title: fetal lung tissue, Sample109

value: male

value: <7.5 ng cotinine/g placenta


title: MII_WT_rep2

status: Public on May 05 2022

type: SRA

city: Chicago

first: Chuan

last: He

state: IL

address: 929 E 57th Street

department: Chemistry

country: USA

institute: University of Chicago

library_source: transcriptomic

data_processing:
Base-calling was performed using CASAVA.
sequencing data were sent to trimmomatic to remove low quality bases and adaptor sequence contaminants under default parameters except for “–length 50”
Remaining reads were then aligned to the mouse transcriptome annotation based on mm10 assembly using hisat2 aligner (v2.1.0), default parameters were used,except for "-k 30"
reads count were called by featureCounts for each samples
Genome_build: mm10
Supplementary_files_format_and_content: csv; reads count

molecule: total RNA

organism: Mus musculus

source_name: MII

growth_protocol: Cells were maintained in DMEM (Invitrogen) supplemented with 15% FBS, 1% nucleosides (100×),1 mM L-glutamine,1% nonessential amino acid, 0.1 mM 2-mercaptoethanol, 1,000 U/ml LIF, 3 μM CHIR99021 and 1 μM PD0325901 37 °C in 5% CO2. Embryos were cultured in G1 plus medium (Vitrolife) at 37°C under 5% CO2 in air.

extract_protocol:
Embryos at GV, MII and morula stages were transferred to 500 μl Trizol Reagent and then mixed well with 100 μl chloroform added. The mixture was transferred Qiagen MaXtract High Density tubes (129046). After centrifuge, upper and aqueous phase was removed. RNA was precipitated by adding equal volume isopropanol and washing by 75% ethanol. Then purified RNA were analyzed by RT-qPCR or subjected to library generation using SMARTer Stranded Total RNASeq Kit (Takara Bio) following manufacturer’s protocol.
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit v2 (Takara) according to the manufacturer’s protocols.

treatment_protocol:
mESCs cells were cross-linked by adding 1% formaldehyde directly to the media for 10 min at RT. Cross-linking was stopped by adding glycine to a final concentration of 0.125 M and incubating for 5 min at RT. The media was removed and the cells were washed twice with ice-cold PBS.
actinomycin D protocol: Four 6-cm plates of WT and Fto-/- mESCs were seeded and controlled to afford the same number of cells, respectively. After 48 h, actinomycin D was added to 5 μg/mL at 6 h and 0 h before trypsinization collection.
EU protocol: Six 6-cm plates of WT and Fto-/- mESCs were seeded and controlled to afford the same number of cells, respectively. After 48 h, 5-Ethynyl Uridine (EU) was added to 0.5 mM at 60 min, 30 min, and 10 min before trypsinization collection.

tag: cell type

value: MII

tag: genotype

value: wild type

tag: molecule subtype

value: totalRNA


title: nhek-fcabs-untargeted-ctr-5 [rbs-wt2-5]

city: Heidelberg

first: Sylvain

last: Delaunay

address: Im Neuenheimer Feld 280

department: Tumor BIology

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
Untargeted fCABseq (Mitochondrial tRNA) NHEK batch1 rep5
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt

data_processing:
Raw sequencing fastq files were trimmed with ‘TrimGalore !’
Reads were aligned to the GRCh38 (hg38) reference genome using Bismark
mtRNA genomic coordinates for the GRCh38 reference genome were obtained from the ENSEMBL database
Original targeted sequencing reads and their multiple sequence alignments on mtRNAs were extracted from sorted Bismark alignment (bam) files using the R packages RSamtools and GenomicAlignments
Assembly: hg38
Supplementary files format and content: Table Delaunay_MT_TM.meth_Kerats_FaDu.txt is a tab delimited text file which contains the calculated total number of reads to the mt-tRNA methionine and the number of Cytosine in position 34 of the targeted tRNA.
Supplementary files format and content: Table Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt is tab delimited text and contains the calculated methylation levels of Cs and coverage on the mitochondrial genome (fragments >20nt)

organism: Homo sapiens

source_name: NHEK

growth_protocol: NHEK cells were maintained in KSFM medium with antibiotics, FaDu cells were maintained in EMEM madium supplement with fetal bovin serum albumin (FBS) 10% with antibiotics, in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted with Trizol kit, according to manufacturers' protocol. tRNA were isolated using Mirvana kit.
for the untargeted samples, the library was created with the Il TruSeq Small RNA kit. For the targeted apporach, the NEBNext Ultra II DNA library prep kit was used.

