title: Paused, MeRIP m6A-IP, rep1

city: Toronto

first: Evelyne

middle: Anne

last: Collignon

state: ON

address: 60 Murray Street, Box42,

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

data_processing:
Libraries were trimmed of adaptors and quality-checked using Trim Galore! v0.4.0, and aligned to the mm10 transcriptome using TopHat2115 v2.0.13. Unmapped reads were then aligned to hg19.
For input samples, raw counts were obtained from the featureCounts function of subread (v1.5.0) with options: -t exon -g gene_id. Counts were imported into R, and analyzed by cell number normalization using the ratio of hg19/mm10 reads with edgeR (v3.32.1).
For m6A-IP samples, peaks were called with MACS2 (using IP samples and their input counterpart as controls and q<0.01). Peaks were annotated by intersecting center positions with RefSeq annotations, and manually verified. Peak analysis was performed using DiffBind v3.0.15, with the options minOverlap=2, score=DBA_SCORE_READS. MeRIP peaks were then first normalized using the ratio of hg19/mm10 reads in each sample for normalization. Then, peak levels were adjusted by dividing values by the ratio Input.sample/Input.average of the corresponding gene to consider expression changes. In the following differential analysis with edgeR, these normalized m6A levels were protected from further re-scaling by fixing the library size for all samples as lib.size = rep(10^6, 6) in the voom function.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with expression levels (log2) for all m6A-RIP peaks, adjusted for gene expression and with cell number normalization.

source_name: embryonic stem cells

growth_protocol: ES cells were grown on gelatin for 2 weeks in FBS/LIF media, under control or paused condition.

extract_protocol:
mESCs were spiked with 2% of human cells (HeLa), then poly(A) RNA was extracted using the Magnetic mRNA Isolation Kit (NEB) with two rounds of enrichment. Immunoprecipitation of m6A methylated RNA (MeRIP) was done using the EpiMark® N6-Methyladenosine Enrichment Kit with 4µg spiked poly(A) RNA.
MeRIP libraries were constructed from 0.5-1ng of input or IP RNA and prepared using the SMARTR-seq RNA library prep v2 kit (TakaraBio), per manufacturer’s recommendations.

treatment_protocol: Paused cells were treated with 200nM INK128 as mTor inhibitor for 2 weeks.

value: embryonic stem cells

value: paused


title: Paused, MeRIP m6A-IP, rep3

status: Public on May 17 2023

type: SRA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: genotype

value: WT

tag: treatment


title: Paused, MeRIP m6A-IP, rep2


title: FBS, MeRIP m6A-IP, rep2

value: control (FBS)


title: FBS, MeRIP m6A-IP, rep1


title: Paused, MeRIP input, rep3


title: FBS, MeRIP m6A-IP, rep3


title: Paused, MeRIP input, rep2


title: Paused, MeRIP input, rep1


title: WT2-1 d6

city: La Jolla

first: Philip

middle: Leo Stefan Maria

last: Gordts

state: CA

department: CMM

country: USA

institute: UCSD

description: Sample 12

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

molecule: total RNA

source_name: MEF

growth_protocol: MEFS (mouse embryonic fibroblasts) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: MEF

tag: cell type

value: fibroblast

value: NDST1 Knockout

value: adipogenic differentiation

tag: time

value: Day 5


title: FBS, MeRIP input, rep3


title: WT2-1 d3

description: Sample 6


title: FBS, MeRIP input, rep2


title: aboveground plant parts, infected with Pst, biol. rep. 3, exp.1

city: Christchurch, Canterbury

first: Moritz

last: Miebach

state: Canterbury

address: 20 Kirkwood Avenue, University of Canterbury Private Bag 4800

department: School of Biological Sciences

country: New Zealand

institute: University of Canterbury

data_processing:
Adapters and low-quality reads (end sequences with base quality <20 and sequences with N content > 10%) were removed from raw sequences and sequences below 75 bp were filtered using cutadapt (v1.9.1) (Martin, 2011).
The resulting reads were mapped against the Arabidopsis thaliana reference genome (TAIR10).
Mapped reads were counted with featureCounts (v1.22.2) (Liao et al., 2014).
Assembly: TAIR10
Supplementary files format and content: The file ‘counts_leafBac.txt’ contains the raw counts of sequencing reads for all samples belonging to the different bacterial leaf coloniser experiment.

organism: Arabidopsis thaliana

source_name: aboveground plant parts

growth_protocol: Plants were grown as previously described in (Miebach et al., 2020). Briefly, sterilised seeds were germinated on ½ MS (Murashige and Skoog medium, including vitamins, Duchefa, Haarlem, Netherlands) 1% phytoagar (Duchefa) filled pipette tips. Healthy looking seedlings were aseptically transferred, without removal from the pipette tip, aseptically into Magenta boxes (Magenta vessel GA-7, Magenta LLC, Lockport, IL, USA) filled with ground Zeolite (sourced from cat litter - Vitapet, Purrfit Clay Litter, Masterpet New Zealand, Lower Hutt, New Zealand) and watered with 60 mL ½ MS. Each box received four seedlings. The boxes were closed with lids that allowed for gas exchange and placed into a climate cabinet (85% relative humidity, 11 h light, 13 dark, 21 °C, 150-200 µmol light intensity). Plants were grown for four weeks before they were treated with bacteria or mock controls.

extract_protocol:
The plant material was collected in RNase-free microcentrifuge tubes (MCT-150-C, Axygen, Corning, USA) and was then immediately flash frozen in liquid N2. Two plants from different growth boxes were pooled per tube to form a biological replicate. Three biological replicates were sampled per treatment and time point. Flash-frozen samples were ground to a fine powder in the collection tube using Teflon pestles (General Lab Supply, Lab Supply, Dunedin, New Zealand). RNA extraction was performed using the Isolate II RNA Plant kit (Bioline, London, England).
RNA library preparation and sequencing was performed by Custom Science (Epping, Australia). RNA quality and purity was assessed using a Nanodrop (ND-2000 Spectrophotometer, Thermo Scientific, Waltham, MA, USA). RNA integrity was verified on a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA) using the RNA 6000 Nano Kit (Agilent). Poly-A enriched libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit (New England Biolabs, Ipswich, USA) for Illumina. RNA sequencing was performed on a NovaSeq 6000 (Illumina, San Diego, USA) platform. Approximately 30,000,000 paired-end reads with a length of 150 bp were generated per sample.

treatment_protocol: Bacterial suspensions were prepared as previously described in (Miebach et al., 2020). Briefly, bacteria were cultivated at 30 °C on minimal media agar plates containing 0.1% pyruvate as a carbon source. Bacterial suspensions were prepared from bacterial colonies suspended in phosphate-buffered saline (PBS, 0.2 g/L NaCl, 1.44 g/L, Na2HPO4 and 0.24 g/L KH2PO4) and washed twice via centrifugation at 4000 × g for 5 min followed by discarding the supernatant and again adding PBS. The optical density (OD 600 nm) was adjusted so that the suspension contained 2 × 10^7 colony forming units (CFU)/mL. Next, 200 µL of bacterial solution was sprayed per plant tissue culture box using an airbrush spray gun (0.2 mm nozzle diameter, Pro Dual Action 3 #83406). To obtain a homogeneous coverage, the distance between the airbrush spray gun and the plants was increased by stacking a plant tissue culture box, with the bottom cut off, onto the plant tissue culture box containing the plants being spray-inoculated.

value: aboveground plant parts

tag: ecotype

value: infection with Pst


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354 at 10^8 cfu/ml, biol. rep. 3, exp.2

data_processing:
Adapters and low-quality reads (end sequences with base quality <20 and sequences with N content > 10%) were removed from raw sequences and sequences below 75 bp were filtered using cutadapt (v1.9.1) (Martin, 2011).
The resulting reads were mapped against the Arabidopsis thaliana reference genome (TAIR10).
Mapped reads were counted with featureCounts (v1.22.2) (Liao et al., 2014).
Assembly: TAIR10
Supplementary files format and content: The file ‘counts_denBac.txt’ contains the raw counts of sequencing reads for all samples belonging to the bacterial density experiment.

growth_protocol: Plants were grown as previously described in (Miebach et al., 2020). Briefly, sterilised seeds were germinated on ½ MS (Murashige and Skoog medium, including vitamins, Duchefa, Haarlem, Netherlands) 1% phytoagar (Duchefa) filled pipette tips. Healthy looking seedlings were aseptically transferred, without removal from the pipette tip, aseptically into Magenta boxes (Magenta vessel GA-7, Magenta LLC, Lockport, IL, USA) filled with ground Zeolite (sourced from cat litter - Vitapet, Purrfit Clay Litter, Masterpet New Zealand, Lower Hutt, New Zealand) and watered with 60 mL ½ MS. Each box received four seedlings. The boxes were closed with lids that allowed for gas exchange and placed into a climate cabinet (85% relative humidity, 11 h light, 13 dark, 21 °C, 150-200 µmol light intensity). Plants were grown for six weeks before they were treated with bacteria or mock controls.

treatment_protocol: Bacterial suspensions were prepared as previously described in (Miebach et al., 2020). Briefly, bacteria were cultivated at 30 °C on minimal media agar plates containing 0.1% pyruvate as a carbon source. Bacterial suspensions were prepared from bacterial colonies suspended in phosphate-buffered saline (PBS, 0.2 g/L NaCl, 1.44 g/L, Na2HPO4 and 0.24 g/L KH2PO4) and washed twice via centrifugation at 4000 × g for 5 min followed by discarding the supernatant and again adding PBS. To explore the influence of bacterial load on plant responses, the bacterial suspensions were adjusted to 10^5, 10^6, 10^7 and 10^8 CFU/mL. Next, 1 ml of bacterial solution was sprayed per plant tissue culture box using an airbrush spray gun (0.2 mm nozzle diameter, Pro Dual Action 3 #83406). To obtain a homogeneous coverage, the distance between the airbrush spray gun and the plants was increased by stacking a plant tissue culture box, with the bottom cut off, onto the plant tissue culture box containing the plants being spray-inoculated.

value: inoculation with Williamsia sp. Leaf354 at 10^8 cfu/ml


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354, biol. rep. 2, exp.1

value: inoculation with Williamsia sp. Leaf354


title: aboveground plant parts, mock-treatment (PBS), biol. rep. 3, exp.1

value: mock (PBS)


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354 at 10^8 cfu/ml, biol. rep. 2, exp.2


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354 at 10^8 cfu/ml, biol. rep. 1, exp.2


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354, biol. rep. 1, exp.1


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354 at 10^6 cfu/ml, biol. rep. 3, exp.2

value: inoculation with Williamsia sp. Leaf354 at 10^6 cfu/ml


title: aboveground plant parts, mock-treatment (PBS), biol. rep. 1, exp.1


title: aboveground plant parts, infected with Pst, biol. rep. 1, exp.1


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354, biol. rep. 3, exp.1


title: aboveground plant parts, inoculated with Microbacterium sp. Leaf347, biol. rep. 3, exp.1

value: inoculation with Microbacterium sp. Leaf347


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354 at 10^7 cfu/ml, biol. rep. 1, exp.2

value: inoculation with Williamsia sp. Leaf354 at 10^7 cfu/ml


title: aboveground plant parts, inoculated with Microbacterium sp. Leaf347, biol. rep. 2, exp.1


title: aboveground plant parts, mock-treatment (PBS), biol. rep. 2, exp.1


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354 at 10^7 cfu/ml, biol. rep. 2, exp.2


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354 at 10^6 cfu/ml, biol. rep. 1, exp.2


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354 at 10^5 cfu/ml, biol. rep. 3, exp.2

value: inoculation with Williamsia sp. Leaf354 at 10^5 cfu/ml


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354 at 10^5 cfu/ml, biol. rep. 2, exp.2


