatment) were treated with small molecule inhibitors for a total time of 6 hours at 37°C and 5% carbon dioxide.

value: Chronic Myeloid Leukemia

value: K562 cell line

value: c-MYC HPRT1 3'UTR

value: Treated with DMSO for 6 hours


title: Motor cortex Male 21mo 16ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_16

value: Motor cortex

value: Male


title: Huh-7 cells treated with RSL-3

city: Simotsuke

first: Tadayoshi

last: Karasawa

state: Tochigi

address: 3311-1 Yakushiji

country: Japan

institute: Jichi Medical University

data_processing:
The sequence data were processed with the MAGeCK algorithm.
The sgRNA cassette was PCR-amplified and barcoded with sequencing adaptor using KOD One PCR Master Mix (TOYOBO).
Supplementary files format and content: Tab-separated values files

growth_protocol: Huh7 cells were transduced with GeCKOv2 library virus at a target MOI of 0.3 in the presence of 8 µg/mL polybrene. The transduced cells were selected by 2 µg/mL of puromycin for 3 days and further expanded under growth media (DMEM supplemented with 10% FCS and antibiotics).

extract_protocol: The genomic DNA was extracted from the survived cells with phenol-chloroform.

treatment_protocol: The transduced cells were either treated with 0.1 µM RSL3 or 0.03 µM RSL3 and 50 mM linoleic acid for 24 h. The survived cells were expanded and selected repeatedly.

value: Human hepatoma


title: Motor cortex Male 26mo 11ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_11


title: TotalRNA_K562_cMYC_3UTRmut_REP2_AZ5576_6hr

value: Treated with 1μM AZ-5576 for 6 hours


title: Huh-7 cells treated with linoleic acid and RSL-3

value: Linoleic acid and RSL-3


title: THP1-ELAVL1-KO-1_DMSO-1

value: Acute Myeloid Leukemia


title: TotalRNA_K562_cMYC_3UTRmut_REP2_DMSO_6hr


title: THP1-ELAVL1-KO-1_DMSO-2

value: THP-1 cell line


title: TotalRNA_K562_cMYC_3UTRmut_REP2_ACTD_6hr

value: Treated with 1μg/mL Actinomycin D for 6 hours


title: TotalRNA_K562_cMYC_3UTRmut_REP1_AZ5576_6hr


title: Huh-7 cells

value: Untreated


title: Motor cortex Male 26mo 14ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_14


title: TotalRNA_K562_cMYC_3UTRctrl_REP2_DMSO_6hr

source_name: K562 c-MYC control 3'UTR cell line clone

value: c-MYC control 3'UTR


title: TotalRNA_K562_cMYC_3UTRmut_REP1_ACTD_6hr


title: Motor cortex Male 12mo 15ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_15


title: TotalRNA_K562_cMYC_3UTRctrl_REP2_AZ5576_6hr


title: TotalRNA_K562_cMYC_3UTRctrl_REP1_AZ5576_6hr


title: Cerebellum Male 12mo 9ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_9

source_name: Cerebellum

value: Cerebellum


title: Motor cortex Female 12mo 10ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_10

value: Female


title: TotalRNA_K562_cMYC_3UTRctrl_REP2_ACTD_6hr


title: B2: HCT116 cells, AVA-ADR-001 treatment, 24h

city: Bengaluru

first: Aditya

last: Kulkarni

state: Karnataka

address: Devarachikkanahalli Main Rd, Bommanahalli

country: India

institute: Aten Porus Lifesciences Pvt Ltd

data_processing:
Fastp (v0.20.0) was used for quality filtering and adapter trimming of the raw data.
A cutoff of 30 was set for the quality phred score and only high quality reads were retained. Hisat2, a splice aware aligner was used to align the reads against the human genome (hg38) from NCBI database28. The transcriptome was assembled and quantified from the aligned reads for each sample using Stringtie29
The expressions of the transcripts are normalized with the Transcripts per million (FPKM) metric. Functional annotation of the assembled transcripts with Gene ontology terms was done with David database
DESeq2 was used to perform differential analysis between Control and Treated. A p-value cutoff of 0.05 and less was used to identify the significantly expressed transcripts and a log2 Fold-change cut of (+2) and higher for Upregulated transcripts and (-2) and less for down regulated transcripts was used.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include log2 fold change values for treated vs control, basemean, p-values, DEGs

growth_protocol: HCT116 and A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNA extraction kit usinng manufacturers' protocol
RNA libraries for RNA-seq were prepared using Library Prep Kit following manufacturer's protocols.

treatment_protocol: A549 and HCT116 cell lines were treated with AVA-ADR-001 (25µM) and 1% DMSO (control) for 24 h. confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),

value: Colorectal cancer cells

value: treated with AVA-ADR-001 for 24 h

tag: time


title: B3: HCT116 cells, DMSO control, untreated

value: DMSO control


title: B2: HCT116 cells, DMSO control, untreated


title: Motor cortex Female 12mo 1ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cor_1


title: TotalRNA_K562_cMYC_3UTRctrl_REP1_DMSO_6hr

value: Chronic Myeloid Leukemia

value: K562 cell line


title: Cerebellum Male 26mo 8ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_8


title: B1: HCT116 cells, AVA-ADR-001 treatment, 24h


title: B3: HCT116 cells, AVA-ADR-001 treatment, 24h


title: TotalRNA_K562_cMYC_3UTRctrl_REP1_ACTD_6hr


title: Cerebellum Female 12mo 7ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_7


title: MACseq_K562_6hr_Plate2

description:
MACseq_metaData.csv
MACseq_rawCounts_plate2.tsv

data_processing:
Paired-end reads were demultiplexed using bcl2fastq (v2.17.1.14) and resulting FASTQ files were quality checked using fastqc (v0.11.6) and read 2 (R2) was trimmed 15 bp from the 5’ end to remove primer bias using cutadapt (v2.1; -u 15).
R2 FASTQ files of paired-end reads were demultiplexed according to well barcodes and filtered for PCR duplicates using Unique Molecular Identifiers (UMIs), both present in read 1 (R1) using the scruff R (v4.0.2) package dumultiplex function (bcStart = 1, bcStop = 10, bcEdit = 0, umiStart = 11, umiStop = 20, keep = 35, minQual = 20, yieldReads = 1e+06).
R2 FASTQ files were then mapped to the GRCh37/hg19 genome and ERCC sequences using alignRsubread (unique = FALSE, nBestLocations = 1, format = "BAM") and resulting BAM files were used to count unique R2 reads mapping to exonic genomic intervals and ERCC sequences using a combined hg19/ERCC GTF file with countUMI (umiEdit = 0, format = "BAM", cellPerWell = 1. Both functions are from the scruff R package.
Assembly: hg19 and ERCC
Supplementary files format and content: MACseq_rawCounts_plate1.tsv (raw counts)
Supplementary files format and content: MACseq_rawCounts_plate2.tsv (raw counts)
Supplementary files format and content: MACseq_metaData.csv (experiment metadata)
Library strategy: MAC-seq

source_name: K562 cell line

growth_protocol: K562 cells were cultured in Roswell Park Memorial Institute (RPMI) medium containing 10% (v/v) heat-inactivated fetal bovine serum (HI-FBS), penicillin (100 U/ml), streptomycin (100 μg/ml) and 2 mM GlutaMAX at 37°C and 5% carbon dioxide.