tag: cell line

value: NHEK

value: Keratinocyte

value: WT

tag: sample type

value: Untargeted fCABseq


title: GV_KO_rep2

description: count.gene.GV.csv

source_name: GV

value: GV

value: Fto Knockout


title: nhek-fcabs-untargeted-ctr-3 [rbs-wt2-3]

description:
Untargeted fCABseq (Mitochondrial tRNA) NHEK batch1 rep3
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt


title: COV014, small RNA

city: Xian

first: chengsheng

last: zhang

state: Shaanxi

address: 277 West Yanta Road, Xi'an, Shaanxi, P.R.China

department: precision medicine center

country: China

institute: First Affiliated Hospital of Xi 'an Jiaotong University

data_processing:
Raw sequencing data was firstly filtered by fastx_toolkit (version: 0.0.13.2, http://hannonlab.cshl.edu/fastx_toolkit/) for discarding the low-quality reads and adaptor sequences were trimmed by cutadapt (version: 1.15) (version: 1.15)
Clean Reads were further treated to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with 100% sequence identity were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-cluster.
Then, the reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA), to remove common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18-26 nucleotide were mapped to human precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’and 5’ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to human mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known human precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p- derived miRNA candidates. For novel miRNAs, the criterion is that the total expression level in 233 samples were >100.The unmapped sequences were BLASTed against the human genomes (ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/), and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi).  The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (<=12); (2) number of base pairs in the stem region of the predicted hairpin (>=16); (3) cutoff of free energy (kCal/mol <=﹣15); (4) length of hairpin (up and down stems + terminal loop >=50); (5) length of hairpin loop (<=20); (6) number of nucleotides in one bulge in mature region (<=8); (7) number of biased errors in one bulge in mature region(<=4); (8) number of biased bulges in mature region (<=2); (9) number of errors in mature region (<=7); (10) number of base pairs in the mature region of the predicted hairpin (>=12); (11) percent of mature in stem (>=80).
Student’t test and paired t-test were used to calculate the differentially expressed miRNAs in different compared groups. P<0.05 and fold changes >1.50 or < 0.67 were selected as the significant level. Low expression of miRNAs was excluded.
Genome_build: GRCh38_v96
Supplementary_files_format_and_content: normalized counts

source_name: Peripheral blood

extract_protocol:
The peripheral blood was collected into standard EDTA blood tubes and stored on ice until processed. The time of centrifugation should be as fast as possible. The upper plasma was separated after centrifuged at 2500 rpm with 20 minutes and frozen in the -80 refrigerator for standby procession. After all plasma samples were collected, the samples were randomly divided into three groups, and RNA was extracted within 3 days. The volume of plasma for RNA extraction was 2-3 ml by Norgen Plasma/Serum Circulating and Exosomal RNA Purification Kit (Slurry Format) (Cat. 42800) kit in a biosafety level 2 (BSL 2) laboratory at the department of inspection, east Hospital, people's Hospital of Wuhan University. 3 μL total RNA was used as input for miRNA library preparation by using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Catalog NO. E7300, New England Biolabs) following the manufacturer’s instruction with modification, which labeled the pre-amplified small RNA molecules with unique molecular identifier (UMI)（LC-Bio Technology Co., LTD）. UMI reduces duplication bias in PCR and sequencing steps. The DNA library was purified by using 6 % PAGE gel, quantified by using QubitTM3 fluorometer (Invitrogen™, Cat. No. Q33216) with Qubit™ dsDNA HS Assay Kit (Invitrogen™, Cat. No. Q32854), examined by using Qsep100TM bio-fragment analyzer (Bioptic Inc., Taiwan, China), and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

tag: gender

value: Female

tag: infection

tag: disease symptom

value: Symptomatic

tag: disease state

value: Severe

tag: disease duration

value: Long-term nucleic acid test positive

tag: tissue

value: Peripheral blood


title: COV015, small RNA

value: Male


title: fetal lung tissue, Sample108

city: Aurora

first: Sunita

last: Sharma

address: 13199 East Montview Blvd

department: Medicine-Pulmonary Sciences & Critical Care

institute: University of Colorado Hospital

data_processing:
Trimming for low-quality base calls and adpator sequeiencs was completed using cutadapt v.2.7. FastQC v0.11.8 was applied to each trimmed .fastq file to assess adaptor removal. Then reads were mapped to counts of known miRNAs using miR-MaGiC with reference to the Homo sapiens miRbase v22.1 database with collapsed functional groups (repo verision 7147b7a).
Samples passing quality-control (≥1x10^5 mapped reads, having available phenotypic information, and being within the 7 - 17 week pseudoglandular period) and autosomal miRNAs passing pre-filtering criteria (non-zero counts in at least 25% of samples; passes DESeq2 independent filtering algorithm;and not mapped to X or Y chromosome) were tested for differences by sex.
Using RUV-Seq v1.22.0, we also obtained four RUVr factors representing unmeasured miRNA expression heterogeneity for inclusion in regression models.
Assembly: Homo sapiens miRBase database v22.1
Supplementary files format and content: Matrix table with raw miRNA counts for every miRNA and every sample