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354 at 10^5 cfu/ml, biol. rep. 1, exp.2


title: aboveground plant parts, mock-treatment (PBS), biol. rep. 3, exp.2


title: aboveground plant parts, mock-treatment (PBS), biol. rep. 2, exp.2


title: aboveground plant parts, infected with Pst, biol. rep. 2, exp.1


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354 at 10^7 cfu/ml, biol. rep. 3, exp.2


title: aboveground plant parts, inoculated with Microbacterium sp. Leaf347, biol. rep. 1, exp.1


title: FBS, MeRIP input, rep1

value: embryonic stem cells


title: CRISPR screen, p53KO, Etoposide, Replicate C

city: Worcester

first: Michael

middle: J

last: Lee

state: MA

address: 368 Plantation Street

institute: UMass Chan Medical School

description:
Column 20
p53KO_Etoposide_C
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx

library_source: genomic

data_processing:
FASTX tool kit used to split barcodes and trim non-variable sgRNA regions
Reads mapped to GeCKOv2 library with Bowtie2 allowing 1 mismatch
Bottom 5% of guides and miRNA sequences removed
sgRNA-level L2FC determined in DESeq2 and then collapsed to gene-level with custom MATLAB script
Assembly: GeCKOv2 library
Supplementary files format and content: tab-delimited file for counts and excel sheet for gene-level L2FC and growth/death rates

molecule: genomic DNA

organism: Homo sapiens

source_name: U-2 OS

growth_protocol: U-2 OS osteosarcoma cells were maintained in high glucose DMEM supplemented with 10% fetal bovine serum, penicillin/streptomycin, and glutamine in a humidified incubator with 5% CO2 at 37C

extract_protocol:
Phenol-chloroform extraction of gDNA
Two consecutive PCRs to amplify sgRNAs from gDNA and add barcodes
sgRNA library

treatment_protocol: Treatment with Etoposide (5uM) for 96 hours

value: U-2 OS

value: Osteosarcoma

value: p53 KO

value: Etoposide

value: 96 hours


title: CRISPR screen, p53KO, Etoposide, Replicate B

description:
Column 19
p53KO_Etoposide_B
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: aboveground plant parts, mock-treatment (PBS), biol. rep. 1, exp.2


title: aboveground plant parts, inoculated with Williamsia sp. Leaf354 at 10^6 cfu/ml, biol. rep. 2, exp.2


title: CRISPR screen, WT, T0, Replicate C

description:
Column 5
WT_T0_C
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx

treatment_protocol: Untreated sample collected at the assay start point

value: p53 WT

value: Untreated

value: 0 hours


title: CRISPR screen, p53KO, Untreated, Replicate A

description:
Column 15
p53KO_Untreated_A
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx

treatment_protocol: Treatment with DMSO (v/v%) for 96 hours


title: CRISPR screen, WT, Etoposide, Replicate C

description:
Column 14
WT_Etoposide_C
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: CRISPR screen, WT, Untreated, Replicate B

description:
Column 10
WT_Untreated_B
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: CRISPR screen, p53KO, Etoposide, Replicate A

description:
Column 18
p53KO_Etoposide_A
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: CRISPR screen, p53KO, Untreated, Replicate C

description:
Column 17
p53KO_Untreated_C
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: CRISPR screen, p53KO, Untreated, Replicate B

description:
Column 16
p53KO_Untreated_B
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: CRISPR screen, p53KO, T0, Replicate A

description:
Column 6
p53KO_T0_A
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: CRISPR screen, WT, Untreated, Replicate A

description:
Column 9
WT_Untreated_A
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: CRISPR screen, WT, Untreated, Replicate C

description:
Column 11
WT_Untreated_C
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: Patients 100, 101

city: Chicago

first: Huiping

last: Liu

state: IL

address: 303 E Superior St Room 5-250

department: Pharmacology

institute: Northwestern University

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Monocytes and Tregs

extract_protocol:
White blood cells from convalescent COVID-19 patients were isolated from whole blood samples. Monocytes and Tregs were labeled with appropriate fluorescent antibodies and sorted using FACS.
Patient cells were labeled with a hashtag barcode oligo and libraries were prepared per manufacturer's instructions. Briefly, Cells were loaded onto a 10X Chromium controller, and librray was constructed using 10X chromium Next GEM Single Cell 5' Library and gel bead kits (v1.1)

value: Monocytes and Tregs


title: CRISPR screen, WT, Etoposide, Replicate B

description:
Column 13
WT_Etoposide_B
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: Patients 061, 062


title: Patients 074, 075, 076, 077


title: Patients 059, 060


title: Patients 086, 087, 088


title: Patients 102, 103


title: Patients 089, 090, 091


title: Patients 053, 054

source_name: Monocytes

value: Monocytes


title: Patient 057


title: CRISPR screen, WT, T0, Replicate B

description:
Column 4
WT_T0_B
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: CRISPR screen, p53KO, T0, Replicate B

description:
Column 7
p53KO_T0_B
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: CRISPR screen, WT, T0, Replicate A

description:
Column 3
WT_T0_A
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: CRISPR screen, WT, Etoposide, Replicate A

description:
Column 12
WT_Etoposide_A
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: Patients 078, 079, 080, 081


title: CRISPR screen, p53KO, T0, Replicate C

description:
Column 8
p53KO_T0_C
CRISPR_p53_counts.txt
CRISPR_p53_GeneLevel.xlsx


title: Patient 056


title: Patients 048, 049, 050


title: Patient 047


title: Patients 093, 094, 095, 096


title: Patients 042, 043


title: Patient 044


title: Patients 022, 023


title: Patients 029, 030


title: Patient 025


title: Patients 036, 037, 038


title: Patients 033, 034


title: Patients 020, 021


title: HCT116_THUMPD2KO2_3

city: Göttingen

first: Katherine

last: Bohnsack

address: Humboldtallee 23

country: Germany

institute: University Medical Centre Göttingen

data_processing:
Raw data were quality checked using FastQC, no reads had to be removed due to low quality. Most reads had a Phred score higher than 28.
For mapping the aligner STAR v2.7.10a with the following settings was used: --outFilterMultimapNmax 10 --outSAMattributes All --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --chimSegmentMin 20 --chimOutType WithinBAM Junctions --quantMode TranscriptomeSAM GeneCounts --outWigType bedGraph --outWigNorm RPM --outWigStrand Unstranded --outFilterMismatchNmax 2 (Li et al., 2009; Quinlan and Hall, 2010).
UCSC Genome Browser tools bedSort and bedGraphToBigWig were used to convert from bedgraph format to bigwig format for visualization of the data in the IGV genome browser (Kent et al., 2010; Thorvaldsdóttir et al., 2013).
Assembly: GRCh38.p13
Supplementary files format and content: bigWig, unstranded genome coverage

source_name: HCT116 THUMPD2KO2 cell culture

growth_protocol: Wild type HCT116 or HCT116 THUMPD2 KO1/2 cells were grown at 37°C in 5% CO2 in McCoy’s 5A medium  supplemented with 10% foetal bovine serum.

extract_protocol:
Total RNA was extracted using TRI reagent (Sigma) according to the manufacturer's instructions. DNase treatment was performed using TURBO DNase at 37°C for 15 min and RNA was re-purified using the RNA clean and concentrator kit (Zymo Research) according to the manufacturer's instructions.
PolyA-enrichment was performed and libraries were constructed by TruSeq total RNA library preparation (Illumina) according to the maufacturer's instructions.

value: THUMPD2 KO


title: HCT116_THUMPD2KO2_2


title: HCT116_THUMPD2KO2_1


title: CTRL_rep2

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

description: Reanalysis of GSM5182607

data_processing:
Cutadapt version 2.4 was used to trim adapter sequences.
Sequence mapping was performed using the tool Hisat2 and the Human reference genome (Ensembl version GRCh38) data.
StringTie (version 1.3.6) tool and a python script prepDE.py from StringTie were used for transcript assembling and extracting read count information, respectively.
The tool edgeR was used for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: Processed data files contain Tab-delimited text files that include Ensembl gene ids and read counts.

source_name: Lung

growth_protocol: A549 lung adenocarcinoma cell line (mycoplasma negative) was cultured in RPMI-1640 media supplemented with 10% FBS, 100U/mL penicillin, 100µg/mL streptomycin, and L-glutamine.

extract_protocol:
RNA was isolated with Trizol.
Library preparation was performed by GeneWiz (www.GENEWIZ.com) using the NEBNext Ultra II RNA Library Prep kit. The libraries were sequenced on HiSeq 4000 to generate the RNA-seq profiles.

treatment_protocol: A459 cells were infected with lentiviral vectors expressing lncRNA PTSL or empty vector and were harvested 48 hrs later (four replicates of each).

value: Lung

value: epithelial

value: Control RNA transfected


title: HCT116_WT_1

source_name: HCT116 WT cell culture

growth_protocol: Wild type HCT116 or HCT116 THUMPD2 KO cells were grown at 37°C in 5% CO2 in McCoy’s 5A medium  supplemented with 10% foetal bovine serum.

value: Wild type


title: PTSL_rep4

value: PTSL transfected


title: PTSL_rep1


title: HCT116_THUMPD2KO1_2

source_name: HCT116 THUMPD2KO cell culture


title: HCT116_WT_2


title: HCT116_THUMPD2KO1_3


title: CTRL_rep4

description: Reanalysis of GSM5182609


title: HCT116_WT_3


title: CTRL_rep3

description: Reanalysis of GSM5182608


title: HCT116_THUMPD2KO1_1


title: PTSL_rep3


title: HU117_K562_MYC1_RAD21_shRNA3_rp2

city: Beijing

first: Jinchun

last: Wu

address: No. 5, Yiheyuan street

country: China

institute: Peking University

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021
Assembly: hg19
Supplementary files format and content: tab file
Library strategy: PEM-seq

source_name: cultured cell

growth_protocol: The authenticated K562 cells (3111C0001CCC000039, National Infrastructure of Cell line resource, China) were cultured in the RPMI1640 with 15% FBS as described.

extract_protocol:
Followed the PEM-seq protocol that described in Yin et al., 2019.
Followed the PEM-seq protocol that described in Yin et al., 2019.

value: WT

value: The cells were transfected with RAD21-shRNA (targeting:GCCCACCAAGAAATTGATGAT) for 36 hrs and transfected with gRNA-Cas9 targeting c-MYC locus for another 2 days.


title: HU117_K562_MYC1_RAD21_shRNA2_rp3

value: The cells were transfected with RAD21-shRNA (targeting:GCTTATAATGCCATTACTTTA) for 36 hrs and transfected with gRNA-Cas9 targeting c-MYC locus for another 2 days.


title: HU117_K562_MYC1_RAD21_shRNA2_rp2


title: PTSL_rep2


title: CTRL_rep1

description: Reanalysis of GSM5182606


title: HU117_K562_MYC1_RAD21_shRNA3_rp3


title: HU117_K562_MYC1_RAD21_shRNA2_rp1


title: HU117_K562_MYC1_RAD21_shRNA1_rp3

value: The cells were transfected with RAD21-shRNA (targeting:GCTAATTGTTGACAGTGTCAA) for 36 hrs and transfected with gRNA-Cas9 targeting c-MYC locus for another 2 days.


title: HU117_K562_MYC1_RAD21_shRNA1_rp1


title: HU117_K562_MYC1_NC_control_for_shRNA_rp3

value: The cells were  transfected with gRNA-Cas9 targeting c-MYC locus for 2 days.


title: HU117_K562_MYC1_RAD21_shRNA1_rp2


title: HU117_K562_MYC1_NC_control_for_shRNA_rp1


title: K562_RAD21_mAC_4_TP53_translocations_repeat1

treatment_protocol: The cells were transfected with gRNA-Cas9 targeting TP53 or MYC1 locus,  then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) cells.

tag: clone

value: The cells were  transfected with gRNA-Cas9 targeting TP53 locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid)  cells.


title: K562_RAD21_mAC_4_TP53_translocations_repeat3


title: K562_RAD21_mAC_4_TP53_translocations_repeat2


title: HU117_K562_MYC1_RAD21_shRNA3_rp1


title: K562_RAD21_mAC_4_MYC1_translocations_repeat3

value: The cells were  transfected with gRNA-Cas9 targeting c-MYC locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid)  cells.


title: K562_RAD21_mAC_1_TP53_translocations_repeat2


title: K562_RAD21_mAC_1_TP53_translocations_repeat3


title: K562_CBEko_Q3C_normalized

description: Cells were fixed with formaldehyde. Fixed cells were then subjected to q3C-seq, similar to the description in 3C-HTGTS (Liu et al., 2021a), except that the 80 cycles of LAM PCR were replaced by one-round primer extension and biotinylated PCR products were ligated with a barcoded bridge adapter, to quantify chromatin interaction. The 4-bp cutter DpnII (NEB, R0543L) was used for the identification of interaction from upstream of CBE. The library construction procedure is similar to PEM-seq.