extract_protocol:
K562 cells (5 x 10^3) from each well were aliquoted into a separate 96-well plate, washed in ice-cold PBS twice and centrifuged (500g at 4°C for 4minutes). Supernatant was removed and cell pellets were frozen at -80°C. In detail, 17 μl lysis buffer were added into each well of a 96-well plate containing cell pellets and incubated at room temperature for 15 min under agitation (900 rpm).
12.5 μl of cell lysate were transferred into each well of a new 96-well plate previously prepared with 1 μl of 10 nM well-specific RT MAC-seq primer and 7.5 μl RT mix; the RT mix contains a TSO primer and external ERCC RNAs. The mixture was incubated for 2 hours at 42 C to create well-barcoded full length cDNA and then all the wells of a plate were combined into a single tube. Concentration and clean-up was done via column purification and RNAClean XP beads and each plate eluted in 22 μl nuclease free water. The purified cDNA was pre-amplified with KAPA HiFi HotStart ReadyMix and MAC-seq PreAmp PCR primer and the quality checked on a D5000 Screentape. One barcoded library was prepared per plate using TD buffer and TDE1 enzyme for tagmentation and KAPA HiFi HotStart Ready Mix and custom primers (MAC-seq P5 PCR and MAC-seq Indexing Mix for amplification. Libraries were purified with DNA Ampure XP beads, quality checked on a DNA1000 tape and quantity verified by qPCR.
3'mRNA-seq

treatment_protocol: K562 cells were treated with transcriptional and epigenetic inhibitors for 6 hours.

value: Treated with transcriptional and epigenetic inhibitors for 6 hours


title: B1: HCT116 cells, DMSO control, untreated


title: Cerebellum Male 12mo 6ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_6

value: Male


title: SLAMseq_K562_4sUwashout_JQ1_T8hr

description:
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Spike-in.tsv
3RNA-SLAM-K562-T-8-JQ1

data_processing:
Single-end reads were demultiplexed using bcl2fastq (v2.17.1.14) and resulting FASTQ files were trimmed for adapter sequences using Trim_galore (v0.6.5) with a stringency overlap of 3bp.
Trimmed FASTQ files were processed with SLAM-dunk (v0.4.3), enabling multi-mapper reconciliation and using a threshold of at least 2 T > C conversions to mark a read as converted. The no 4sU control sample was processed first to find single nucleotide polymorphisms (SNPs), which was then used to filter the subsequent samples.
`bedtools merge` was then used to merge the 3' UTRs of each Ensembl transcript by gene (v77 identifiers for hg38) for use in the SLAM-dunk counting step.
Decay rates for each gene were determined using precision-weighted nonlinear regression to fit an exponential curve to the decreasing quantity of SLAM-seq labelled reads measured post-washout of 4-thiouridine.
Assembly: hg38 and dm6
Supplementary files format and content: K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Total.tsv (raw total RNA counts)
Supplementary files format and content: K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Nascent.tsv (raw nascent RNA counts)
Supplementary files format and content: K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Spike-in.tsv (raw spike-in counts)
Library strategy: SLAM-seq

extract_protocol:
K562 cells were washed in ice-cold PBS and resuspended in 300μL TRIzol. To extract RNA, one-fifth volume of chloroform was added to TRIzol lysates, followed by shaking, incubation at room temperature for 2 minutes and centrifugation (16000g at 4°C for 15 minutes). The aqueous phase was isolated and RNA was precipitated using DTT (10mM), 100% isopropanol (1 volume) and GlycolBlue co-precipitant, incubated at room temperature for 10 minutes and centrifuged (16000g at 4°C for 20 minutes). Supernatant was removed, RNA pellets were washed in 75% (v/v) ethanol and DTT (100μM) and centrifuged (7500g at room temperature for 5 minutes). Supernatant was removed and RNA pellets dried for 10 minutes prior to reconstitution in Ultrapure DNAse/RNAse-free distilled water supplemented with DTT (1mM) and incubation at 55°C for 10 minutes. Thiol-containing bases were reduced by incubating RNA (10μg) with IAA (10mM, 50 mM NaPO4 pH 8.05 and 50% (v/v) DMSO) in a final volume of 50μL for 15 minutes at 55°C. Reaction was stopped by quenching IAA with DTT (20μM). RNA was precipitated using 3M NaOAc pH 5.2 (5μL), 100% ethanol (125μL) and GlycolBlue co-precipitant, incubated at -80°C for 30 minutes and centrifuged (16000g at 4°C for 30 minutes). Supernatant was removed and RNA pellet was washed in 75% (v/v) ethanol and centrifuged (16000g at 4°C for 10 minutes) twice, dried at room temperature for 10 minutes and reconstituted in Ultrapure DNAse/RNAse-free distilled water. RNA clean-up was performed by incubating RNA solution in 2 volumes of AMPure XP Beads, for 2 minutes at room temperature. Beads were washed in 80% (v/v) ethanol twice, dried at room temperature for 3 minutes and resuspended in Ultrapure DNAse/RNAse-free distilled water. Eluate was collected and S2 spike-in material (5%) was added to RNA.
QuantSeq 3′mRNA-seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria)
3'mRNA-seq

treatment_protocol: K562 cells were treated with 30μM 4-thiouridine for 12 hours at 37°C and 5% carbon dioxide, whereby culture medium was exchanged every 3 hours for the duration of the pulse.  K562 cells were then washed in sterile ice-cold PBS twice and resuspended in pre-warmed (37°C) culture medium containing 3mM uridine and either DMSO, 1μM JQ1 or 1μM AZ-5576. K562 cells were then harvested at 0- , 2-, 4-, 8- hours post-uridine chase.

tag: time point

value: 8 hours post 4-thiouridine wash-out and 1μM JQ1 addition


title: Cerebellum Male 28mo 59ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_59


title: SLAMseq_K562_4sUwashout_AZ5576_T8hr

description:
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Spike-in.tsv
3RNA-SLAM-K562-T-8-AZ5576

value: 8 hours post 4-thiouridine wash-out and 1μM AZ-5576 addition


title: SLAMseq_K562_4sUwashout_JQ1_T4hr

description:
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Spike-in.tsv
3RNA-SLAM-K562-T-4-JQ1

value: 4 hours post 4-thiouridine wash-out and 1μM JQ1 addition


title: A3: A549 cells, DMSO control, untreated

value: Lung adenocarcinoma cells


title: SLAMseq_K562_4sUwashout_AZ5576_T4hr

description:
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Spike-in.tsv
3RNA-SLAM-K562-T-4-AZ5576

value: 4 hours post 4-thiouridine wash-out and 1μM AZ-5576 addition


title: A3: A549 cells, AVA-ADR-001 treatment, 24h


title: Cerebellum Male 28mo 58ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_58


title: SLAMseq_K562_4sUwashout_DMSO_T2hr

description:
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Spike-in.tsv
3RNA-SLAM-K562-T-2-UT

value: 2 hours post 4-thiouridine wash-out and DMSO addition


title: Cerebellum Male 28mo 57ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_57


title: A2: A549 cells, AVA-ADR-001 treatment, 24h


title: A2: A549 cells, DMSO control, untreated


title: SLAMseq_K562_4sUwashout_AZ5576_T2hr

description:
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Spike-in.tsv
3RNA-SLAM-K562-T-2-AZ5576

value: 2 hours post 4-thiouridine wash-out and 1μM AZ-5576 addition


title: SLAMseq_K562_4sUwashout_T0hr

description:
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Spike-in.tsv
3RNA-SLAM-K562-T-0

value: 0 hours post 4-thiouridine wash-out


title: TTseq_K562_REP2_UT_5min

description:
K562_TTseq_synthesis_measurements_ReadCounts_Total.tsv
K562_TTseq_synthesis_measurements_ReadCounts_Spike-in.tsv
K562_TTseq_synthesis_measurements_synthesis_rates.txt

