title: MCE2-rep30 (scRepli-seq)

city: Tsu

first: Takuya

last: Hayakawa

state: Mie

address: 1577 Kuriyamachiya

department: Bioresources

institute: Mie University

data_processing:
For E/L Repliseq data analysis, the raw Fastq files were trimmed to remove adapter sequences using the cutadapt program before mapping. We performed two-step adapter trimming, first removing the Illumina adapter according to the index of each NGS library and then removing the SEQXE adapter. mm9 reference genome (chr1–19, chrX, chrY) assemblies were used. Mapping to the mm9 reference genome used the Picard tool to remove duplicated reads and defining MAPQ>10 as uniquely mapped reads. We also filtered out the reads that overlapped with the mm9 blacklists. After blacklist filtering, we counted the reads from the early- and late-S-phase BrdU-IP samples in sliding windows of 300 kb at 40-kb intervals, and performed reads per million (rpm) normalization. The ratio of early-S-phase to late-S-phase read counts log2 ((early-S reads)/ (late-S reads)) was calculated for each bin. The average RT profiles were obtained by calculating log2 ((averaged early-S)/(averaged late-S)).
For single-cell Repli-seq data analysis, the raw Fastq files were subjected to two-step adapter trimming, first removing the Illumina adapter according to the index of each NGS library and then removing the SEQXE adapter. After mapping to the mm9 reference genome, we filtered out duplicated reads that had an identical chromosome start position and strand information relating to an existing read. We also filtered out reads that overlapped with the mm9 blacklists. We then counted the reads in sliding windows of 200 kb at 40-kb intervals and used AneuFinder’s correctMappability command for normalizing mid-S-phase data on the basis of the G1 control. From the mappability-corrected mid-S-phase read counts, the genome-wide median was obtained and was used to generate log2((mappability-corrected mid-S reads)/median) scores, which we defined as the single-cell mid-S-phase RT score. Positive and negative RT scores are classified as early and late RT. The binarization (replicated or unreplicated) for each genomic bin was performed by using the findCNVs command in AneuFinder as described previously (Miura et al., Nature Protocols 2020).
Assembly: mm9
Supplementary files format and content: bedGraph
Library strategy: Repli-seq

growth_protocol: Mouse 3T3-L1 cells (JCRB, lot.#07232012) were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Nacalai tesque), supplemented with 10% fetal bovine serum (FBS, lot.#S05692S1820, Biowest), 2 mM L-glutamine (Nacalai tesque), 168 µM penicillin (Nacalai tesque) and 137.5 µM streptomycin (Sigma Aldrich) in a humidified 5% CO2 incubator at 37℃.

extract_protocol:
For E/L Repliseq experiments, cells were labeled for 2 h with 50 µM BrdU (Sigma-Aldrich) before being fixed with 70% ethanol. We used a Sony SH800 cell sorter in ultrapurity mode to fractionate the early- and late-S phase populations based on DNA content (PI intensity). We followed our routine BrdU-immunoprecipitation (IP)-based protocol except that we used a Bioruptor (Cosmo Bio, Tokyo, Japan) for gDNA sonication to obtain DNA fragments of 100~700 bp. After BrdU-IP, the purity of early and late S phase cell fractions was validated by PCR using specific primer sets that detect early and late replicating regions. The immunoprecipitated DNA samples were then subjected to whole genome amplification (WGA) using a SeqPlex kit (Sigma-Aldrich, SEQXE). Amplified early- and late-replicating DNA were used to construct NGS libraries.
For single-cell Repli-seq experments, single mid-S-phase cells were sorted with a Sony SH800 cell sorter in single-cell mode based on DNA content (propidium iodide intensity). Single cells were sorted directly into a 96-well plate with 6 µl of cell lysis buffer [447 µl H2O, 3 µl Proteinase K (Sigma, P4850), 50 µl 10× single-cell lysis and fragmentation buffer (Sigma, L1043)], incubated at 55°C for 1 h and then at 99°C for 4 min for genomic DNA isolation and fragmentation. Then, 6 µl of the genomic DNA solution was subjected to WGA using a SeqPlex kit (Sigma, SEQXE). Amplified gDNA was used to construct NGS libraries.
Next generation sequencing (NGS) libraries were constructed using an NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs), according to the manufacturer’s instructions

treatment_protocol: Mouse 3T3-L1 cells were seeded in 6-well plates and grown until confluency. At 2 days post-confluency (defined as day 0), cells were treated with DMEM containing 10% FBS supplemented with 10 µg/mL insulin (Sigma-Aldrich), 0.25 µM dexamethazone (Dex, Sigma-Aldrich) and 0.5 mM 3-isobutyl-1methylxanthine (IBMX, Sigma-Aldrich) for 48 h to induce adipogenesis. These cells were then treated with DMEM containing 5 µg/mL insulin and the medium was replaced every 2 days up to 8 days (day 10) for full differentiation into mature adipocytes.

tag: sample state

value: Single cell

tag: cell cycle phase

value: MidS


title: MCE2-rep28 (scRepli-seq)

status: Public on Dec 22 2022

type: SRA

country: Japan

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line

tag: treatment


title: MCE2-rep27 (scRepli-seq)


title: MCE2-rep32 (scRepli-seq)


title: MCE2-rep29 (scRepli-seq)


title: MCE2-rep26 (scRepli-seq)


title: H9c2 cells day 0 without RA, replicate 1

city: Monterrey

first: Victor

last: Trevino

state: Nuevo León

address: Ave. Eugenio Garza Sada 2501 Sur

department: Investigación e Innovación

country: Mexico

institute: Tecnológico de Monterrey

library_source: transcriptomic

data_processing:
FASTQ files uploaded to GALAXY platform
QC, Trimming in GALAXY
Mapped to Rat genome in GALAXY using HiSat2
Reads counted by FeatureCounts tool in GALAXY
Transcripts not showing reads in any sample were removed.
Assembly: Rattus norvegicus Rnor_6.0.98

molecule: total RNA

organism: Rattus norvegicus

source_name: Heart; Myocardium

growth_protocol: The H9c2 cell line obtained from ATCC (Manassas, VA, USA) was cultured in Dulbecco´s modified Eagle´s medium (DMEM) (SIGMA), supplemented with 3.7 g/L sodium bicarbonate (SIGMA S5761), 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin in 75 cm2 tissue culture flasks at 37°C in a humidified atmosphere of 5% CO2. Cells were fed every 2–3 days and subcultured when reaching 70–80% confluence to prevent the loss of the differentiation potential. Cell differentiation was initiated by H9c2 cells at a density of 35,000 cells/ml in 25 cm2 tissue culture flasks for 24 hours for cell attachment. Then, decreasing FBS from 10% to 1% in the media, followed by Retinoic Acid (RA) supplementation [1, 5].

extract_protocol:
The collection of total RNA extracts was performed following the TRIzol™ reagent protocol instructions (Invitrogen). Add 0.3–0.4 mL of TRIzol™ reagent per 1 × 105-107 cells directly to the culture dish to lyse the cells. The suspension was homogenized pipetting the lysate up and down several times and incubating for 5 min at room temperature to permit the complete dissociation of the nucleoproteins complex. After this time, 0.2 mL of chloroform was added per 1 mL of TRIzol™ reagent used for lysis and incubated for 3 min on ice. Samples were centrifuged for 15 min at 12,000 x g at 4°C, and the aqueous phase that contained the RNA was transferred to a new tube. For the RNA precipitation, we added 0.5 mL of isopropanol to the aqueous phase per 1 mL of TRIzol™ reagent used for lysis, and the sample was incubated for 10 min on ice. The samples were then centrifuged for 10 min at 12,000 x g at 4°C. The supernatant was discarded, and the pellet was resuspended in 1 mL of 75% ethanol per 1 mL of TRIzol™ reagent used for lysis. The sample was vortexed for 5 sec and immediately centrifuged for 5 min at 7500 x g at 4°C; the supernatant was discarded, and the RNA pellet was dried for 10 min on ice. Pellet was resuspended in 50 µL of RNase-free water. Total RNA was quantified using a UV analysis Synergy™ HT Multi-Detection Microplate Reader (Biotek Instruments). To examine RNA integrity and DNA contamination, 0.5 μg of RNA was electrophoretically separated in an agarose gel. Samples were then saved at -80°C.
TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions.

treatment_protocol: The RA (1 μM) addition was performed daily in dark conditions for 14 days. All-trans-RA was prepared in DMSO and stored at -20°C in dark conditions to avoid degradation [1]. For Ca2+ signaling experiments, cells were plated in 6-well plates with coverslips at a density of 15,000 cells/ 400 µL. Cells were incubated at 37°C for 30 minutes, afterward added 600 µL of DMEM supplemented with 10 % FBS. After 24 hours, FBS was decreased to 1 % and treated with 1 μM daily for 7 or 14 days, as previously stated.

tag: tissue

value: Heart; Myocardium

tag: cell type

value: myoblast

tag: genotype

value: WT

value: control

tag: time

value: Day 0

tag: replicate


title: MCE2-rep31 (scRepli-seq)


title: MCE2-rep20 (scRepli-seq)


title: MCE2-rep23 (scRepli-seq)


title: MCE2-rep17 (scRepli-seq)


title: MCE2-rep19 (scRepli-seq)


title: MCE2-rep18 (scRepli-seq)


title: MCE2-rep16 (scRepli-seq)


title: MCE2-rep15 (scRepli-seq)


title: MCE2-rep14 (scRepli-seq)


title: MCE2-rep13 (scRepli-seq)


title: MCE2-rep10 (scRepli-seq)


title: MCE2-rep9 (scRepli-seq)


title: MCE2-rep5 (scRepli-seq)


title: MCE2-rep7 (scRepli-seq)


title: MCE2-rep6 (scRepli-seq)


title: MCE2-rep25 (scRepli-seq)


title: MCE2-rep4 (scRepli-seq)


title: MCE2-rep24 (scRepli-seq)


title: MCE1-rep32 (scRepli-seq)


title: MCE2-rep11 (scRepli-seq)


title: MCE1-rep30 (scRepli-seq)


title: MCE2-rep3 (scRepli-seq)


title: MCE2-rep2 (scRepli-seq)


title: MCE2-rep1 (scRepli-seq)


title: MCE2-rep22 (scRepli-seq)


title: MCE2-rep8 (scRepli-seq)


title: MCE2-rep21 (scRepli-seq)


title: MCE1-rep22 (scRepli-seq)


title: MCE1-rep25 (scRepli-seq)


title: MCE1-rep23 (scRepli-seq)


title: MCE2-rep12 (scRepli-seq)


title: MCE1-rep28 (scRepli-seq)


title: MCE1-rep31 (scRepli-seq)


title: MCE1-rep29 (scRepli-seq)


title: MCE1-rep21 (scRepli-seq)


title: MCE1-rep20 (scRepli-seq)


title: MCE1-rep24 (scRepli-seq)


title: MCE1-rep19 (scRepli-seq)


title: MCE1-rep18 (scRepli-seq)


title: MCE1-rep17 (scRepli-seq)


title: MCE1-rep15 (scRepli-seq)


title: MCE1-rep27 (scRepli-seq)


title: MCE1-rep14 (scRepli-seq)


title: MCE1-rep13 (scRepli-seq)


title: MCE1-rep12 (scRepli-seq)


title: MCE1-rep11 (scRepli-seq)


title: MCE1-rep10 (scRepli-seq)


title: MCE1-rep8 (scRepli-seq)


title: MCE1-rep9 (scRepli-seq)