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021
Assembly: hg19
Supplementary files format and content: bedGraph
Library strategy: q3C-seq

value: CBE-/+


title: K562_RAD21_mAC_1_TP53_translocations_repeat1


title: K562_WT_TP53_translocations_repeat3


title: K562_RAD21_mAC_4_MYC1_translocations_repeat2


title: K562_WT_TP53_translocations_repeat1


title: K562_RAD21_mAC_4_MYC1_translocations_repeat1


title: K562_RAD21_mAC_1_MYC1_translocations_repeat3


title: K562_WT_MYC1_translocations_repeat3


title: K562_RAD21_mAC_1_MYC1_translocations_repeat2


title: K562_RAD21_mAC_1_MYC1_translocations_repeat1


title: K562_WT_MYC1_translocations_repeat1


title: HU117_K562_MYC1_NC_control_for_shRNA_rp2


title: K562_WT_MYC1_translocations_repeat2


title: K562_WT_Q3C_normalized_control_for_CBEko

treatment_protocol: Cells were fixed with formaldehyde. Fixed cells were then subjected to q3C-seq, similar to the description in 3C-HTGTS (Liu et al., 2021a), except that the 80 cycles of LAM PCR were replaced by one-round primer extension and biotinylated PCR products were ligated with a barcoded bridge adapter, to quantify chromatin interaction. The 4-bp cutter DpnII (NEB, R0543L) was used for the identification of interaction from upstream of CBE. The library construction procedure is similar to PEM-seq.


title: HU117_K562_CBEko_heterozygous_PEM-seq_rp2

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021, adjust the barcode to 12-nt (https://github.com/liumz93/PEM-Q).
Assembly: hg19
Supplementary files format and content: tab file
Library strategy: PEM-seq

treatment_protocol: The cells were  transfected with gRNA-Cas9 targeting , with indicated treatment, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) cells.

value: cells were transfected with gRNA-Cas9 (GGGCTATAATAAGGCCCTTG) for 48 hours and sorting for cherry positive cells.


title: HU117_K562_WT_sg-for-CBE_PEM-seq_rp3


title: HU116_HU120_NAIL_EdUHU_WT

data_processing:
END-seq data were trimmed by cutadapt using arguments: –g “ACACTCTTTCCCTACACGACGCTCTTCCGATCT” –G “AGACGTGTGCTCTTCCGATCT” and aligned to human hg19 assembly using BWA mem algorithm. Duplicates were removed using picard MarkDuplicates with argument “REMOVE_DUPLICATES = true”. After duplication, the DSB break points were identified and the numbers of DNA breaks were normalized to the same DSBs from other ERIZ regions. NAIL-seq data were processed followed the pipeline described in Liu et al., 2021 and Wong et al., 2021
Assembly: hg19
Supplementary files format and content: bedgraph and bigwig
Library strategy: END-seq

extract_protocol: END-seq were performed as described in (Wong et al., 2021), with minor modifications. NAIL-seq were performed as described in Liu et al., 2021

value: cells were arrested by CDKi for 36h, and released into EdU and HU for 24hrs.


title: HU117_K562_WT_sg-for-CBE_PEM-seq_rp2


title: HU117_K562_WT_sg-for-CBE_PEM-seq_rp1


title: HU117_K562_CBEko_heterozygous_PEM-seq_rp1


title: HU117_K562_CBEko_heterozygous_PEM-seq_rp3


title: K562_WT_TP53_translocations_repeat2


title: HU116_HU120_NAIL_EdUHU_CBE_ko_heterozygous


title: HU116_HU120_Early-S_HU_END-seq_CBEko_heterozygous

value: cells were arrested by CDKi for 36h, and released into 10mM HU for 24h. Then the samples were applied to END-seq.


title: HU102_K562_MYC1_5uM_aphidicolin_rp1

treatment_protocol: The cells were  transfected with gRNA-Cas9 targeting c-MYC locus, with indicated treatment, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) cells.

value: The cells were  transfected with gRNA-Cas9 targeting c-MYC locus and treated with 5 uM aphidicolin for 2 days, RFP positive cells were sorted for library.


title: HU102_K562_MYC1_20uM_etoposide_rp1

value: The cells were  transfected with gRNA-Cas9 targeting c-MYC locus and treated with 20 uM etoposide for 2 days, RFP positive cells were sorted for library.


title: HU116_HU120_Early-S_HU_END-seq_WT


title: HU102_K562_MYC1_5uM_aphidicolin_rp3


title: HU102_K562_MYC1_1mMHU_rp1

value: The cells were  transfected with gRNA-Cas9 targeting c-MYC locus and treated with 1 mM HU for 2 days, RFP positive cells were sorted for library.


title: HU102_K562_MYC1_5uM_aphidicolin_rp2


title: HU102_K562_MYC1_20uM_etoposide_rp3


title: HU102_K562_MYC1_20uM_etoposide_rp2


title: HU102_K562_MYC1_1mMHU_rp2


title: HU102_K562_MYC1_NC_rp1

value: The cells were  transfected with gRNA-Cas9 targeting c-MYC locus for 2 days and sorted for RFP positive cells.


title: HU102_K562_MYC1_1mMHU_rp3


title: HU102_K562_MYC1_NC_rp2


title: K562_RAD21_mAC_1_IAA_E212X_rp3

description: The cells were pretreated by 2ug/ml dox for 12 hours and transfected with plasmid carrying E212X RAD21 mutant for 12 hours in dox. Cells were subsequently treated with 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting c-MYC locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) and mClover negative cells.

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021
Assembly: hg19
Supplementary files format and content: bed file containing genome-wide break sites
Library strategy: PEM-seq

extract_protocol: Followed the PEM-seq protocol that described in Yin et al., 2019.


title: K562_RAD21_mAC_1_IAA_Q592X_rp1

description: The cells were pretreated by 2ug/ml dox for 12 hours and transfected with plasmid carrying Q592X RAD21 mutant for 12 hours in dox. Cells were subsequently treated with 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting c-MYC locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) and mClover negative cells.


title: K562_RAD21_mAC_1_IAA_Q592X_rp2


title: K562_RAD21_mAC_1_IAA_Q592X_rp3


title: K562_RAD21_mAC_1_IAA_E212X_rp2


title: K562_RAD21_mAC_1_IAA_E212X_rp1


title: K562_RAD21_mAC_1_IAA_wt-RAD21_rp1

description: The cells were pretreated by 2ug/ml dox for 12 hours and transfected with plasmid carrying wild type RAD21 for 12 hours in dox. Cells were subsequently treated with 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting c-MYC locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) and mClover negative cells.


title: K562_RAD21_mAC_1_IAA_wt-RAD21_rp2


title: K562_RAD21_mAC_1_IAA_wt-RAD21_rp3


title: K562_RAD21_mAC_1_IAA_no_mutant_rp3

description: The cells were pretreated by 2ug/ml dox for 24 hours and then 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting c-MYC locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) and mClover negative cells.


title: K562_RAD21_mAC_1_IAA_no_mutant_rp2


title: K562_WT_IAA_no_mutant_rp3


title: K562_WT_IAA_no_mutant_rp2


title: K562_WT_IAA_no_mutant_rp1


title: HU102_K562_MYC1_NC_rp3


title: K562_RAD21_mAC_4_IAA_END_seq

data_processing:
Reads were trimmed by cutadapt using arguments: –g “ACACTCTTTCCCTACACGACGCTCTTCCGATCT” –G “AGACGTGTGCTCTTCCGATCT” and aligned to human hg19 assembly using BWA mem algorithm. Duplicates were removed using picard MarkDuplicates with argument “REMOVE_DUPLICATES = true”. After duplication, the DSB break points were identified and the numbers of DNA breaks were normalized to the same DSBs from spike-in.
Assembly: hg19
Supplementary files format and content: bedfile containing genome-wide break sites
Library strategy: END-seq

extract_protocol:
After solidification, plugs were incubated with cell lysis buffer (1 mg/mL Protease K, 10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 50 mM EDTA, and 0.4% SDS) at 37ºC for 1 hour and then at 50ºC for 7 hours. The plugs were washed by wash buffer (10 mM Tris-HCl pH 8.0, 50 mM EDTA) for 3 times and then incubated with RNase A(Invitrogen) at 37ºC for 1 hour. After being extensively washed, plugs were treated with blunting, A-Tailing as described in END-seq protocol (Wong et al., 2021), and then ligated with END-seq adapter 1 (up: 5’-phos- GATCGGAAGAGCGTCGTGTAGGGAAAGAGT-3’-biotin; down: 5’-NH2- ACTCTTTCCCTACACGACGCTCTTCCGATCT-3’). After ligation, plugs were melted and treated by β-Agarase I. The recovered genomic DNA were then sheared to a length between 150-400 bp by sonication (Covaris) and the biotinylated DNA fragments were purified by streptavidin beads (MyOne C1, Invitrogen).
After purification, the DNA underwent end repair, dA-Tailing, and ligated with END-seq adapter 2 (up: 5’- AGACGTGTGCTCTTCCGATCT; down: 5’-phos-GATCGGAAGAGCACACGTCT). The ligated products were tagged with Illumina adapters and sequenced on Hi-seq, 2×150 bp.

value: END-seq were performed as described in (Wong et al., 2021), with minor modifications. Three million WT or RAD21-depleted K562 cells were mixed 30,000 spike-in cells that harbored a DSB induced by SpCas9 at the c-MYC locus. Cells were harvested, resuspended in the cell suspension buffer (PBS with 5 mM EDTA), embedded in low-melting agarose, and then transferred in to plugs (Bio-Rad Plug Molds, 1703713). After solidification, plugs were incubated with cell lysis buffer (1 mg/mL Protease K, 10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 50 mM EDTA, and 0.4% SDS) at 37ºC for 1 hour and then at 50ºC for 7 hours. The plugs were washed by wash buffer (10 mM Tris-HCl pH 8.0, 50 mM EDTA) for 3 times and then incubated with RNase A(Invitrogen) at 37ºC for 1 hour. After being extensively washed, plugs were treated with blunting, A-Tailing as described in END-seq protocol (Wong et al., 2021), and then ligated with END-seq adapter 1 (up:5’-phos- GATCGGAAGAGCGTCGTGTAGGGAAAGAGT-3’-biotin; down:5’-NH2- ACTCTTTCCCTACACGACGCTCTTCCGATCT-3’). After ligation, plugs were melted and treated by β-Agarase I. The recovered genomic DNA were then sheared to a length between 150-400 bp by sonication (Covaris) and the biotinylated DNA fragments were purified by streptavidin beads (MyOne C1, Invitrogen). After purification, the DNA underwent end repair, dA-Tailing, and ligated with END-seq adapter 2 (up:5’- AGACGTGTGCTCTTCCGATCT; down:5’-phos-GATCGGAAGAGCACACGTCT). The ligated products were tagged with Illumina adapters and sequenced on Hi-seq, 2×150 bp.


