title: RNA_sequencing_MCF7_TEX_2

city: Amsterdam

data_processing:
RNA-seq: FASTQ files were aligned to the human hg19 genome using STAR (STAR_2.5.0a). File conversions were done using samtools. Reads on exons were counted using HTSEQ (0.5.4p3).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file (.bw) for each sequencecs fastq file

extract_protocol: RNA was extracted from Hela cells using Trizol reagent (15596-018, Ambion life technologies) according to the manufactures protocol followed by DNase I treatment. Library preparation was done using illumina Truseq Stranded mRNA Library Prep kit.

tag: treatment

value: MCF7 + TEX


title: RNA_sequencing_ALKBH5_KD_1

status: Public on Aug 26 2022

type: SRA

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

library_source: transcriptomic

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010) with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: TotalRNAs_readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes.

molecule: total RNA

organism: Homo sapiens

source_name: HeLa

growth_protocol: HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C. Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq.

extract_protocol: RNA was extracted from U2OS and HEK293 cells using QIAzol Reagent (Qiagen; 79306) and Trizol reagent for HeLa cells (15596-018, Ambion life technologies) according to the manufactures protocol followed by DNase I treatment. PolyA selected RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; E7490) for U2OS and HEK293 and Oligotex kit (QIAGEN) for HeLa cells and further processed with the NEBNext Ultra Directional RNA Library Prep Kit (NEB; E7420S) for U2OS and HEK293 or SMARTer® Stranded RNA-Seq Kit (Takara; 634839) and illumina Truseq Stranded mRNA Library Prep kit. for HeLa cells or 3′–3′-mRNA-Seq Library Prep Kit (lexogen; 015UG009V0211).

treatment_protocol: siRNAs against ALKBH5 were purchased from Life Technologies ( ALKBH5 siRNA catalogue number 4392420, ID s29686 and s29687; Cells were transfected for using Dharmafect I reagent (Dharmacon) following the manufacturer’s instructions (2 siRNAs per target gene) for 72h.

tag: cell type

value: HeLa

value: RNA sequencing of ALKBH5 KD


title: MAC1_STAT3_MWZ7484

city: Memphis

first: Brian

middle: J

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

country: USA

institute: St. Jude Children's Research Hospital

library_source: genomic

data_processing:
Single-end data were aligned to the hg19 revision of the human reference genome using bowtie v1.2.2 with parameters -k 2 -m 2 --best.
Paired-end data were aligned to the hg19 revision of the human reference genome using bowtie v1.2.2 in paired-end mode with parameters -k 2 -m 2 --best -X 600.
Paired-end alignments were converted into fragments using samtools view, samtools sort, and bedtools bamtobed.
Single-end read coverage was calculated using MACS v1.4 with parameters -w -S --space=50 --nomodel --shiftsize=200.
Paired-end fragment coverage was calculated in 50bp bins genome-wide using bedtools makewindows and bedtools intersect and were normalized to the millions of mapped reads.
Assembly: hg19
Supplementary files format and content: Paired-end bigWig files contain reads-per-million-normalized coverage of fragments in 50bp bins.
Supplementary files format and content: Single-end bigWig files contain reads-per-million-normalized coverage of reads in 50bp bins.

molecule: genomic DNA

growth_protocol: Cells were grown in T75 flasks in RPMI media containing 10% FBS and 1% pen-strep.

extract_protocol:
For each target, 5 μg of antibody coupled to 2 μg of magnetic Dynabeads (Life Technologies) was added to 3 ml of sonicated nuclear extract from formaldehyde-fixed cells. Chromatin was immunoprecipitated overnight, cross-links were reversed, and DNA was purified by precipitation with phenol:chloroform:isoamyl alcohol. DNA pellets were resuspended in 25 μl of TE buffer.
Swift 2S automated library prep (manufacturer's instructions).

tag: cell line

value: ALCL

tag: antibody


title: SD4 control

city: Nathan

first: Tessa

middle: M

last: Page

state: QLD

address: 170 Kessels Road

department: Science and Environment

country: Australia

institute: Griffith University

data_processing:
Customised sequencing was performed on a single lane of an Illumina NovaSeq 6000, sequencing 26 bp on read 1, and 100 bp on read 2.
Raw sequence data were processed using Illumina BCL2FASTQ.
Quality control was performed with FastQC.
CEL-Seq-pipeline (https://github.com/yanailab/CEL-Seq-pipeline) for demultiplexing and mapping.
Assembly: Reference transcriptomes were created using transcriptomes for P. onkodes and S. durum (NCBI BioProject PRJNA518156, accession numbers GHIN00000000.1 and GHIO00000000.1 for S. cf. durum and P. cf. onkodes, respectively).
Supplementary files format and content: csv matrix of counts data for Porolithon onkodes
Supplementary files format and content: csv matrix of counts data for Sporolithon durum

organism: Sporolithon durum

source_name: pigmented tissue

growth_protocol: Coralline algae were cultured for three months in flow through aquarium where temperature and pH were altered.

extract_protocol:
Fragments of CCA were thoroughly cleaned prior to sampling for molecular analysis under a microscope and all epiphytes, as far as possible, were removed. CCA were rinsed with filtered seawater and RNAlater® and then blotted with a kimwipe to remove bacterial film. RNA was extracted following a modified TRIzol protocol.
cDNA synthesis, library preparation, and sequencing followed the single-cell sequencing (CEL-Seq2) protocol detailed in Hashimonshony et al. 2016

treatment_protocol: Fragments of CCA (20 per species) were divided across four treatments [“control” (unmanipulated seawater conditions, 27.2 ºC, 8.0 pH/450 µatm pCO2), “T” (elevated temperature and ambient pH, 29.5 ºC, 8.0 pH/450 µatm pCO2), “pH” (reduced pH and ambient temperature, 27.2 ºC, 7.7 pH/1000 µatm pCO2), or “T+pH” (elevated temperature and reduced pH, 29.5 ºC, 7.7 pH/1000 µatm pCO2)] with five biological replicates (n = 5) per treatment for a duration of three months.

tag: tissue

value: pigmented tissue

value: control


title: RNA_sequencing_MCF7_TEX_1


title: SD2 elevated temperature

value: elevated temperature


title: Q13Xeno_Input_MWZ8047

source_name: Mouse xenograft

value: Mouse xenograft


title: human WBC, GB4030163 (iDNase-seq)

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 10 Center Dr

department: Systems Biology Center

institute: NHLBI

data_processing:
Basecalls performed
The raw fastq files are read and separated into 480 files corresponding to 96 pairs of cell barcodes over 5 replicates. The 480 pairs are shown in barcode_480.txt. A read is considered as belonging to one of the barcodes if the beginning of read 1 or read 2 contains the same pair of barcodes in the left and right column respectively.  After separting each set of fastq files into 480 files, some base pairs starting from 5' are trimmed and the remaining reads are mapped to the human genome using bowtie2.
The top 30 barcodes are selected from each well based on read count, so 30 nuclei are sorted for each well with doublets removed, where the number removed was calculated based on the collision rate like in (Science. 2015 May 22; 348(6237): 910–914). These are denoted as single cells because of the low likelihood of two cells in the same well having the same barcode. We required that qualifying cells have more than 100 reads and a FRiP greater than 0.1. With these requirements, 4489 cells were obtained, and we were able to identify 218,042 DHSs. For each cell, we calculated the reads that were located within the DHS and stored the results in a matrix.
Genome_build: hg18
barcode_480.txt: two columns, the left column refers to a DNA barcode starting from the 5' end while the right column refers to a DNA barcode starting from the 3' end
peaks_218042_WBC.txt: first column is for chromsome, second column is for DHS start site, and third column is for DHS end site
iDNase_4489_cells_218042_peaks_counts_at_WBC.mtx: This file contains read count data for single cells in MatrixMarket format. Each row corresponds to a non-zero entry with the row, column, and then value specified. Reading the matrix results in a 218042 x 4489 matrix of peaks by cells where each element represents the number of reads located within a DHS site for some single cell.

source_name: WBC

extract_protocol:
DNase-seq human 1.25M 2-step crosslink human healthy T/B/NK/monocyte, final 0.1U/μl DNase digestion 37°C 5 minutes, T cell split #1-15 wells, B cell split #16-30 wells, NK cell split #31-45 wells, monocyte split #46-61 wells, TdT&T4 methods adding P7 barcode adaptor (12.5μl volumn/well 37°C 60 minutes), pool, dilution, counting and redistribute into 96-well plate, total 20 nuclei per well seal completely, 65°C overnight; direct PCR1 (12 cycles), pool all the DNA, EXO I 30 minutes, A-tailing and P5 ligation(rt overnight) , column purification and PCR2(16 cycles), run-e-gel and cut from 200-500bp rc#1 i5-01
The isolated 50M of PBMC suspended by 50ml PBS /MgCl2 are firstly fixed by adding 400μl freshly prepared 0.25M Disuccinimidyl glutarate (DSG, ThermoFisher Scientific, catalog no.20593) and incubate at room temperature for 45 minutes with rotation. After protein-protein fixation by DSG and washing three times by PBS, cells suspended by culture medium DMEM supplemented with 10% FBS are further fixed by the addition of 1:15 volume of 16% (w/v) methanol-free formaldehyde solution (Thermo Fisher Scientific) and incubate at room temperature for 10 minutes. The fixing reaction is terminated by a 1:10 volume of 1.25 M glycine and incubate at room temperature for 5 minutes. The fixed cells are collected by centrifugation at 1320rpm for 7 minutes and washed with PBS. The cells are stored in aliquots (1 × 10e6 cells per tube) at −80°C until use.

value: WBC


title: Q13Xeno_STAT3_MWZ8047


title: s_42_764012_tetfzd1_het_p0_neg7dox

city: Kansas City

first: Congrong

middle: Ron

last: Yu

state: Missouri

institute: Stowers Insitute for Medical Research

description: DOX from P0 to P7

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
Reads were aligned to UCSC genome mm10 with STAR aligner (version STAR_2.6.1c ), using Ensembl 91 gene models.
TPM values were generated using RSEM (version v1.3.0 ).
Genome_build: mm10
Supplementary_files_format_and_content: csv, STAR count table and TPM table

organism: Mus musculus

source_name: olfactory epithelium

extract_protocol:
TRIzol
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold

tag: genotype

value: olfactory epithelium

tag: development stage


title: human WBC, GB4030162 (iDNase-seq)


title: RNA_sequencing_MCF7_Control_1


title: s_39_764015_tetfzd1_het_p0_neg7dox

description: DOX from P0 to P7


title: RNA_sequencing_MCF7_Control_2


title: Q13Xeno_H3K27ac_MWZ8047


title: Cytosolic_RNA_sequencing_TEX_2

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010) with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: TotalRNA_htseq_readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes.