data_processing:
Single-end reads were demultiplexed using bcl2fastq (v2.17.1.14) and resulting FASTQ files were aligned to the genome using STAR (v2.7).
Mapped reas were then summarized using featureCounts in Subread (v2.0.1): counting reads with a minimum Mapping Quality Score (MQS) of 7 in the union of all transcript isoforms of each Ensembl gene. Only genes with at least 10 reads per million across at least two samples within an experiment were retained for further analysis.
Raw read counts for each gene were converted to reads per million using adjusted library sizes calculated with edgeR’s TMM implementation on the spike-in read counts.
Sythesis rates were determined by dividing the TT-seq adjusted reads per million for each gene by the length and sampling time, producing a scaled FPKM h-1 averaged across replicates.
Assembly: hg38 and dm6
Supplementary files format and content: K562_TTseq_synthesis_measurements_ReadCounts_Total.tsv (raw total RNA counts)
Supplementary files format and content: K562_TTseq_synthesis_measurements_ReadCounts_Spike-in.tsv (raw spike-in RNA counts)
Supplementary files format and content: K562_TTseq_synthesis_measurements_synthesis_rates.txt (raw sythesis measurements)
Library strategy: TT-seq

extract_protocol:
K562 cells were centrifuged (500g at 4°C for 5 minutes) and resuspended in TRIzol (5mL). One-fifth volume of chloroform was added to lysates, followed by shaking, incubation at room temperature for 2 minutes and centrifugation (13000g at 4°C for 10 minutes). The aqueous phase was isolated and RNA was precipitated using 100% isopropanol (1 volume), incubated at room temperature for 10 minutes and centrifuged (13000rpm at 4°C for 10 minutes). Supernatant was removed and RNA pellet was washed in 70% (v/v) ethanol, reconstituted in Ultrapure DNAse/RNAse-free distilled water (100μL) and denatured at 65°C for 10 minutes. S2 spike-in (15μg) was added to RNA (150μg), material was adjusted to a final volume 100μL and sonicated in microTUBE AFA Fiber screw cap tubes using the Covaris S220 Focused-ultrasonicator at a maximum power for 15 seconds. Thiol-specific biotinylation of RNA was performed in a final volume of 1.5mL by incubation with 10 mM tris (pH 7.4), 1 mM EDTA, 20% (v/v) dimethylformamide (200 μg/ml), and 300 μg of EZ-Link HPDP-Biotin for 1.5 hours at room temperature. An equal volume of chloroform was added to reaction, followed by shaking, incubation at room temperature for 2 minutes and centrifugation (500g at 4°C for 5 minutes). Aqueous phase was isolated and an equal volume of chloroform was added, followed by shaking, incubation at room temperature for 2 minutes and centrifugation (500g at 4°C for 5 minutes). This step was repeated an additional one time. Aqueous phase was isolated and RNA was precipitated using 5M NaCl (10% volume) and 100% isopropanol (1 volume) and centrifugation (20000g at 4°C for 20 minutes). RNA pellets were washed in 75% (v/v) ethanol, reconstituted in Ultrapure DNAse/RNAse-free distilled water (100μL) and denatured at 65°C for 10 minutes. Biotinylated RNA was separated from the total RNA pool by incubation with streptavidin beads at room temperature for 15 min with constant rotation. μMACs columns pre-equilibrated with room temperature wash buffer (100 mM tris-HCl (pH 7.4), 10 mM EDTA, 1 M NaCl, and 0.1% (v/v) Tween 20) were used to bind streptavidin beads, which were then washed using 900μL wash buffer that was heated to 65 °C or at room temperature, 5 times each. Biotinylated RNA was eluted into 700μL Buffer RLT from the RNeasy MinElute Cleanup Kit through two additions of 100 mM DTT (100μl) 3 min apart, and then isolated using the same kit according to manufacturer’s instructions. RNA concentration was quantified using the Agilent 2200 TapeStation System with High Sensitivity RNA ScreenTape and Sample Buffer.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (without additional fragmentation), where ribodepletion was performed using the NEBNext rRNA Depletion Kit.
Total RNA-seq

treatment_protocol: K562 cells (5 x 107 per treatment condition) were treated with 1mM 4-thiouridine for either 5 or 15 minutes at 37°C and 5% carbon dioxide.

value: UT 5min


title: MACseq_K562_6hr_Plate1

description:
MACseq_metaData.csv
MACseq_rawCounts_plate1.tsv


title: SLAMseq_K562_4sUwashout_DMSO_T8hr

description:
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Spike-in.tsv
3RNA-SLAM-K562-T-8-UT

value: 8 hours post 4-thiouridine wash-out and DMSO addition


title: A1: A549 cells, AVA-ADR-001 treatment, 24h


title: Cerebellum Female 21mo 56ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_56

value: Cerebellum

value: Female


title: Cerebellum Female 15mo 54ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_54


title: A1: A549 cells, DMSO control, untreated

value: DMSO control


title: SLAMseq_K562_4sUwashout_DMSO_T4hr

description:
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Spike-in.tsv
3RNA-SLAM-K562-T-4-UT

value: Chronic Myeloid Leukemia

value: 4 hours post 4-thiouridine wash-out and DMSO addition


title: TTseq_K562_REP1_UT_15min

value: K562 cell line

value: UT 15min


title: TTseq_K562_REP2_UT_15min


title: SLAMseq_K562_REP2_4sUwashout_T8hr

description:
K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv
SLAM-K562-S2-T-8-2

data_processing:
Single-end reads were demultiplexed using bcl2fastq (v2.17.1.14) and resulting FASTQ files were trimmed for adapter sequences using Trim_galore (v0.6.5) with a stringency overlap of 3bp.
Trimmed FASTQ files were processed with SLAM-dunk (v0.4.3), enabling multi-mapper reconciliation and using a threshold of at least 2 T > C conversions to mark a read as converted. The no 4sU control sample was processed first to find single nucleotide polymorphisms (SNPs), which was then used to filter the subsequent samples.
`bedtools merge` was then used to merge the 3' UTRs of each Ensembl transcript by gene (v77 identifiers for hg38) for use in the SLAM-dunk counting step.
Decay rates for each gene were determined using precision-weighted nonlinear regression to fit an exponential curve to the decreasing quantity of SLAM-seq labelled reads measured post-washout of 4-thiouridine.
Assembly: hg38 and dm6
Supplementary files format and content: K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv (raw total RNA counts)
Supplementary files format and content: K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv (raw nascent RNA counts)
Supplementary files format and content: K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv (raw spike-in counts)
Library strategy: SLAM-seq

treatment_protocol: K562 cells were treated with 30μM 4-thiouridine for 12 hours at 37°C and 5% carbon dioxide, whereby culture medium was exchanged every 3 hours for the duration of the pulse.  K562 cells were then washed in sterile ice-cold PBS twice and resuspended in pre-warmed (37°C) culture medium containing 3mM uridine (Sigma Aldrich, U6381). K562 cells were then harvested at 0- ,1-, 2-, 4-, 8-, 12- hours post-uridine chase.

value: 8 hours post 4-thiouridine wash-out


title: SLAMseq_K562_REP1_4sUwashout_T12hr

description:
K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv
SLAM-K562-S2-T-12-1

value: 12 hours post 4-thiouridine wash-out


title: A549_IFN_Topo_Eto_top30_mCherry_R3

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: A549_IFN_Topo_Eto_top30_mCherry_R3.count

data_processing:
The initial demultiplexing based on Illumina indices was performed using the bcl2fastq conversion software (v2.20.0).
The oligo-dT barcode sequences were extracted from Read 1 reads using cutadapt (v2.1) and utilized for subsequent internal demultiplexing using BRBseqTools-1.6.jar ( http://github.com/DeplanckeLab/BRB-seqTools).
The BRBseqTools demultiplexed data was aligned to a custom genome (COVGT#5-containing GRCh38) using STAR (v2.7.8a).
The count matrices were subsequently generated using HTSeq (v2.0.2).
Assembly: GRCh38.107 + COVGT#5
Supplementary files format and content: Tab-delimited text file with raw counts for each sample
Library strategy: BRB-seq

source_name: lung adenocarcinoma

growth_protocol: 293T and A549 cell lines were cultured in DMEM or RPMI medium (Gibco) respectively, supplemented with 10% fetal bovine serum (FBS; from Gibco) and penicillin and streptomycin (pen/strep; 100 U/ml; Gibco) at 37°C in a 5% CO2 and 95% air.