source_name: fetal lung tissue

extract_protocol:
Total RNA was extracted from 30mg of homogenized prenatal lung tissue with the miRNeasy Mini Kit per manufacturer instructions.
Samples were block-randomized by age, sex, and smoke exposure status to four batches of miRNA library preparation (Small RNA Sequencing Kit v3 for Illumina Platforms; Bio Scientific) and sequencing (HiSeq2500; Illumina; San Diego, CA, USA).

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

value: female

tag: smokebinary

value: >=7.5 ng cotinine/g placenta

tag: run


title: NB37 (RNA-seq)

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

data_processing:
Demultiplexing of bcl files into .fastq files was performed using cellranger 3.0.1 mkfastq software (10x Genomics) and alignments to the human (GRCh38) genome reference sequences were performed using cellranger count. The reference included all protein coding genes as well as mitochondrial genes for downstream analysis.
Assembly: GRCh38/hg38
Supplementary files format and content: count matrix in csv

source_name: neuroblastoma

extract_protocol:
10X Genomics Single cell 3' gene expression V2
Fresh tissue obtained from surgery was collected in Media 199 (Gibco) supplemented with 2% (v/v) FBS on ice. Single cell suspensions of the tumors were obtained by cutting the tumor in to small pieces (1mm3) followed by enzymatic dissociation for 45 minutes at 37°C with shaking at 120 rpm using Collagenase I, Collagenase II, Collagenase III, Collagenase IV (all at a concentration of 1 mg/ml; Worthington Biochemical) and Dispase (2mg/ml; Thermo Fisher) in the presence of DNAse I solution (Thermo Fisher Scientific; 1:100) and RNase Out (Thermo Fisher; 1:1000). Cells were then resuspended in fetal bovine serum (FBS) with 5% DMSO and cryopreserved in liquid nitrogen.Cryopreserved cells from neuroblastoma samples were thawed and stained with anti-CD235-PE (Biolegend) and Calcein AM (Thermo Fisher) for 30 minutes at 4°C.  Cells were washed twice with Media199 containing 2% FBS followed by DAPI and/or 7AAD staining (1 ug/ml). Flow sorting for live and non-erythroid cells (DAPI/7AAD-negative, Calcein AM-positive, CD235-negative) was performed on a BD FACS Aria III equipped with a 100um nozzle (BD Biosciences, San Jose, CA) instrument.

value: neuroblastoma

tag: risk group

value: Low

tag: tumor type

value: Primary


title: COV012, small RNA

tag: repeated samples

value: COV031, COV042, COV077(dead)


title: fetal lung tissue, Sample106

value: male

value: <7.5 ng cotinine/g placenta


title: GV_WT_rep2

description: count.gene.GV.csv

tag: cell type

tag: genotype

value: wild type

tag: molecule subtype

value: totalRNA


title: FtoKO_60M_rep2

description: count.gene.EU.csv

source_name: mESC

extract_protocol:
Total RNA was purified by TRIzol reagents (Thermo Scientific) and nascent RNA was captured using Click-iT Nascent RNA Capture Kit (Invitrogen) following the manufacturer’s protocols.
Library preparation was performed using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 following the manufacturer’s protocols.

value: mESC

value: Fto Knockout

value: nascent RNA


title: fetal lung tissue, Sample107


title: NB34 (RNA-seq)

tag: age

value: High

value: Recurrence


title: GV_WT_rep1

description: count.gene.GV.csv

value: GV


title: COV016, small RNA

tag: gender

value: Male

tag: infection

tag: disease symptom

value: Symptomatic

value: Severe

value: Peripheral blood


title: NB26 (RNA-seq)

data_processing:
Demultiplexing of bcl files into .fastq files was performed using cellranger 3.0.1 mkfastq software (10x Genomics) and alignments to the human (GRCh38) genome reference sequences were performed using cellranger count. The reference included all protein coding genes as well as mitochondrial genes for downstream analysis.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count matrix in csv

value: Low


title: fetal lung tissue, Sample104


title: COV009, small RNA

tag: disease state

tag: disease duration

value: Short-term nucleic acid test positive

tag: tissue


title: COV011, small RNA


title: NB23 (RNA-seq)