molecule: cytoplasmic RNA

growth_protocol: HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C. Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq. To inhibit RNA polymerase II transcription activity,

extract_protocol: Three million isolated HeLa cells were subjected to Nuclear and cytoplasmic RNA extraction using the Cytoplasmic and Nuclear RNA Purification Kit (Norgen Biotek, 21000) following additional step of an on-column DNA removal using DNase I treatment.

treatment_protocol: For RNA-seq analysis DNase I-treated, poly(A) selected RNA was treated with Terminator 5′-Phosphate-Dependent Exonuclease (Epicentre; TER51020) according to the manufacturer’s instructions followed enzyme deactivation

value: RNA sequencing of cytoplasmic RNA plus TEX treatment


title: s_37_764198_tetfzd1_het_p3

description: no DOX


title: human WBC, GB4030160 (iDNase-seq)


title: human WBC, GB4030161 (iDNase-seq)


title: MAC1_BATF3_MWZ7126


title: s_3_773592_tetfzd1_wt_p0

description: no DOX

value: Omp-IRES-tTA


title: human WBC, GB4030159 (iDNase-seq)


title: s_4_773589_tetfzd1_het_p0

description: no DOX


title: human WBC, GB4030157 (iDNase-seq)


title: Nuclear_RNA_sequencing_TEX_2

molecule: nuclear RNA

value: RNA sequencing of nuclear RNA plus TEX treatment


title: human WBC, GB4030158 (iDNase-seq)


title: s_35_764200_tetfzd1_ctrl_p3

description: no DOX


title: SUPM2_H3K27ac_MWZ7415


title: Nuclear_RNA_sequencing_TEX_1

value: RNA sequencing of nuclear RNA plus TEX


title: s_36_764199_tetfzd1_ctrl_p3

description: no DOX


title: Q13Xeno_BATF3_MWZ8047


title: s_41_764013_tetfzd1_het_p0_neg7dox

description: DOX from P0 to P7


title: Cytosolic_RNA_sequencing_Control_2

value: RNA sequencing of Cytoplasmic RNA


title: s_28_773588_tetfzd1_het_p0

description: no DOX


title: SUPM2_Input_MWZ7415


title: human WBC, GB4030156 (iDNase-seq)


title: K299_IgG_MWZ8081

data_processing:
Raw sequencing reads were aligned to the hg19 revision of the human reference genome using bowtie v1.2.2 in paired-end mode with parameters -k 2 -m 2 --best -X 600.
Read alignments were converted into fragments using samtools view, samtools sort, and bedtools bamtobed.
Fragment coverage was calculated in 50bp bins genome-wide using bedtools makewindows and bedtools intersect and were normalized to the millions of mapped reads.
Assembly: hg19
Supplementary files format and content: bigWig files contain reads-per-million-normalized coverage of fragments in 50bp bins.
Library strategy: CUT&RUN-Seq

extract_protocol:
Live cells were washed and incubated with activated concanavalin A beads for 10 min at room temperature. Cells were then resuspended in antibody buffer containing 0.01% digitonin, 1 ml of each antibody was added to individual cell aliquots, and tubes were rotated at 4°C overnight. The following day, targeted chromatin digestion and release were performed with 2.5 ml of Cutana pA/G-MNase and 100 mM CaCl2. Retrieved genomic DNA was purified with a MinElute PCR purification kit and eluted in 10 ml of buffer EB.
Swift 2S automated library prep (manufacturer's instructions).

value: IgG


title: K299_STAT3_MWZ8081


title: human WBC, GB4030155 (iDNase-seq)


title: Nuclear_RNA_sequencing_Control_2

value: RNA sequencing of Nuclear RNA


title: K299_BATF3_MWZ8081


title: Cytosolic_RNA_sequencing_TEX_1


title: FEPD_IgG_MWZ8081

source_name: FE-PD

value: FE-PD


title: s_25_755734_tetfzd1_wt_p0_neg7dox

description: DOX from P0 to P7


title: s_2_773591_tetfzd1_wt_p0

description: no DOX


title: Nuclear_RNA_sequencing_Control_1

value: HeLa


title: s_20_755736_tetfzd1_wt_p0_neg7dox

description: DOX from P0 to P7


title: human WBC, GB4030152 (iDNase-seq)


title: FEPD_BATF3_MWZ8081


title: RNA_Sequencing_siRNA_CPSF3L_TEX_1

treatment_protocol: siRNAs against PCF11 catalogue number 4392420 ID s28363 and s28364; INTS11 siRNA catalogue number 4392420 ID s29893 and s29895; Negative control siRNA catalogue number 4390844). Cells were transfected for using Dharmafect I reagent (Dharmacon) following the manufacturer’s instructions (2 siRNAs per target gene) for 72h. For RNA-seq analysis DNase I-treated, poly(A) selected RNA was treated with Terminator 5′-Phosphate-Dependent Exonuclease (Epicentre; TER51020) according to the manufacturer’s instructions followed enzyme deactivation.

value: RNA sequencing with siRNA against CPSF3L plus TEX treatment


title: s_1_773590_tetfzd1_wt_p0

description: no DOX


title: RNA_Sequencing_siRNA_CPSF3L_TEX_2


title: JB6_MYC_MWZ10054

value: ALCL

value: MYC


title: human WBC, GB4030151 (iDNase-seq)


title: s_17_755739_tetfzd1_wt_p0_neg7dox

description: DOX from P0 to P7


title: Cytosolic_RNA_sequencing_Control_1


title: human WBC, GB4030150 (iDNase-seq)


title: RNA_Sequencing_siRNA_PCF11_TEX_2

value: RNA sequencing with siRNA against PCF11 plus TEX treatment


title: human WBC, GB4030149 (iDNase-seq)


title: human WBC, GB4030154 (iDNase-seq)


title: JB6_IgG_MWZ8081


title: JB6_STAT3_MWZ8081


title: s_15_766483_fzd1ko_homo_p3

description: no DOX


title: SD17 control

value: pigmented tissue

value: control


title: human WBC, GB4030153 (iDNase-seq)

value: WBC


title: s_14_766642_fzd1ko_homo_p7

description: no DOX

value: olfactory epithelium


title: RNA_Sequencing_siRNA_PCF11_TEX_1


title: FEPD_STAT3_MWZ8081


title: JB6_BATF3_MWZ8081


title: s_144_766481_fzd1ko_homo_p0

description: no DOX


title: RNA_sequencing_Control2_TEX_for_ KD_PCF11_CPSF3L

value: RNAsequencing Control plus TEX treatment for PCF11 and CPSF3L KD.


title: human WBC, GB4030147 (iDNase-seq)


title: MAC2A_IgG_MWZ7847


title: RNA_sequencing_Control1_TEX_for_ KD_PCF11_CPSF3L


title: s_143_766480_fzd1ko_homo_p0

description: no DOX


title: human WBC, GB4030146 (iDNase-seq)


title: s_142_766479_fzd1ko_homo_p0

description: no DOX


title: RNA_Sequencing_siRNA_CPSF3L_2

treatment_protocol: siRNAs against PCF11 catalogue number 4392420 ID s28363 and s28364; INTS11 siRNA catalogue number 4392420 ID s29893 and s29895; Negative control siRNA catalogue number 4390844). Cells were transfected for using Dharmafect I reagent (Dharmacon) following the manufacturer’s instructions (2 siRNAs per target gene) for 72h.

value: RNA sequencing with siRNA against CPSF3L


title: RNA_Sequencing_siRNA_CPSF3L_1

value: RNAsequencing with siRNA against CPSF3L


title: human WBC, GB4030145 (iDNase-seq)


title: MAC2A_MYC_MWZ10054


title: MAC2A_STAT3_1_MWZ7847


title: human WBC, GB4030144 (iDNase-seq)


title: human WBC, GB4030148 (iDNase-seq)


title: s_138_772506_tetfzd1_wt_p7

description: no DOX

value: Omp-IRES-tTA


title: s_139_772507_tetfzd1_wt_p7

description: no DOX


title: RNA_sequencing_Control2_for_ KD_PCF11_CPSF3L

value: RNA sequencing Control for PCF11 and CPSF3L KD


title: RNA_Sequencing_siRNA_PCF11_1

value: treatment:RNA sequencing with siRNA against PCF11


title: MAC2A_DMSO_IRF4_MWZ7564


title: MAC2A_DMSO_BATF3_MWZ75674


title: RNA_Sequencing_siRNA_PCF11_2

value: RNA sequencing with siRNA against PCF11


title: human WBC, GB4030143 (iDNase-seq)


title: s_13_766482_fzd1ko_homo_p3

description: no DOX


title: human WBC, GB4030142 (iDNase-seq)


title: s_134_772491_tetfzd1_wt_p0_neg3dox

description: DOX from P0 to P3


title: MAC2A_DMSO_IKZF1_MWZ7564


title: s_132_772489_tetfzd1_wt_p0_neg3dox

description: DOX from P0 to P3


title: MAC2A_BRD4_MWZ7847


title: RNA_sequencing_Control1_for_ KD_PCF11_CPSF3L


title: RNA_sequencing_A_AMANITINE_TEX_1.fastq.gz

data_processing:
RNA-seq: FASTQ files were aligned to the human hg19 genome using STAR (STAR_2.5.0a). File conversions were done using samtools. Reads on exons were counted using HTSEQ (0.5.4p3).
Genome_build: hg19
Supplementary_files_format_and_content: Total_RNAs_Readcounts.txt is a tab delimited txt file containing raw read counts obtaned with htseq over exons of protein coding genes. Also included is RNA_sequencing_A_AMANITINE_TEX_1.bw as bigwig file

source_name: U2OS cells

growth_protocol:
HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C.  Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq.
To inhibit RNA polymerase II transcription activity, U2OS cells were incubated with α-amanitin (10 µg/ml; Santa Cruz SC-202440) for 6h at 37 °C.