title: MCE1-rep26 (scRepli-seq)


title: MCE1-rep6 (scRepli-seq)


title: MCE1-rep7 (scRepli-seq)


title: MCE1-rep4 (scRepli-seq)


title: MCE1-rep3 (scRepli-seq)


title: Control-rep33 (scRepli-seq)

value: Control


title: MCE1-rep2 (scRepli-seq)


title: MCE1-rep16 (scRepli-seq)


title: Control-rep35 (scRepli-seq)


title: Control-rep34 (scRepli-seq)


title: Control-rep31 (scRepli-seq)


title: Control-rep30 (scRepli-seq)


title: Control-rep26 (scRepli-seq)


title: Control-rep27 (scRepli-seq)


title: Control-rep29 (scRepli-seq)


title: Control-rep22 (scRepli-seq)


title: Control-rep28 (scRepli-seq)


title: Control-rep23 (scRepli-seq)


title: Control-rep19 (scRepli-seq)


title: Control-rep18 (scRepli-seq)


title: Control-rep20 (scRepli-seq)


title: Control-rep24 (scRepli-seq)


title: MCE1-rep5 (scRepli-seq)


title: Control-rep16 (scRepli-seq)


title: MCE1-rep1 (scRepli-seq)


title: Control-rep14 (scRepli-seq)


title: Control-rep13 (scRepli-seq)


title: Control-rep15 (scRepli-seq)


title: Control-rep17 (scRepli-seq)


title: Control-rep11 (scRepli-seq)


title: Control-rep10 (scRepli-seq)


title: Control-rep25 (scRepli-seq)


title: Control-rep21 (scRepli-seq)


title: Control-rep8 (scRepli-seq)


title: Control-rep7 (scRepli-seq)


title: Control-rep9 (scRepli-seq)


title: Control-rep5 (scRepli-seq)


title: Control-rep4 (scRepli-seq)


title: Control-rep6 (scRepli-seq)


title: Control-rep2 (scRepli-seq)


title: Control-rep1 (scRepli-seq)


title: G1-rep1 (scRepli-seq)


title: Control-rep3 (scRepli-seq)


title: G1-rep3 (scRepli-seq)


title: rBMSCs_ControlC

city: Milano

first: Carolina

last: Testa

address: Piazza Leonardo da Vinci 32

country: Italy

institute: Politecnico di Milano

description: rBMSCs grown on 2D Nichoid

data_processing:
Per-base quality check of fastq files with FastQC v0.11.9
Samples mapping to the reference genome Rnor_6.0 with STAR v.2.7.0a
Readcounts generation with Htseq v0.12.4
Assembly: Rnor_6.0
Supplementary files format and content: Readcounts text files

source_name: Mesenchymal stem cells

extract_protocol:
Total RNA was isolated with the TRIzol reagent following the standard protocol
cDNA libraries were prepared using Universal Plus mRNA-Seq kit and standard Illumina protocols

value: Rat bone marrow mesenchymal stem cells

value: Bone marrow

tag: protocol

value: 2D Nichoid


title: G1-rep2 (scRepli-seq)


title: rBMSCs_ControlB

description: rBMSCs grown on 2D Nichoid


title: Control-rep32 (scRepli-seq)


title: MCE2-Late-rep2 (E/L Repli-seq)

value: BrdU-IP

value: LateS


title: rBMSCs_ControlA

description: rBMSCs grown on 2D Nichoid


title: MCE2-Early-rep2 (E/L Repli-seq)

value: EarlyS


title: rBMSCs_NichoidC

description: rBMSCs grown in 3D Nichoid

value: 3D Nichoid


title: MCE2-Late-rep1 (E/L Repli-seq)


title: rBMSCs_NichoidB

description: rBMSCs grown in 3D Nichoid


title: MCE2-Early-rep1 (E/L Repli-seq)


title: Control situation - Replicate 1

city: Nice

first: Melanie

last: Pousse

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

data_processing:
Sequencing was performed by BGI. Illumina HiSeq  Xten 2 ×150-bp paired-end was used for sequencing. More than 40 million raw reads were obtained for each sample. The RNA-seq experiment was performed in two biological replicates for vehicle groups, three biological replicates for treated groups.
Raw RNA-seq reads were filtrated by SOAPnuke with default setting to remove adapters and low quality reads and the remaining reads were trimmed into 100bp for downstream analysis
Reads were aligned using STAR v2.6.1d on zebrafish zv10 release with parameter –quantMode GeneCounts
Differential expression analysis was performed using DESeq2 R package
Genome_build: zv10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts for each sample

organism: Danio rerio

source_name: Adult brain

growth_protocol: These experiments were performed in the Zebrafish Tübingen strain. Zebrafish were raised and maintained under standard conditions as described previously. All experiments were performed in accordance with the guidelines of the Animal Care and Use Committee of Shanghai Jiao Tong University.

extract_protocol:
Total RNA from adult zebrafish brain were extracted by TRIzol Reagent (ambion). Add 2 brains in 1mL of TRIzol Reagent and homogenize the tissue. Add 0.2mL of chloroform per 1mL of TRIzol Reagent used for lysis. Centrifuge the sample for 15 minutes at 12,000×g at 4℃. Keep the aqueous phase containing the RNA. Add 0.5mL of isopropanol per tube and mix them. Centrifuge the sample for 5 minutes at 12,000×g at 4℃ to pellet the RNA. Wash the RNA with 75% ethanol. Centrifuge for 2 minutes at 12,000×g at 4℃ and discard the supernatant. Air dry RNA pellet for 5-10 minutes
Library was performed by BGI. Briefly, the total RNA was processed with the NEBNext Ultra RNA Library Prep kit for Illumina.

treatment_protocol: All drug solutions were freshly prepared with PBS (MPH 1.08mg/kg, Valproate 300mg/kg). The fish foods were soaked in drug solution, then fed the zebrafish for 3 days and performed behavioral analysis on the fourth day.

tag: strain

value: Tubingen

value: Brain

tag: age

value: 6 months

value: wild type


title: Control situation - Replicate 2


title: rBMSCs_NichoidA

description: rBMSCs grown in 3D Nichoid


title: a4 mutant treated with Valproate - Replicate 3

value: ppp2r2c m/m

value: Valproate 300mg/kg


title: MCE1-Late-rep2 (E/L Repli-seq)


title: a4 mutant treated with Ritalin - Replicate 2

value: MPH 1.08mg/kg


title: a4 mutant treated with Ritalin - Replicate 3


title: a4 mutant treated with Valproate - Replicate 1


title: a4 mutant treated with Ritalin - Replicate 1


title: a4 mutant - Replicate 2


title: MCE1-Early-rep2 (E/L Repli-seq)


title: a4 mutant treated with Valproate - Replicate 2


title: MCE1-Early-rep1 (E/L Repli-seq)


title: red1288-345DEL-FTP direct RNA

city: Melbourne

first: Attila

last: Horvath

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description: RIP-purified RNA was used for direct RNA seq. using ONT.

data_processing:
Nanopore reads were aligned with minimap (2.10) with long-read spiced alignment (with splice and -k7 parameters).
Strand-specific bigwig tracks were generated using bamCoverage to the pombe genome (ASM294v2) with the parameter ‘—binSize 1’.
Genome_build: ASM294v2
Bigwig tracks were generated after normalisation by the sum of the raw signals of chromosome I and II multiplied by 100 million.

organism: Schizosaccharomyces pombe

source_name: S. pombe grown in YEA liquid culture to an OD600 of around 2

growth_protocol: S. pombe strains used for the study were grown in YEA liquid culture to an OD of 0.8 - 2.2 according to experiment performed.

extract_protocol:
RIP-RNA: Cell pellets that were snap-frozen and ground was resuspended in purification buffer and the clarified supernatants prepared post centrifugation were incubated with IgG beads. After IgG binding TEV cleavage was performed using AcTEV protease and the eluate collected was incubated with anti-Flag beads. Flag bound proteins were subsequently eluted using flag peptide and two third of the flag eluate was taken for DNase treatment and the RNA was purified using RNA Clean and Concentrator Kit.
Direct RNA seq.: 200ng of RIP-purified RNA was used for library preparation using Oxford Nanopore direct RNA sequencing library kit (SQK-RNA002; Version: DRS_9080_v2_revM_14Ag2019) protocol. The prepared libraries were run on individual flow cells following manufacturer guidelines.

treatment_protocol: Samples for ChIP seq. was treated using formaldehyde solution to a final concentration of 1% at room temperature (RT) for 15 min and quenched by addition of glycine to a final concentration of 150 mM for 5 min at RT

tag: strain number

value: MatMsmt0, leu1-32, ura4-D18, ade6-M216, red1288-345DEL-3xFTP::hyg


title: MCE1-Late-rep1 (E/L Repli-seq)


title: Control-Late-rep2 (E/L Repli-seq)


title: a4 mutant - Replicate 1


title: red1-FTP direct RNA

value: MatMsmt0, leu1-32, ura4-D18, ade6-M216, red1-3xFTP::hyg


title: Control-Early-rep2 (E/L Repli-seq)

value: Control


title: Control-Late-rep1 (E/L Repli-seq)


title: Control-Early-rep1 (E/L Repli-seq)


title: LCL HiC

city: Boston

first: Sizun

last: Jiang

state: MA

address: 3 Blackfan Circle

country: USA

institute: BIDMC/Harvard

description: raw sequencing reads

data_processing:
Raw reads were pooled and processed with HiC-Pro pipeline (version v2.10.0) with default parameters  to obtain interactions under genome build hg19.
Contact maps were generated with bins under different resolutions (5k, 10k, 25kb, 50k, 100kb, 500kb)
Contact maps were normalized with iterative correction and eigenvector decomposition (ICE).
Normalized contact maps with necessary re-formatting were used to generate visualization files (.hic) and Pearson correlation of contact matrix using Juicer tools (version 1.8.9) with pre command.
Contact domain boundaries were identified using insulation score with parameters -is 500000 -ids 200000 -im mean -bmoe 1 -nt 0.1 based on normalized contact matrix under 25kb resolution
Assembly: hg19
Supplementary files format and content: .hic file for visulization; .bed text file for domain boundaries; .bed text file for bin annotation; .matrix file for pair-wise bin interations

organism: Homo sapiens

source_name: Resting B Lymphocytes

growth_protocol: Primary B cells were purified from human blood collars using RosetteSep and EasySep B cell kits (StemCell). LCLs were generated from RBLs infected with B95.8 strain EBV for 28 days

extract_protocol:
Hi-C
Hi-C

treatment_protocol: Cells were crosslinked and then lysed with nuclei permeabilized. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.Standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NextSeq 500 sequencer.

tag: cell type source

value: Primary B Cells

value: Resting B Lymphocytes


title: RBL HiC

description: raw sequencing reads

growth_protocol: Primary B cells were purified from human blood collars using RosetteSep and EasySep B cell kits (StemCell).