value: Intermediate

value: Primary


title: COV008, small RNA


title: GV_KO_rep1

description: count.gene.GV.csv


title: COV010, small RNA

value: Female

value: Moderate


title: FtoKO_60M_rep1

description: count.gene.EU.csv


title: NB22 (RNA-seq)


title: FtoKO_30M_rep2

description: count.gene.EU.csv


title: COV013, small RNA


title: FtoKO_10M_rep2

description: count.gene.EU.csv


title: NB24 (RNA-seq)


title: fetal lung tissue, Sample105

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

value: female

value: <7.5 ng cotinine/g placenta


title: NB20 (RNA-seq)


title: fetal lung tissue, Sample100

tag: Sex

value: male

tag: smokebinary

value: >=7.5 ng cotinine/g placenta

tag: run


title: FtoKO_10M_rep1

description: count.gene.EU.csv

value: mESC

value: Fto Knockout

value: nascent RNA


title: NB21 (RNA-seq)

tag: risk group

value: High

tag: tumor type


title: COV007, small RNA

value: Male

value: Symptomatic

value: Long-term nucleic acid test positive

tag: repeated samples


title: fetal lung tissue, Sample102


title: fetal lung tissue, Sample103


title: FtoKO_30M_rep1

description: count.gene.EU.csv

tag: cell type

tag: genotype

tag: molecule subtype


title: NB18 (RNA-seq)

tag: age


title: COV004, small RNA

tag: gender

tag: infection

tag: disease symptom

value: Severe

value: Peripheral blood


title: fetal lung tissue, Sample101


title: NB17 (RNA-seq)


title: WT_60M_rep1

description: count.gene.EU.csv

value: wild type


title: COV006, small RNA

tag: disease state

tag: disease duration

value: Short-term nucleic acid test positive

tag: tissue


title: COV002, small RNA


title: NB16 (RNA-seq)

value: Primary


title: COV001, small RNA


title: NB19 (RNA-seq)

value: Low


title: fetal lung tissue, Sample10

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term


title: NB13 (RNA-seq)

value: Recurrence


title: WT_30M_rep1

description: count.gene.EU.csv


title: WT_30M_rep2

description: count.gene.EU.csv


title: COV005, small RNA

value: Female


title: WT_10M_rep1

description: count.gene.EU.csv


title: NB12 (RNA-seq)


title: multi_PYMT_cd11b_lo_myeloid

city: San Francisco

first: Arjun

middle: Arkal

last: Rao

state: CA

address: 505 Parnassus Ave, S-447

department: CoLabs

institute: University of California, San Francisco

description: cd11b-lo-enriched Myeloid sort of spontaneous tumors from a pool of 4 mice

data_processing:
sequencer-generated bcl files were converted to fastqs using the cellranger mkfastq (cellranger version 3.0.2) command with default parameters.
fastq files were aligned to the mouse reference genome (with ENSEMBL v93 annotation) using cellranger count (cellranger version 3.0.2). This step also generated the submitted raw feature-barcode matrices
Genome_build: mm10
Supplementary_files_format_and_content: *raw_feature_bc_matrix.h5: raw count matrix from cellranger in the h5ad format;More information on 10X filetypes at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

molecule: polyA RNA

source_name: mammary ductal epithelium

extract_protocol:
Tumors from different stages were digested with collagenase IV and Dnase I for 30min, cells were filtered and pooled. Cells were stained 20min at 4°C with the antibody mix and myeloid cells were sorted in total or enriched for CD11b+ or CD11b- myeloid cells, according to CD45+CD90.2-B220-NK1.1-Ly6G-CD11b+ or CD11c.
After sorting, all cell preparations were pelleted and resuspended at 1x103cells/ml in 0.04%BSA/PBS and loaded onto the Chromium Controller (10X Genomics). Samples were processed for single-cell encapsulation and cDNA library generation using the Chromium Single Cell 3’v2 Reagent Kits (10X Genomics) according to manufacturer’s protocol. The library was subsequently sequenced on an Illumina HiSeq4000 (Illumina).