extract_protocol: RNA was extracted from U2OS and HEK293 cells using QIAzol Reagent (Qiagen; 79306) and Trizol reagent for HeLa cells (15596-018, Ambion life technologies) according to the manufactures protocol followed by DNase I treatment.  PolyA selected RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; E7490) for U2OS and HEK293 and Oligotex kit (QIAGEN) for HeLa cells and further processed with the NEBNext Ultra Directional RNA Library Prep Kit (NEB; E7420S) for U2OS and HEK293 or SMARTer® Stranded RNA-Seq Kit (Takara; 634839) and illumina Truseq Stranded mRNA Library Prep kit.  for HeLa cells or 3′–3′-mRNA-Seq Library Prep Kit (lexogen; 015UG009V0211).

treatment_protocol:
To inhibit RNA polymerase II transcription activity, U2OS cells were incubated with α-amanitin (10 µg/ml; Santa Cruz SC-202440) for 6h at 37 °C.
For RNA-seq analysis DNase I-treated, poly(A) selected RNA was treated with Terminator 5′-Phosphate-Dependent Exonuclease (Epicentre; TER51020) according to the manufacturer’s instructions followed enzyme deactivation.

value: A-Amanitine + TEX


title: human WBC, GB4030141 (iDNase-seq)


title: human WBC, GB4030139 (iDNase-seq)


title: human WBC, GB4030138 (iDNase-seq)


title: RNA_sequencing_A_AMANITINE_Control_2.fastq.gz

data_processing:
RNA-seq: FASTQ files were aligned to the human hg19 genome using STAR (STAR_2.5.0a). File conversions were done using samtools. Reads on exons were counted using HTSEQ (0.5.4p3).
Genome_build: hg19
Supplementary_files_format_and_content: Total_RNAs_Readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_A_AMANITINE_Control_2.bw bigwig file

growth_protocol: HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C. Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq. To inhibit RNA polymerase II transcription activity, U2OS cells were incubated with α-amanitin (10 µg/ml; Santa Cruz SC-202440) for 6h at 37 °C.

value: A-Amanitine Control


title: s_12_773587_tetfzd1_het_p0

description: no DOX


title: RNA_sequencing_A_AMANITINE_TEX_2.fastq.gz

data_processing:
RNA-seq: FASTQ files were aligned to the human hg19 genome using STAR (STAR_2.5.0a). File conversions were done using samtools. Reads on exons were counted using HTSEQ (0.5.4p3).
Genome_build: hg19
Supplementary_files_format_and_content: Total_RNAs_Readcounts.txt is a tab delimited txt file containing raw read counts obtaoned with htseq over exons of protein coding genes. Also included is RNA_sequencing_A_AMANITINE_TEX2.bw as bigwig file

growth_protocol: HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C.  Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq. To inhibit RNA polymerase II transcription activity, U2OS cells were incubated with α-amanitin (10 µg/ml; Santa Cruz SC-202440) for 6h at 37 °C.

treatment_protocol:
To inhibit RNA polymerase II transcription activity, U2OS cells were incubated with α-amanitin (10 µg/ml; Santa Cruz SC-202440) for 6h at 37 °C. Terminator phosphate-dependent TEX treatment:
For RNA-seq analysis DNase I-treated, poly(A) selected RNA was treated with Terminator 5′-Phosphate-Dependent Exonuclease (Epicentre; TER51020) according to the manufacturer’s instructions followed enzyme deactivation.


title: human WBC, GB4030140 (iDNase-seq)


title: s_119_772135_tetfzd1_het_p10

description: no DOX


title: RNA_sequencing_A_AMANITINE_Control_1.fastq.gz

data_processing:
RNA-seq: FASTQ files were aligned to the human hg19 genome using STAR (STAR_2.5.0a). File conversions were done using samtools. Reads on exons were counted using HTSEQ (0.5.4p3).
Genome_build: hg19
Supplementary_files_format_and_content: Total_RNAs_Readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes. Also included is RNA_sequencing_A_AMANITINE_Control_1.bw as bigwig file

treatment_protocol: To inhibit RNA polymerase II transcription activity, U2OS cells were incubated with α-amanitin (10 µg/ml; Santa Cruz SC-202440) for 6h at 37 °C.


title: MAC2A_Ruxo_MWZ982_2

data_processing:
Raw reads were aligned to the hg19 revision of the human reference genome to which the sequences of the ERCC spike-in probes were added using hisat2 v2.1.0 in paired-end mode.
Expression was quantified for all RefSeq genes using htseq-count with parameters -i gene_id --stranded=reverse -m intersection-strict.
Assembly: hg19
Supplementary files format and content: *.txt: Counts files contain reads assigned to each gene by htseq-count.

growth_protocol: Cells were grown in 6-well plates in RPMI media containing 10% FBS and 1% pen-strep.

extract_protocol:
Cells were collected, pelleted and snap freezed on liquid nitrogen. Pellets were lysed in Trizol and ERCC-spike in RNA was added directly to the suspension, normalized to cell number. RNA from the aqueous phase was then purified using QIAgen RNeasy columns according to the manufacturer’s protocol, and eluted in 30 uL RNase-free water.
Swift 2S automated library prep (manufacturer's instructions).

treatment_protocol: Cells were treated with DMSO or crizotinib/ruxolitinib (1uM) for 24h.

value: Ruxolitinib, 1uM, 24h


title: s_11_766484_fzd1ko_homo_p3

description: no DOX


title: MAC2A_Ruxo_MWZ982_3

value: ALCL


title: human WBC, GB4030135 (iDNase-seq)


title: s_130_772487_tetfzd1_wt_p0_neg3dox

description: DOX from P0 to P3


title: s_114_771884_tetfzd1_het_p0_neg14dox

description: DOX from P0 to P14


title: s_115_772131_tetfzd1_wt_p10

description: no DOX


title: s_125_772141_tetfzd1_het_p7

description: no DOX


title: human WBC, GB4030136 (iDNase-seq)


title: RNA_sequencing_NUDT21_siRNA_TEX_2.fastq.gz

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: Total_RNAs_Readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_NUDT21_siRNA_TEX_2.bw bigwig file

treatment_protocol: siRNAs against NUDT21 were purchased from Life Technologies (NUDT21 siRNA catalogue number 4392420, ID s21770 and s21772; Negative control siRNA catalogue number 4390844). Cells were transfected for using Dharmafect I reagent (Dharmacon) following the manufacturer’s instructions (2 siRNAs per target gene) for 72h.For RNA-seq analysis DNase I-treated, poly(A) selected RNA was treated with Terminator 5′-Phosphate-Dependent Exonuclease (Epicentre; TER51020) according to the manufacturer’s instructions followed enzyme deactivation.

value: HeLa

value: RNA sequencing of NUDT21 siRNA + TEX


title: human WBC, GB4030137 (iDNase-seq)


title: MAC2A_Ruxo_MWZ982_1


title: MAC2A_DMSO_MED1_MWZ7564


title: MAC2A_DMSO_MWZ982_1

value: DMSO


title: RNA_sequencing_NUDT21_siRNA_2.fastq.gz

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: Total_RNAs_Readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_NUDT21_siRNA_2.bw bigwig file

treatment_protocol: siRNAs against NUDT21 were purchased from Life Technologies (NUDT21 siRNA catalogue number 4392420, ID s21770 and s21772; Negative control siRNA catalogue number 4390844). Cells were transfected for using Dharmafect I reagent (Dharmacon) following the manufacturer’s instructions (2 siRNAs per target gene) for 72h.

value: RNA sequencing of NUDT21 siRNA


title: MAC2A_DMSO_MWZ982_3


title: human WBC, GB4030134 (iDNase-seq)

value: WBC


title: human WBC, GB4030133 (iDNase-seq)


title: JB6_Criz_MWZ9302_3

value: Crizotinib, 1uM, 24h


title: human WBC, GB4030132 (iDNase-seq)


title: RNA_sequencing_NUDT21_siRNA_1.fastq.gz

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: Total_RNAs_Readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_NUDT21_siRNA_1.bw bigwig file


title: s_113_771447_tetfzd1_het_p0_neg10dox

description: DOX from P0 to P10

value: olfactory epithelium


title: MAC2A_DMSO_MWZ982_2


title: RNA_sequencing_NUDT21_Control_1_TEX_1.fastq.gz

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: Total_RNAs_Readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_NUDT21_Control_1_TEX_1.bw bigwig file

extract_protocol: NA was extracted from U2OS and HEK293 cells using QIAzol Reagent (Qiagen; 79306) and Trizol reagent for HeLa cells (15596-018, Ambion life technologies) according to the manufactures protocol followed by DNase I treatment.  PolyA selected RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; E7490) for U2OS and HEK293 and Oligotex kit (QIAGEN) for HeLa cells and further processed with the NEBNext Ultra Directional RNA Library Prep Kit (NEB; E7420S) for U2OS and HEK293 or SMARTer® Stranded RNA-Seq Kit (Takara; 634839) and illumina Truseq Stranded mRNA Library Prep kit.  for HeLa cells or 3′–3′-mRNA-Seq Library Prep Kit (lexogen; 015UG009V0211).

treatment_protocol: For RNA-seq analysis DNase I-treated, poly(A) selected RNA was treated with Terminator 5′-Phosphate-Dependent Exonuclease (Epicentre; TER51020) according to the manufacturer’s instructions followed enzyme deactivation. siRNAs against NUDT21 were purchased from Life Technologies (NUDT21 siRNA catalogue number 4392420, ID s21770 and s21772; Negative control siRNA catalogue number 4390844). Cells were transfected for using Dharmafect I reagent (Dharmacon) following the manufacturer’s instructions (2 siRNAs per target gene) for 72h.

value: Control NUDT21 siRNA + TEX


title: JB6_Criz_MWZ9302_2


title: human WBC, GB4030131 (iDNase-seq)


title: s_110_771502_tetfzd1_het_p14

description: no DOX


title: s_111_771687_tetfzd1_het_p10

description: no DOX


title: RNA_sequencing_NUDT21_siRNA_TEX_1.fastq.gz

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: Total_RNAs_Readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_NUDT21_siRNA_TEX_1.bw bigwig file

treatment_protocol: siRNAs against NUDT21 were purchased from Life Technologies (NUDT21 siRNA catalogue number 4392420, ID s21770 and s21772; Negative control siRNA catalogue number 4390844). Cells were transfected for using Dharmafect I reagent (Dharmacon) following the manufacturer’s instructions (2 siRNAs per target gene) for 72h. For RNA-seq analysis DNase I-treated, poly(A) selected RNA was treated with Terminator 5′-Phosphate-Dependent Exonuclease (Epicentre; TER51020) according to the manufacturer’s instructions followed enzyme deactivation.