extract_protocol:
Total RNA was extracted using the TRIzol Reagent (Invitrogen) with subsequent isopropanol precipitation, DNase I treatment and purification with AMPure XP beads (Beckman Coulter). The concentration of the RNA was quantified by Qubit RNA HS Assay Kit (Invitrogen). The integrity of the RNA was determined with the High-Sensitivity RNA ScreenTape System (Agilent).
60 ng of total RNA per sample was used as input for constructing multiplexed 3’-cDNA libraries using barcoded oligo-dT primers (Datlinger et al., 2021) in an adapted version of Bulk RNA barcoding and sequencing (BRB-seq) protocol (Alpern et al., 2019). The final multiplexed library pools were quantified with Qubit dsDNA HS Assay Kit (Invitrogen) and Collibri™ Library Quantification Kit (Invitrogen), and the proper library fragment distribution was assessed by the TapeStation High-Sensitivity D1000 ScreenTapes kit (Agilent).

treatment_protocol: 293T and A549 reporter cells were induced with IFN mix (20ng/ml IFNa-2a, 20ng/ml IFNa-2b, 20ng/ml IFNb, 10ng/ml IL-28, 5ng/ml IFNg) or 3p-hpRNA (0.1ug/ml) followed by TOPi (30nM Topotecan, 100nM Etoposide) or JAKi (100nM Baricitinib, 300nM Tofacitinib) treatement.

value: lung adenocarcinoma

value: WT

value: IFN mix + TOPi


title: Cerebellum Female 18mo 55ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_55


title: A549_IFN_Topo_Eto_top30_mCherry_R2

description: A549_IFN_Topo_Eto_top30_mCherry_R2.count


title: SLAMseq_K562_REP1_4sUwashout_T8hr

description:
K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv
SLAM-K562-S2-T-8-1


title: SLAMseq_K562_REP2_4sUwashout_T12hr

description:
K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv
SLAM-K562-S2-T-12-2


title: Cerebellum Female 21mo 52ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_52


title: SLAMseq_K562_4sUwashout_JQ1_T2hr

description:
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_with_inhibitors_ReadCounts_Spike-in.tsv
3RNA-SLAM-K562-T-2-JQ1

value: 2 hours post 4-thiouridine wash-out and 1μM JQ1 addition


title: SLAMseq_K562_REP2_4sUwashout_T4hr

description:
K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv
SLAM-K562-S2-T-4-2

value: 4 hours post 4-thiouridine wash-out


title: A549_IFN_Topo_Eto_top30_mCherry_R1

description: A549_IFN_Topo_Eto_top30_mCherry_R1.count


title: SLAMseq_K562_REP1_4sUwashout_T4hr

description:
K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv
SLAM-K562-S2-T-4-1


title: Cerebellum Female 18mo 51ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_51


title: A549_IFN_top30_mCherry_R3

value: IFN mix


title: SLAMseq_K562_REP1_4sUwashout_T2hr

description:
K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv
SLAM-K562-S2-T-2-1

value: 2 hours post 4-thiouridine wash-out


title: Cerebellum Female 15mo 50ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_50


title: SLAMseq_K562_REP2_4sUwashout_T2hr

description:
K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv
SLAM-K562-S2-T-2-2


title: Cerebellum Male 26mo 5ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_5

value: Male


title: SLAMseq_K562_REP2_4sUwashout_T1hr

description:
K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv
SLAM-K562-S2-T-1-2

value: 1 hour post 4-thiouridine wash-out


title: SLAMseq_K562_REP1_4sUwashout_T1hr

description:
K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv
SLAM-K562-S2-T-1-1


title: SLAMseq_K562_REP2_4sUwashout_T0hr

description:
K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv
SLAM-K562-S2-T-0-2

value: 0 hours post 4-thiouridine wash-out


title: A549_IFN_top30_mCherry_R2


title: TTseq_K562_REP1_UT_5min

description:
K562_TTseq_synthesis_measurements_ReadCounts_Total.tsv
K562_TTseq_synthesis_measurements_ReadCounts_Spike-in.tsv
K562_TTseq_synthesis_measurements_synthesis_rates.txt

value: UT 5min


title: A549_IFN_top30_mCherry_R1


title: SLAMseq_K562_REP1_4sUwashout_T0hr

description:
K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv
SLAM-K562-S2-T-0-1

value: Chronic Myeloid Leukemia


title: Cerebellum Female 3mo 53ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_53

value: Cerebellum

value: Female


title: SLAMseq_K562_no4sU_control

description:
K562_SLAMseq_decay_measurements_ReadCounts_Total.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Nascent.tsv
K562_SLAMseq_decay_measurements_ReadCounts_Spike-in.tsv
SLAM-K562-S2-no4sU

value: K562 cell line

value: No 4-thiouridine control


title: Cerebellum Female 21mo 48ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_48


title: A549_IFN_Bari_Tofa_bottom40_mCherry_R3

description: A549_IFN_Bari_Tofa_bottom40_mCherry_R3.count

value: IFN mix + JAKi


title: SLAMseq_K562_REP2_AZ5576

description:
K562_SLAMseq_ReadCounts_Total.tsv
K562_SLAMseq_ReadCounts_Nascent.tsv
K562_SLAMseq_ReadCounts_Spike-in.tsv

data_processing:
Single-end reads were demultiplexed using bcl2fastq (v2.17.1.14) and resulting FASTQ files were trimmed for adapter sequences using Trim_galore (v0.6.5) with a stringency overlap of 3bp.
Trimmed FASTQ files were processed with SLAM-dunk (v0.4.3), enabling multi-mapper reconciliation and using a threshold of at least 2 T > C conversions to mark a read as converted. The no 4sU control sample was processed first to find single nucleotide polymorphisms (SNPs), which was then used to filter the subsequent samples.
`bedtools merge` was then used to merge the 3' UTRs of each Ensembl transcript by gene (v77 identifiers for hg38) for use in the SLAM-dunk counting step.
Assembly: hg38 and dm6
Supplementary files format and content: K562_SLAMseq_ReadCounts_Total.tsv (raw total RNA counts)
Supplementary files format and content: K562_SLAMseq_ReadCounts_Nascent.tsv (raw nascent RNA counts)
Supplementary files format and content: K562_SLAMseq_ReadCounts_Spike-in.tsv (raw spike-in counts)
Library strategy: SLAM-seq

treatment_protocol: K562 cells were treated with transcriptional inhibitors for 2 hours, with 100μM 4-thiouridine in the final hour of treatment.