title: K562_WT_IAA_END_seq

treatment_protocol: END-seq were performed as described in (Wong et al., 2021), with minor modifications. Three million WT or RAD21-depleted K562 cells were mixed 30,000 spike-in cells that harbored a DSB induced by SpCas9 at the c-MYC locus. Cells were harvested, resuspended in the cell suspension buffer (PBS with 5 mM EDTA), embedded in low-melting agarose, and then transferred in to plugs (Bio-Rad Plug Molds, 1703713).


title: K562_RAD21_mAC_1_IAA_END_seq


title: siMock3

city: Xi'an

first: Qiong

last: Ma

state: Shaanxi

address: Orthopaedic Oncology Institute.Tangdu Hospital, Fourth Military Medical University，569 Xinsi Road, Baqiao District, Xi’an, Shaanxi

institute: Orthopedic Oncology Institute, Department of Orthopedic Surgery, Tangdu Hospital, Fourth Military Medical University

data_processing:
Quality control  Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome  Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Novel transcripts prediction  The mapped reads of each sample were assembled by StringTie (v1.3.3b)  (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level  featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: Hisat2 v2.0.5
Supplementary files format and content: gzip-compressed archive containing raw data sequenced for each group.

extract_protocol:
1RNA degradation and contamination was monitored on 1% agarose gels.  2RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) .  3RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse  Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: osteosarcoma cells

tag: transfection

value: siMock


title: siFUBP1_1


title: siFUBP1_3


title: siMock2


title: siMock1


title: sample28_normal

city: Hong  Kong

first: Yueqin

last: ZHU

state: China

address: Sassoon Road

institute: Hong Kong University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (v0.21.0)
Trimmed sequence reads were mapped to GRCh38/rn6  using STAR(v2.7.7a)
Read count extraction and normalization were performed using RSEM(v1.3.3)
Assembly: GRCh38/rn6
Supplementary files format and content: tab-delimited text files include read count for each sample

source_name: liver grafts,normal,patient

extract_protocol:
Total RNA was extracted from liver grafts using TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver graft

tag: disease

value: normal


title: siFUBP1_2


title: sample25_normal


title: sample19_normal


title: sample26_normal


title: sample18_steatotic

source_name: liver grafts,steatotic,patient

value: steatotic


title: sample22_normal


title: sample27_normal


title: sample23_normal


title: sample24_normal


title: sample20_normal


title: sample17_steatotic


title: sample21_normal


title: sample14_steatotic


title: K562_RAD21_mAC_1_IAA_no_mutant_rp1


title: sample15_steatotic


title: sample12_steatotic


title: sample11_steatotic


title: sample13_steatotic


title: sample16_steatotic


title: sample10_steatotic


title: sample9_steatotic


title: sample8_steatotic


title: sample7_steatotic


title: sample6_steatotic


title: sample3_steatotic


title: sample4_steatotic


title: sample5_steatotic


title: sample1_steatotic


title: q3C, K562, RAD21-mAC, #4, IAA, G1, 1k

description: G1-arrested cells with or without RAD21 were purified by FACS isolation and then fixed with formaldehyde. Fixed cells were then subjected to q3C-seq, similar to the description in 3C-HTGTS (Liu et al., 2021a), except that the 80 cycles of LAM PCR were replaced by one-round primer extension and biotinylated PCR products were ligated with a barcoded bridge adapter, to quantify chromatin interaction. The 4-bp cutter DpnII (NEB, R0543L) was used for the identification of interaction from CBE upstream of c-MYC. The library construction procedure is similar to PEM-seq. Data of q3C-seq was applied to the PEM-Q pipeline for further processing.


title: q3C, K562, WT, IAA, G1, 1k

treatment_protocol: G1-arrested cells with or without RAD21 were purified by FACS isolation and then fixed with formaldehyde. Fixed cells were then subjected to q3C-seq, similar to the description in 3C-HTGTS (Liu et al., 2021a), except that the 80 cycles of LAM PCR were replaced by one-round primer extension and biotinylated PCR products were ligated with a barcoded bridge adapter, to quantify chromatin interaction. The 4-bp cutter DpnII (NEB, R0543L) was used for the identification of interaction from CBE upstream of c-MYC. The library construction procedure is similar to PEM-seq.

value: WT


title: sample2_steatotic


title: HU074 K562 WT G1 CTCF ChIP seq

description: Applying ChIP-seq to check the amount of chromatin-bound CTCF.

data_processing:
Trimmed the adapter sequences in the reads using cutadapt
Aligned reads to the human genome(assembly hg19) using BWA-MEM
The bigwig files were generated using bamCoverage with RPKM normalization according to total mapped reads.
Assembly: hg19
Supplementary files format and content: bigwig files containing signal of RAD21 or CTCF ChIP-seq

extract_protocol:
Collected cells were fixed by 1% formaldehyde (Sigma, F1635, fresh-made) for 10 min at 25oC and quenched by 125 mM glycine (VWR-amerasco 0167) for 5 min. Thoroughly washed by PBS, cells were lysed on ice for 15 min with ice-cold NP40 lysis buffer (10 mM Tris-HCl, pH 7.5; 150 mM NaCl; 0.05% NP40) supplied with protease inhibitors (PIs) (Bimake, B14012). The nuclei fraction was isolated, washed by PBS/1 mM EDTA, and then lysed with glycerol buffer (20 mM Tris-HCl, pH 8.0; 75 mM NaCl; 0.5 mM EDTA; 0.85 mM DTT; 50% glycerol) and nuclei lysis buffer (10 mM HEPES, pH 7.6; 1 mM DTT; 7.5 mM MgCl2; 0.2 mM EDTA; 0.3 M NaCl; 1 M urea; 1% NP40). The chromatin was pelleted by centrifuge, washed twice by PBS/1 mM EDTA, and eventually suspended in sonication buffer (20 mM Tris-HCl, pH 8.0; 150 mM NaCl; 2 mM EDTA; 0.1% SDS; 1% Triton X-100; 4 mM CaCl2) with PIs. Chromatin fractions were then treated with 50 U MNase (NEB, M2047S) for 10-12 min at 37oC, and the digestion was quenched by adding 5 mM EGTA and 5 mM EDTA. After that, pre-digested chromatin was sonicated by a Biorupter (Energy: High; On: 30 s; Off: 60 s; 15 cycles; 4oC). 30 mL of soluble chromatin fraction was kept as input and the rest was subjected to ChIP analysis.
For ChIP-seq, an antibody against  RAD21 (Abcam, ab992)  or CTCF (millipore, 07-729)was incubated with the soluble chromatin fraction for 2 hours at 4oC. 40 mL protein G dynabeads (Invitrogen, 10003D) were then added overnight. Next, beads were sequentially washed by high-salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 2 mM EDTA; 20 mM Tris-HCl, pH 8.0) for twice, LiCl buffer (0.25 M LiCl; 1% NP-40; 10 mM Tris-HCl; pH 8.0, 1 mM EDTA) for once, and TE buffer for three times. Chromatin bound on beads was eluted twice with elution buffer (20 mM Tris-HCl, pH 8.0; 10 mM EDTA; 1% SDS) at 65 oC, each for 15 min. Eluate fraction was treated with RNase A (Thermo Fisher, EN0531), Proteinase K (Invitrogen, 25530015), and de-crosslinked at 65 oC overnight. Purified DNA was end-repaired, tailed with poly-dC, tagged with biotin, captured by Streptavidin C1 beads (Invitrogen, 65002), and ligated with an adapter. The beads-bound DNA was thoroughly washed, tagged with Illumina sequences, and sequenced with Hi-seq (2×150 bp).

treatment_protocol: Cells were directly subjected to ChIP-seq procedure with CTCF antibody (Millipore, 07-729).

tag: antibody

value: anti-CTCF (Millipore, 07-729)


title: HU075 K562 RAD21 mAC 1 IAA RAD21 ChIP seq

description: Applying ChIP-seq to check the amount of chromatin-bound RAD21.

treatment_protocol: Cells were treated with dox for 24 hours, and then with IAA for 6 hours, after sorting for mClover negative cells, cells were collected and then subjected to ChIP-seq procedure with RAD21 antibody(Abcam, ab992).

value: anti-RAD21 (Ab992, Abcam)


title: HU075 K562 WT G1 RAD21 ChIP seq

treatment_protocol: Cells were treated with CDK inhibitor for 42h, cells were collected and then subjected to ChIP-seq procedure with RAD21 antibody(Abcam, ab992).


title: HU093, EdUHU, K562, RAD21-mAC-4, IAA, Repeat3

description: EdUHU_K562_RAD21_4_IAA_3_Repeats_merge.bw

data_processing:
Library strategy: NAIL-seq
The "RepFind" pipeline was applied as described in  Liu et al., 2021.
Assembly: hg19
Supplementary files format and content: bigwig files were generated using bamCoverage

extract_protocol:
Genomic DNA was isolated, tagged with biotin by click-iT reaction, subjected to the sequential isolation of EdU.
After on-beads ligation, purified DNA was tagged with Illumina sequencing primers and sequenced on Hi-seq, 2×150 bp.
Nail-seq (Liu et al., 2021)

treatment_protocol: cells were treat with CDK4/6 inhibitor for 42h, at 24h and 6h prior to release, dox and IAA were added respectively, cells were released into EdU/HU/DOX/IAA for 24h, and mClover negative cells were sorted for NAIL-seq libraries

value: IAA


title: HU075 K562 WT RAD21 ChIP seq

treatment_protocol: Cells were directly subjected to ChIP-seq procedure with RAD21 antibody (Abcam, ab992).


title: HU075 K562 WT IAA G1 RAD21 ChIP seq

treatment_protocol: Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were collected and then subjected to ChIP-seq procedure with RAD21 antibody(Abcam, ab992).


title: HU075 K562 RAD21 mAC 4 G1 IAA RAD21 ChIP seq

treatment_protocol: Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, mClover-negative cells were sorted and then subjected to ChIP-seq procedure with RAD21 antibody(Abcam, ab992).


title: HU075 K562 RAD21 mAC 4 IAA RAD21 ChIP seq


title: EdUHU, K562, CTCF-mAC_5C9, IAA, Repeat1


title: HU093, EdUHU, K562, WT, IAA, Repeat3


title: HU088, EdUHU, K562, RAD21-mAC-4, IAA, Repeat2


title: HU088, EdUHU, K562, RAD21-mAC-1, IAA, Repeat2

description: EdUHU_K562_RAD21_1_IAA_3_Repeats_merge.bw


title: HU093, EdUHU, K562, RAD21-mAC-1, IAA, Repeat3


title: HU075 K562 WT IAA RAD21 ChIP seq


title: EdUHU, K562, WT, IAA, Repeat1


title: HU088, EdUHU, K562, WT, IAA, Repeat2


title: HU090, B24, K562, RAD21-mAC-4, IAA, G1, antiMCM5, ChIP-input

description:
Comparing the disribution of chromatin-bound MCM5 after RAD21 depletion.
HU090_K562_RAD21-mAC_4_IAA_G1_antiMCM5_ChIP_Fold_change.bw

data_processing:
Trimmed the adapter sequences in the reads using cutadapt
Aligned reads to the human genome(assembly hg19) using BWA-MEM
The bigwig files were generated using bamCoverage with RPKM normalization
Signals were normalized to fold change defined by the ratio of ChIP-ed signals over input signals by bigwigCompare
Assembly: hg19
Supplementary files format and content: bigwig files containing signal of MCM ChIP-seq