title: human WBC, GB4030130 (iDNase-seq)


title: s_109_771501_tetfzd1_het_p14

description: no DOX


title: JB6_DMSO_MWZ9302_3


title: JB6_Criz_MWZ9302_1


title: JB6_DMSO_MWZ9302_1


title: human WBC, GB4030129 (iDNase-seq)


title: RNA_sequencing_NUDT21_Control_2_TEX_2.fastq.gz

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: Total_RNAs_Readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_NUDT21_Control_2_TEX_2.bw bigwig file

value: Control for NUDT21 siRNA + TEX


title: JB6_DMSO_MWZ9302_2


title: human WBC, GB4030126 (iDNase-seq)


title: RNA_sequencing_NUDT21_Control_2.fastq.gz

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: Total_RNAs_Readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_NUDT21_Control_2.bw bigwig file

value: Control for NUDT21 siRNA


title: human WBC, GB4030128 (iDNase-seq)


title: s_107_771451_tetfzd1_wt_p10

description: no DOX

value: Omp-IRES-tTA


title: human WBC, GB4030127 (iDNase-seq)


title: Ribosome_profiling_ALKBH5_siRNA_2.fastq.gz

data_processing: For the Ribosome profiling analysis, reads in FASTQ format were trimmed for adapters using cutadapt, and were aligned to human hg19 trancriptome (gencode v19) using bowtie. Samtools (Li et al., 2009) and bedtools (Quinlan and Hall, 2010) were used for file format conversion (SAM to BAM and BAM to BED). Finally, CDS alignment was retained using PERL script which was covered into tabular format using custom PERL script, generating read count data for every one of the hundred windows covering the length of transcript, generated using BEDTOOLS. Peaks were identified with a custom R script using the findPeaks function from the package PRACMA. The fraction of reads for every peak identified in a transcript were identified by percentile normalization. Processed data files Ribosome_htseq_readcounts.txt is a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. Ribosome_profiling_ALKBH5_siRNA_2.bw is a bigwig file

molecule: other

source_name: HeLa cells

growth_protocol: HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C.  Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq.

treatment_protocol: Libraries from cultured cells were prepared as described previously (Loayza-Puch et al., 2013), with an addition of harringtonine treatment for 5 minutes that added to the cell culture medium (final concentration of 2 µg/ml -Santa Cruz sc-204771A) prior to CHX treatment. siRNAs against ALKBH5 were purchased from Life Technologies (ALKBH5 siRNA catalogue number 4392420, ID s29686 and s29687;  Negative control siRNA catalogue number 4390844). Cells were transfected for using Dharmafect I reagent (Dharmacon) following the manufacturer’s instructions (2 siRNAs per target gene) for 72h.

value: ALKBH5 KD in Ribosome profiling plus Harringtonine


title: s_106_771450_tetfzd1_wt_p10

description: no DOX


title: s_104_770926_tetfzd1_wt_p0_neg1dox

description: DOX from P0 to P1


title: Ribosome_profiling_Control_siRNA_2.fastq.gz

data_processing: For the Ribosome profiling analysis, reads in FASTQ format were trimmed for adapters using cutadapt, and were aligned to human hg19 trancriptome (gencode v19) using bowtie. Samtools (Li et al., 2009) and bedtools (Quinlan and Hall, 2010) were used for file format conversion (SAM to BAM and BAM to BED). Finally, CDS alignment was retained using PERL script which was covered into tabular format using custom PERL script, generating read count data for every one of the hundred windows covering the length of transcript, generated using BEDTOOLS. Peaks were identified with a custom R script using the findPeaks function from the package PRACMA. The fraction of reads for every peak identified in a transcript were identified by percentile normalization. Processed data files Ribosome_htseq_readcounts.txt is a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. Ribosome_profiling_Control_siRNA_2.bw is a bigwig file

extract_protocol: Libraries from cultured cells were prepared as described previously (Loayza-Puch et al., 2013), with an addition of harringtonine treatment for 5 minutes that added to the cell culture medium (final concentration of 2 µg/ml -Santa Cruz sc-204771A) prior to CHX treatment.

value: Control for Ribosome profiling plus Harringtonine


title: human WBC, GB4030125 (iDNase-seq)

data_processing:
Basecalls performed
The raw fastq files are read and separated into 480 files corresponding to 96 pairs of cell barcodes over 5 replicates. The 480 pairs are shown in barcode_480.txt. A read is considered as belonging to one of the barcodes if the beginning of read 1 or read 2 contains the same pair of barcodes in the left and right column respectively.  After separting each set of fastq files into 480 files, some base pairs starting from 5' are trimmed and the remaining reads are mapped to the human genome using bowtie2.
The top 30 barcodes are selected from each well based on read count, so 30 nuclei are sorted for each well with doublets removed, where the number removed was calculated based on the collision rate like in (Science. 2015 May 22; 348(6237): 910–914). These are denoted as single cells because of the low likelihood of two cells in the same well having the same barcode. We required that qualifying cells have more than 100 reads and a FRiP greater than 0.1. With these requirements, 4489 cells were obtained, and we were able to identify 218,042 DHSs. For each cell, we calculated the reads that were located within the DHS and stored the results in a matrix.
Genome_build: hg18
barcode_480.txt: two columns, the left column refers to a DNA barcode starting from the 5' end while the right column refers to a DNA barcode starting from the 3' end
peaks_218042_WBC.txt: first column is for chromsome, second column is for DHS start site, and third column is for DHS end site
iDNase_4489_cells_218042_peaks_counts_at_WBC.mtx: This file contains read count data for single cells in MatrixMarket format. Each row corresponds to a non-zero entry with the row, column, and then value specified. Reading the matrix results in a 218042 x 4489 matrix of peaks by cells where each element represents the number of reads located within a DHS site for some single cell.


title: Ribosome_profiling_ALKBH5_siRNA_1.fastq.gz

data_processing: For the Ribosome profiling analysis, reads in FASTQ format were trimmed for adapters using cutadapt, and were aligned to human hg19 trancriptome (gencode v19) using bowtie. Samtools (Li et al., 2009) and bedtools (Quinlan and Hall, 2010) were used for file format conversion (SAM to BAM and BAM to BED). Finally, CDS alignment was retained using PERL script which was covered into tabular format using custom PERL script, generating read count data for every one of the hundred windows covering the length of transcript, generated using BEDTOOLS. Peaks were identified with a custom R script using the findPeaks function from the package PRACMA. The fraction of reads for every peak identified in a transcript were identified by percentile normalization. Processed data files Ribosome_htseq_readcounts.txt is a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. Ribosome_profiling_ALKBH5_siRNA_1.bw as bigwig file


title: Ribosome_profiling_Control_siRNA_1.fastq.gz

data_processing: For the Ribosome profiling analysis, reads in FASTQ format were trimmed for adapters using cutadapt, and were aligned to human hg19 trancriptome (gencode v19) using bowtie. Samtools (Li et al., 2009) and bedtools (Quinlan and Hall, 2010) were used for file format conversion (SAM to BAM and BAM to BED). Finally, CDS alignment was retained using PERL script which was covered into tabular format using custom PERL script, generating read count data for every one of the hundred windows covering the length of transcript, generated using BEDTOOLS. Peaks were identified with a custom R script using the findPeaks function from the package PRACMA. The fraction of reads for every peak identified in a transcript were identified by percentile normalization. Processed data files Ribosome_htseq_readcounts.txt is a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. Ribosome_profiling_Control_siRNA_1.bw is a bigwig file

treatment_protocol: Libraries from cultured cells were prepared as described previously (Loayza-Puch et al., 2013), with an addition of harringtonine treatment for 5 minutes that added to the cell culture medium (final concentration of 2 µg/ml -Santa Cruz sc-204771A) prior to CHX treatment.

value: Control for Ribosomal profiling plus Harringtonine


title: human WBC, GB4030124 (iDNase-seq)


title: RNA_sequencing_NUDT21_Control_1.fastq.gz

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: Total_RNAs_Readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_NUDT21_Control_1.bw bigwig file

extract_protocol: RNA was extracted from U2OS and HEK293 cells using QIAzol Reagent (Qiagen; 79306) and Trizol reagent for HeLa cells (15596-018, Ambion life technologies) according to the manufactures protocol followed by DNase I treatment.  PolyA selected RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; E7490) for U2OS and HEK293 and Oligotex kit (QIAGEN) for HeLa cells and further processed with the NEBNext Ultra Directional RNA Library Prep Kit (NEB; E7420S) for U2OS and HEK293 or SMARTer® Stranded RNA-Seq Kit (Takara; 634839) and illumina Truseq Stranded mRNA Library Prep kit.  for HeLa cells or 3′–3′-mRNA-Seq Library Prep Kit (lexogen; 015UG009V0211)


title: s_103_770925_tetfzd1_wt_p0_neg1dox

description: DOX from P0 to P1

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
Reads were aligned to UCSC genome mm10 with STAR aligner (version STAR_2.6.1c ), using Ensembl 91 gene models.
TPM values were generated using RSEM (version v1.3.0 ).
Genome_build: mm10
Supplementary_files_format_and_content: csv, STAR count table and TPM table


title: s_101_771062_tetfzd1_het_p0_neg14dox

description: DOX from P0 to P14


title: s_108_771452_tetfzd1_het_p10

description: no DOX


title: s_102_770924_tetfzd1_wt_p0_neg1dox

description: DOX from P0 to P1


title: 5‘_end_sequencing_ALKBH5_KD_2.fastq.gz

data_processing:
5' end RNA-sequencing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13).TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12) witth “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Aligned Reads on exons were counted using HTSEQ (0.5.4p3).
HTSEQ was used to count reads at exons of genes. Normalization was done using DESEQ.
Genome_build: hg19 for human data, mm10 for mouse data
Supplementary_files_format_and_content: Processed data file 5prime_htseq_readcounts.txt is a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. also included is 5‘_end_sequencing_ALKBH5_KD_2.bw as bigwig file

extract_protocol: 20 μg of total RNA was polyA selected and then was treated with E.coli purified  AlkB for demethylation of the RNA as previously describe (Zheng et al., 2015). Next, we construction uncapped 5′-specific sequencing libraries as previously describe (Pelechano et al., 2016).