value: Treated with 1μM AZ-5576 for 2 hours, with 100μM 4-thiouridine in the final hour of treatment


title: SLAMseq_K562_REP2_JQ1

value: Treated with 1μM JQ1 for 2 hours, with 100μM 4-thiouridine in the final hour of treatment


title: A549_IFN_Bari_Tofa_bottom40_mCherry_R2

description: A549_IFN_Bari_Tofa_bottom40_mCherry_R2.count

value: lung adenocarcinoma

value: WT


title: Cerebellum Female 3mo 49ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_49


title: Cerebellum Female 18mo 47ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_47


title: SLAMseq_K562_REP1_JQ1


title: SLAMseq_K562_REP1_DMSO

value: Treated with DMSO for 2 hours and with 100μM 4-thiouridine in the final hour of treatment


title: SLAMseq_K562_REP2_A485

value: Treated with 1μM A-485 for 2 hours, with 100μM 4-thiouridine in the final hour of treatment


title: SLAMseq_K562_REP1_AZ5576


title: A549_IFN_Bari_Tofa_bottom40_mCherry_R1

description: A549_IFN_Bari_Tofa_bottom40_mCherry_R1.count


title: SLAMseq_K562_REP1_A485


title: Cerebellum Female 15mo 46ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_46


title: A549_CTRL_25_75_mCherry_R3

value: untreated


title: Cerebellum Female 3mo 45ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_45


title: WGBS Control CD11b+ Biol. Rep. 2, HiSeq 2500

city: La Jolla

first: Isaac

middle: F.

last: López-Moyado

address: 9420 Athena Cir

department: Division of Signaling and Gene Expression

institute: La Jolla Institute for Immunology

data_processing:
For WGBS analysis, we employed BSMAP (v2.9) (Xi and Li, 2009) to align paired-end reads from bisulfite-treated samples to the mm10 mouse reference genome allowing 4 mismatches. Reads mapping to multiple locations in the reference genome with the same mapping score were removed as well as the 5' ends bearing quality lower than 20 (mapping parameters: -n 1 -v 4 -w 2 -r 0 -q 20 -R -p 8). Duplicate reads caused by PCR amplification were removed by BSeQC (v1.0.3) (Lin et al., 2013) using default parameters. An effective genome size of 1.87e9 (as suggested in BSeQC for Mus musculus genome) was employed to calculate maximum coverage at the same genomic location. In addition, BSeQC was employed for removing DNA methylation artifacts introduced by end repair during adaptor ligation. For paired-end sequencing, overlapping segments of two mates of a pair were reduced to only one copy to avoid considering the same region twice during the DNA methylation quantification. To estimate CpG DNA methylation, we employed the methratio.py tool included in BSMAP (v2.9) (Xi and Li, 2009), merging DNA methylation at each CpG di-nucleotide (combining CpG methylation ratios on both DNA strands).
Assembly: mm10
Supplementary files format and content: Methylation summary matrices were generated using the methratio.py tool included in BSMAP (v2.9), and summarize the ratio of bisulfite-unconverted to total cytosines (C_count/[C_count+CT_count]).

source_name: Bone marrow

growth_protocol: To delete TET genes, total bone marrow cells from Control (Rosa26-LSL-YFP) or Tet1/2/3 f/f Rosa26-LSL-YFP 6-8-week-old mice were lentivirally infected with a Cre vector. These cells were transferred into lethally irradiated CD45.1+ mice with 2 x 10^6 helper bone marrow cells from CD45.1+ mice.

extract_protocol:
CD11b+ cells were isolated by flow cytometry and DNA was isolated using the PureLink genomic DNA mini kit (Life technologies).
DNA was fragmented to an average size of 200 bp using the Adaptive Focused Acoustics Covaris E220 instrument. Before bisulfite treatment, fully unmethylated λ (lambda) DNA (Promega) was spiked into the mouse genomic DNA at a ratio of 1:200. DNA library was prepared by NEBNext® DNA Library Prep Master Mix Set for Illumina (New England BioLabs). Methylated adapters (NeBNext Multiplex Oligos for Illumina, New England BioLabs) were used to determine the bisulfite conversion efficacy. DNA was bisulfite-treated using the MethylCode Bisulfite Conversion Kit (Life Technologies). After the bisulfite conversion the purified DNA was amplified for 4 cycles (low amplification) using Kapa HiFi Uracil+ (Kapa Biosystems). Two independent WGBS samples per genotype were evaluated.

value: Bone marrow

value: Lentivirally transduced with Cre


title: WGBS Control CD11b+ Biol. Rep. 1, HiSeq 2500


title: A549_CTRL_25_75_mCherry_R2


title: SLAMseq_K562_REP2_DMSO


title: Cerebellum Female 21mo 44ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_44


title: Cerebellum Female 15mo 42ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_42


title: SLAMseq_K562_REP2_ACTD

value: Treated with 1μg/mL Actinomycin D for 2 hours, with 100μM 4-thiouridine in the final hour of treatment


title: WGBS TetTKO CD11b+ Biol. Rep. 1, HiSeq 2500

value: Tet1/2/3 f/f Rosa26-YFPLSL


title: A549_CTRL_25_75_mCherry_R1


title: Cerebellum Female 18mo 43ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_43


title: A549_3p_hpRNA_Topo_Eto_top40_mCherry_R2

description: A549_3p_hpRNA_Topo_Eto_top40_mCherry_R2.count

value: 3p-hpRNA + TOPi


title: Total RNA-seq Control CD11b+ Biol. Rep. 2, HiSeq 2500

description: WT_Cd11b_2_totalRNAseq_UNIQUE_ENSEMBL.cntTable

data_processing:
For total RNA-seq analysis, quality and adapter trimming was performed on raw RNA-seq reads using TrimGalore! 431 v0.4.5 with default parameters, retaining reads with minimal length of 25 bp. Ribosomal RNA reads were filtered out using Tagdust2. Resulting reads were aligned to mouse genome mm10 using STAR v2.5.3a (Dobin et al., 2013). Bioconductor libraries rtracklayer and GenomicAlignments were used to generate a table of counts from gene annotations. The DESeq2 package v1.30.0 was used to normalize the raw counts and identify differentially expressed genes (greater than 2-fold change with adjusted p-value < 0.05).
Assembly: mm10
Supplementary files format and content: Table of raw counts of genes

growth_protocol: To delete TET genes, total bone marrow cells from Control (Rosa26-LSL-YFP), Tet2/3 f/f Rosa26-LSL-YFP, or Tet1/2/3 f/f Rosa26-LSL-YFP 6-8-week-old mice were lentivirally infected with a Cre vector. These cells were transferred into lethally irradiated CD45.1+ mice with 2 x 10^6 helper bone marrow cells from CD45.1+ mice.

extract_protocol: 10 million cells were sorted and then whole RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). Ribo-zero RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina) with minor modifications. The starting RNA was 800 ng. Ribosomal RNAs were depleted using magnetic beads. Next, RNA was fragmented, and cDNA was synthesized using Superscript II (Invitrogen). After A-tailing and adaptor ligation, libraries were generated by amplifying the cDNA for 10 cycles.