extract_protocol:
Collected cells were fixed by 1% formaldehyde (Sigma, F1635, fresh-made) for 10 min at 25oC and quenched by 125 mM glycine (VWR-amerasco 0167) for 5 min. Thoroughly washed by PBS, cells were lysed on ice for 15 min with ice-cold NP40 lysis buffer (10 mM Tris-HCl, pH 7.5; 150 mM NaCl; 0.05% NP40) supplied with protease inhibitors (PIs) (Bimake, B14012). The nuclei fraction was isolated, washed by PBS/1 mM EDTA, and then lysed with glycerol buffer (20 mM Tris-HCl, pH 8.0; 75 mM NaCl; 0.5 mM EDTA; 0.85 mM DTT; 50% glycerol) and nuclei lysis buffer (10 mM HEPES, pH 7.6; 1 mM DTT; 7.5 mM MgCl2; 0.2 mM EDTA; 0.3 M NaCl; 1 M urea; 1% NP40). The chromatin was pelleted by centrifuge, washed twice by PBS/1 mM EDTA, and eventually suspended in sonication buffer (20 mM Tris-HCl, pH 8.0; 150 mM NaCl; 2 mM EDTA; 0.1% SDS; 1% Triton X-100; 4 mM CaCl2) with PIs. Chromatin fractions were then treated with 50 U MNase (NEB, M2047S) for 10-12 min at 37oC, and the digestion was quenched by adding 5 mM EGTA and 5 mM EDTA. After that, pre-digested chromatin was sonicated by a Biorupter (Energy: High; On: 30 s; Off: 60 s; 15 cycles; 4oC). 30 mL of soluble chromatin fraction was kept as input and the rest was subjected to ChIP analysis.
For ChIP-seq, an antibody against  MCM5 (1:50; Abcam, ab75975) was incubated with the soluble chromatin fraction for 2 hours at 4oC. 40 mL protein G dynabeads (Invitrogen, 10003D) were then added overnight. Next, beads were sequentially washed by high-salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 2 mM EDTA; 20 mM Tris-HCl, pH 8.0) for twice, LiCl buffer (0.25 M LiCl; 1% NP-40; 10 mM Tris-HCl; pH 8.0, 1 mM EDTA) for once, and TE buffer for three times. Chromatin bound on beads was eluted twice with elution buffer (20 mM Tris-HCl, pH 8.0; 10 mM EDTA; 1% SDS) at 65 oC, each for 15 min. Eluate fraction was treated with RNase A (Thermo Fisher, EN0531), Proteinase K (Invitrogen, 25530015), and de-crosslinked at 65 oC overnight. Purified DNA was end-repaired, tailed with poly-dC, tagged with biotin, captured by Streptavidin C1 beads (Invitrogen, 65002), and ligated with an adapter. The beads-bound DNA was thoroughly washed, tagged with Illumina sequences, and sequenced with Hi-seq (2×150 bp).

treatment_protocol: Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, mClover negative cells were sorted and then subjected to ChIP-seq procedure without MCM5 antibody enrichment.

tag: chip antibody


title: HU090, B22, K562, WT, IAA, G1, antiMCM5, ChIP-input

description:
Comparing the disribution of chromatin-bound MCM5 after RAD21 depletion.
HU090_K562_WT_IAA_G1_antiMCM5_ChIP_Fold_change.bw

treatment_protocol: Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were collected and then subjected to ChIP-seq procedure without MCM5 antibody enrichment.


title: HU090, B23, K562, RAD21-mAC-1, IAA, G1, antiMCM5, ChIP-input

description:
Comparing the disribution of chromatin-bound MCM5 after RAD21 depletion.
HU090_K562_RAD21-mAC_1_IAA_G1_antiMCM5_ChIP_Fold_change.bw


title: HU090, B21, K562, RAD21-mAC-4, IAA, G1, antiMCM5, ChIP

treatment_protocol: Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, mClover-negative cells were sorted and then subjected to ChIP-seq procedure with MCM5 antibody (Abcam, ab75975).

value: MCM5 antibody (Abcam, ab75975)


title: HU090, B20, K562, RAD21-mAC-1, IAA, G1, antiMCM5, ChIP


title: HU086_HU089_K562_WT_IAA_BrdU_B17_RPKM_1000

description: for identification of early replication regions

extract_protocol:
Genomic DNA was isolated, tagged with biotin by click-iT reaction, subjected to the sequential isolation of BrdU (by antibody on Protein G beads) and then EdU (by streptavidin beads).
After on-beads ligation, purified DNA was tagged with Illumina sequencing primers and sequenced on Hi-seq, 2×150 bp.
Nail-seq (Liu et al., 2021)

treatment_protocol: EdU-and-BrdU labeling, G1-arrested WT or RAD21-depleted cells were released into fresh medium for 3 or 4 hours, respectively.Then, cells were labeled by 20 uM EdU for 15 min, washed with pre-warmed fresh medium, and then incubated with 50 uM BrdU for 15 min. Of note, Dox and IAA persisted in the medium during release and labeling with nucleoside analogs. After that, cells were thoroughly washed by ice-cold PBS and subjected to FACS purification of RAD21-depletion cells.

value: cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were released into DOX/IAA for 3h, labelled by EdU and then BrdU, each for 15 min and purified BrdU-enriched DNA


title: HU090, B19, K562, WT, IAA, G1, antiMCM5, ChIP

treatment_protocol: Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were collected and then subjected to ChIP-seq procedure with MCM5 antibody (Abcam, ab75975).


title: HU086_HU089_K562_Rad21_mAC_4_IAA_EdU_R12_RPKM_1000

value: cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were released into DOX/IAA for 4h, labelled by EdU and then BrdU, each for 15 min and sorted for mClover-negative cells,  purified genomic DNA and enriched EdU-labelled DNA


title: HU085, B17, PRO-seq, K562, WT, IAA, replicate1, G1

description: Comparing the expression difference of WT and RAD21-depleted cells

data_processing:
Library strategy: PRO-seq
The adapter sequences on R1 and R2 were trimmed using cutadapt.
Reads were aligned to a combined genome (assembly hg19 combined with dm6) using bowtie.
Duplicates or reads with multiple alignments, and reads in the blacklist regions were removed.
Reads uniquely aligned to hg19 were normalized by the spike-in reads with a normalization factor measured by 1000000 / (the number of reads aligned to the dm6 genome).
Assembly: combined genome (assembly hg19 combined with dm6)
Supplementary files format and content: bigwig files containing transcription signal.

extract_protocol:
Cell nucleis were isolated and subjected to nuclear run-on for PRO-seq libraries as described in Mahat et al., 2016.
Following PRO-seq description in Mahat et al., 2016.

treatment_protocol: Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were collected and then subjected to nuclear run-on following the PRO-seq procedure.

tag: fraction

value: nascent RNA


title: HU085, B21, PRO-seq, K562, RAD21-mAC-1, IAA, G1

treatment_protocol: Cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, mClover negative cells were sorted and then subjected to nuclear run-on following the PRO-seq procedure.


title: HU086_HU089_K562_WT_IAA_EdU_B38_RPKM_1000

value: cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were released into DOX/IAA for 3h, labelled by EdU and then BrdU, each for 15 min and purified EdU-enriched DNA


title: HU086_HU089_K562_Rad21_mAC_4_IAA_BrdU_B21_RPKM_1000

value: cells were treated with CDK inhibitor for 42h, at the 12h the dox was added, at the 36h the IAA was added, at 42h, cells were released into DOX/IAA for 4h, labelled by EdU and then BrdU, each for 15 min and sorted for mClover-negative cells,  purified genomic DNA and enriched BrdU-labelled DNA


title: HU085, B22, PRO-seq, K562, RAD21-mAC-4, IAA, G1


title: HU086_HU089_K562_Rad21_mAC_1_IAA_BrdU_B20_RPKM_1000


title: HU088_K562_WTIAA_MYC1_translocations_repeat3

description: The cells were pretreated by 2ug/ml dox for 24 hours and then 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting c-MYC locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) cells.

data_processing:
Library strategy: PEM-seq
Followed the PEM-Q pipeline described in Liu et al., 2021
Assembly: hg19
Supplementary files format and content: tab file

treatment_protocol: The cells were pretreated by 2ug/ml dox for 24 hours and then 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting c-MYC locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) and mClover negative cells.


title: EdUHU, K562, RAD21-mAC-1, IAA, Repeat1


title: HU088_K562_WTIAA_MYC1_translocations_repeat2


title: HU086_HU089_K562_Rad21_mAC_1_IAA_EdU_R11_RPKM_1000


title: HU090_K562_WT_IAA_TP53_translocations_repeat2

description: The cells were pretreated by 2ug/ml dox for 24 hours and then 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting TP53 locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) cells.

treatment_protocol: The cells were pretreated by 2ug/ml dox for 24 hours and then 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting TP53 locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) and mClover negative cells.


title: HU088_K562_WTIAA_MYC1_translocations_repeat1


title: EdUHU, K562, RAD21-mAC-4, IAA, Repeat1


title: HU088_K562_RAD21_mAC_4_IAA_MYC1_translocations_repeat2


title: HU090_K562_RAd21_mAC_4_IAA_TP53_translocations_repeat3

description: The cells were pretreated by 2ug/ml dox for 24 hours and then 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting TP53 locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) and mClover negative cells.


title: HU090_K562_WT_IAA_TP53_translocations_repeat1


title: HU088_K562_RAD21_mAC_4_IAA_MYC1_translocations_repeat3


title: HU088_K562_RAD21_mAC_1_IAA_MYC1_translocations_repeat3


title: HU088_K562_RAD21_mAC_1_IAA_MYC1_translocations_repeat1

description: The cells were pretreated by 2ug/ml dox for 24 hours and then 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting MYC locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) and mClover negative cells.


title: HU085, B18, PRO-seq, K562, WT, IAA, replicate2, G1


title: HU090_K562_WT_IAA_TP53_translocations_repeat3


title: HU088_K562_RAD21_mAC_4_IAA_MYC1_translocations_repeat1


title: HU090_K562_RAd21_mAC_4_IAA_TP53_translocations_repeat1


title: HU077, K562, RAD21, mAC, 4, IAA, 6h, EdU, G2, RPKM2000

description:
Depicting replication timing in K562 RAD21-depleted cells.
HU077_RAD21-mAC-4_IAA_6h_RT_S50.bedgraph.txt

data_processing:
Library strategy: NAIL-seq
Following NAIL-seq "RepFind" pipeline as described in Liu et al., 2021
Assembly: hg19
Supplementary files format and content: bigwig, bedgraph (S50 curve)

extract_protocol:
Genomic DNA was isolated, tagged with biotin by click-iT reaction, subjected to the sequential isolation EdU (by streptavidin beads).
Following NAIL-seq protocol as described in Liu et al., 2021

treatment_protocol: The cells were treated by 2ug/ml dox for 24 hours, then treated by IAA for 6 or 24 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the indicated fraction with Hoechest

value: IAA for 6 hours


title: HU077, K562, RAD21, mAC, 4, IAA, 6h, EdU, G1, RPKM2000


title: HU090_K562_RAd21_mAC_4_IAA_TP53_translocations_repeat2


title: HU077, K562, RAD21, mAC, 4, IAA, 6h, EdU, S2, RPKM2000


title: HU077, K562, RAD21, mAC, 4, IAA, 24h, EdU, S1, RPKM2000

description:
Depicting replication timing in K562 RAD21-depleted cells.
HU077_RAD21-mAC-4_IAA_24h_RT_S50.bedgraph.txt

value: IAA for 24 hours


title: HU077, K562, RAD21, mAC, 4, IAA, 24h, EdU, G2, RPKM2000


title: HU088, K562, WT, IAA, repeat2, 24h, EdU, S4, RPKM2000

description:
Depicting replication timing in K562 WT cells.
HU088_K562_WT_IAA_repeat2_S50.bedgraph

treatment_protocol: The cells were treated by 2ug/ml dox for 24 hours, then treated by IAA for 24 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the indicated fraction with Hoechest


title: HU088, K562, WT, IAA, repeat2, 24h, EdU, S3, RPKM2000


title: HU077, K562, RAD21, mAC, 4, IAA, 24h, EdU, S2, RPKM2000


title: HU077, K562, RAD21, mAC, 4, IAA, 24h, EdU, S4, RPKM2000


title: HU077, K562, RAD21, mAC, 4, IAA, 24h, EdU, G1, RPKM2000


title: HU077, K562, RAD21, mAC, 4, IAA, 24h, EdU, S3, RPKM2000


title: HU088, K562, WT, IAA, repeat2, 24h, EdU, G2, RPKM2000


title: HU088, K562, WT, IAA, repeat2, 24h, EdU, S1, RPKM2000


title: HU077, K562, RAD21, mAC, 4, IAA, 6h, EdU, S4, RPKM2000


title: HU088_K562_RAD21_mAC_1_IAA_MYC1_translocations_repeat2

description: The cells were pretreated by 2ug/ml dox for 24 hours and then 500uM IAA for 6 hours, then transfected with gRNA-Cas9 targeting c-MYC locus, with dox and IAA for additional 48 hours, then sorted for mCherry positive (marker on gRNA-Cas9 plasmid) and mClover negative cells.