treatment_protocol: SiRNAs against ALKBH5 were purchased from Life Technologies ( ALKBH5 siRNA catalogue number 4392420, ID s29686 and s29687;   Cells were transfected for using Dharmafect I reagent (Dharmacon) following the manufacturer’s instructions (2 siRNAs per target gene) for 72h.

value: ALKBH5 KD in 5'end sequencing


title: H1975-OL+EV-3

city: Nanjing

first: Feng

last: Jiang

state: Jiangsu

address: Baiziting 42

country: China

institute: Jiangsu Institute of Cancer Research

description: RNA-SEQ_H1975_expression matrix

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0.
For circRNA expression analysis, the reads were to mapped genome using the STAR and DCC was used to identify the circRNA and to estimate the circRNA expression.
Differentially expressed genes were identified using the edgeR program.
Assembly: hg38
Supplementary files format and content: Excel and csv files include normalized abundance measurements for each Sample

source_name: Lung

growth_protocol: H1975 and PC9 cells were cultured in DMEM with 10% FBS (Corning). Before the experiment, cells were tested for mycoplasma, cross-contamination between species and authenticity. Cell lines in the experiments were used within 20 passages.

extract_protocol:
H1975 or PC9 cells were treated with Osi (500 nM) or Ge (100 nM) for 3 days, after which apoptotic cells were washed away with ice-cold PBS, and the total RNA of the remaining cells together with the cells before treatment was extracted using TRIzol reagent.
The Total RNA was incubated for 30 min at 37 °C with 10 units RNase R (Geneseed) .Then，RNA-seq library was prepared with approximately 2μg of total RNA usingRNA-seq (H/M/R) Library Prep Kit for Illumina® (Geneseed).

treatment_protocol: H1975 cells were treated with DMSO or Osi, while PC9 cells were treated with DMSO or Ge for 3 days followed by circRNA-sequencing

value: Lung

value: NSCLC

value: WT

value: Osimertinib (500nM)+Linsitinib (500nM) for 8 days


title: human WBC, GB4030123 (iDNase-seq)


title: 5‘_end_sequencing_ALKBH5_KD_1.fastq.gz

data_processing:
5' end RNA-sequencing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13).TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12) witth “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Aligned Reads on exons were counted using HTSEQ (0.5.4p3).
HTSEQ was used to count reads at exons of genes. Normalization was done using DESEQ.
Genome_build: hg19 for human data, mm10 for mouse data
Supplementary_files_format_and_content: Processed data file 5prime_htseq_readcounts.txt is a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. also included is 5‘_end_sequencing_ALKBH5_KD_1.bw as bigwig file.

treatment_protocol: iRNAs against ALKBH5 were purchased from Life Technologies ( ALKBH5 siRNA catalogue number 4392420, ID s29686 and s29687;   Cells were transfected for using Dharmafect I reagent (Dharmacon) following the manufacturer’s instructions (2 siRNAs per target gene) for 72h.

value: ALKBH5 KD in 5' end sequencing


title: 5‘_end_sequencing_Control_2.fastq.gz

data_processing:
5' end RNA-sequencing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13).TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12) witth “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Aligned Reads on exons were counted using HTSEQ (0.5.4p3).
HTSEQ was used to count reads at exons of genes. Normalization was done using DESEQ.
Genome_build: hg19 for human data, mm10 for mouse data
Supplementary_files_format_and_content: Processed data file 5prime_htseq_readcounts.txt is a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. also included is 5‘_end_sequencing_Control_2.bw as bigwig file

growth_protocol:
HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C.
Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq.

value: Control for 5' end sequencing


title: H1975-OL+EV-2

description: RNA-SEQ_H1975_expression matrix


title: human WBC, GB4030122 (iDNase-seq)

value: WBC


title: s_100_771061_tetfzd1_het_p0_neg14dox

description: DOX from P0 to P14


title: single-cell_adult olfactory epithelia

data_processing:
Data was processed with 10X genomic Cell ranger pipline
Genome_build: mm10
Supplementary_files_format_and_content: h5, processed count matrix.

molecule: polyA RNA

source_name: olfactory epithelia dissociation

extract_protocol:
papain dissociation
10X genomic Chromium

tag: strain

value: wildtype

value: adult

value: olfactory epithelia


title: human WBC, GB4030121 (iDNase-seq)


title: 5‘_end_sequencing_Control_1.fastq.gz

data_processing:
5' end RNA-sequencing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13).TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12) witth “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Aligned Reads on exons were counted using HTSEQ (0.5.4p3).
HTSEQ was used to count reads at exons of genes. Normalization was done using DESEQ.
Genome_build: hg19 for human data, mm10 for mouse data
Supplementary_files_format_and_content: Processed data file 5prime_htseq_readcounts.txt is a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. also included is 5‘_end_sequencing_Control_1.bw as bigwig file


title: human WBC, GB4030119 (iDNase-seq)


title: single-cell_P14 olfactory epithelia


title: human WBC, GB4030120 (iDNase-seq)


title: H1975-OC-3

description: RNA-SEQ_H1975_expression matrix

value: cIGF1R overexpression

value: Osimertinib (500nM)+cIGF1R overexpression for 8 days


title: human WBC, GB4030118 (iDNase-seq)


title: 3‘_end_sequencing_Control_1.fastq.gz

data_processing:
Trimming and filtering of raw reads: NextSeq basecall files were converted to FASTQ files using bcl2fastq (v.2.17.1.14). Reads were screened and preprocessed similarly to the described above, an additional step of removing polyA sequences from the 3′ ends of reads was performed with cutadapt, using a 75-mer oligo-A sequence as the “adapter” and a minimal overlap of 2. Genome_build: hg19.
Supplementary_files_format_and_content: Processed data files 3prime_htseq_readcounts.txt is a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. Also included is 3‘_end_sequencing_Control_1.bw as bigwigfile.

value: Control for 3' end sequencing


title: H1975-OC-2

description: RNA-SEQ_H1975_expression matrix


title: single-cell_E18.5 olfactory epithelia


title: H1975-DMSO+EV-3

description: RNA-SEQ_H1975_expression matrix

value: DMSO+EV for 8 days


title: RNA_sequencing_XRN_2.fastq.gz

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: TotalRNA_htseq_readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_XRN_2.bw as bigwig file

treatment_protocol: For RNA-seq analysis DNase I-treated, poly(A) selected RNA was treated with XRN1 (NEB M0338S) according to the manufacturer’s instructions followed enzyme deactivation.

value: RNA sequencing of Control + XRN1


title: human WBC, GB4030117 (iDNase-seq)


title: Purified mature olfactory sensory neuron at P7 from OMP-GFP animal

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
Reads were aligned to UCSC genome mm10 with STAR aligner (version STAR_2.6.1c ), using Ensembl 91 gene models.
TPM values were generated using RSEM (version v1.3.0 ).
Genome_build: mm10
Supplementary_files_format_and_content: TPM table and STAR count table

source_name: mature olfactory sensory neuron

extract_protocol:
Cells were first sorted by FACS. RNA was extracted using TRIzol.
TruSeq Stranded mRNA library Prep kit (Illumina) was used to construct library.

value: OMP-GFP

value: mature olfactory sensory neuron


title: H1975-OC-1

description: RNA-SEQ_H1975_expression matrix

value: Lung


title: RNA_sequencing_TEX_2.fastq.gz

data_processing: ASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: TotalRNA_htseq_readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_TEX_2.bw bigwig file

treatment_protocol: For RNA-seq analysis DNase I-treated, poly(A) selected RNA was treated with Terminator 5′-Phosphate-Dependent Exonuclease (Epicentre; TER51020) according to the manufacturer’s instructions followed enzyme deactivation.

value: Ribosome sequencing of Control + TEX


title: RNA_sequencing_XRN_1.fastq.gz

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: TotalRNA_htseq_readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_XRN_1.bw is a bigwig file

value: RNA sequencing of Control treated with XRN1


title: Purified progenitor cells at P9 from Neurog1-GFP animal

source_name: intermediate progenitor cell

value: intermediate progenitor cell


title: H1975-DMSO+EV-2

description: RNA-SEQ_H1975_expression matrix

value: NSCLC

value: WT


title: H1975-OL+EV-1

description: RNA-SEQ_H1975_expression matrix

value: Osimertinib (500nM)+Linsitinib (500nM) for 8 days


title: Purified progenitor cells at P3 from Neurog1-GFP animal


title: H1975-DMSO+EV-1

description: RNA-SEQ_H1975_expression matrix


title: 3‘_end_sequencing_Control_2.fastq.gz

data_processing:
Trimming and filtering of raw reads: NextSeq basecall files were converted to FASTQ files using bcl2fastq (v.2.17.1.14). Reads were screened and preprocessed similarly to the described above, an additional step of removing polyA sequences from the 3′ ends of reads was performed with cutadapt, using a 75-mer oligo-A sequence as the “adapter” and a minimal overlap of 2. Genome_build: hg19.
Supplementary_files_format_and_content: Processed data files 3prime_htseq_readcounts.txt is a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. Also included is 3‘_end_sequencing_Control_2.bw as bigwigfile.