title: AGO2_eclip_rep2

city: Brno

first: Vaclav

last: Hejret

address: Kamenice 5

country: Czech Republic

institute: Masaryk University

data_processing:
bcl2fastq v. 2.20.0.422 software used for basecalling
The adapters and quality trimming of raw fastq reads was performed using Trimmomatic v. 0.36
Trimmed chimeric eCLIP reads were mapped against the human genome (hg38) and using STAR v. 2.5.3 with default parameters default parameters except --outFilterMismatchNoverReadLmax 0.1  --outFilterMismatchNoverLmax 0.1  --outFilterScoreMinOverLread 0.85 –outFilterMatchNminOverLread 0.85 to detect and separate single genomic reads
Remaining reads were mapped against the in-house database of noncoding RNAs using STAR v. 2.5.3 with default parameters default parameters except --outFilterMismatchNoverReadLmax 0.1 --outFilterMismatchNoverLmax 0.1 –outFilterScoreMinOverLread 0.14 --outFilterMatchNminOverLread 0.14 to detect both single noncoding RNA and noncoding RNA parts of chimeric reads.
Softclipped parts of chimeric reads were extracted and mapped against the human genome (hg38) using STAR v. 2.5.3 with default parameters default parameters except --outFilterMismatchNoverReadLmax 0.1 --outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.75 --outFilterMatchNminOverLread 0.75 to specify genomic parts of chimeric reads.
Obtained chimeric reads were further deduplicated, collapsed and filtered using in-house script.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include obtained chimeric interactions for each sample

growth_protocol: Standard HEK293 TREx growth conditions

extract_protocol:
Ago2-PTH miR-eCLIP in HEK293 TREx
Library preparation was executed based on miR-eCLIP protocol by Van Nostrand et al 2022
miR-eCLIP (eCLIPseq)

treatment_protocol: Overamplification of tRNA fragments: TCCGGCTCGAAGGACCA and TCCCGGGTTTCGGCACC

value: Human embryonic kidney


title: Control-rep12 (scRepli-seq)

value: Single cell

value: MidS


title: AGO2_eclip_rep1


title: red1W298A/F305A-FTP direct RNA

value: MatMsmt0, leu1-32, ura4-D18, ade6-M210, red1W298A/F305A-3xFTP::hyg


title: day6-after-differentiation-stimuli-rep3 (RNA-seq)

data_processing:
RNA-seq raw data were checked the quality by FastQC. Index sequences that added during library preparation were trimmed using cutadapt software. The trimmed data were mapped to the reference genome of mouse mm9 (chr1–19, chrX, chrY) using Hisat2. After mapping, the number of read and TPM values were calculated using Stringtie software.
Assembly: mm9
Supplementary files format and content: TPMs

molecule: polyA RNA

extract_protocol:
RNA was extracted according to the standard protocol using TRIzol (Invitrogen). The concentration of extracted total RNA and the RNA integrity number (RIN) were measured using the 4200 TapeStation system (Agilent Technologies). mRNA was enriched from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB# E7490).
RNA-seq library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB# E7770) and fragment sizes of the obtained library were measured using a TapeStation.

value: day6 after differentiation stimuli


title: day8-after-differentiation-stimuli-rep1 (RNA-seq)

value: day8 after differentiation stimuli


title: 4 d ibrutinib biol rep 2

city: Würzburg

first: Hilka

last: Rauert-Wunderlich

address: Josef-Schneider-Str. 2 , E2

department: Institute of Pathology

country: Germany

institute: University of Würzburg

data_processing:
To assure high sequence quality, Illumina reads were quality and adapter-trimmed via Cutadapt v2.5
Processed reads were mapped to the human reference genome (Ensembl GRCh38) using STAR v2.7.2b with default parameters. Raw read counting with featureCounts v1.6.4 using the RefSeq annotation.
Differential Expression analysis with DESeq2 v1.24.0
Assembly: GRCh38.p13
Supplementary files format and content: CSV: Raw read table

source_name: Mantle cell lymphoma cells

growth_protocol: REC-1 cells were cultured for 4 d at 0.5 × 106 cells per 6 ml growth medium (RPMI 1640, 10% heat-inactivated fetal bovine serum, 2 mM L-Glutamine) at 37 °C in humidified atmosphere with 5% CO2 .

extract_protocol:
Cells were harvested and viable cells were separated by centrifugation using OptiPrep™ Density Gradient Medium (14% (w/v) iodixanol; Serumwerk Bernburg, Bernburg, Germany). RNA from viable cells was isolated by AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) according to manufacturer's protocol.
The RIN for all samples was ≥ 8 according to 2100 Bioanalyzer analysis with RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA). DNA libraries suitable for sequencing were prepared from 500 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA, USA) according to manufacturer’s instructions (1/2 volume). After 15 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~330 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips. Sequencing of pooled libraries, spiked with 1% PhiX control library, was performed at 25 million reads/sample in single-end mode with 75 nt read length on the NextSeq 500 platform (Illumina) using a High output sequencing kits.  Bcl2fastq2 v2.20.0.422 (Illumina) was used to generate demultiplexed FASTQ files.

treatment_protocol: Cells were treated with 400 nM ibrutinib (Selleck Chemicals, Absource Diagnostics, Munich, Germany; dissolved in DMSO) for 4 d, 3 d, and 2 d, and one sample was untreated. The experiment was repeated twice to generate three biological replicates.

value: Mantle cell lymphoma cells

value: B cells

value: 400 nM ibrutinib for 4 d


title: 4 d ibrutinib biol rep 3


title: 4 d ibrutinib biol rep 1


title: 3 d ibrutinib biol rep 1

value: 400 nM ibrutinib for 3 d


title: day6-after-differentiation-stimuli-rep2 (RNA-seq)


title: 3 d ibrutinib biol rep 2


title: 3 d ibrutinib biol rep 3


title: day4-after-differentiation-stimuli-rep3 (RNA-seq)

value: day4 after differentiation stimuli


title: Control-3

type: RNA

city: jilin city

first: guangyu

last: xu

address: Binjiang Road 3999,jilin city,132013

country: China

institute: College of Pharmacy, Beihua University

description: Gene expression after 1d in mouse liver

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide.The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 9 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 700μL RNA using the RNeasy Mini Kit (Qiagen p/n 74104) according to the manufacturer's instructions, followed by RNAeasy column purification. The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The total liver RNA was extracted with Trizol reagent (Invitrogen, Gaithersburg, MD, USA) and the mRNA was purified according to the instructions of RNeasy mini kit (Qiagen, Valencia, CA, USA). RNA samples were assessed for RNA integrity, inhibitor and DNA contamination by referring to the kit instructions. The quality of mRNA was detected by agarose gel electrophoresis, and the content was determined by UV spectrophotometer.

treatment_protocol: After they were acclimated to the laboratory environment for 35d, 24 male mice were randomly divided into 2 groups: blank control group (CON), DECB group, 12 mice in each group. Mice in the CON group were given normal saline (0.08mL/20g), those in the DECB group were given DECB (0.08mL/20g) intragastrically once daily continuously for 35d.

value: liver

tag: gender

value: male


title: Control-2

description: Gene expression after 1d in mouse liver


title: DECB-4

description: Gene expression after 30d in mouse liver


title: DECB-6


title: day8-after-differentiation-stimuli-rep3 (RNA-seq)


title: Control-1

description: Gene expression after 1d in mouse liver


title: day6-after-differentiation-stimuli-rep1 (RNA-seq)


title: DECB-5


title: day8-after-differentiation-stimuli-rep2 (RNA-seq)


title: Untreated biol rep 3

value: untreated


title: Untreated biol rep 2


title: 2 d ibrutinib biol rep 1

value: 400 nM ibrutinib for 2 d


title: 2 d ibrutinib biol rep 2


title: 2 d ibrutinib biol rep 3


title: day4-after-differentiation-stimuli-rep2 (RNA-seq)


title: Untreated biol rep 1


title: day4-after-differentiation-stimuli-rep1 (RNA-seq)


title: PRF0 Clone#11 unsorted population

city: Dallas

first: Joshua

last: Mendell

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
Raw data from machine are de-multiplexed and converted to fastq files using bcl2fastq
Galaxy: Clip adapter GTTTTAGA and CGGTGTTTC
Galaxy: Collapse sequences
Galaxy: FASTA-to-tabular
MAGeCK sgRNA enrichment
Assembly: hg38
Supplementary files format and content: Table of raw and normalized read counts of sgRNAs

growth_protocol: Cell lines were obtained from ATCC. HCT116 cells (male) were cultured in DMEM media (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Sigma-Aldrich) and 1X Penicillin-Streptomycin (Gibco)

extract_protocol:
Genomic DNA was isolated from unsorted cells using the MasterPure Complete DNA Purification kit (Lucigen) and from sorted cells by phenol-chlorofom extraction
Sequencing libraries were generated using two sequential rounds of PCR using Herculase II Fusion DNA polymerase (Agilent). In the first round of PCR, 5µg of genomic DNA from unsorted cells was used in each of 24 100 µl reactions, and all recovered genomic DNA from sorted cells was split into two 100 µl reactions. Following 18 cycles of PCR1 amplification, 5 µl from the pooled reaction product was used in the second round of PCR (11 – 13 cycles), using primers containing barcodes and Illumina sequencing adaptors
OTHER: CRISPR screen custom DNA library

treatment_protocol: Transduced cells were selected with 1 µg/mL puromycin (Thermo Fisher Scientific)

value: colon cancer cell line

value: PRF0 Clone #11

value: Unsorted


title: PRF0 Clone#17 unsorted population

value: PRF0 Clone #17


title: PRF-1 Clone#6 unsorted population

value: PRF-1 Clone #6


title: PRF-1 Clone#16 unsorted population

value: PRF-1 Clone #16


title: PRF0 Clone#17 bottom eGFP/mCh population

value: Sorted:Bottom eGFP/mCherry


title: MCE2-rep3 (RNA-seq)


title: PRF0 Clone#11 bottom eGFP/mCh population


title: MCE2-rep1 (RNA-seq)


title: PRF-1 Clone#16 bottom eGFP/mCh population


title: MCE1-rep3 (RNA-seq)


title: PRF-1 Clone#16 top eGFP/mCh population

value: Sorted:Top eGFP/mCherry


title: MCE1-rep2 (RNA-seq)


title: EBNA3A OFFChIP-seq RAD21 Rep2

data_processing:
ChIP-seq reads were aligned to human genome hg19 using Bowtie v2.4.1 under default settings except the parameter −k was set to 1. Bams were merged from replicates using samtools v1.10, and the regions overlapped with blacklist regions were removed with bedtools v2.26.0. ChIP-seq peaks were called and tracks were normalized using MACS v2.2.7 with the parameter --SPMR by comparing ChIP to INPUT control.
Cut&Run reads were aligned to human genome hg19 using Bowtie v2.4.1 with the parameters -I 10 -X 700 --local --very-sensitive-local --no-discordant --no-mixed --no-unal --phred33 -k 1. Bams were merged from replicates using samtools v1.10, and the regions overlapped with blacklist regions were removed with bedtools v2.26.0. Cut&Run peaks were called and tracks were normalized using MACS v2.2.7 with the parameter --SPMR.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: EBNA3A OFFChIP-seq RAD21

growth_protocol: Cells were grown in RPMI1640 media supplemented with 10% fetal bovine serum.

extract_protocol:
ChIP was done using the ChIP assay kit protocol (Millipore). Cut and run was done following the protocol from CUTANA™ ChIC/CUT&RUN Kit (Epicypher).
Libraries were prepared using NEB library preparation kit.

treatment_protocol: Cell were grown in the presence or absence of 4-HT for 14 days.