title: HU088, K562, WT, IAA, repeat1, 24h, EdU, S4, RPKM2000

description:
Depicting replication timing in K562 WT cells.
HU088_K562_WT_IAA_repeat1_S50.bedgraph


title: HU088, K562, WT, IAA, repeat2, 24h, EdU, S2, RPKM2000


title: HU090_K562_RAd21_mAC_1_IAA_TP53_translocations_repeat2


title: HU088, K562, WT, IAA, repeat1, 24h, EdU, S2, RPKM2000


title: HU088, K562, WT, IAA, repeat1, 24h, EdU, S1, RPKM2000


title: HU077, K562, RAD21, mAC, 4, IAA, 6h, EdU, S1, RPKM2000


title: HU088, K562, WT, IAA, repeat1, 24h, EdU, S3, RPKM2000


title: HU090_K562_RAd21_mAC_1_IAA_TP53_translocations_repeat1


title: HU090_K562_RAd21_mAC_1_IAA_TP53_translocations_repeat3


title: HU077, K562, RAD21, mAC, 4, IAA, 6h, EdU, S3, RPKM2000


title: HU088, K562, WT, IAA, repeat1, 24h, EdU, G2, RPKM2000


title: HU088, K562, WT, IAA, repeat1, 24h, EdU, G1, RPKM2000


title: QKI7 ribo rep2 [oe.2.ip]

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

description: ribozero RNA

data_processing:
library strategy: Ribo-seq
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
reads were aligned to the GRCh38 genome assembly using STAR
the TPM were calculated using RSEM 1.2.31 with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: table delimited text file containing the expression of genes

source_name: QKI7 OE ribo-seq

growth_protocol: Human U2OS cell lines were obtained from American Type Culture Collection (ATCC), and cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% penicillin/ streptomycin at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
The ribosomes from the cell lysates were collected by ultracentrifugation and the ribosome footprints (17-34nts) were recovered from polyacrylamide TBE-Urea gel.
The end structures of the RNA fragments were repaired by T4 polynucleotide kinase (T4 PNK, M0201S, New England Biolabs): (1) 3’ end healing reaction (10 μl): 7 μl RNA sample, 1 μl 10×T4 PNK buffer, 1 μl T4 PNK, and 1 μl SUPERase In RNase Inhibitor were mixed and incubated for 1 h at 37 ℃; (2) 5’-end phosphorylation: 1 μl 10 mM ATP and 1 μl extra T4 PNK were added to the reaction and the mixture was kept for 30 min at 37 ℃. The RNA was purified by ethanol precipitation. The libraries were constructed after depletion of rRNA, and sequenced on Illumina Hiseq2500 with single end 51-bp read length.

treatment_protocol: The cells were treated with 0.5mM NaAsO2 for 1 hour before harvesting the cells.

tag: rna fragment

value: ribosome footprint RNA

value: Bone Osteosarcoma


title: HU088, K562, WT, IAA, repeat2, 24h, EdU, G1, RPKM2000


title: vector ribo rep2 [vector.2.ip]

description: ribozero RNA

source_name: vector ribo-seq


title: U2OS QKI7 input rep1 [qki7.1.in]

description: ribozero RNA

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
reads were aligned to the GRCh38 genome assembly using STAR
the TPM were calculated using RSEM 1.2.31 with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: table delimited text file containing the expression of genes

source_name: QKI7-bound transcripts  RIP-seq input (U2OS)

growth_protocol: The U2OS cells with forced expression of QKI7 were expanded in DMEM medium with 10% FBS, 1 X penicillin-streptomycin and plasmocin prophylactic for 1-2 weeks and the cells were collected at 70-80% confluency in 150 mm dish

extract_protocol:
After cross-link with UV, the cells were collected by trypsinization, lysed in 1 ml M-PER buffer (78501, Thermo Fisher Scientific) with 100 U/ml RNase inhibitor and 1 × protease inhibitor on ice for 20 min, and sonicated in a Bioruptor Pico device (Diagenode) with 30s on/30s off for 10 cycles. Then the lysates were collected and subject to RIP with Flag antibody and Protein A/G Magnetic Beads. The RIP RNAs were recovered from the beads with RNA clean and concentrater kit. Both Input and RIP RNAs were used for sequencing.
KAPA Stranded mRNA-Seq Kit (Illumina Platforms) was utilized to construct library and sequencing was performed on an Illumina Hiseq 2500.

treatment_protocol: Without special treatment

tag: rip antibody


title: U2OS QKI7 RIP rep2 [qki7.2.ip]

description: ribozero RNA

source_name: QKI7-bound transcripts  RIP-seq IP (U2OS)

value: Flag (Cat#:F3165, Sigma-Aldrich)


title: QKI7 input rep2 [oe.2.in]

description: ribozero RNA

source_name: QKI7 OE input

value: Input RNA


title: QKI7 ribo rep1 [oe.1.ip]

description: ribozero RNA


title: U2OS input rep2

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
m7G-seq reads were aligned to the GRCh38 genome assembly using STAR
peaks were called using exomePeak.
the m7G peaks were annotated using an ad hoc perl script.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak files were generated using exomePeak

source_name: U2OS input

extract_protocol:
Total RNAs were isolated from the whole cells with QIAzol and poly(A) RNAs were enriched from total RNA with oligo(dT) polystyrene beads.The anti-m7G antibody (Cat#: RN017M, MBL international) was applied for m7G immunoprecipitation.
Both input and m7G IP samples were utilized for next-generation sequencing (NGS). The library preparation was constructed using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) and was quantified by BioAnalyzer High Sensitivity DNA chip, and then was deeply sequenced on the Illumina HiSeq 2500.

tag: merip antibody


title: U2OS IP rep1

source_name: U2OS m7G IP

value: m7G antibody (Cat#:RN017M, MBL international)


title: U2OS IP rep2


title: vector ribo rep1 [vector.1.ip]

description: ribozero RNA


title: HepG2 IP rep2

source_name: HepG2 m7G IP

growth_protocol: Human HepG2 cell lines were obtained from American Type Culture Collection (ATCC), and cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% penicillin/ streptomycin at 37°C in a 5% CO2 humidified incubator.

value: Hepatocellular carcinoma


title: vector input rep1 [vector.1.in]

description: ribozero RNA

source_name: vector input


title: HepG2 input rep1

source_name: HepG2 input


title: U2OS input rep1


title: HepG2 input rep2


title: QKI7 input rep1 [oe.1.in]

description: ribozero RNA


title: HepG2 IP rep1


title: v1H9

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

data_processing:
Sequencing outputs of the bulk and NCADpos libraries were run through CellRanger mkfastq, version 3.0.2 (10x GENOMICS).
The resulting fastq files were run through CellRanger count, version 3.0.2, to obtain bam alignment files using GRCh38 as a reference and to obtain unique molecular identifiers (UMIs) matrices.
To remove doublets and poor-quality cells, cells were excluded from subsequent analysis if they were outliers in terms of number of genes, number of UMIs, and percentage of mitochondrial genes using the R package scater (ver.1.10.1; nmads = 3). Normalization of cell-specific biases and removal of technical noise were performed using scran package (ver. 1.10.2).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files including either UMI counts or normalized logcounts for individual genes (rows) in individual cells (QCed; columns). Gene symbols and ENSEMBL gene IDs were in the first and second column, respectively. Barcodes in the first row consist of cellular barcodes.

source_name: v1H9 transformed hESCs (also called v-hESC-1)

growth_protocol: The cells were maintained as previously described (Sachlos et al., 2012, Werbowetski-Ogilvie et al., 2009) in feeder-free culture on Matrigel-coated plates with mouse embryonic fibroblast (MEF)-conditioned media (Xu et al., 2001) supplemented with 8 ng/ml bFGF.

extract_protocol:
The cells were encapsulated into single droplets using Chromium Controller (10x GENOMICS) according to the manufacturer's protocol.
Libraries were prepared using Chromium Single Cell 3' Reagent Kits v3 (10x GENOMICS) according to the manufacturer's protocol.

tag: Sex

value: female

value: v1H9 transformed hESCs


title: U2OS QKI7 RIP rep1 [qki7.1.ip]

description: ribozero RNA


title: U2OS QKI7 input rep2 [qki7.2.in]

description: ribozero RNA


title: SKD00402R-P24

city: Solna

first: Martin

last: Enge

address: Solnavägen 1

country: Sweden

institute: Karolinska Institutet

data_processing:
Demultiplexed RNA reads were aligned using STAR 2.7.7a, duplicate reads removed using Picard 2.22.0 and read counts summarized using HTSeq 0.9.1. Cutoffs of 20000 counts and 500 features were used.
Assembly: GRCm38 with ERCC-spike ins and the reporter-gene EYFP

source_name: Aorta

extract_protocol:
Aortae was perfused for 1 min with PBS at room temperature and then dissected. Lumen side was exposed and digested with 1 mg/mL collagenase I, 1 mg/mL dispase, and 150 μg/mL DNase-I for 30 min at 37 °C. The cell suspension was strained and then depleted of Cd45+ cells with Cd45 magnetic beads (protocol according to manufacturer). To purify endothelial cells, the suspension was stained with Cd45 and Cd31 antobodies, as well as a cell viability dye. FACS sorting was used to sort out Cd45-, Cd31+, viable endothelial cells, as well as some Cd45-, Cd31-, viable cells for control. Cells were sorted into 384 well plates with lysis buffer.
Library was constructed using smartseq2 protocol, as previously has been described. Briefly, primer annealing, followed by RT and cDNA amplification was followed by cleanup of PCR products. The cDNA was tagmented and final library anmplified using custom barcodes, then pooled and cleaned with SPRI beads. Libraries were then sequenced.