title: Purified mature olfactory sensory neuron at P2 from OMP-GFP animal


title: PC9-Ge-2

value: Gefitinib (500nM) for 3 days


title: PC9-Ge-3


title: Purified progenitor cells at P7 from Neurog1-GFP animal


title: human WBC, GB4030114 (iDNase-seq)

data_processing:
Basecalls performed
The raw fastq files are read and separated into 480 files corresponding to 96 pairs of cell barcodes over 5 replicates. The 480 pairs are shown in barcode_480.txt. A read is considered as belonging to one of the barcodes if the beginning of read 1 or read 2 contains the same pair of barcodes in the left and right column respectively.  After separting each set of fastq files into 480 files, some base pairs starting from 5' are trimmed and the remaining reads are mapped to the human genome using bowtie2.
The top 30 barcodes are selected from each well based on read count, so 30 nuclei are sorted for each well with doublets removed, where the number removed was calculated based on the collision rate like in (Science. 2015 May 22; 348(6237): 910–914). These are denoted as single cells because of the low likelihood of two cells in the same well having the same barcode. We required that qualifying cells have more than 100 reads and a FRiP greater than 0.1. With these requirements, 4489 cells were obtained, and we were able to identify 218,042 DHSs. For each cell, we calculated the reads that were located within the DHS and stored the results in a matrix.
Genome_build: hg18
barcode_480.txt: two columns, the left column refers to a DNA barcode starting from the 5' end while the right column refers to a DNA barcode starting from the 3' end
peaks_218042_WBC.txt: first column is for chromsome, second column is for DHS start site, and third column is for DHS end site
iDNase_4489_cells_218042_peaks_counts_at_WBC.mtx: This file contains read count data for single cells in MatrixMarket format. Each row corresponds to a non-zero entry with the row, column, and then value specified. Reading the matrix results in a 218042 x 4489 matrix of peaks by cells where each element represents the number of reads located within a DHS site for some single cell.

value: WBC


title: human WBC, GB4030116 (iDNase-seq)


title: human WBC, GB4030115 (iDNase-seq)


title: RNA_sequencing_TEX_1.fastq.gz

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: TotalRNA_htseq_readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_TEX_1.bw bigwig file

value: RNA sequencing of Control treated with TEX


title: human WBC, GB4030112 (iDNase-seq)


title: Purified mature olfactory sensory neuron at P16 from OMP-GFP animal

value: olfactory epithelia


title: RNA_sequencing_Control_for TEX_XRN1_1.fastq.gz

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: TotalRNA_htseq_readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_Control_for TEX_XRN1_1.bw bigwig file

value: RNA sequencing Control for TEX and XRN1


title: Polysomal_RNA_sequencing_Control_1.fastq.gz

data_processing:
RNA-seq (as well as 3’, 5’, Polysome): FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13). Mouse FASTQ files were alignes with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12) witth “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Aligned Reads on exons were counted using HTSEQ (0.5.4p3).
Ribo-seq: Fastq file preprocessing consisted of adapter removal using cutadapt using the parameters (--quality-base=33  -O 7 -e 0.15 -m 20 -q 5) and removal of rRNA and tRNA contaminants by means of alignment against a reference using bowtie2with parameters (--seed 42 -p1 –local). The actual alignment of pre-processed fastq files was done with tophat2  and bowtie2  against GRCh37/hg19  using parameters ( --seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25). In a subsequent step the primary aligned reads filtered for a minimum mapping quality of 10.  HTSEQ was used to count reads at exons of genes. Normalization was done using DESEQ.
3‘ end sequencing: same as Rnaseq with additionally removal of polyA sequences from the 3′ ends of reads which was performed with cutadapt, using a 75-mer oligo-A sequence as the “adapter” and a minimal overlap of 2.
Genome_build: hg19 for human data, mm10 for mouse data
Supplementary_files_format_and_content: Processed data file Polysome_htseq_readcounts.txt is a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. Also included is  Polysomal_RNA_sequencing_Control_1.bw bigwig file

extract_protocol: Polysomal RNA isolation was performed as described previously (Slobodin et al., 2017). Briefly, Sucrose gradients for separation of polysomes were usually prepared by gentle sequential addition of 2.2ml of the different sucrose solutions (e.i., 47, 37, 27, 17 and 7% in Tris-HCl pH = 7.5 (f.c. 20mM), MgCl2 (f.c. 10mM) and KCl (f.c. 100mM), supplemented with 2mM DTT, Ribosafe RNase inhibitor (Bioline, 1 μl/ml) and CHX (100 μg/ml) into a 12 mL tube (Beckman, 9/16 × 3 1/2 in.) and left overnight at 4°C to achieve continuous gradient prior to the centrifugation. Cells were treated with CHX and harvest after washing with PBS with CHX and lysed. The lysates were centrifuged 1300xg for 10 min at 4°C and the supernatants were transferred into new tubes. From the cleared lysates, 500 μL were loaded on top of each gradient, mounted on SW41TI rotor and centrifuged at 36000rpm for 2 hr at 4°C. Following the centrifugation, each gradient was split into 15 equal fractions of 760 μl. Fractions 9-13 were collected for RNA isolation using TRIsure (Bioline) according to the manufacturer’s instructions, polyA selected followed by RNA library preparation as previously describe (Takara; 634839).

value: Control Polysomal RNA sequencing


title: Polysomal_RNA_sequencing_Control_2.fastq.gz

data_processing:
RNA-seq (as well as 3’, 5’, Polysome): FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13). Mouse FASTQ files were alignes with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12) witth “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Aligned Reads on exons were counted using HTSEQ (0.5.4p3).
Ribo-seq: Fastq file preprocessing consisted of adapter removal using cutadapt using the parameters (--quality-base=33  -O 7 -e 0.15 -m 20 -q 5) and removal of rRNA and tRNA contaminants by means of alignment against a reference using bowtie2with parameters (--seed 42 -p1 –local). The actual alignment of pre-processed fastq files was done with tophat2  and bowtie2  against GRCh37/hg19  using parameters ( --seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25). In a subsequent step the primary aligned reads filtered for a minimum mapping quality of 10.  HTSEQ was used to count reads at exons of genes. Normalization was done using DESEQ.
3‘ end sequencing: same as Rnaseq with additionally removal of polyA sequences from the 3′ ends of reads which was performed with cutadapt, using a 75-mer oligo-A sequence as the “adapter” and a minimal overlap of 2.
Genome_build: hg19 for human data, mm10 for mouse data
Supplementary_files_format_and_content: Processed data file is GSE149204_Polysome_htseq_readcounts.txt as a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. Also included is Polysomal_RNA_sequencing_Control_2.bw as bigwig file


title: human WBC, GB4030113 (iDNase-seq)


title: PC9-DMSO-2

value: DMSO for 3 days


title: PC9-DMSO-3


title: RNA_sequencing_Control_for TEX_XRN1_2.fastq.gz

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010)  with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: TotalRNA_htseq_readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes and RNA_sequencing_Control_for TEX_XRN1_2.bw bigwig file


title: human WBC, GB4030109 (iDNase-seq)


title: Purified progenitor cells at P16 from Neurog1-GFP animal


title: PC9-DMSO-1

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0.
For circRNA expression analysis, the reads were to mapped genome using the STAR and DCC was used to identify the circRNA and to estimate the circRNA expression.
Differentially expressed genes were identified using the edgeR program.
Assembly: hg38
Supplementary files format and content: Excel and csv files include normalized abundance measurements for each Sample


title: Specimen_53 [200]

city: Philadelphia

first: Yijing

last: Su

state: PA

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

data_processing:
Library strategy: split-seq
Basecalls performed using BCL2fastq
RNAseq reads were aligned to the hg38 genome assembly using STAR 2.7.6a
Data processing was preprocessed using Drop-seq-1.13
Assembly: hg38
Supplementary files format and content: cell barcode
Supplementary files format and content: abundance measurements

source_name: human hippocampus

extract_protocol:
Tissue were minced with a razor blade and homogenized using a tissue grinder in a 1 ml of HB buffer (1 mM DTT), 0.15 mM spermine, 0.5 mM spermidine, EDTA-free protease inhibitor, 0.3% IGEPAL-630, 0.25 M sucrose, 25 mM MgCl2, 20 mM Tricine-KOH) for 5 to 10 strokes, then filtered through a 40 mm strainer, underlayer with a cushion buffer (0.5 mM MgCl2, 0.5 mM DTT, EDTA-free protease inhibitor, 0.88 M sucrose) and centrifuged at 2800g for 10 minutes in a swinging bucket centrifuge at 4 ºC. Nuclei were collected as pellets. Nuclei were then centrifuged for 3 mins at 500g at 4 ˚C. The pellet was resuspended in 1 ml of cold PBS-RI (1x PBS + 0.05U/μl RNase Inhibitor). The nuclei were passed through a 40 μm strainer. 3 ml of cold 1.33% formaldehyde solution was then added to 1 ml of cells. Nuclei were fixed for 10 mins before adding 160 μl of 5% Triton X-100. Nuclei were then permeabilized for 3 mins and centrifuged at 500g for 3 mins at 4 ˚C. Nuclei were resuspended in 500 l of PBS-RI before adding 500 μl of cold 100 mM Tris-HCl pH 8. Then, nuclei were spun down at 500g for 3 mins at 4 ˚C and resuspended in 300 μl of cold 0.5 X PBS-RI. Finally, nuclei were again passed through a 40 μm strainer and then counted on a hemocytometer, diluted to 1,000,000 cells/ml.
mRNA from single nuclei were tagged 3 rounds with barcoded primers, with in-cell ligations using T4 DNA ligase. Plates were incubated for 30 mins at 37 ºC with gentle sharking (50 rpm) to allow hybridization and ligation to occur. The ligation products were purified with Dynabeads MyOne Streptavidin C1 beads. After washing beads once with 10 mM Tris and 0.1% Tween-20 solution and once with water, beads were resuspended into a solution containing 110 μl of 2X Kapa HiFi HotStart Master Mix, 8.8 μl of 10 μM stocks of primers BC_0062 and BC_0108, and 92.4 μl of water. PCR thermocycling was performed as follows: 95 °C for 3 mins, then five cycles at 98 °C for 20 seconds, 65 °C for 45 seconds, 72 °C for 3 mins. After these five cycles, Dynabeads beads were removed from PCR solution and EvaGreen dye was added at a 1X concentration. Samples were again placed in a qPCR machine with the following thermocycling conditions: 95 °C for 3 mins, cycling at 98 °C for 20 seconds, 65 °C for 20 seconds, and then 72 °C for 3 mins, followed by a single 5 mins at 72 °C after cycling. Once the qPCR signal began to plateau, reactions were removed.

value: hippocampus

tag: group

value: Adolescent

tag: age

value: 13 Yrs


title: Specimen_53 [1K]


title: PC9-Ge-1

value: Lung


title: human WBC, GB4030108 (iDNase-seq)


title: human WBC, GB4030111 (iDNase-seq)


title: human WBC, GB4030110 (iDNase-seq)


title: Specimen_52

value: Aging

value: 85 Yrs


title: CD45+ CD11b+ cells from whole brain of mice cured from late-stage T. b. brucei infection, 9 days post treatment