value: Lymphoblastoid Cell Line

tag: genotype/variation

value: EBNA3A off


title: PRF-1 Clone#6 bottom eGFP/mCh population


title: EBNA3A 4HT ChIP-seq INPUT

source_name: EBNA3A 4HT ChIP-seq INPUT


title: EBNA3A OFFChIP-seq  INPUT

source_name: EBNA3A OFFChIP-seq  INPUT


title: PRF-1 Clone#6 top eGFP/mCh population


title: MCE1-rep1 (RNA-seq)


title: Control-rep2 (RNA-seq)

value: Control


title: EBNA3A OFF Cut&Run CTCF Rep2

data_processing:
library strategy: Cut & Run
ChIP-seq reads were aligned to human genome hg19 using Bowtie v2.4.1 under default settings except the parameter −k was set to 1. Bams were merged from replicates using samtools v1.10, and the regions overlapped with blacklist regions were removed with bedtools v2.26.0. ChIP-seq peaks were called and tracks were normalized using MACS v2.2.7 with the parameter --SPMR by comparing ChIP to INPUT control.
Cut&Run reads were aligned to human genome hg19 using Bowtie v2.4.1 with the parameters -I 10 -X 700 --local --very-sensitive-local --no-discordant --no-mixed --no-unal --phred33 -k 1. Bams were merged from replicates using samtools v1.10, and the regions overlapped with blacklist regions were removed with bedtools v2.26.0. Cut&Run peaks were called and tracks were normalized using MACS v2.2.7 with the parameter --SPMR.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: EBNA3A OFF Cut&Run CTCF


title: MCE2-rep2 (RNA-seq)


title: Control-rep3 (RNA-seq)


title: Control-rep1 (RNA-seq)


title: EBNA3A OFF Cut&Run CTCF Rep1


title: EBNA3A 4HT ChIP-seq RAD21 Rep2

source_name: EBNA3A 4HT ChIP-seq RAD21

value: EBNA3A on


title: EBNA3A 4HT ChIP-seq RAD21 Rep1


title: EBNA3A OFFChIP-seq RAD21 Rep1


title: PRF0 Clone#17 top eGFP/mCh population


title: PRF0 Clone#11 top eGFP/mCh population


title: EBNA3A OFF Cut&Run K27AC Rep2

source_name: EBNA3A OFF Cut&Run K27AC


title: EBNA3A ON  Cut&Run K27AC Rep2

source_name: EBNA3A ON  Cut&Run K27AC


title: EBNA3A OFF Cut&Run K27AC Rep1


title: EBNA3A ON Cut&Run CTCF Rep1

source_name: EBNA3A ON Cut&Run CTCF


title: EBNA3A ON Cut&Run K27AC Rep1

source_name: EBNA3A ON Cut&Run K27AC


title: Liver metastasis

city: Nanjing

first: linlin

last: ji

state: Jiangsu

address: 305 Zhongshan East Road, Xuanwu District

institute: Nanjing University

description: GEXSCOPE®

library_source: transcriptomic single cell

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver metastasis of colorectal cancer

extract_protocol:
The fresh tissues were stored in the sCelLiveTM Tissue Preservation Solution (Singleron) on ice after the surgery within 30 mins. The specimens were washed with Hanks Balanced Salt Solution (HBSS) for three times, minced into small pieces, and then digested with 3 mL sCelLiveTM Tissue Dissociation Solution (Singleron) by Singleron PythoN™ Tissue Dissociation System at 37 °C for 15 min. The cell suspension was collected and filtered through a 40-micron sterile strainer. Afterwards, the GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) was added, and the mixture[Cell: RCLB=1:2 (volume ratio)] was incubated at room temperature for 5-8 min to remove red blood cells. The mixture was then centrifuged at 300 × g 4 ℃ for 5 mins to remove supernatant and suspended softly with PBS.
Single-cell suspensions (2×105 cells/mL) with PBS  were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) . Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: liver metastasis of colorectal cancer

value: colon cells

value: kras(+), braf(+)

tag: Sex

value: female

tag: tumor stage

value: ⅣA


title: HEK293_p300_H3K27Ac_2

city: Stanford

first: Michael

middle: Gregory

last: Chavez

state: CA

address: 443 Via Ortega, Rm 062

department: Bioengineering

institute: Stanford University

data_processing:
For RNA-seq, mapping and quantification was performed by Novogene. Briefly, mapping was performed with STAR v2.5 against hg19 with a mismatch parameter equal to 2. Initial quantification of transcript abundance was performed by HTSeq v0.6.1. We performed differential expression analysis using DESeq2 v1.24.0. MA plots were generated in DESeq2 by contrasting the two conditions using the log fold change shrinkage method.
For ChIP-seq, initial analysis was performed by Active Motif. Reads were aligned to hg19 using the BWA algorithm on default settings and stored in BAM format. Reads were extended in silico at their 3′ ends to a length of 200 bp. The genome was divided into 32-nt bins and fragment density was calculated in each bin. Peak locations were determined using the MACS algorithm with a cutoff of p value of 10-7. Regions were merged across samples for comparison across samples and stored in bigWig files. We imported these bigWig files directly to deepTools to create correlation results and visualization of H3K27Ac about a genomic locus.
Genome_build: hg19

extract_protocol:
RNA-seq was performed from duplicates for each condition. To prepare samples, cells were induced with dox for 48 hours and GFP+/BFP+ double positive cells were sorted on a BD Influx flow cytometer (BD Biosciences). WT cells containing only an sgRNA were sorted for BFP+ cells. 1 million cells were sorted for each sample and total RNA was purified using RNeasy Plus mini kit (Qiagen). H3K27ac ChIP-seq was performed from duplicates for each condition. To prepare samples, cells were induced with dox for 48 hours. To fix the cells, 1/10 volume of freshly-prepared Formaldehyde solution (11% Formaldehyde, 0.1M NaCl, 1mM EDTA, 50mM HEPES in water) was added to existing media for 15 minutes at room temperature. The fixation was stopped by adding 1/20 volume of 2.5M Glycine solution for 5 minutes at room temperature. After the glycine incubation cells were scraped from the culture surface. Cells were collected and kept on ice for the remainder of the procedure. The cells were centrifuged at 800xg for 10 minutes and then re-suspended in 10 mL chilled PBS-Igepal. Cells were centrifuged again and resuspended in 10 mL PBS-Igepal and 100ul of PMSF (100mM). Cells were centrifuged a third time and cell pellets were snap-frozen on dry ice and stored at -80C. ChIP-seq was performed by Active Motif.
Total RNA quantification and qualification was done by Nanodrop for RNA purity, agarose gel electrophoresis and Agilent 2100 for RNA integrity. mRNA was purified using poly-T oligo-attached magnetic beads and fragmented. cDNA was synthesized using M-MuLV Reverse Transcriptase and DNA Polymerase I and purified using AMPure XP beads.The 3' ends of the cDNA were adenylated and a NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. AMPure XP system (Beckman Coulter, Beverly, USA) was utilized to enrich for fragments of 150-200bp length. Finally, the final library is obtained by PCR amplification and purification of PCR products by AMPure XP beads. Libraries were diluted to 1.5ng/ul (Qubit2.0) and insert size detected by Agilent 2100. Q-PCR is used to accurately quantify the library effective concentration (> 2nM). Samples were then pooled and run on Illumina sequencers. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

value: dCas9-p300 + sgHBB


title: HEK293_p300_H3K27Ac_1


title: Rectum-03T

description: GEXSCOPE®

source_name: colorectal cancer

value: colorectal cancer


title: Rectum-03N

description: GEXSCOPE®

source_name: normal colorectal mucosa

value: normal colorectal mucosa


title: HEK293_VPR_H3K27Ac_2

value: dCas9-VPR + sgHBB


title: HEK293_VPR_H3K27Ac_1


title: HEK293_WT_HEK293_H3K27Ac_1

value: No treatment


title: HEK293_VPRP_H3K27Ac_2

value: dCas9-VPRP + sgHBB


title: HEK293_VPRP_H3K27Ac_1


title: EBNA3A ON Cut&Run CTCF Rep2


title: HEK293_VPRP_D1399Y_H3K27Ac_1

value: dCas9-p300 (D1399Y) + sgHBB


title: HS_NPC_RNAseq_Mock_R1

city: San Francisco

first: Kristoffer

middle: Edgar

last: Leon

address: 1650 Owens Street

institute: University of California, San Francisco

description:
processed data file:
ZIKV_Mock_results_bulk_DESeq2.csv

data_processing:
Alignments to the human genome performed by STAR
Counts performed by HT-Seq or Bedtools
DESeq2 used for differental analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts or differential expression analysis provided above

growth_protocol: NPCs were differentiated and maintained using EFH media (Stemline Neural Stem Cell Media [Sigma Aldrich], EGF [R&D Biosystems], rhFGF basic [R&D Biosystems],). NPCs were dissociated and plated onto Matrigel-coated plates (Corning) prior to infecting with ZIKV (MOI of 1)

extract_protocol:
Whole-cell lysates were generated in CLIP lysis buffer (50 mM HEPES, 200 mM NaCl, 1 mM EDTA, 10% glycerol, 0.1% NP-40, 0.2% Triton X-100, 0.5% N-lauroylsarcosine) and briefly sonicated using a probe-tip Branson sonicator to solubilize chromatin.
Eluted cDNA was transferred to a new PCR tube containing 15 mL of 2X Phusion HF-PCR Master Mix (NEB), 0.5 mL of 30 mM P3/P6 PCR1 oligo mix and 0.5 ml of 15x SYBR Green I (ThermoFisher Scientific). Real-time quantitative PCR was preformed: 98°C 2 min, 15 cycles of 98°C 15 seconds, 65°C 30 seconds, 72°C, 30 seconds, with data acquisition set to the 72°C extension. PCR1 reactions were cleaned up by adding of 4.5 mL of isopropanol, 54 mL of AMPure XP beads and incubation for 10 min. Beads were washed once with 80% ethanol, dried for 5 min, and eluted in 15 ml of water. Illumina flow cell adaptors were added by adding 15 mL 2X Phusion HF-PCR Master Mix and 0.4 mL P3solexa/P6solexa oligo mix and amplified:  98°C 2 min, 3 cycles of 98°C 15 seconds, 65°C 30 seconds, 72°C, 30s seconds. Final libraries were purified by addition of 48 mL of AMPure XP beads and incubation for 5 min. Beads were washed twice with 70% ethanol, dried for 5 min, and eluted in 20 mL of water.

treatment_protocol: Briefly, viral inoculum was added to DMEM with 2% FBS or EFH followed by a two-hour incubation at 37C with a rock every 15 minutes. After infection was completed, inoculum was aspirated and then fresh DMEM with 10% FBS or EFH was added to the cells. Infected cells were cultured for 48 hours prior to harvesting for all sequencing and IF experiments.