title: WGBS TetTKO CD11b+ Biol. Rep. 2, HiSeq 2500


title: Cerebellum Female 3mo 41ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_41

data_processing:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v0.3.7, parameters: --paired --length 25). Trimmed sequences were aligned using STAR (v2.5.3a). Multi-mapped reads were filtered. Data visualization and analysis was performed using SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), custom RStudio (https://www.rstudio.com/) scripts and the following Bioconductor packages: Deseq2 (Love et al., 2014), topGO (Alexa and Rahnenfuhrer, 2010) and org.Mm.eg.db.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file including raw counts for each sample

value: Cerebellum


title: Total RNA-seq Control CD11b+ Biol. Rep. 1, HiSeq 2500

description: WT_Cd11b_1_totalRNAseq_UNIQUE_ENSEMBL.cntTable


title: A549_3p_hpRNA_Topo_Eto_top40_mCherry_R3

description: A549_3p_hpRNA_Topo_Eto_top40_mCherry_R3.count


title: Cerebellum Female 21mo 40ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_40

value: Female


title: Total RNA-seq TetTKO CD11b+ Biol. Rep. 1, HiSeq 2500

description: TKO_Cd11b_1_totalRNAseq_UNIQUE_ENSEMBL.cntTable


title: A549_3p_hpRNA_Topo_Eto_top40_mCherry_R1

description: A549_3p_hpRNA_Topo_Eto_top40_mCherry_R1.count


title: A549_3p_hpRNA_top30_mCherry_R3


title: A549_3p_hpRNA_top30_mCherry_R2


title: Total RNA-seq Tet2/3 DKO CD11b+ Biol. Rep. 2, HiSeq 2500

description: DKO_Cd11b_2_totalRNAseq_UNIQUE_ENSEMBL.cntTable

value: Tet2/3 f/f Rosa26-YFPLSL


title: Total RNA-seq TetTKO CD11b+ Biol. Rep. 2, HiSeq 2500

description: TKO_Cd11b_2_totalRNAseq_UNIQUE_ENSEMBL.cntTable


title: Cerebellum Female 18mo 39ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_39


title: ATAC-seq Control LSK Biol. Rep. 1

data_processing:
ATAC-seq datasets were mapped employing BWA v0.7.13. BWA-aln was used in paired-end mode, and Mus musculus mm10 was used as reference genome. Reads were filtered out if they had a MAPQ score of less than 30, and only reads that were at least 25 bp were considered for the rest of the analysis. ATAC-seq signal was quantified over the list of hematopoietic enhancers published in PMID: 25103404. The DESeq2 package v1.30.0 was used to identify differentially accessible enhancers (greater than 2-fold change with adjusted p-value < 0.05).
Assembly: mm10
Supplementary files format and content: Table of raw counts of ATAC-seq signal overlapping hematopoietic enhancers from PMID: 25103404.

extract_protocol: For ATAC-seq library preparation, 50,000 cells were collected by centrifugation and washed once with 50 µl of ice-cold PBS and centrifuged at 600g for 5 min at 4°C. Cell pellets were resuspended in 50 µl of cold lysis buffer [10 mM tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630] and spun down immediately at 500g for 10 min at 4°C. Supernatant was discarded and nuclei were resuspended in 50 µl of transposition reaction mix (25 µl of 1× TD buffer from Illumina, 2.5 µl of Tn5 transposase, and 22.5 µl of H2O), incubated at 37°C for 30 min, and DNA was purified with a Qiagen MinElute kit (Qiagen). Library was amplified with KAPA HiFi HotStart Real-time PCR Master Mix (Roche) using indexed primers and sequenced on an Illumina HiSeq 2500 (paired end 50-bp reads).

treatment_protocol: To induce conditional excision of floxed alleles using the Mx1-Cre recombinase, pIpC (polyinosinic–polycytidylic acid, Sigma: 300 μg per mouse) in PBS was injected five times intraperitoneally every other day for a total of five injections. The day of the last tamoxifen injection was designated Day 0.

value: LSK

value: Tet2/3 f/f

value: poly-I:C treatment


title: Cerebellum Female 3mo 37ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_37


title: SLAMseq_K562_REP1_ACTD

description:
K562_SLAMseq_ReadCounts_Total.tsv
K562_SLAMseq_ReadCounts_Nascent.tsv
K562_SLAMseq_ReadCounts_Spike-in.tsv

value: Chronic Myeloid Leukemia

value: K562 cell line


title: ATAC-seq Control LSK Biol. Rep. 2


title: Total RNA-seq Tet2/3 DKO CD11b+ Biol. Rep. 1, HiSeq 2500

description: DKO_Cd11b_1_totalRNAseq_UNIQUE_ENSEMBL.cntTable


title: Cerebellum Female 15mo 38ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_38


title: Cerebellum Male 18mo 35ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_35

value: Male


title: A549_3p_hpRNA_top30_mCherry_R1

value: lung adenocarcinoma

value: WT


title: Wildtype harvested following 5 hours of sleep deprivation, replicate 3 [RNA-Seq]

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

description:
WTSD5_PFC_3
Counts matrices (gene and transcript) provided as supplementary files: RNAseq_gene.txt, RNAseq_transcript.txt

data_processing:
RNA-Seq
HiSeq Cobtrol Software (HC) version 2.2.68 was used for base calling. The raw bcl files were converted to fastq files using software program bcl2fastq2.17.1.14.  Adaptors were trimmed from the fastq files during the conversion.
Salmon version 1.3.0 was used for this analysis. A "salmon index" was built with decoys using GRCm38 and Gencode (vM25). For each FASTQ file, "salmon quant" was used to perform quantification.
Assembly: GRCm38
Supplementary files format and content: Count matrices (gene and transcript levels) provided as supplementary files
snRNA-seq
HiSeq Cobtrol Software (HC) version 2.2.68 was used for base calling. The raw bcl files were converted to fastq files and demultiplexed using software program bcl2fastq2.17.1.14 with cellranger mkfastq.
Salmon version 1.3.0 was used for this analysis. A "salmon index" was built with decoys (including intronic regions) using GRCm38 and Gencode (vM25). For each FASTQ file, "salmon alevin" was used to perform quantification.
Assembly: GRCm38
Supplementary files format and content: Count matrix provided as supplementary file

source_name: Pre-Frontal Cortex

growth_protocol: C57BL6/J mice were house in standard cages on a 12:12 h light:dark cycle with food and water ad libitum.

extract_protocol:
RNA was extracted from thawed tissue using the Qiagen RNAeasy Microarray Tissue kit with RWT buffer. The tissue was lysed and homogenized using a TissueLyzer. 1ml of Qiazol was added to the pre-sterilized 2ml round bottom tubes with one 5mm steel bead inside, before adding the tissue. The TissueLyzer was operated for 2x3 min at 50Hz. Samples were spun down prior to opening the tubes. Lysate was transferred to a clean 2 ml tube. RNA was isolated through phase separation. 200 µl pf chloroform was added followed by vigorous shaking. Samples were then incubated at room temperature for 3 min. Next, samples were centrifuged at 12,000 g (max centrifuge) for 15 min at 4 C. The aqueous phase was transferred to a new tube. Total RNA was purified (Binding and washing with the RNAeasy column). 600 µl (1 volume) of 100% EtOH was added. 600 µl was then transferred to an RNAeasy mini spin column placed inside of a 2ml collection tube and centrifuged at max speed for 15s at room temperature. This was repeated with the remaining 600 µl. The loaded columns were washed using 500 µl of RWT (Qiagen) and centrifuged at max speed for 15 s at room temperature. The flow through was discarded and the collection tube was kept. The membrane was washed twice with 500 µl of RPE buffer (Qiagen) followed by 15s (first wash) and 2 min (second wash) centrifugation at max speed at room temperature. The spin column was placed on a new collection tube and centrifuged at max speed for a minute (to prevent EtOH carryover). RNA was eluted from the column. The column was placed into a 1.5 ml Eppendorf. 30 µl of RNAse free water was added and centrifuged at max speed for 1 min at room temperature. The volume was pipetted in the Eppendorf tube back into the column and the previous step was repeated. 1 µl was used to quantify using a Nanodrop Spectrophotometer. The RNA was freezed at -80 C after quantification.
The integrity of total RNA was assessed using Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) with the High Sensitivity RNA Analysis Kit.  RNA Quality Numbers (RQNs) from 1 to 10 were assigned to each sample to indicate its integrity or quality.  “10” stands for a perfect RNA sample without any degradation, whereas “1” marks a completely degraded sample.  RNA samples with RQNs ranging from 8 to 10 were used for RNA library preparation with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA).  Briefly, mRNA was isolated from 2.5 µg of total RNA using poly-T oligo attached to magnetic beads and then subjected to fragmentation, followed by cDNA synthesis, dA-tailing, adaptor ligation and PCR enrichment.  The sizes of RNA libraries were assessed by Fragment Analyzer with the High Sensitivity NGS Fragment Analysis Kit.  The concentrations of RNA libraries were measured by StepOnePlus Real-Time PCR System (ThermoFisher Scientific, San Jose, CA) with the KAPA Library Quantification Kit (Kapabiosystems, Wilmington, MA).  The libraries were diluted to 2 nM with RSB (10 mM Tris-HCl, pH8.5) and denatured with 0.1 N NaOH.  Eighteen pM libraries were clustered in a high-output flow cell using HiSeq Cluster Kit v4 on a cBot (Illumina).  After cluster generation, the flow cell was loaded onto HiSeq 2500 for sequencing using HiSeq SBS kit v4 (Illumina).  DNA was sequenced from both ends (paired-end) with a read length of 100 bp.