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description:
Cured_9d_whole_brain
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq.
Demultiplexed data was processed using the Cellranger count pipeline.
Assembly: mm10
Supplementary files format and content: h5 files including raw counts (output CellRanger Count) per sample.
Supplementary files format and content: Text metadata files with information per cell.

source_name: whole brain

extract_protocol:
Sample preparation for sort: Tissues were dissociated as described in the manuscript. To limit dissociation-induced gene expression, cured vs. control samples were dissociated in the presence of actinomycin D (ActD), as previously described (Van Hove et al., 2019). After tissue dissociation and antibody staining (anti-CD45, anti-CD11b), cells were sorted into RPMI medium, supplemented with 10% (v/v) FCS, 300 μg/ml L-glutamine, 100 units/ml penicillin, 100 μg/ml streptomycin, 1 mM sodium pyruvate (Gibco), 1% (v/v) MEM non-essential amino acids (Gibco) and 1% (v/v) β-mercaptoethanol (Sigma).
Post-sort sample preparation: Sorted cells were centrifuged for 6 min at 4°C at 450 g and resuspended in PBS with 0.04% bovine serum albumin in an estimated concentration of 1000 cells/µl.
To generate single-cell gel beads in emulsion (GEM), single cell suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics). For most samples, the GEMs and scRNA-seq libraries were prepared with the GemCode Single Cell 3’ Gel Bead and Library kit v2 (10x Genomics) and the Chromium i7 Multiplex kit (10x Genomics), according to the manufacturer’s instructions. For the cured versus control samples, a Chromium Next Gem Single Cell 3’ Gel Bead and Library kit v3.1 (10x Genomics) was used. In essence, GEM reverse-transcription was achieved in a 96-deep-well plate by an incubation reaction module at 53°C for 45 min, 85°C for 5 min, finishing at 4°C, generating barcoded complementary DNA (cDNA). Subsequently, GEMs were broken and cDNA was cleaned up with DynaBeads MyOne Silane Beads (ThermoFisher Scientific) and SPRIselect Reagent Kit (Beckman Coulter). Full-length, barcoded cDNA was amplified by a polymerase chain reaction (PCR) in a 96-deep-well reaction module at 98°C for 3 min, 14 cycles of 98°C for 15 s, 67°C for 20 s and 72°C for 1 min, a final cycle at 72°C for 1 min and ending at 4°C. After clean-up using SPRIselect Reagent Kit and enzymatic fragmentation, Illumina-ready sequencing libraries were generated, by library construction through addition of R1 (read 1 primer), P5, P7, i7 sample index and R2 (10x Genomics), via end-repair, A-tailing, adapter ligation, post-ligation SPRIselect cleanup/size selection and sample index PCR. The cDNA content of pre-fragmentation and post-sample index PCR samples was analysed using a 2100 BioAnalyzer (Agilent). The sequencing libraries were loaded onto an Illumina HiSeq4000 or an Illumina NovaSeq6000 flow cell, using the sequencing settings recommended by 10x Genomics.

value: whole brain

tag: condition

value: cured, 9d


title: CD45+ CD11b+ cells from whole brain of mice cured from late-stage T. b. brucei infection, 7 days post treatment

description:
Cured_7d_whole_brain
10x Genomics

value: cured, 7d


title: H1975-Osi-3

value: NSCLC

value: WT

value: Osimertinib (500nM) for 3 days


title: CD45+ CD11b+ cells from whole brain of mice cured from late-stage T. b. brucei infection, 3 days post treatment

description:
Cured_3d_whole_brain
10x Genomics

value: cured, 3d


title: human WBC, GB4030107 (iDNase-seq)

value: WBC


title: H1975-Osi-2


title: human WBC, GB4030106 (iDNase-seq)


title: H1975-Osi-1


title: Specimen_51


title: Specimen_53 [500]


title: human WBC, GB4030105 (iDNase-seq)


title: H1975-DMSO-3


title: CD45+ cells from choroid plexus of C57BL/6JRj mice

description:
Naive_CP
10x Genomics

source_name: choroid plexus

value: choroid plexus

value: non-infected


title: human WBC, GB4030104 (iDNase-seq)


title: CD45+ CD11b+ cells from choroid plexus of late-stage T. b. brucei infected mice

description:
Infected_CP_YFP
10x Genomics

value: T. b. brucei infected


title: Specimen_49

value: hippocampus

value: Adult

value: 66 Yrs


title: Specimen_48

value: 39 Yrs


title: H1975-DMSO-1

value: Lung

value: DMSO for 3 days


title: human WBC, GB4030103 (iDNase-seq)


title: CD45int CD11b+ CX3CR1hi cells from whole brain of late-stage T. b. brucei infected mice

description:
Infected_Microglia_whole_brain
10x Genomics

value: whole brain

value: CD45int CD11b+ CX3CR1hi


title: Specimen_47

value: 27 Yrs


title: CD45+ CD11b+ cells from whole brain of late-stage T. b. brucei infected mice

description:
Cured_0d_whole_brain
10x Genomics

value: T. b. brucei infected, cured, 0d


title: Specimen_46

value: Adolescent

value: 14 Yrs


title: CD45int CD11b+ CX3CR1hi cells from whole brain of non-infected mice

description:
Naive_Microglia_whole_brain
10x Genomics


title: Specimen_50

value: 71 Yrs


title: human WBC, GB4030101 (iDNase-seq)

value: WBC


title: Specimen_45

value: Child

value: 6 Yrs


title: human WBC, GB4030099 (iDNase-seq)


title: Huh7 LR3

city: Beijing

first: Juan

last: Liu

state: China

address: No 168, Litang Road

institute: Beijing Tsinghua Changgung Hosptial

description: Huh7 LR3

data_processing:
Low quality reads, such as only adaptor, unknown nucleotides>5%, or Q20 <20%  (percentage of sequences with sequencing error rates <1%), were removed by perl script.  The clean reads that were filtered from the raw reads were mapped to honeybee (Apis  mellifera) genome (OGSv3.2) using Tophat2 (Kim, Pertea et al. 2013) software. The  aligned records from the aligners in BAM/SAM format were further examined to remove  potential duplicate molecules. Gene expression levels were estimated using FPKM values  (fragments per kilobase of exon per million fragments mapped) by the Cufflinks software  (Trapnell, Williams et al. 2010)
DESeq (Anders and Huber 2010) and Q-value were employed and used to evaluate  differential gene expression between queen and worker honeybee. After that, gene  abundance differences between those samples were calculated based on the ratio of the  2  FPKM values. The false discovery rate (FDR) control method was used to identify the  threshold of the P-value in multiple tests in order to compute the significance of the  differences. Here, only gene with an absolute value of log2 ratio ≥2 and FDR significance  score <0.01 were used for subsequent analysis.
Genes were compared against various protein database by BLASTX, including the  National Center for Biotechnology Information (NCBI) non-redundant protein (Nr)  database, Swiss-Prot database with a cut-off E-value of 10-5. Furthermore, genes were  searched against the NCBI non-redundant nucleotide sequence (Nt) database using  BLASTn by a cut-off E-value of 10-5. Genes were retrieved based on the best BLAST hit  (highest score) along with their protein functional annotation.
To annotate the gene with gene ontology (GO) terms, the Nr BLAST results were  imported into the Blast2 GO program (Conesa, Gotz et al. 2005). GO annotations for the  genes were obtained by Blast2GO. This analysis mapped all of the annotated genes to  GO terms in the database and counted the number of genes associated with each term.  Perl script was then used to plot GO functional classification for the unigenes with a GO  term hit to view the distribution of gene functions. The obtained annotation was enriched  and refined using TopGo (R package). The gene sequences were also aligned to the  Clusters of Orthologous Group (COG) database to predict and classify functions (Tatusov,  Galperin et al. 2000). KEGG pathways were assigned to the assembled sequences by perl  script.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA of each sample was extracted from the honeybee larvae according to the  instruction manual of the TRlzol Reagent (Life technologies, California, USA). RNA  integrity and concentration were checked using an Agilent 2100 Bioanalyzer (Agilent  Technologies, Inc., Santa Clara, CA, USA). The mRNA was isolated by NEBNext Poly  (A) mRNA Magnetic Isolation Module (NEB, E7490).
The cDNA library was constructed following the manufacturer’s instructions of NEBNext Ultra RNA Library Prep Kit for Illumina（NEB, E7530）and NEBNext Multiplex Oligos for Illumina（NEB,E7500）.

value: Human hepatocellular carcinoma cells

value: WT

value: continuous exposure to lenvatinib (1–20 μM)

tag: time

value: 10 months


title: Huh7 LR2

description: Huh7 LR2


title: Huh7 LR1

description: Huh7 LR1


title: Huh7 P3

description: Huh7 P3

value: no treatment


title: CD45hi CD11b+ cells from whole brain of late-stage T. b. brucei infected mice

description:
Infected_CD45hi_whole_brain
10x Genomics

value: CD45hi CD11b+

value: T. b. brucei infected


title: human WBC, GB4030098 (iDNase-seq)

extract_protocol:
DNase-seq human 1.25M 2-step crosslink human healthy T/B/NK/monocyte, final 0.1U/μl DNase digestion 37°C 5 minutes, T cell split #1-15 wells, B cell split #16-30 wells, NK cell split #31-45 wells, monocyte split #46-61 wells, TdT&T4 methods adding P7 barcode adaptor (12.5μl volumn/well 37°C 60 minutes), pool, dilution, counting and redistribute into 96-well plate, total 20 nuclei per well seal completely, 65°C overnight; direct PCR1 (12 cycles), pool all the DNA, EXO I 30 minutes, A-tailing and P5 ligation(rt overnight) , column purification and PCR2(16 cycles), run-e-gel and cut from 200-500bp rc#1 i5-01
The isolated 50M of PBMC suspended by 50ml PBS /MgCl2 are firstly fixed by adding 400μl freshly prepared 0.25M Disuccinimidyl glutarate (DSG, ThermoFisher Scientific, catalog no.20593) and incubate at room temperature for 45 minutes with rotation. After protein-protein fixation by DSG and washing three times by PBS, cells suspended by culture medium DMEM supplemented with 10% FBS are further fixed by the addition of 1:15 volume of 16% (w/v) methanol-free formaldehyde solution (Thermo Fisher Scientific) and incubate at room temperature for 10 minutes. The fixing reaction is terminated by a 1:10 volume of 1.25 M glycine and incubate at room temperature for 5 minutes. The fixed cells are collected by centrifugation at 1320rpm for 7 minutes and washed with PBS. The cells are stored in aliquots (1 × 10e6 cells per tube) at −80°C until use.