value: iPSC-derived neural progenitor cells

value: mock-infected


title: Rep1-Mock-Cyto

description:
processed data file:
HTSeq_Mock_Zikv_Nuc_Cyto_counts.xlsx

source_name: Mock-Cyto

tag: fraction

value: Cyto


title: HS_NPC_RNAseq_Mock_R2

tag: cell line


title: Rep2-Mock-Nuc

source_name: Mock-Nuc

tag: treatment

value: Nuc


title: Rep1-ZIKV-Cyto

source_name: ZIKV-Cyto

value: ZIKV-infected


title: Rep1-ZIKV-Nuc

source_name: ZIKV-Nuc


title: Rep2-Mock-Cyto


title: HS_NPC_RNAseq_ZIKV_R1


title: Mock 2 CLIP

description:
processed data file:
UPF1_CLIP_NPC_MockZikvRead_3UTR_Analysis.xlsx

data_processing:
library strategy: CLIP-seq
Alignments to the human genome performed by STAR
Counts performed by HT-Seq or Bedtools
DESeq2 used for differental analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts or differential expression analysis provided above

source_name: Mock CLIP

tag: clip-antibody

value: Bethyl laboratories, A300-38A


title: ZIKV2 CLIP

source_name: ZIKV CLIP

tag: cell type


title: ZIKV1 CLIP


title: HS_NPC_RNAseq_ZIKV_R2


title: Rep2-ZIKV-Cyto


title: Mock 1 CLIP


title: Adipocyte, EAKO, ATAC

first: Kai

last: Li

address: #818, East Tianyuan Road

institute: Nanjing Medical University

data_processing:
Alignment by BWA
Filtering by Samtools
Narrow peaks by Macs2
BigWig files by Deeptools bamCoverage
Deseq2 for differential analysis
Assembly: mm10
Supplementary files format and content: BigWig files
Supplementary files format and content: fastq files

source_name: subcutaneous adipose

extract_protocol:
Mature adipocytes were obtained from adipose tissue in the inguinal position of male mice at 8-10 weeks old. Type I collagenase (2mg/ml, Sigma, SCR103) was preconfigured using DMEM basic medium (Gibco, C11995500BT) containing 2% volume of FBS (Gibco), 100 U/ml penicillin, 100 μg/ml streptomycin, and stored in the dark after removal of bacteria by filtration using a 0.22 μM filter. The volume ratio of collagenase to adipose tissue was maintained at 2:1. Then the adipose pad was cut into pieces to 1mm³ and digested in 37℃ water bath for 1h, during which the tube was reversed and mixed every five minutes. The digested adipocytes were filtered (70 μm), then centrifuged at 1000 rpm for 10 min. Up layer mature adipocyte were collected and treated according to the manufacturer’s instructions by using in situ DNA Binding Library for Illumina Cut&Tag kits (Yeasen, 12598E12).
native nuclei were purified from adipocytes，and washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). For CUT&Tag, 1x10^5 nuclei bound to Concanavalin A-coated beads were incubated with indicated primary antibodies (Ets1, Active Motif, #39581, 1:50; H3K27ac, Active Motif, #91193, 1:50; normal rabbit IgG, Merck Millipore #12-370; normal mouse IgG, Merck Millipore #12-371) and second antibodies (anti-rabbit IgG antibody, goat monoclonal: Millipore AP132; anti-mouse IgG antibody, goat polyclonal: Millipore AP124). Transposase pA-Tn5 was used to induce DNA tagmentation, followed by Proteinase K digestion and PCI extraction. The ethanol precipitated DNA was immediately subjected to PCR amplification by Universal and barcoded i7 primer using NEBNext HiFi 2x PCR Master mix. The amplified library was purified without size selection. ChIP-seq libraries were prepared from 3-5ng DNA using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions. Post-amplification libraries were size selected at 250–450bp in length using AMPure XP beads ((Beckman Counter)) and were quantified using the Library Quantification Kit for Illiumina (Kapa Biosystems, KK4603). For ATAC seq,  the Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer's manual. 50,000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃. The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen). All CUT&Tag and ATAC Libraries were pooled to a final concentration of 10nM and sequenced paired-end using the Illumina NovaSeq 6000.

tag: tissue

value: subcutaneous adipose

value: primary adipocyte

value: adipocyte

tag: genotype

value: Ets1 Knockout

value: Mature adipocytes obtained by density gradient centrifugation


title: HEK293_VPRP_D1399Y_H3K27Ac_2


title: Adipocyte, Flox, ATAC

value: wild type (Knockout)


title: Rep2-ZIKV-Nuc


title: RPMI-EV-rep3

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

data_processing:
RNA sequencing reads were aligned to the GRCh38 build of the Human genome using the Subread aligner. Only uniquely mapped reads were retained. Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included.
Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least two libraries. Counts were converted to log2 counts per million, quantile normalized and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. P values from Bayes moderated t-tests were adjusted to control the false discovery rate (FDR) across all comparisons. Genes were called differentially expressed if they achieved a FDR of 0.05 or less. Other criteria were also applied for calling DE genes; the criteria are mentioned in our paper.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-RPKM values for each sample

source_name: RPMI-8226 cell line + EV sgRNA

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: All cell lines were treated with doxycycline for 48 hours to induce guide expression

tag: expression

value: EV sgRNA

value: Multiple Myeloma (MM) cell line


title: Adipocyte, EAKO, H3k27ac ChIP

tag: antibody


title: RPMI-EV-rep1


title: RPMI-EV-rep2


title: RPMI-21B-rep2

source_name: RPMI-8226 cell line + Irf4 sgRNA

value: Irf4 sgRNA


title: RPMI-21B-rep3


title: Rep1-Mock-Nuc


title: Adipocyte, Flox, H3k27ac ChIP


title: RPMI-21B-rep1


title: HepaRG cells, PA+BMS-2

city: Beijing

first: Juan

last: Liu

state: China

address: No 168, Litang Road

institute: Beijing Tsinghua Changgung Hosptial

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. 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 N base 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.
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.
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.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HepaRG

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. Total amounts and integrity of RNA were assessed using the RNA Nano 6000  Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.

value: HepaRG

value: human hepatic cell line

value: WT

value: PA+BMS


title: HepaRG cells, PA+BMS-1


title: HepaRG cells, PA+BMS-3


title: OPM2-EV-rep3

source_name: OPM2 cell line + EV sgRNA


title: HepaRG cells, PA+OA-3

value: PA+OA


title: OPM2-EV-rep1


title: OPM2-EV-rep2


title: Adipocyte, EA+/+, H3k27ac ChIP

value: Ets1 Knockin


title: Adipocyte, EC+/+, H3k27ac ChIP

value: wild type (Knockin)


title: OPM2-21B-rep1

source_name: OPM2 cell line + Irf4 sgRNA


title: OPM2-21B-rep2


title: HepaRG cells, PA+OA-2


title: Adipocyte, cold stress, Ets1 ChIP

value: wild type C57


title: OPM2-21B-rep3


title: Adipocyte, room temperature, Ets1 ChIP

value: subcutaneous adipose


title: MM1S-EV-rep2

source_name: MM1S cell line + EV sgRNA


title: MM1S-21B-rep3

source_name: MM1S cell line + Irf4 sgRNA


title: MM1S-21B-rep2


title: MM1S-21B-rep1


title: HepaRG cells, PA-2

value: PA


title: H929-EV-rep3

source_name: H929 cell line + EV sgRNA


title: HepaRG cells, PA-1


title: H929-EV-rep2


title: MM1S-EV-rep3


title: HepaRG cells, PA+OA-1


title: KO G-CSF spleen, rep4

city: Saint Louis

first: laura

last: schuettpelz

state: MO

address: 660 S. Euclid

institute: washington university

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.  Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: mm10
Supplementary files format and content: Merged_differential_expression_results_2018_RNAseq.xlsx

source_name: HSC

extract_protocol:
NucleoSpin RNA XS (Machery-Nagel) of sorted HSCs from bone marrow or spleen
SMARTer Ultra Low RNA (Illumina)

value: spleen

value: HSC

value: KO

value: G-CSF


title: KO G-CSF spleen, rep2


title: KO G-CSF spleen, rep3


title: H929-21B-rep3

source_name: H929 cell line + Irf4 sgRNA


title: WT G-CSF spleen, rep3


title: WT G-CSF spleen, rep4


title: HEK293_WT_HEK293_H3K27Ac_2

value: No treatment


title: H929-21B-rep2

value: Multiple Myeloma (MM) cell line


title: HepaRG cells, PA-3


title: H929-21B-rep1

value: Irf4 sgRNA


title: WT G-CSF spleen, rep2


title: HepaRG cells, control-3

value: HepaRG

value: control


title: SortedCells_Screen3

city: Camperdown

first: Matthew

last: Waller

state: NSW

address: D17 - Charles Perkins Centre, Johns Hopkins Drive, The University of Sydney

department: School of Life and Environmental Sciences

institute: University of Sydney

data_processing:
Sequenced reads were trimmed and aligned to reference sgRNA library (Addgene #92379) using MAGeCK v0.5.9 to produce raw read counts
Genome_build: Calabrese Set A (Addgene #92379) used for read alignment
Supplementary_files_format_and_content: Each txt file contains raw read counts for corresponding sample as determined by MAGeCK v0.5.9

growth_protocol: HEK293T-CRISPRa cells grown in DMEM supplemented with 10% HyClone FBS and 1% Penicillin-Streptomycin

extract_protocol:
Genomic DNA was extracted from cells using ISOLATE II Genomic DNA Kit (Bioline, BIO-52067). 25 ug genomic DNA was used as input for unsorted diversity control samples and 5 ug for sorted samples. PCR was assembled with NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, M0541L), 0.4 uM P5 index primer mix and 0.4uM P7 indexing primer. PCR cycling conditions and primers were adapted from Sanson et al., 2018. Briefly, reactions were held at 95°C for 1 min, followed by 28 cycles of 94°C for 30 s, 53°C for 30 s and 72°C for 30 s, followed by a final 72°C extension step for 10 min. Amplicons were gel extracted and purified using the ISOLATE II PCR & Gel Kit (Bioline, BIO-52060) and the quality and concentration of DNA assessed via 2100 BioAnalyzer Instrument (Agilent Technologies, G2939BA). Next generation sequencing was performed on Illumina Novoseq 6000.
NA

treatment_protocol: Transduced HEK293T-CRISPRa cells were selected on puromycin, then incubated with Alexa Fluor 488-conjugated SARS-CoV-2 Spike protein for 30 min at 4 degrees celcius before FACS.

tag: puromycin selection

value: 8 days

tag: spike protein used

value: Hexapro

tag: sorted

value: Yes


title: EBV Infection RNA PolII HiChIP Day 28 Replicate 1

data_processing:
Library strategy: HiChIP
Raw reads from biological replicates were pooled and processed with the HiC-Pro pipeline (version v2.10.0) against a MboI digested hg19 genome build
Long ranged interactions were identified with hichipper v0.7.3 using the parameters for peaks (COMBINED, ALL).
Read depth normalization for long ranged interactions identified was performed based off the number of valid PET counts per library.
Genome_build: hg19
Supplementary_files_format_and_content: .mango long ranged interaction files normalized to valid mapped PET counts per library

source_name: Primary Resting B Lymphocyte HiChIP RNAPII Day 28 Replicate 1

growth_protocol: Cells were grown in RPMI supplemented with 1% L-glutamate, 1% Pen/Strep and 10% FBS.

extract_protocol: Hi-ChIP

treatment_protocol: Cells for each biological replicate were collected and crosslinked by using 1% formaldehyde for 10 min. Chromatin was digested using MboI restriction enzyme (New England Biolabs) followed by end-repair, ligation, and sonication. Sheared chromatin was pre-cleared and 3-fold diluted as described in ChIP method and then incubated with RNAPII antibody (8WG16) at 4°C for overnight. Chromatin-antibody complex was captured by Dynabead Protein-A bead. Biotin was incorporated by adding Biotin-14-dATP(Thermo Fisher) followed by capture with Streptavidin C-1 bead (Thermo Fisher). Captured DNA was quantified using Qubit (Thermo Fisher). An appropriate of Tn5 used and the number of PCR cycles performed were based on the post-ChIP Qubit amounts. PCR products were size selected by PAGE purification (300–700 bp). All libraries were sequenced on the Illumina NextSeq 500 sequencer.