treatment_protocol: Begining at light onset, sleep deprived mice were kept awake for 5 hours via gentle handling. Prefrontal cortex tissue was collected at the conclusion of sleep deprivation (SD5, E) and immediately flash frozen in liquid nitrogen. Control animals that were left in their home cage to sleep were dissected at the same time of day (HC5, C).

value: Pre-Frontal Cortex

value: Brain cell

tag: age

value: 8-12 weeks

value: male

value: Sleep Deprivation

tag: insert size


title: Wildtype harvested following 5 hours of sleep deprivation, replicate 5 [RNA-Seq]

description:
WTSD5_PFC_5
Counts matrices (gene and transcript) provided as supplementary files: RNAseq_gene.txt, RNAseq_transcript.txt


title: Wildtype harvested following 5 hours of sleep deprivation, replicate 4 [RNA-Seq]

description:
WTSD5_PFC_4
Counts matrices (gene and transcript) provided as supplementary files: RNAseq_gene.txt, RNAseq_transcript.txt


title: ATAC-seq Tet2/3 iDKO LSK Biol. Rep. 1

value: Bone marrow

value: Tet2/3 f/f Mx1-Cre


description: A549_3p_hpRNA_Bari_Tofa_bottom40_mCherry_R1.count

value: 3p-hpRNA + JAKi


title: ATAC-seq Tet2/3 iDKO LSK Biol. Rep. 2


title: Cerebellum Male 15mo 34ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_34

extract_protocol:
RNeasy Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT. Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.

value: Cerebellum


title: Cerebellum Male 3mo 33ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_33


title: Wildtype harvested following 5 hours of sleep deprivation, replicate 1 [RNA-Seq]

description:
WTSD5_PFC_1
Counts matrices (gene and transcript) provided as supplementary files: RNAseq_gene.txt, RNAseq_transcript.txt


description: A549_3p_hpRNA_Bari_Tofa_bottom40_mCherry_R2.count


title: Wildtype homecage control harvested at ZT hour 5, replicate 4 [RNA-Seq]

description:
WTHC5_PFC_4
Counts matrices (gene and transcript) provided as supplementary files: RNAseq_gene.txt, RNAseq_transcript.txt

value: Control


description: A549_3p_hpRNA_Bari_Tofa_bottom40_mCherry_R3.count


title: Wildtype harvested following 5 hours of sleep deprivation, replicate 2 [RNA-Seq]

description:
WTSD5_PFC_2
Counts matrices (gene and transcript) provided as supplementary files: RNAseq_gene.txt, RNAseq_transcript.txt


title: 293T_IFN_Topo_Eto_top30_mCherry_R1

description: 293T_IFN_Topo_Eto_top30_mCherry_R1.count

source_name: kidney; Embryo

value: kidney; Embryo

value: IFN mix + TOPi


title: Wildtype homecage control harvested at ZT hour 5, replicate 5 [RNA-Seq]

description:
WTHC5_PFC_5
Counts matrices (gene and transcript) provided as supplementary files: RNAseq_gene.txt, RNAseq_transcript.txt


title: Cerebellum Male 18mo 31ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_31


title: 293T_IFN_Topo_Eto_top30_mCherry_R2

description: 293T_IFN_Topo_Eto_top30_mCherry_R2.count


title: Wildtype homecage control harvested at ZT hour 5, replicate 2 [RNA-Seq]

description:
WTHC5_PFC_2
Counts matrices (gene and transcript) provided as supplementary files: RNAseq_gene.txt, RNAseq_transcript.txt


title: 293T_IFN_Topo_Eto_top30_mCherry_R3

description: 293T_IFN_Topo_Eto_top30_mCherry_R3.count


title: Wildtype homecage control harvested at ZT hour 5, replicate 3 [RNA-Seq]

description:
WTHC5_PFC_3
Counts matrices (gene and transcript) provided as supplementary files: RNAseq_gene.txt, RNAseq_transcript.txt


title: 293T_IFN_top20_mCherry_R3

value: IFN mix


title: Cerebellum Male 15mo 30ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_30


title: Cerebellum Male 21mo 32ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_32


title: Pit_T3_Sun_ATAC_3

city: Bethesda

first: Hong

last: Liu

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

description:
Pit_T3_Sun_ATAC_merged.wig
Pit_T3-regulated_Sun_ATAC_1776.txt

data_processing:
Libraries were multiplex sequenced in one lane using Illumina HiSeq2500 Sequencer at NIDDK Genomics Facility
ChIP-seq and ChAP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-6); For ChIP-Seq of factors: Windows (50), Gaps (50), FDR (1e-3)
Single-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the counts/reads per million mapped reads (CPM) on exonic regions as expression measurements for each gene.
ATAC-seq bam files were analyzed with Genomatix programs (Macs2 and edgeR) for the open-chromatin peaks.
Genome_build: mm9
Supplementary_files_format_and_content: comma delimited files include CPM values for each gene; tab-delimited text files include FPKM values for each sites

source_name: pituitary (purified)

extract_protocol:
Nuclei were isolated from 1 or 2 pooled, frozen pituitaries from Thrb-b2Cre/+;Rosa26Sun1-GFP/Sun1-GFP mice by homogenization in 0.5 mL ice cold nuclei isolation buffer (NIB)  with EDTA-free protease inhibitor using a 1 mL glass homogenizer and pestle A. The homogenate was filtered through a cell strainer then centrifuged at 500 g for 5 min at 4 C. The nuclear pellet was washed with resuspension buffer (RSB) containing 0.4% IGEPAL®CA-630. The pellet was resuspended in 10 mL RSB with 0.4% IGEPAL-630, incubated with 10 μg of anti-GFP antibody (Abcam ab290, RRID: AB_303395) for 30 min, then incubated with 60 μL of Dynabeads for 20 min. Bead-bound nuclei were passed through a 20 μm strainer and washed in 3 x 5 mL, 2 x 1 mL, and 1 x 1 mL RSB with 0.4% IGEPAL-630. Approximately 50,000 bead-bound nuclei were incubated in a 50 μL volume containing 25 μL of 2X Tagment DNA buffer, 2.5 μL Tn5 transposase, 0.5 μL of 1% digitonin, and 22 μL nuclease-free water for 30 min at 37°C.  Fragmented genomic DNA was recovered using MinElute spin columns ), then amplified by five cycles of quantitative PCR. Typically, 4 - 7 PCR cycles were added to the initial 5 cycles. Amplified DNA was purified on AMPure XP beads (Beckman A63881), analyzed on an Agilent Bioanalyzer, then sequenced (50 base, single end) on an Illumina HiSeq 2500 instrument.
DNA was amplified with PCR using Nextera i7- and i5-index primers for Illumina protocols