title: H1975-DMSO-2

value: Lung

value: NSCLC

value: DMSO for 3 days


title: Specimen_43

value: hippocampus

value: Infant

value: 0.1 Yrs


title: Huh7 P2

description: Huh7 P2


title: wild-type  zebrafish embryos Ribo-seq 72 hpf replicate 2

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

description: Ribosomal RNA

data_processing:
The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR, and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by limma package.
Assembly: GRCz11

organism: Danio rerio

source_name: zebrafish cells

growth_protocol: embryos were cultured in a Petri dish filled with 0.3X Danieau buffer

extract_protocol: For bulk RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols. For Ribo-seq, WT and mycn mutant embryos were collected at 3 dpf, digested with cold 0.5% trypsin to a single-cell suspension, and homogenized in lysis buffer for 20–50 times. The homogenate centrifuged at 12,000 g for 15 min at 4°C, and the supernatants were digested with RNase for 30 mins and aborted by 1M EGTA followed by layering on top of a 10%–50% sucrose-gradient solution. Ultracentrifugation was performed at 36,000 rpm for 2 hrs (hours) at 4°C. After centrifugation, the fractions were collected according to the absorbance at optical density OD260 by a TRAIX detector. Then the RNA was purified and used to construct the library for sequencing.

treatment_protocol: WT and Mycn mutant zebrafish embryos were collected for RNA sequencing or Ribo-seq at 72 hpf

value: AB

value: embryonic cells

value: 72 hpf


title: Mycn mutant  zebrafish embryos Ribo-seq 72 hpf replicate 1

description: Ribosomal RNA

value: Mycn mutant


title: human WBC, GB4030097 (iDNase-seq)

value: WBC


title: human WBC, GB4030102 (iDNase-seq)


title: Mycn mutant  zebrafish embryos Ribo-seq 72 hpf replicate 2

description: Ribosomal RNA


title: wild-type  zebrafish embryos Ribo-seq 72 hpf replicate 1

description: Ribosomal RNA


title: Huh7 P1

description: Huh7 P1

value: Human hepatocellular carcinoma cells

value: WT


title: Specimen_44


title: Mycn mutant  zebrafish embryos RNA-seq 72 hpf

description: total RNA


title: human WBC, GB4030096 (iDNase-seq)


title: human WBC, GB4030095 (iDNase-seq)


title: Patient2B

city: Stanford

first: Melanie

last: Plastini

state: CA

address: 290 Campus Drive

institute: Stanford University

data_processing:
Reads were trimmed using Trim Galore v0.6.4 and aligned to hg39 human reference genome (UCSC Genome Browser) using default parameters.
STAR was used to map the number of read pairs aligned to each gene.
Differential gene expression analysis was conducted using EdgeR to generate p-values and calculate normalized expression measures of each gene in Fragments Per Kilobase per million Mapped reads (FPKM). Only genes with a log2CPM > 1 and log2|FC| ≥ 0.585 were included in heatmaps, volcano plots, and DAVID Gene Ontology (GO) Term analysis.
Assembly: hg39
Supplementary files format and content: STAR output files ReadsPerGene.out.tab were used with the EdgeR package in are to create the all FPKMs text file and the final PPMSvsControl differential expression text file

source_name: O4+ oligodendrocyte lineage cells

growth_protocol: Differentiation of hiPSCs into OLs was carried out according to the “fast protocol” published by Douvaras and Fossati (Douvaras and Fossati, 2015). Briefly, hiPSCs were thawed and expanded in StemFlex medium (ThermoFisher) to form colonies for differentiation. Colonies were then dissociated into single cells using Accutase (Life Technologies, #A11105-01), seeded in poly-L-ornithine- and laminin-coated 6-well plates at 1x105 cells/well density, and cultured in StemFlex medium for 2 days before differentiation, which was induced by switching to neural induction medium (NIM) containing freshly added SB434542 (TGFb inhibitor), LDN-193189 (BMP inhibitor) and retinoic acid (RA) (day 0). Medium was changed daily for 8 days. From day 8 to 12, cells were exposed to RA and smoothened agonist (SAG). On day 12, cells were mechanically dissociated, transferred to non-coated 6-well plates and grown in suspension until day 20. On day 20, cells were switched to PDGF containing medium until day 30. On day 30, cell aggregates were replated onto poly-L-ornithine- and laminin-coated 6-well plates, switched to mitogen-free medium, and grown adherent for the rest of the differentiation through day 75. On Day 76, cultures were immunolabeled for O4 and FACS-sorted either for RNA extraction and subsequent RNA-seq and qPCR, or to be replated onto 24-well plates containing poly-L-ornithine- and laminin-coated coverslips to perform immunostaining and high content analysis (HCA).

extract_protocol:
RNA from FACS-sorted cells was isolated using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems, #KIT0204) according to the manufacturer’s protocol. Sorted O4+ cells were resuspended in 100 ml RNA extraction buffer and incubated at 42°C for 30 min. Samples were spun down and the RNA-containing supernatant further purified of residual genomic DNA by on-column digestion with RNase-free DNase (Qiagen, #79254).
RNA integrity was measured with the Agilent 2100 BioAnalyzer, and only RNA with RNA integrity number (RIN) above 7 was used for sequencing. Library preparation and sequencing was conducted by experienced personnel at the John P. Hussman Institute for Human Genomics (Miller School of Medicine, University of Miami) using an Illumina NovaSeq sequencing system. Paired-end, 125 base pair reads were generated.

treatment_protocol: Cells were grown without treatment or stimulation

value: iPSC-derived oligodendrocyte lineage cells

value: progressive multiple sclerosis iPSC lines

value: untreated


title: Patient2A


title: wild-type  zebrafish embryos RNA-seq 72 hpf

description: total RNA


title: CD45+ CD11b+ cells from whole brain of mice cured from late-stage T. b. brucei infection, 8 weeks post treatment

description:
Cured_8w_whole_brain
10x Genomics

value: whole brain

value: cured, 8w


title: Exp 2 DIO-NASH vehicle w12 Rep 9

city: Hørsholm

first: Martin

middle: Rønn

last: Madsen

state: Please Select

address: Hørsholm Kongevej 11

department: Computation Biology

country: Denmark

institute: Gubra

data_processing:
Reads were mapped to the GRCm38.p96 Ensembl mouse genome using STAR v.2.5.2a with default parameters.
Counts in protein coding genes was quantified using STAR and can be found in supplementary.
Assembly: GRCm38
Supplementary files format and content: .txt file of RPKM-normalized gene expression

source_name: Liver

extract_protocol: Illumina TruSeq Stranded mRNA Library Prep kit (#20020594, Illumina, San Diego, CA, USA)

value: Liver

value: DIO-NASH + vehicle w12

tag: weeks treatment


title: Exp 2 DIO-NASH vehicle w12 Rep 8


title: Exp 2 DIO-NASH vehicle w12 Rep 7


title: Patient1C


title: ml5_Dark_7d_3

city: Shanghai

first: Moyang

address: dongchuan road 800

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Assembly: TAIR10;IRGSP-1.0; SL3.0
Supplementary files format and content: tab-delimited text files include count for each Sample

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
10 μg/mg doxycycline treated and  control check leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf

value: ml5 knockdown

value: Dark

value: Day 7


title: ml5_Dark_7d_2


title: Patient1B


title: Exp 2 DIO-NASH vehicle w12 Rep 10


title: human WBC, GB4030093 (iDNase-seq)


title: human WBC, GB4030091 (iDNase-seq)


title: Exp 2 DIO-NASH vehicle w12 Rep 6


title: ml5_Dark_7d_1


title: human WBC, GB4030094 (iDNase-seq)


title: Exp 2 DIO-NASH vehicle w12 Rep 5


title: ml5_Dark_0d_3

value: Day 0


title: Exp 2 DIO-NASH vehicle w12 Rep 4


title: Exp 2 DIO-NASH vehicle w12 Rep 3


title: Exp 2 DIO-NASH vehicle w12 Rep 2


title: human WBC, GB4030092 (iDNase-seq)


title: Control3E

value: control induced pluripotent stem cell (iPSC) lines


title: human WBC, GB4030090 (iDNase-seq)


title: human WBC, GB4030089 (iDNase-seq)


title: Control3D


title: ml5_Dark_0d_2


title: human WBC, GB4030088 (iDNase-seq)


title: ml2_Dark_7d_3

value: ml2 knockdown


title: Control2A


title: ml5_Dark_0d_1


title: Exp 2 DIO-NASH Chow Reversal w12 Rep 10

value: DIO-NASH Chow Reversal w12


title: ml2_Dark_0d_3


title: Exp 2 DIO-NASH vehicle w12 Rep 1


title: Exp 2 DIO-NASH Chow Reversal w12 Rep 8


title: human WBC, GB4030086 (iDNase-seq)

value: WBC


title: Control1B


title: Control1C


title: human WBC, GB4030087 (iDNase-seq)


title: Exp 2 DIO-NASH Chow Reversal w12 Rep 7


title: human WBC, GB4030085 (iDNase-seq)


title: Exp 2 DIO-NASH Chow Reversal w12 Rep 9


title: human WBC, GB4030084 (iDNase-seq)


title: ml2_Dark_0d_2


title: ml2_Dark_7d_2


title: Control2B


title: Exp 2 DIO-NASH Chow Reversal w12 Rep 6


title: human WBC, GB4030083 (iDNase-seq)


title: ml2_Dark_7d_1


title: Exp 2 DIO-NASH Chow Reversal w12 Rep 5


title: Exp 2 DIO-NASH Chow Reversal w12 Rep 3


title: ml2_Dark_0d_1


title: Exp 2 DIO-NASH Chow Reversal w12 Rep 4


title: WT_Dark_7d_2

value: WT


title: Exp 2 DIO-NASH Chow Reversal w12 Rep 2


title: WT_Dark_7d_1