value: Resting B Lymphocytes

value: RNAPII

tag: agent

value: EBV

tag: time point

value: day 28


title: SortedCells_Screen2

value: 3 days

value: Krammer lab


title: HepaRG cells, control-1

value: human hepatic cell line

value: WT


title: EBV Infection RNA PolII HiChIP Day 28 Replicate 2

source_name: Primary Resting B Lymphocyte HiChIP RNAPII Day 28 Replicate 2


title: EBV Infection RNA PolII HiChIP Day 0 Replicate 2

source_name: Primary Resting B Lymphocyte HiChIP RNAPII Day 0 Replicate 2

value: day 0


title: EBV Infection RNA PolII HiChIP Day 0 Replicate 1

source_name: Primary Resting B Lymphocyte HiChIP RNAPII Day 0 Replicate 1


title: EBNA3A-HT HiChIP H3K27ac 3A Off Replicate 2

description: E3A H3K27ac HiChIP

data_processing:
Library strategy: Hi-ChIP
Raw reads from biological replicates were pooled and processed with the HiC-Pro pipeline (version v2.10.0) against a MboI digested hg19 genome build
Long ranged interactions were identified with hichipper v0.7.3 using the parameters for peaks (COMBINED, ALL).
Read depth normalization for long ranged interactions identified was performed based off the number of valid PET counts per library.
genome build: hg19
.mango long ranged interaction files normalized to valid mapped PET counts per library

source_name: EBNA3A-HT Lymphoblastoid Cell Lines

growth_protocol: The EBNA3A-HT Lymphoblastoid Cell Lines were grown in RPMI supplemented with 1% L-glutamate, 1% Pen/Strep and 10% FBS.

treatment_protocol: Cells for each biological replicate were collected and crosslinked by using 1% formaldehyde for 10 min. Chromatin was digested using MboI restriction enzyme (New England Biolabs) followed by end-repair, ligation, and sonication. Sheared chromatin was pre-cleared and 3-fold diluted as described in ChIP method and then incubated with H3K27ac antibody (Abcam ab4729) at 4°C for overnight. Chromatin-antibody complex was captured by Dynabead Protein-A bead. Biotin was incorporated by adding Biotin-14-dATP(Thermo Fisher) followed by capture with Streptavidin C-1 bead (Thermo Fisher). Captured DNA was quantified using Qubit (Thermo Fisher). An appropriate of Tn5 used and the number of PCR cycles performed were based on the post-ChIP Qubit amounts. PCR products were size selected by PAGE purification (300–700 bp). All libraries were sequenced on the Illumina NextSeq 500 sequencer.

value: Lymphoblastoid Cell Lines

value: EBNA3A-HT Lymphoblastoid Cell Lines


title: EBNA3A-HT HiChIP H3K27ac 3A Off Replicate 1

description: E3A H3K27ac HiChIP


title: WT G-CSF spleen, rep1

value: spleen

value: HSC

value: G-CSF


title: H929-EV-rep1

value: EV sgRNA

value: Multiple Myeloma (MM) cell line


title: EBNA3A-HT HiChIP H3K27ac 3A On Replicate 1

description: E3A H3K27ac HiChIP


title: KO G-CSF spleen, rep1

value: KO


title: KO G-CSF BM, rep4

value: BM


title: pro-B Site1.3PrKO2

city: Chicago

first: Amy

last: Kenter

state: IL

address: 835 S Wolcott

institute: UIC

description: VDJ-seq library

data_processing:
The MiXCR pipeline was used to identify and group clonotypes by their CDRs to determine V gene usage.
Tables of unique CDR3 identified for each sample are provided as processed files. Tables include read counts, fraction, and sequence quality for each unique CDR3 region as well as the possible IGHV, IGHD and IGHJ gene names, scores, and sequence.
Assembly: mm9
Library strategy: VDJ-Seq

source_name: BM derived NE1-/- pro-B cells

growth_protocol: Bone marrow derived primary pro-B cells were FACS purified from WT (C57Bl/6), NE1-/- and Site I.3Pr-/- mice.

extract_protocol:
Genomic DNA (gDNA) was isolated from purified CD19+ pro-B cells.
The V(D)J-seq protocol using gDNA was performed while omitting the negative depletion step and using custom JH primers. GDNA was sonicated to a range of 500 bp to 1000 bp using a Covaris S2 (Covaris).  Library barcoding was carried out using NEBNext Multiplex Oligos for Illumina (E7600S).

treatment_protocol: CD19+ cells were isolated using anti-CD19 conjugated MACS beads, pre-incubated with CD16/32 Fc Block and FACS purified using antibodies for CD19-BB515, CD93-PE/Cy7, IgM Fab-AF647, CD2-PE, CD43-BV421.

tag: strain

value: pro-B


title: SortedCells_Screen1

value: Hexapro

value: Yes


title: pro-B Site1.3PrKO1

description: VDJ-seq library


title: DiversityControl_Screen3

value: 8 days

value: No


title: KO G-CSF BM, rep3


title: KO G-CSF BM, rep2


title: KO G-CSF BM, rep1


title: 592mic-2

city: Hefei

first: Kan

last: He

address: 111 Jiulong Road

department: School of life sciences

institute: Anhui University

data_processing:
PE150 platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT2 v2.0.5.
We used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05.
Bidirectional clustering analysis was performed for all different genes in the samples using R language Pheatmap(1.0.8) software package.
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

source_name: breast cancer cells

growth_protocol: MCF-7 cells were cultured in DMEM  supplemented with 10% FBS , penicillin (100 U/ml), and streptomycin (100 µg/ml).

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext Ultra II RNA Library Prep Kit for Illumina was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: MiR-592 mimics and mimics NC were transferred to MCF-7 cells, respectively.

value: breast cancer cells

value: transfected with miR-592 mimics


title: spike-specific B cells D15,scRNAseq

city: Erlangen

first: Simon

last: Schaefer

state: Bavaria

address: Glueckstr. 6

department: Genetics

institute: FAU Erlangen

description:
10X HTO+ADT
Antibody-derived oligonucleotide (ADT) + Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
The scRNA-seq reads were aligned to the human reference genome GRCh38  (UCSC, CA, USA), after generation of cell-gene matrices via Cell Ranger v6.1.2 (10xGenomics). Cell Ranger v6.1.2 multi pipeline was applied for scRNA-seq and VDJ-seqanalysis, while CITE seq Count v1.4.5 was applied to count the surface features
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0,refdata-gex-GRCh38-2020-A
Supplementary files format and content: CITE-seq-Count output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: B cells

extract_protocol:
Live CD19+ IgG+ spike-FusionRed-binding memory B cells were sorted on a MoFlo Astrios Cell Sorter. FusionRed-negative CD19+  IgG+ B cells were sorted in parallel and mixed with spike sorted B cells. FACS staining  solution also contained barcoded hashtags for sample identifications (BioLegend) as well as barcoded RBD.
Libraries for single-cell transcriptome sequencing and scBCR sequencing were prepared using the, Chromium Single-Cell 5′ Library Gel Bead and Construction Kit, v2 Dual index Chemistry Kit and Chromium Single-Cell V(D)J BCR Enrichment Kit (10x Genomics, CA, USA).
For CITE-seq a unique molecular 5´ feature barcode was added to purified spike-FusionRed protein by the 5’ feature Barcode Antibody conjugation Kit – Lightning Link® (Abcam) exactly as described by the manufacturer. RBD was also labelled by adifferent feature barcode.

value: B cells

tag: library type

value: HTO+ADT

tag: antibodies/tags


title: DiversityControl_Screens1and2

value: 3 days


title: spike-specific B cells D22,scRNAseq


title: RNAseq-M12GFP_3

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

description:
RSEM_gene_counts.tsv.gz
RSEM_gene_FPKM.tsv.gz
RSEM_gene_TPM.tsv.gz

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore
Reads were mapped with STAR(v2.7.1a) to mm10 (Gencode M22) reference genome using parameters "--readFilesCommand unpigz -c -p 4 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --genomeLoad NoSharedMemory --outSAMmapqUnique 60 --outSAMmultNmax 1 --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM"
Read duplication was marked with MarkDuplicates from GATK (v4.1.2.0)
RSEM was used to quantify read counts per gene
Genome_build: mm10
Supplementary_files_format_and_content: gene-based raw counts, as well as TPM and  FPKM normalized txt files

source_name: spontaneous lung metastasis (E0771GFP derivative)

growth_protocol: Cells were maintained in RPMI 1640 (Thermo Fisher) supplemented with 10% calf serum with iron (Hyclone) and 1% penicillin/streptomycin.

extract_protocol:
RNA was isolated from total cell lysates with the Rneasy Plus Mini kit (Qiagen, 74136) following manufacturer's instructions.
Total RNA was polyA enriched and prepared for RNA sequencing with TruSeq stranded mRNA library prep kit (Illumina).

treatment_protocol: Cells were treated with doxycycline (1 mg/mL) and with TGF-beta1 (2 ng/mL) or vehicle control.

tag: genotype/variation

value: M12GFP cells


title: HepaRG cells, control-2

source_name: HepaRG

value: HepaRG

tag: cell line

value: human hepatic cell line

value: WT

value: control


title: RNAseq-M12GFP_2

tag: treatment


title: EBNA3A-HT HiChIP H3K27ac 3A On Replicate 2

first: Sizun

last: Jiang

address: 3 Blackfan Circle

institute: BIDMC/Harvard

description: E3A H3K27ac HiChIP

value: Lymphoblastoid Cell Lines

value: EBNA3A-HT Lymphoblastoid Cell Lines


title: RNAseq-M12GFP_1


title: 592micNC-2

value: transfected with  mimics NC


title: KO saline BM, rep3

value: BM

value: HSC

value: KO

value: saline


title: spike-specific B cells D31,scRNAseq


title: KO saline BM, rep2


title: RNAseq-M11GFP_3

value: M11GFP cells

value: breast cancer cells


title: spike-specific B cells D14 scRNAseq

value: B cells


title: spike-specific B cells, B cells, D31,scRNAseq,VDJ

description:
BCR RNA
10x Genomics

data_processing:
The scRNA-seq reads were aligned to the human reference genome GRCh38  (UCSC, CA, USA), after generation of cell-gene matrices via Cell Ranger v6.1.2 (10xGenomics). Cell Ranger v6.1.2 multi pipeline was applied for scRNA-seq and VDJ-seqanalysis, while CITE seq Count v1.4.5 was applied to count the surface features
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0,refdata-gex-GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Live CD19+ IgG+ spike-FusionRed-binding memory B cells were sorted on a MoFlo Astrios Cell Sorter. FusionRed-negative CD19+  IgG+ B cells were sorted in parallel and mixed with spike sorted B cells. FACS staining  solution also contained barcoded hashtags for sample identifications (BioLegend) as well as barcoded RBD.
Libraries for single-cell transcriptome sequencing and scBCR sequencing were prepared using the, Chromium Single-Cell 5′ Library Gel Bead and Construction Kit, v2 Dual index Chemistry Kit and Chromium Single-Cell V(D)J BCR Enrichment Kit (10x Genomics, CA, USA).