value: Rosa26Sun1-GFP; Thrb2-Cre

value: Thrb2 positive pituitary cells  (purified)

value: MMI + T3 treatment (hyperthyroid)

tag: antibody

value: anti-GFP (ab290, Abcam)


title: Cerebellum Male 21mo 36ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_36

value: Male


title: Pit_T3_Sun_ATAC_4


title: Wildtype homecage control harvested at ZT hour 5, replicate 1 [RNA-Seq]

description:
WTHC5_PFC_1
Counts matrices (gene and transcript) provided as supplementary files: RNAseq_gene.txt, RNAseq_transcript.txt

value: Pre-Frontal Cortex

value: Brain cell

value: WT


title: Pit_T3_Sun_ATAC_2


title: Cerebellum Male 21mo 28ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_28


title: 293T_IFN_top20_mCherry_R2


title: Pit_T3_Sun_ATAC_1


title: 293T_IFN_Bari_Tofa_bottom40_mCherry_R2

description: 293T_IFN_Bari_Tofa_bottom40_mCherry_R2.count

value: IFN mix + JAKi


title: Pit_mmi_Sun_ATAC_3

description:
Pit_mmi_Sun_ATAC_merged.wig
Pit_T3-regulated_Sun_ATAC_1776.txt

value: MMI treatment (hypothyroid)


title: Cerebellum Male 18mo 27ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_27


title: Cerebellum Male 12mo 3ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_3


title: Cerebellum Male 3mo 29ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_29


title: 293T_IFN_top20_mCherry_R1


title: Pit_T3_ChIP_IgG_2

source_name: pituitary

extract_protocol:
Samples containing 12 pooled, frozen pituitaries were cross-linked in 1% formaldehyde for 10 min at room temperature, then glycine added at final concentration 125 mM to quench the reaction. Samples were centrifuged at 1,400 g for 2 min at room temperature. The pellet was washed by vortexing in 10 mL ice-cold PBS with protease inhibitor, pelleted again, suspended in 2 mL ice-cold cell lysis buffer and homogenized using 40 plunges with pestle A in a 1 mL glass homogenizer on ice. The sample centrifugated at 3,800 g, for 10 min at 4 °C. The nuclear pellet was resuspended in 1.5 mL nuclear lysis buffer, incubated at room temp for 10 min, then mixed with an additional 1.5 mL of buffer. The sample was sonicated in a 15 mL conical tube then centrifuged at 18,000 g for 10 min at 4 °C, to yield supernatant (sample) for analysis. For ChIP-seq assays of histone marks, 3 mL of supernatant was incubated with specific antibody on a rotator at 4°C overnight, then mixed with 20 ul pre-washed Magna ChIP Protein A+G beads for 2 h. The beads were washed sequentially in dilution buffer, then a low-salt wash , then a high-salt wash, then an ice-cold LiCl wash, then rinsed twice in 1 ml TE buffer. Bound proteins were eluated from the beads using 250 μl elution buffer, then cross-links reversed by addition of 10 μl 5 M NaCl with incubation at 65°C for 4 h.  To release DNA, 5 μl proteinase K (20 mg/mL) was added to a final concentration of 0.5 mg/mL together with the addition of 5 uL of 0.5 M EDTA, and 10 uL of 1 M Tris pH 6.5, then incubated at 56 °C for 1 h. DNA was collected using a magnet rack, purified by QIAquick PCR Purification Kit (QIAGEN, 28104) and quantified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, #Q32851).
ChIP-seq libraries were generated using Illumina Truseq kit (Cat# 15034288).

treatment_protocol: Mice were kept in a 12h light / 12 h dark cycle and tissues taken in the light phase between ~14.00 - 18.00 hours. To induce hypothyroidism, 0.05% Methimazole (MMI) and 1% potassium perchlorate (KClO4) were added to the drinking water for 4 or 5 weeks. Subgroups under this treatment were made hyperthyroid for the final week by co-administration of 0.5 μg/ml T3 in the drinking water

value: wild type

value: pituitary tissue

value: Rabbit IgG


title: Pit_T3_ChIP_IgG_1


title: 293T_CTRL_25_75_mCherry_R5

value: untreated


title: Pit_mmi_Sun_ATAC_1


title: 293T_IFN_Bari_Tofa_bottom40_mCherry_R3

description: 293T_IFN_Bari_Tofa_bottom40_mCherry_R3.count

value: kidney; Embryo


title: Pit_mmi_Sun_ATAC_2


title: Cerebellum Male 3mo 25ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_25

value: Cerebellum


title: Cerebellum Male 21mo 24ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_24


title: Pit_mmi_Sun_ATAC_4


title: 293T_IFN_Bari_Tofa_bottom40_mCherry_R1

description: 293T_IFN_Bari_Tofa_bottom40_mCherry_R1.count


title: Pit_T3_ChIP_H3K4m3_1

value: anti-H3K4me3 (07-473, Millipore)


title: Pit_T3_ChIP_H3K27ac_1

value: anti-H3K27ac (ab4729, Abcam)


title: Pit_T3_ChIP_H3K27ac_2


title: Pit_T3_ChIP_H3K4m3_2


title: Cerebellum Male 15mo 26ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_26


title: Pit_T3_ChIP_H3K4m3_3


title: 293T_CTRL_25_75_mCherry_R3


title: Pit_T3_ChIP_IgG_3


title: 293T_CTRL_25_75_mCherry_R4


title: Cerebellum Male 18mo 23ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_23


title: Cerebellum Male 15mo 22ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_22


title: 293T_CTRL_25_75_mCherry_R2


title: Pit_mmi_ChIP_IgG_3


title: Pit_T3_ChIP_H3K4m1_2

value: anti-H3K4me1 (ab8895, Abcam)


title: 293T_CTRL_25_75_mCherry_R1


title: Pit_T3_ChIP_H3K27ac_3

value: MMI + T3 treatment (hyperthyroid)


title: Pit_T3_ChIP_H3K4m1_1


title: Cerebellum Male 3mo 21ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_21


title: Pit_mmi_ChIP_IgG_2


title: 293T_3p_hpRNA_Topo_Eto_top30_mCherry_R3

description: 293T_3p_hpRNA_Topo_Eto_top30_mCherry_R3.count

value: 3p-hpRNA + TOPi


title: Cerebellum Male 21mo 20ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_20

value: Male


title: Pit_mmi_ChIP_H3K27ac_3


title: Pit_mmi_ChIP_H3K27ac_1


title: Pit_mmi_ChIP_H3K27ac_2


title: 293T_3p_hpRNA_Topo_Eto_top30_mCherry_R2

description: 293T_3p_hpRNA_Topo_Eto_top30_mCherry_R2.count


title: Pit_mmi_ChIP_H3K4m3_3


title: Pit_T3_ChIP_H3K4m1_3


title: 293T_3p_hpRNA_Topo_Eto_top30_mCherry_R1

description: 293T_3p_hpRNA_Topo_Eto_top30_mCherry_R1.count


title: Pit_mmi_ChIP_H3K4m3_1


title: Pit_mmi_ChIP_H3K4m3_2


title: Cerebellum Male 26mo 2ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_2


title: Cerebellum Male 15mo 18ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_18


title: 293T_3p_hpRNA_top20_mCherry_R5


title: Pit_mmi_ChIP_H3K4m1_3


title: Cerebellum Male 3mo 17ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_17


title: Pit_mmi_ChIP_IgG_1


title: Pit_mmi_ChIP_H3K4m1_2


title: 293T_3p_hpRNA_top20_mCherry_R4


title: Cerebellum Male 21mo 16ID

description:
Unstranded mRNA-seq
sample name:
BulkSeq_cer_16


title: Pit_mmi_ChIP_H3K4m1_1