value: DoubleNegative

tag: tissue

value: Aorta

tag: strain

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP

tag: age

value: 3 months


title: SKD00402R-P23

tag: genotype


title: vector input rep2 [vector.2.in]

description: ribozero RNA

tag: cell line

tag: cell type


title: SKD00402R-P22


title: SKD00402R-P21


title: SKD00402R-P16


title: SKD00402R-P20


title: SKD00402R-P17


title: SKD00402R-P19


title: SKD00402R-P15


title: SKD00402R-P14


title: SKD00402R-P18


title: SKD00402R-P13


title: SKD00402R-P10


title: SKD00402R-P09


title: SKD00402R-P12


title: SKD00402R-P11


title: SKD00402R-P06


title: SKD00402R-P05


title: SKD00402R-P03


title: SKD00402R-P01


title: SKD00402R-O24


title: SKD00402R-O23


title: SKD00402R-O22


title: SKD00402R-O21


title: SKD00402R-O20


title: SKD00402R-O17


title: SKD00402R-O19


title: SKD00402R-O18


title: SKD00402R-P08


title: SKD00402R-P07


title: SKD00402R-P02


title: SKD00402R-O05


title: SKD00402R-O13


title: SKD00402R-O11


title: SKD00402R-O10


title: SKD00402R-O16


title: SKD00402R-O12


title: SKD00402R-O08


title: SKD00402R-O09


title: SKD00402R-O15


title: SKD00402R-O14


title: SKD00402R-O01


title: SKD00402R-N24

value: Endothelial


title: SKD00402R-N23


title: SKD00402R-N22


title: SKD00402R-P04


title: SKD00402R-N21


title: SKD00402R-O06


title: SKD00402R-N20


title: SKD00402R-O07


title: SKD00402R-O04


title: SKD00402R-N19


title: SKD00402R-N15


title: SKD00402R-N18


title: SKD00402R-N17


title: SKD00402R-N16


title: SKD00402R-O03


title: SKD00402R-N14


title: SKD00402R-N13


title: SKD00402R-O02


title: SKD00402R-N11


title: SKD00402R-N09


title: SKD00402R-N12


title: SKD00402R-N06


title: SKD00402R-N08


title: SKD00402R-N10


title: SKD00402R-N07


title: SKD00402R-N03


title: SKD00402R-N05


title: SKD00402R-M24


title: SKD00402R-M17


title: SKD00402R-N02


title: SKD00402R-M20


title: SKD00402R-M22


title: SKD00402R-M23


title: SKD00402R-M21


title: SKD00402R-N01


title: SKD00402R-M16


title: SKD00402R-M19


title: SKD00402R-M18


title: SKD00402R-M11


title: SKD00402R-M12


title: SKD00402R-M14


title: SKD00402R-M13


title: SKD00402R-M15


title: SKD00402R-M10


title: SKD00402R-M09


title: SKD00402R-M08


title: SKD00402R-M07


title: SKD00402R-N04


title: SKD00402R-M06


title: SKD00402R-M04


title: SKD00402R-M05


title: SKD00402R-M02


title: SKD00402R-L23


title: SKD00402R-M03


title: SKD00402R-M01


title: SKD00402R-L19


title: SKD00402R-L24


title: SKD00402R-L17


title: SKD00402R-L16


title: SKD00402R-L14


title: SKD00402R-L21


title: SKD00402R-L20


title: SKD00402R-L22


title: SKD00402R-L18


title: SKD00402R-L08


title: SKD00402R-L09


title: SKD00402R-L13


title: SKD00402R-L02


title: SKD00402R-L01


title: SKD00402R-L11


title: SKD00402R-L15


title: SKD00402R-K22


title: SKD00402R-L10


title: SKD00402R-L12


title: SKD00402R-K20


title: SKD00402R-L07


title: SKD00402R-L06


title: SKD00402R-L05


title: SKD00402R-L03


title: SKD00402R-K14


title: SKD00402R-K12


title: SKD00402R-L04


title: SKD00402R-K09


title: SKD00402R-K08


title: SKD00402R-K23


title: SKD00402R-K21


title: SKD00402R-K19


title: SKD00402R-K18


title: SKD00402R-K24


title: SKD00402R-K16


title: SKD00402R-K17


title: SKD00402R-K03


title: SKD00402R-K01


title: SKD00402R-K13


title: SKD00402R-J19


title: SKD00402R-J22


title: SKD00402R-J20


title: SKD00402R-J18


title: SKD00402R-K11


title: SKD00402R-J17


title: SKD00402R-J15


title: SKD00402R-K07


title: SKD00402R-K06


title: SKD00402R-K10


title: SKD00402R-K04


title: SKD00402R-K05


title: SKD00402R-J13


title: SKD00402R-K02


title: SKD00402R-J24


title: SKD00402R-J11


title: SKD00402R-K15


title: SKD00402R-J12


title: SKD00402R-J14


title: SKD00402R-J16


title: SKD00402R-J21


title: SKD00402R-J23


title: SKD00402R-J08


title: SKD00402R-J10


title: SKD00402R-J02


title: SKD00402R-I22


title: SKD00402R-I23


title: SKD00402R-I21


title: SKD00402R-J04


title: SKD00402R-J03


title: SKD00402R-I20


title: SKD00402R-I17


title: SKD00402R-J01


title: SKD00402R-J09


title: SKD00402R-I19


title: SKD00402R-J06


title: SKD00402R-I18


title: SKD00402R-I14


title: SKD00402R-I16


title: SKD00402R-I13


title: SKD00402R-I12


title: SKD00402R-I11


title: SKD00402R-I15


title: SKD00402R-I10


title: SKD00402R-J07


title: SKD00402R-J05


title: SKD00402R-I09


title: SKD00402R-I07


title: SKD00402R-I06


title: SKD00402R-I05


title: SKD00402R-I24


title: SKD00402R-I04


title: SKD00402R-I03


title: SKD00402R-I01


title: SKD00402R-I02


title: SKD00402R-H24


title: SKD00402R-H20


title: SKD00402R-H22


title: SKD00402R-H23


title: SKD00402R-H21


title: SKD00402R-H14


title: SKD00402R-H16


title: SKD00402R-H15


title: SKD00402R-H13


title: SKD00402R-H18


title: SKD00402R-H19


title: SKD00402R-H17


title: SKD00402R-H11


title: SKD00402R-H12


title: SKD00402R-H09


title: SKD00402R-H10


title: SKD00402R-H08


title: SKD00402R-I08


title: SKD00402R-H06


title: SKD00402R-H07


title: SKD00402R-H05


title: SKD00402R-H03


title: SKD00402R-H04


title: SKD00402R-G22


title: SKD00402R-H02


title: SKD00402R-G23


title: SKD00402R-G24


title: SKD00402R-H01


title: SKD00402R-G21


title: SKD00402R-G20


title: SKD00402R-G18


title: SKD00402R-G15


title: SKD00402R-G19


title: SKD00402R-G13


title: SKD00402R-G17


title: SKD00402R-G14


title: SKD00402R-G09


title: SKD00402R-G07


title: SKD00402R-G06


title: SKD00402R-G11


title: SKD00402R-G08


title: SKD00402R-F23


title: SKD00402R-G03


title: SKD00402R-G01


title: SKD00402R-F24


title: SKD00402R-G12


title: SKD00402R-G10


title: SKD00402R-G05


title: SKD00402R-G02


title: SKD00402R-G04


title: SKD00402R-F21


title: SKD00402R-F22


title: SKD00402R-F19


title: SKD00402R-G16


title: SKD00402R-F20


title: SKD00402R-F18


title: SKD00402R-F17


title: SKD00402R-F16


title: SKD00402R-F12


title: SKD00402R-F15


title: SKD00402R-F11


title: SKD00402R-F14


title: SKD00402R-F09


title: SKD00402R-F13


title: SKD00402R-F10


title: SKD00402R-F05


title: SKD00402R-F06


title: SKD00402R-F02


title: SKD00402R-F03


title: SKD00402R-E19


title: SKD00402R-F08


title: SKD00402R-F07


title: SKD00402R-E21


title: SKD00402R-F01


title: SKD00402R-E20


title: SKD00402R-E22


title: SKD00402R-E24


title: SKD00402R-E23


title: SKD00402R-E17


title: SKD00402R-E15


title: SKD00402R-E12


title: SKD00402R-E14


title: SKD00402R-E11


title: SKD00402R-E07


title: SKD00402R-E06


title: SKD00402R-F04


title: SKD00402R-E18


title: SKD00402R-E04


title: SKD00402R-E03


title: SKD00402R-E16


title: SKD00402R-E01


title: SKD00402R-E02


title: SKD00402R-D16


title: SKD00402R-D15


title: SKD00402R-D23


title: SKD00402R-D22


title: SKD00402R-D18


title: SKD00402R-D24


title: SKD00402R-E13


title: SKD00402R-E10


title: SKD00402R-D13


title: SKD00402R-D14


title: SKD00402R-D11


title: SKD00402R-D12


title: SKD00402R-E08


title: SKD00402R-E09


title: SKD00402R-D09


title: SKD00402R-E05


title: SKD00402R-D10


title: SKD00402R-D08


title: SKD00402R-D06


title: SKD00402R-D07


title: SKD00402R-D04


title: SKD00402R-D02


title: SKD00402R-D21


title: SKD00402R-D19


title: SKD00402R-D20


title: SKD00402R-D05


title: SKD00402R-D01


title: SKD00402R-D17


title: SKD00402R-C19


title: SKD00402R-C18


title: SKD00402R-C22


title: SKD00402R-C23


title: SKD00402R-C17


title: SKD00402R-C24


title: SKD00402R-C20


title: SKD00402R-C16


title: SKD00402R-C15


title: SKD00402R-C13


title: SKD00402R-C12


title: SKD00402R-D03


title: SKD00402R-C08


title: SKD00402R-C09


title: SKD00402R-C10


title: SKD00402R-C07


title: SKD00402R-C21


title: SKD00402R-C06


title: SKD00402R-C05


title: SKD00402R-C14


title: SKD00402R-C04


title: SKD00402R-C02


title: SKD00402R-C03


title: SKD00402R-C01


title: SKD00402R-C11


title: hMEC_sip63_rep1

type: RNA

city: Rome

first: Stefano

last: Scalera

address: Via Elio Chianesi 53

country: Italy

institute: IRCCS Regina Elena National Cancer Institute

description: Gene expression of hMEC after p63 interference replicate1

hyb_protocol: Hybridization done according to Agilent Gene expression hybridization kit

scan_protocol: Scanned on Agilent SureScan Microarray Scanner (Agilent Technologies G2600D SG12434244)

data_processing: Data pre-processing steps of background-correction, normalization and summarization were performed in R using functions in Limma library. The raw intensity for each probe is the median feature pixel intensity with the median background subtracted. Data was quantile normalized followed by log2 transform. Signals from probes measuring same ncRNA were averaged.

source_name: hMEC p63 interference replicate1

label_protocol: Labbeling was done according to Nimblegen one color DNA Labeling kit

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: hMEC


title: HCC1954_sip63_rep1

description: Gene expression of HCC1954 after p63 interference replicate1

source_name: HCC1954 p63 interference replicate1


title: HCC1954_control_rep2

description: Gene expression of HCC1954 control replicate2

source_name: HCC1954 control replicate2


title: SKD00402R-B24


title: hMEC_sip63_rep2

description: Gene expression of hMEC after p63 interference replicate2

source_name: hMEC p63 interference replicate2


title: HEKn_sip63_rep2

description: Gene expression of HEKn after p63 interference replicate2

source_name: HEKn p63 interference replicate2

value: HEKn


title: SKD00402R-B22


title: HCC1954_sip63_rep2

description: Gene expression of HCC1954 after p63 interference replicate2

source_name: HCC1954 p63 interference replicate2


title: HEKn_sip63_rep1

description: Gene expression of HEKn after p63 interference replicate1

source_name: HEKn p63 interference replicate1


title: hMEC_control_rep1

description: Gene expression of hMEC control replicate1

source_name: hMEC control replicate1


title: HCC1954_control_rep1

description: Gene expression of HCC1954 control replicate1

source_name: HCC1954 control replicate1


title: SKD00402R-B18


title: SKD00402R-B21


title: FaDu_sip63_rep1

description: Gene expression of FaDu after p63 interference replicate1

source_name: FaDu p63 interference replicate1

value: FaDu


title: SKD00402R-B23


title: SKD00402R-B19


title: SKD00402R-B20


title: HEKn_control_rep2

description: Gene expression of HEKn control replicate2

source_name: HEKn control replicate2


title: FaDu_sip63_rep2

description: Gene expression of FaDu after p63 interference replicate2

source_name: FaDu p63 interference replicate2


title: hMEC_control_rep2

description: Gene expression of hMEC control replicate2

source_name: hMEC control replicate2


title: HEKn_control_rep1

description: Gene expression of HEKn control replicate1

source_name: HEKn control replicate1


title: SKD00402R-B16


title: SKD00402R-B17


title: NaCl-D3, B

city: Nagoya

first: Hakuto

last: Kageyama

state: Aichi

address: 1-501, Shiogamaguchi, Tempaku-ku

country: Japan

institute: Meijo University

description:
Processed data B
NaCl-D3-B

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated.
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with Bowtie. Transcript abundances are measured with mapped read count within gene region. In case of strand specific library, sense or anti-sense read counts are extracted by strand.
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage.
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing.
Assembly: Synechoccus elongatus PCC7942 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000012525.1/)
Supplementary files format and content: Excel files include raw read counts for each sample