title: KO saline BM, rep1


title: 592micNC-1


title: HEK293_VPRP_NonTarget_2_RNA

value: dCas9-VPRP +  non-target guide


title: spike-specific B cells, B cells, D22,scRNAseq,VDJ

description:
BCR RNA
10x Genomics


title: RNAseq-M11GFP_2


title: spike-specific B cells ,B cells, D15,scRNAseq,VDJ

description:
BCR RNA
10x Genomics


title: WT G-CSF BM, rep3

value: G-CSF


title: RNAseq-M11GFP_1


title: HEK293_VPRP_NonTarget_1_RNA


title: 592mic-1

value: transfected with miR-592 mimics


title: WT G-CSF BM, rep2


title: WT G-CSF BM, rep1


title: spike-specific B cells, B cells, D31,scRNAseq,GEX

description:
total mRNA
10x Genomics


title: RNAseq-E0771GFP-ZBTB18OE_iTGFBR2-vehicle_3

source_name: E0771 cells (CH3 BioSystems cat. #94A001)

value: E0771GFP cells (ZBTB18 overexpression + doxycycline-inducible TGFBR2 overexpression + treatment with doxycycline and vehicle)


title: RNAseq-E0771GFP-ZBTB18OE_iTGFBR2-vehicle_2

value: ZBTB18 overexpression + doxycycline-inducible TGFBR2 overexpression + treatment with doxycycline and vehicle


title: HEK293_WT_2_RNA

value: No treatment


title: HEK293_WT_1_RNA


title: WT saline BM, rep3

value: WT


title: RNAseq-E0771GFP-ZBTB18OE_iTGFBR2-TGFbeta1_3

value: E0771GFP cells (ZBTB18 overexpression + doxycycline-inducible TGFBR2 overexpression + treatment with doxycycline and TGF-beta1)


title: spike-specific B cells, B cells, D22,scRNAseq,GEX

description:
total mRNA
10x Genomics


title: WT saline BM, rep4


title: HEK293_p300_D1399Y_sgHBB_2_RNA

value: dCas9-p300 (D1399Y) + sgHBB


title: HEK293_p300_D1399Y_sgHBB_1_RNA


title: WT saline BM, rep2


title: spike-specific B cells, B cells, D14,scRNAseq,GEX

description:
total mRNA
10x Genomics


title: RNAseq-E0771GFP-ZBTB18OE_iTGFBR2-TGFbeta1_2

value: ZBTB18 overexpression + doxycycline-inducible TGFBR2 overexpression + treatment with doxycycline and TGF-beta1


title: RNAseq-E0771GFP-ZBTB18OE_iTGFBR2-TGFbeta1_1


title: WT saline BM, rep1

value: BM


title: HEK293_p300_sgHBB_1_RNA

value: dCas9-p300 + sgHBB


title: spike-specific B cells, B cells, D14,scRNAseq,VDJ

description:
BCR RNA
10x Genomics


title: RNAseq-E0771GFP-ZBTB18OE_3

value: E0771GFP cells (ZBTB18 overexpression)

value: ZBTB18 overexpression


title: EBNA3C-HT 4C-seq AICDA 3C Off Replicate 1

data_processing:
Library strategy: 4c-seq
Reads were mapped with Bowtie2 with parameters (-N 0 -5 0).
Self ligating and undigested fragments were removed from the analysis.
Reads were analyzed with the 4Cker R package to identify regions of differential interactions

source_name: EBNA3C-HT Lymphoblastoid Cell Lines

growth_protocol: EBNA3C-HT lymphoblastoid Cell Lines were grown in RPMI supplemented with 1% L-glutamate, 1% Pen/Strep and 10% FBS.

extract_protocol: Cells were treated with 1% formaldehyde to crosslink, and the nuclei were isolated via resuspension in lysis buffer (500 μl 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630 and 50 μl protease inhibitors). Then, the nuclei were washed with 1× NEBuffer2 (New England Biolabs) and treated with 0.3% SDS at 65 °C. HindIII digestion was performed at 37 °C overnight, and then, a proximity ligation was performed at 4 °C for 24 h. After reverse cross-linking with a Proteinase K (Ambion, USA) treatment, the DNA was purified using a phenol–chloroform (Solarbio) extraction with ethanol precipitation. The second digestion step was performed using DpnII overnight. Then, we performed a second ligation and ethanol precipitation to extract the DNA. The DNA was finally purified using a QIAquick PCR purification kit (QIAGEN, Germany) according to the manufacturer’s protocol. After the PCR reaction, we purified the 4C library using AMPure beads (Beckman, Germany). Libraries were sequenced on the Illumina HiSeq2500 sequencer.

value: Lymphoblastoid Cell Lines

value: EBNA3C-HT Lymphoblastoid Cell Lines


title: HEK293_VPR_sgHBB_2_RNA

value: dCas9-VPR + sgHBB


title: EBNA3C-HT 4C-seq AICDA 3C Off Replicate 2


title: Wild-type, CD45.1+  P3/P4 macrophages 2007

first: Izabel

last: Patik

state: Massachusetts

address: 300 Longwood Ave

department: Division of Gastroenterology, Hepatology, and Nutrition

institute: Boston Children's Hospital

description:
WTmix 3
AN11

data_processing:
Reads were aligned to the mm10 mouse genome assembly and gene counts were quantified using STAR (v2.7.3a).
Gene counts were normalized using the trimmed mean of M-values (TMM) approach in edgeR (v 3.15)
Since all mice in this study were Cdcs1 knockouts, we excluded all Cdcs1 proximal genes, which might have escaped the targeted knockout. Specifically, we ignored genes found within 1Mb up and downstream of the expanded Cdcs1 locus, as defined by Bleich et al. (2010) [PMID: 19856416]
Since wildtype (WT) mice were male and mice of all other groups were female, we excluded sex dimorphic genes in all comparisons involving WT. Specifically, we ignored genes found to be sexually dimorphic in at least three cell types as reported by Lu and Mar (2020) [PMID: 33153500]
Assembly: mm10
Supplementary files format and content: log-TMM normalized gene-level expression, ignoring genes found to be sexually dimorphic in at least three cell types as reported by Lu and Mar (2020) [PMID: 33153500], and ignoring genes found within 1Mb up and downstream of the expanded Cdcs1 locus, as defined by Bleich et al. (2010) [PMID: 19856416]

source_name: sorted Ly6C- colonic lamina propria macrophages

growth_protocol: Mice were kept under SPF conditions to induce sponteneious colitis development.

extract_protocol:
Animals were euthanized by CO2 and colonic lamina propria cells were isolated. Briefly, colons and cecums were dissected and epithelial cells were stripped by 10mM EDTA in HDMI for 30 min at 37°C. Remaining tissue was transferred to 50 ml conical tubes minced and digested using Collagenase VIII (Sigma-Aldrich, C2139-5G) in HBSS (with Ca /Mg) for 30-45 min at 37°C. Cells were then filtered through 70µm cell strainer and washed twice in 1xPBS. Viability and cell numbers were determined using an automated cell counter (TECAN) and stained with the antibody cocktail and analyzed using a LSRFortessa (BioLegend, San Diego, CA, USA ). 5000-25000 P3/P4 LP macrophages from bone marrow chimeras 8 weeks following reconstitution were FACS-sorted (gated on: CD103-, Ly6G-, CD11b+, CD11cint, CD64+, Ly6C-, CD45.1+ or CD45.2+) directly into RLT buffer (Qiagen) on a FACS Aria II (BD Life Sciences) and mRNA was extracted using the RNeasy Micro kit (Qiagen).
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7. The finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced on an Illumina NovaSeq 6000 targeting 40 million 50bp read pairs per library at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: Recipient mice were irradiated (Gamma Cell 40, 137Cs) with a split dose of 1200 Rads 4h apart. The following day bone marrow was harvested from the hind leg bones of donor mice by flushing with sterile PBS. Bone marrow cells were counted and 4 x 106 cells/mouse were injected into irradiated recipients via retro-orbital injections in 150 µl sterile PBS. Drinking water was supplemented with trimethoprim/sulfamethoxazole (Aurobindo Pharmaceuticals) in their drinking water for 3 weeks (240 mg/ 250 ml water). Animals were euthanized 8 weeks following reconstitution.

tag: received bone_marrow's_genotype

value: 1:1 mix of Cdcs1, wild-type and Il10ra-/-


title: RNAseq-E0771GFP-ZBTB18OE_iTGFBR2-vehicle_1

tag: cell type

value: breast cancer cells


title: Il10ra-/-, CD45.2+ P3/P4 macrophages 2007

description:
KOmix 3
AN12

value: sorted Ly6C- colonic lamina propria macrophages


title: RNAseq-E0771GFP-ZBTB18OE_2


title: EBNA3C-HT 4C-seq AICDA 3C On Replicate 1

tag: tissue


title: RNAseq-E0771GFP-ZBTB18OE_1


title: HEK293_VPRP_sgHBB_2_RNA

data_processing:
For RNA-seq, mapping and quantification was performed by Novogene. Briefly, mapping was performed with STAR v2.5 against hg19 with a mismatch parameter equal to 2. Initial quantification of transcript abundance was performed by HTSeq v0.6.1. We performed differential expression analysis using DESeq2 v1.24.0. MA plots were generated in DESeq2 by contrasting the two conditions using the log fold change shrinkage method.
For ChIP-seq, initial analysis was performed by Active Motif. Reads were aligned to hg19 using the BWA algorithm on default settings and stored in BAM format. Reads were extended in silico at their 3′ ends to a length of 200 bp. The genome was divided into 32-nt bins and fragment density was calculated in each bin. Peak locations were determined using the MACS algorithm with a cutoff of p value of 10-7. Regions were merged across samples for comparison across samples and stored in bigWig files. We imported these bigWig files directly to deepTools to create correlation results and visualization of H3K27Ac about a genomic locus.
Genome_build: hg19

value: dCas9-VPRP + sgHBB


title: Il10ra-/-, CD45.2+ P3/P4 macrophages 2006

description:
KOmix 2
AN10


title: spike-specific B cells ,B cells, D15,scRNAseq,GEX

description:
total mRNA
10x Genomics

value: B cells


title: RNAseq-E0771GFP_3

value: E0771GFP cells


title: Wild-type, CD45.1+  P3/P4 macrophages 2006

description:
WTmix 2
AN9


title: Il10ra-/-, CD45.2+ P3/P4 macrophages 2005

description:
KOmix 1
AN8


title: HEK293_p300_sgHBB_2_RNA


title: HEK293_VPRP_sgHBB_1_RNA


title: EBNA3C-HT 4C-seq CDKN2A 3C Off Replicate 1

description: E3C 4C-seq at CDKN2A

data_processing:
Library strategy: 4c-seq
Reads were mapped with Bowtie2 with parameters (-N 0 -5 0).
Self ligating and undigested fragments were removed from the analysis.
Reads were analyzed with the 4Cker R package to identify regions of differential interactions
genome build: hg19
.bedgraph files mapped for each 4C-seq biological replicate.

treatment_protocol: Cells were treated with 1% formaldehyde to crosslink, and the nuclei were isolated via resuspension in lysis buffer (500 μl 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630 and 50 μl protease inhibitors). Then, the nuclei were washed with 1× NEBuffer2 (New England Biolabs) and treated with 0.3% SDS at 65 °C. HindIII digestion was performed at 37 °C overnight, and then, a proximity ligation was performed at 4 °C for 24 h. After reverse cross-linking with a Proteinase K (Ambion, USA) treatment, the DNA was purified using a phenol–chloroform (Solarbio) extraction with ethanol precipitation. The second digestion step was performed using DpnII overnight. Then, we performed a second ligation and ethanol precipitation to extract the DNA. The DNA was finally purified using a QIAquick PCR purification kit (QIAGEN, Germany) according to the manufacturer’s protocol. After the PCR reaction, we purified the 4C library using AMPure beads (Beckman, Germany). Libraries were sequenced on the Illumina HiSeq2500 sequencer.