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: bacterial cell

growth_protocol: Cyanobacterial cells were photoautotrophically cultured at 30ºC in blue-green 11 (BG11) media under continuous cool white fluorescent light intensity of 70 µE m-2 s-1.

extract_protocol:
Total RNA was extracted utilizing TRIzol LS Reagent (Thermo Fisher Scientific), according to the manufacturer’s protocol.
RNA samples were utilized to construct the libraries, which were sequenced.

value: bacterial cell

value: WT

tag: stress

value: 0.4 M NaCl stress for 3 day

tag: time

value: Day 3


title: Str50-D1, B

description:
Processed data B
Str50-D1-B

value: 50 mg/L streptomycin stress for 1 day

value: Day 1


title: NaCl-D1, B

description:
Processed data B
NaCl-D1-B

value: 0.4 M NaCl stress for 1 day


title: Str50-D3, B

description:
Processed data B
Str50-D3-B

value: 50 mg/L streptomycin stress for 3 day


title: A253_sip63_rep2

description: Gene expression of A253 after p63 interference replicate2

source_name: A253 p63 interference replicate2


title: FaDu_control_rep2

description: Gene expression of FaDu control replicate2

source_name: FaDu control replicate2


title: A253_control_rep2

description: Gene expression of A253 control replicate2

source_name: A253 control replicate2


title: FaDu_control_rep1

description: Gene expression of FaDu control replicate1

source_name: FaDu control replicate1


title: Control, B

description:
Processed data B
Control-B

value: control

value: Day 0


title: SKD00402R-B15

source_name: Aorta

value: Aorta


title: Str50-D3, A

description:
Processed data A
Str50-D3-A


title: A253_control_rep1

description: Gene expression of A253 control replicate1

source_name: A253 control replicate1


title: SKD00402R-B14

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP


title: NaCl-D3, A

description:
Processed data A
NaCl-D3-A


title: SKD00402R-B10

value: 3 months


title: SKD00402R-B11

value: Endothelial


title: NaCl-D1, A

description:
Processed data A
NaCl-D1-A


title: SKD00402R-B09


title: SKD00402R-B12


title: PSA4 VDJ

city: London

first: Leonie

last: Taams

state: london

address: CIBCI, 1.26, New Hunts House

country: United Kingdom

institute: King's College London

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 6.1.1. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: .csv files containing VDJ information

source_name: Synovial Fluid

extract_protocol:
Synovial fluid mononuclear cells (SFMC) were isolated from four patients with psoriatic arthritis by density gradient centrifugation using Lymphoprep (Axis-Shield, Oslo, Norway). Cells were cryopreserved and stored in liquid nitrogen in culture medium containing 90% FCS and 10% DMSO (Fisher Scientific, Loughborough, UK). After thawing, 2 million SFMCs were labelled with fluorescently labelled antibodies for flow sorting as well as CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing) antibodies.  CD8+ T-cells were sorted on a FACSAria/LSRII. 20,000 cells per patient were loaded for gene expression and immune profiling using the 10X Genomics Chromium Single Cell platform.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol with feature barcoding and VDJ sequencing, 10x Genomics).

value: Synovial Fluid

value: psoriatic arthritis

value: memory CD8+ T cells


title: Control, A

description:
Processed data A
Control-A

value: bacterial cell


title: A253_sip63_rep1

description: Gene expression of A253 after p63 interference replicate1

source_name: A253 p63 interference replicate1


title: SKD00402R-B08


title: PSA4 GEX

description: 10x Genomics


title: SKD00402R-B06


title: Str50-D1, A

description:
Processed data A
Str50-D1-A

value: WT


title: SKD00402R-B13


title: PSA3 VDJ

description: 10x Genomics


title: SKD00402R-B07


title: SKD00402R-B02


title: SKD00402R-B01


title: PSA2 CSP

description: 10x Genomics


title: PSA3 GEX

description: 10x Genomics


title: SKD00402R-B03


title: PSA2 VDJ

description: 10x Genomics


title: PSA2 GEX

description: 10x Genomics


title: PSA3 CSP

description: 10x Genomics


title: SKD00402R-A23


title: PSA1 CSP

description: 10x Genomics


title: SKD00402R-A24


title: PSA1 VDJ

description: 10x Genomics


title: PSA4 CSP

description: 10x Genomics


title: PSA1 GEX

description: 10x Genomics


title: SKD00402R-A22


title: SKD00402R-A21


title: SKD00402R-A20


title: Rice seedling shoot treated with rehydration for 24 h, biological replicate #2

city: Chuncheon

first: Dong-Hoon

last: Jeong

state: Gangwon-do

address: Room #8306, Department of Life Science, 1 Hallymdaehak-gil

department: Dept. of Life Science

country: South Korea

institute: Hallym University

data_processing:
The paired-end raw sequencing reads were processed and mapped to the rice genome (Rice Genome Annotation Project, MSU v7.0) using the CLC Genomics Workbench 20.0.4. Gene expression levels were normalized to reads per kilobase of transcript per million mapped reads (RPKM).
Supplementary files format and content: Exel file including RPKM values for each Sample

organism: Oryza sativa Japonica Group

source_name: Eleven-day-old seedling shoots

growth_protocol: Dehusked rice seeds (Oryza sativa L. ssp. Japonica cv. Nipponbare) were sterilized and germinated on half-strength Murashige and Skoog (MS) medium (Duchefa Biochemie) containing 0.2% (w/v) phytagel (Sigma-Aldrich, St. Louis, MO, USA) in a sterile plastic box. The plants were grown in a growth chamber under continuous light conditions at 25 °C.

extract_protocol:
Total RNA was isolated from the tissues using the Tri-RNA Reagent (Favorgen, FATRR 001).
RNA-seq libraries were constructed using a TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA; RS-122-2101), according to the manufacturer’s protocol. RNA-seq libraries were sequenced on the Illumina MiSeq platform.

treatment_protocol: For the drought treatment, 10-day-old seedlings were air-dried with a paper towel for 8 h. Control plants were sampled at the same time as the drought treatment. Rehydration was performed by re-watering the 8 h-dehydrated seedlings for 24 or 72 h.

value: Eleven-day-old seedling shoots

tag: cultivar

value: Nipponbare

value: wild-type

tag: treatment

value: 24 h rehydration after 8h dehydration


title: Rice seedling shoot treated with dehydration for 8 h, biological replicate #2

source_name: Ten-day-old seedling shoots

value: Ten-day-old seedling shoots

value: 8 h dyhydration


title: Rice seedling shoot treated with rehydration for 24 h, biological replicate #1


title: SKD00402R-B05


title: Rice seedling shoot control, biological replicate #1

value: No treatment control


title: Rice seedling shoot treated with dehydration for 8 h, biological replicate #1


title: Rice seedling shoot control, biological replicate #2


title: SKD00402R-A16


title: SKD00402R-A19


title: SKD00402R-A17


title: SKD00402R-A18


title: SKD00402R-A14


title: SKD00402R-A11


title: SKD00402R-A15


title: SKD00402R-A12


title: SKD00402R-A10


title: SKD00402R-A13


title: SKD00402R-A09


title: SKD00402R-A07


title: SKD00402R-A06


title: SKD00402R-A08


title: SKD00402R-A05


title: SKD00402R-A02


title: SKD00402R-A04


title: SKD00402R-A03


title: SKD00402R-A01


title: SKD00401R-P24

value: DoubleNegative


title: SKD00401R-P23

value: Aorta


title: BTIC129_C1_TSPOshRNA

city: Regensburg

first: Julia

last: Lorenz

address: Franz-Josef-Strauß-Allee 11

department: Neuropathology

institute: Regensburg university hospital

data_processing:
fastq files were aligned to version 87 of Homo_sapiens reference genome GRCh38 using the HiSat2 aligner.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm (v2.0.1).
Batch effects were removed with Combat_Seq of the SVA package using a negative binomial regression model
Expression data was normalized using the normalization function of DeSeq2 package or RPKM values
Differentially expressed genes (³1.0-fold and £5% false discovery rate) were identified by negative binomial generalized linear models statistics using the DeSeq2 package
Assembly: version 87 of Homo_sapiens reference genome GRCh38
Supplementary files format and content: tab-delimited text files include adjusted counts for each cell line (BITC13/BITC129)

source_name: glioblastoma-derived brain tumor initiating cell (BTICs)

growth_protocol: 4 x 10^5 TSPO proficient or deficient BTICs/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 24 hours.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Illumina Stranded mRNA Prep kit (Illumina) and processed as per manufacturer’s instructions.

treatment_protocol: BTICs were left untreated

tag: background strain

value: GB WHO IV, female, 63y at diagnosis

value: TSPO sh

value: untreated


title: BTIC129_B1_TSPOshRNA


title: RAW_infected_srfJ_rep2

city: Sevilla

first: Francisco

last: Ramos-Morales

state: Sevilla

address: Avda Reina Mercedes, 6

department: Genética

country: Spain

institute: Universidad de Sevilla

description: Gene expression data from RAW264.7 cells infected with srfJ mutant of Salmonella

hyb_protocol: Labelled cDNA was hybridized to Clariom S Assay, MOUSE arrays  (Affymetrix) following the manufacturer’s instructions

scan_protocol: The arrays were scanned in a 3000 7G Scanner from Affymetrix

data_processing: Data processing was carried out with GeneChip Command Console 2.0 (Affymetrix) to generate .CEL and .CHP assays. Normalization was performed using the SST (signal space transformation)-RMA (robust multiple-array average) method. The Transcriptome Analysis Console (TAC) was used for data analysis.

label: biotin

source_name: RAW264.7 cells infected with srfJ mutant Salmonella, biological rep2

label_protocol: Biotinylated single-stranded cDNA was prepared from 100 ng per sample of total intact RNA extracted from 6 independent samples (3 from RAW264.7 cells infected with wild-type Salmonella and 3 from RAW264.7 cells infected with srfJ mutant of Salmonella).

growth_protocol: RAW264.7 cells (ECAC no. 91062702) were cultured in DMEM supplemented with 10% foetal calf serum. 2 mM L-glutamine, 100 U/ml penicillin and 100 microg/ml streptomycin were included in the culture media. Cells were maintained in a 5% CO2 humidified atmosphere at 37ºC

extract_protocol: Total RNA from RAW264.7 cells was isolated using 1 ml of TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. An additional purification step was carried out with the RNeasy Min Elute Cleanup Kit (Qiagen).

treatment_protocol: RAW264.7 cells were plated in 24-well plates at 1.5 x 10E5 cells per well and incubated for 24 h at 37ºC with 5% CO2. Bacteria were grown in LB medium for 24 h at 37ºC with shaking and added at a multiplicity of infection of 250. The cell culture was washed twice with phosphate-buffered saline (PBS) 1 h postinfection, overlaid with DMEM containing 100 ug/ml gentamicin, and incubated for another hour. The culture was then washed twice with PBS, covered with DMEM with gentamicin (16 ug/ml), and incubated for 6 h.

tag: bacteria

value: S. enterica serovar Typhimurium srfJ null mutant


title: BTIC129_A1_TSPOshRNA


title: SKD00401R-P22

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP

value: 3 months


title: RAW_infected_srfJ_rep3

source_name: RAW264.7 cells infected with srfJ mutant Salmonella, biological rep3


title: BTIC129_C1_ControlshRNA

value: control sh


title: SKD00401R-P21