title: RNAseq-E0771GFP_2


title: EBNA3C-HT 4C-seq CDKN2A 3C On Replicate 2

description: E3C 4C-seq at CDKN2A


title: Wild-type, CD45.1+  P3/P4 macrophages 2005

description:
WTmix 1
AN7


title: RNAseq-E0771GFP_1


title: UO3.IP

city: Jinzhong

first: Qing

address: Taigu, Shanxi Province, PR China

institute: Shanxi Agricultural university

data_processing:
Cutadapt software (v1.9.3) was used to eliminate the reads containing adaptor contaminants and low quality bases.
HISAT2 software was applied to align clean reads of all libraries to the reference genome of E. tenella
MACS software was used to identify methylated sites on RNAs (peaks),and differentially methylated sites were identified by diffReps
The m6A-enriched motifs were identified with DREME.
Assembly: ETH001 RefSeq GCF_000499545.2
Supplementary files format and content: The xlsx format sheet (named Gene Expression Profiling) showed gene_id,counts of all samples of the gene, normalized counts by edgeR, and annotation of the genes.
Supplementary files format and content: The xlsx format sheet (named Methylated_RNA_sites.mRNA) showed information about methylation sites,methylated RNA,enrichment information,and annotations.
Library strategy: MeRIP-seq

organism: Eimeria tenella

source_name: Unsporulated oocysts

extract_protocol:
Input: Total RNA was extracted from oocysts with TRIzol reagent (Invitrogen Carlsbad, CA, USA).IP:Total RNA was extracted from oocysts with TRIzol reagent (Invitrogen Carlsbad, CA, USA), and then subjected to immunoprecipitation (IP) by using the GenSeq® m6A-IP Kit (Cloudseq Biotech, Inc., Shanghai, China) following the manufacturer’s specifications.
RNA libraries for IP and input samples were constructed with the GenSeq® Low Input Whole RNA Library Prep Kit (Cloudseq Biotech, Inc., Shanghai, China) according to the manufacture’s instructions.

value: SD-01 strain

value: Unsporulated oocysts


title: EBNA3C-HT 4C-seq AICDA 3C On Replicate 2

city: Boston


title: Il10ra-/-, CD45.2+ P3/P4 macrophages 2009

description:
KO 3
AN6

value: Cdcs1, Il10ra-/-


title: RNAseq-E0771GFP-EV_2

value: E0771GFP cells (empty vector)

value: empty vector


title: HEK293_VPR_sgHBB_1_RNA


title: Il10ra-/-, CD45.2+ P3/P4 macrophages 2008

description:
KO 2
AN5


title: UO2.IP


title: UO2.Input


title: EBNA3C-HT 4C-seq CDKN2A 3C Off Replicate 2

description: E3C 4C-seq at CDKN2A


title: RNAseq-E0771GFP-EV_3


title: RNAseq-E0771GFP-EV_1


title: Il10ra-/-, CD45.2+ P3/P4 macrophages 2003

description:
KO 1
AN4


title: GSC3028_shKLHDC8A-2_Replicate2

city: La Jolla

first: Derrick

last: Lee

address: 9500 Gilman Dr

institute: University of California, San Diego

data_processing:
The Fastq files of the RNA-seq data were processed to read quality control by running ‘FastQC’ (Galaxy version 0.72) in Galaxy (usegalaxy.org) and then to remove the adapters by running ‘Trim Galore!’ (Galaxy version 0.4.3.1). The trimmed reads were mapped to human genome 38 by ‘HISAT2’ (Galaxy version 2.1.0+galaxy 4) and the mapped reads were then counted with ‘featureCounts’ (Galaxy version 1.6.3+galaxy 2). The counts were processed to differentially expressed gene analysis with R package ‘DESeq2’ (Version 1.14.1). Volcano plots were generated using GraphPad Prism. Downregulated genes upon EYA2 knockdown were processed to GO analysis (http://geneontology.org/). Pre-ranked genes by fold change were processed to GSEA (Gene Set Enrichment Analysis; Broad institute).
Assembly: hg19
Supplementary files format and content: counts.txt
Supplementary files format and content: Counts of all RNA-seq files including replicates

growth_protocol: Xenografted tumors were dissociated using a papain dissociation system according to the manufacturer’s instructions. Cells were then cultured in Neurobasal medium supplemented with 2% B27, 1% L-glutamine, 1% sodium pyruvate, 1% penicillin/streptomycin, 10 ng/ml basic fibroblast growth factor (bFGF), and 10 ng/ml epidermal growth factor (EGF) for at least 6 hours to recover expression of surface antigens. Because cell surface markers are not uniformly informative for marking GSCs, we utilized a combination of functional criteria to validate GSCs. Both GSCs and DGCs were derived immediately following dissociation or following transient xenograft passage in immunocompromised NSG mice using prospective sorting followed by assays to confirm stem cell marker expression, sphere formation, and secondary tumor initiation. Cells were labeled with CD133/2(293C)-Allophycocyanin (APC) antibody kit (Miltenyi Biotec, 130098826), and the CD133+ cells were sorted and analyzed by flow cytometry. The sorted CD133+ cells were cultured in NBM-B27 medium containing 20 ng/ml of both epidermal growth factor (EGF) (R&D system, 236-EG-01M) and recombinant human FGF basic (FGF) (R&D system, 4114-TC-01M) for a short period before treatment and analyzed. GSC phenotypes were validated by expression of stem cell markers (SOX2 and OLIG2) and functional assays of self-renewal. Corresponding differentiated glioma cells were obtained by culturing the GSCs in DMEM medium supplemented with 10% FBS for at least 2 weeks.

extract_protocol:
Totoal RNA from GSCs transduced with shCONT or shKLHDC8A were collected with miRNeasy mini kit (Qiagen) and processed to library construction with TruSeq RNA library Prep Kit (illumine).
Totoal RNA from GSCs transduced with shCONT or shKLHDC8A were collected with miRNeasy mini kit (Qiagen) and processed to library construction with TruSeq RNA library Prep Kit (illumine).

treatment_protocol: Lentiviral clones expressing two or three non-overlapping shRNAs directed against human KLHDC8A (TRCN0000138219 and TRCN00000138761), or a non-targeting control shRNA were obtained from Sigma-Aldrich. 293FT cells were used to generate lentiviral particles through co-transfection of the packaging vectors pCMV-dR8.2 dvpr and pCI-VSVG using a standard calcium phosphate transfection method in DMEM plus 10% FBS. 12 hours later after transfection, medium was changed to neurobasal complete medium. Neurobasal complete medium containing lentiviral particles was collected by filtering with 0.45uM filter for immediate use or stock in -80°C.

value: Glioblatoma stem cells

tag: genotype

value: KLHDC8A knockdown


title: GSC3028_shKLHDC8A-2_Replicate1


title: Wild-type, CD45.1+  P3/P4 macrophages  2004

description:
WT 3
AN3

value: Cdcs1, wild-type


title: RNA-seq Ikzf1 rep4

city: Montreal

first: Awais

last: Javed

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

description: Raw salmon counts/DESeq2

data_processing:
Raw CUT&RUN fastq reads were aligned using bowtie2 mm9 genome on Galaxy platform. MACS2 was used for peak calling using FDR 0.5 . Bamcoverage was used to generate bigwig files.
Salmon quant function was used to quantify effective length of transcripts and transcript per million value from RNA-seq raw fastq reads using mm10 transcriptome. Salmon quants output files were used to calculate Log2FC and statistical values using DESeq2 for differential analysis. Annotate DESeq2 package on Galaxy platform was used to annotate gene_ids to symbols.
Genome_build: mm10, mm9
Supplementary_files_format_and_content: Bigwig tracks files for CUT&RUN conditions and bed peak files for scored peaks.
Supplementary_files_format_and_content: Matrix table with Log2FC and FDR values of comparisons between the two conditions.

source_name: Retina

growth_protocol: RNA-seq: P0 CD1 retinas were dissociated using Accutase and transfected using the Amaxa Neural Stem Cell Kit according to the manufacturer’s protocol.  Cells were seeded into 6-well plates coated with PLL/ Laminin, and cultured as previously described (Gomes et al., 2011).  After 9 hr, cells were harvested and dissociated with Accutase followed by FAC-sorting for GFP. Control GFP condition contained 4 x105 cells per biological replicate (n=4) and Ikzf1 condition contained 3 x 105 cells per biological replicate (n=4). CUT&RUN: Whole retinas were dissected and CUT&RUN was performed as previously described (Skene et al., 2018), with a few added modifications. For Ikzf1, CAG-Ikzf1-IRES-GFP electroporated P0 retinal explants were cultured as previously described in Elliott et al. 2008.

extract_protocol:
RNA-seq: rRNA was depleted using Ribo-Zero™ Magnetic Gold Kit for rRNA depletion (Human/Mouse/Rat) (Epicentre for Illumina #MRZG12324) according to manufacturer’s guidelines. CUT&RUN: Extraction of DNA fragments was performed as described in (Skene and Henikoff, 2018) using the Qiagen Nucleotide Romoval Kit.
RNA-seq: . Libraries were diluted and pooled equimolar and then sequenced in pair end 50 cycles (PE50) on a v4 flowcell (Illumina - HiSeq PE Cluster Kit v4 cBot - PE-401-4001) of the Illumina HiSeq 2500 System. CUT&RUN: Libraries were prepared using Manufacturer's protocols using the KAPA HyperPrep Kit (Roche).

treatment_protocol: RNA-seq: Cells were sorted directly into lysis buffer and purified using the RNeasy micro kit from Qiagen. Samples quantity (RNA Integrity Number = RIN) and quality were assessed using the Agilent RNA 6000 Pico Kit (Agilent #5067-1513) on the Bioanalyzer 2100. rRNA was depleted using Ribo-Zero™ Magnetic Gold Kit for rRNA depletion (Human/Mouse/Rat) (Epicentre for Illumina #MRZG12324) according to manufacturer’s guidelines. Library preparations were done using SMARTer® Stranded RNA-Seq Kit (Clontech Laboratories, Inc. #634836 or #634837) according to manufacturer’s guidelines. CUT&RUN: For Ikzf1, 50,000 GFP+ve cells were sorted directly into the buffer with Concanavalin-A beads. For Ikzf4, E14 and P0 retinas, 1,500,000 cells were used for each stage. The entire procedure was done in 200μl PCR tubes. 0.01% digitonin concentration was used and pAG-MNase digestion was performed for 30min on ice.

value: Retinal progenitor cells

tag: condition


title: Wild-type, CD45.1+  P3/P4 macrophages  2002

description:
WT 2
AN2


title: GSC3028_shKLHDC8A-1_Replicate2


title: RNA-seq Ikzf1 rep3

description: Raw salmon counts/DESeq2


title: UO3.Input


title: zebrafish wild-type explant 10hpf

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

data_processing:
Illumina sequencing reads were aligned to the zebrafish mRNA reference genome (GRCz11) using the 10x Genomics CellRanger pipeline (version 3.0.2) with default parameters.
Assembly: GRCz11
Supplementary files format and content: tar compressed  files included filtered_gene_bc_matrices after running CellRanger pipeline

source_name: zebrafish cells

growth_protocol: explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium

extract_protocol: Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 (10x Genomics, PN-1000075) according to the manufacturer’s protocol for 10000 cells recovery.

treatment_protocol: phenol red was injected to one cell of embryonic animal pole at 128 cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage, then, were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 10hpf(corresponding to embryonic developmental stage) separately.

value: AB

value: embryonic cells

tag: age

value: wild type


title: SO3.Input

source_name: Sporulated oocysts

value: Sporulated oocysts