tag: mouse model

value: MMTV-PyMT-mCherry-OVA

value: spontaneous

value: mammary tumor


title: HC66, small RNA

value: Healthy control

value: Healthy control-repeated


title: WT_60M_rep2

description: count.gene.EU.csv

value: mESC

value: nascent RNA


title: WT_10M_rep2

description: count.gene.EU.csv


title: fetal lung tissue, Sample1

tag: Sex

value: female

tag: smokebinary

value: <7.5 ng cotinine/g placenta

tag: run


title: multi_PYMT_cd11b_hi_myeloid

description: cd11b-hi-enriched Myeloid sort of spontaneous tumors from a pool of 4 mice

tag: tumor type


title: multi_PYMT_bulk_myeloid

description: Bulk Myeloid sort of spontaneous tumors from a pool of 4 mice


title: NB09 (RNA-seq)

tag: risk group

value: High


title: tissues

city: Seoul

first: Jae-Yol

last: Lim

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Department of Otorhinolaryngology

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
raw base call files were demultiplexed with cellranger (v 5.0.0), bcl2fastq (v2.20.0)
reads were aligned to the GRCh38 genome assembly using cellranger 4.0.0
demultiplexing fastq with VCF was done with singularity 3.7.1 with parameters -q -p 4 -e 100 -f -o -I -k cellranger/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
h5ad files have information about cellular source where they are derived from, either PG, SMG, or SLG.
Cell sources were determined by SNP, in point of the fact that human has different SNPs and all PG, SMG, and SLG samples were derived from different persons.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5ad files are final version after cell clustering.

source_name: salivary gland tissues

growth_protocol: Human salivary gland organoids were embedded in matrigel and cultured for 2 weeks in human salivary gland growth media.

extract_protocol:
Single cell suspension were prepared with TrypLE Express.
Chromium Next GEM Single Cell 3` Reagent Kit was used for library construction

treatment_protocol: Organoids were differentiated for 3 days in differentiation media.

value: mixed tissue sample:human PG, SMG, SLG


title: NB11 (RNA-seq)


title: NB02 (RNA-seq)


title: FtoKO_0h_rep2

description: count.gene.lifetime.csv

extract_protocol:
The entire nuclear fraction was separated and total RNA was purified by TRIzol reagents (Thermo Scientific) followed by rRNA depletion using RiboMinus Eukaryote kit (Thermo Scientific).
Library preparation was performed using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 following the manufacturer’s protocols.

tag: cell type

tag: genotype

value: Fto Knockout

tag: molecule subtype

value: nuclear total RNA


title: organoids

source_name: salivary gland organoids

value: mixed organoid sample:human PG, SMG, SLG


title: HC67, small RNA

tag: age

tag: gender

tag: infection

value: Peripheral blood


title: ortho_PYMT_bulk_myeloid

description: Bulk Myeloid sort of orthotopically injected tumors from a pool of 5 mice

source_name: mammary fat pad

growth_protocol: Cells were cultured at 37°C in DMEM containing 10% FCS/1% penicillin-streptomycin-glutamine. On the day of injection, cells were washed in PBS and 200 000 were injected in the mammary fat pat of female,

value: orthotopically induced


title: COV003, small RNA

value: Female

tag: disease symptom

value: Symptomatic

tag: disease state

value: Severe

tag: repeated samples


title: FtoKO_6h_rep2

description: count.gene.lifetime.csv


title: HC62, small RNA

value: Male

tag: tissue


title: FtoKO_0h_rep1

description: count.gene.lifetime.csv


title: HC61, small RNA

value: Healthy control


title: FtoKO_6h_rep1

description: count.gene.lifetime.csv


title: WT_0h_rep2

description: count.gene.lifetime.csv

value: wild type


title: HC63, small RNA

value: Healthy control-repeated


title: Leaves, Col-0, 30C, DC3000 Rep 1

city: East Lansing

first: Sheng Yang

state: MI - Michigan

address: 612 Wilson Rd.

department: DOE Plant Research Lab

institute: Michigan State University

data_processing:
Raw single-end RNA sequencing reads were preprocessed to remove sequence adapters and low-quality reads using Trimmomatic version 0.32.
Leading and trailing low-quality bases (below quality score 20) were trimmed, and reads with less than 36 bp in length were removed.
Cleaned reads were aligned to the Arabidopsis thaliana TAIR 10 reference genome using STAR version 2.5.2b.
Reads per gene were counted using featureCounts version 1.22.3.
Genome_build: Arabidopsis thaliana TAIR 10
Supplementary_files_format_and_content: comma-delimited text file includes RPKM values for each Sample ...

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Arabidopsis thaliana plants were grown in soil (2:1 “Arabidopsis mix”: perlite) covered with standard Phiferglass mesh for 3-4 weeks at 23°C and 60% relative humidity under a 12 h light/12 h dark regimen (85 ± 10 µmol m-2 s-1).

extract_protocol:
20 to 60 mg of fresh leaf tissues were flash-frozen in liquid nitrogen and ground using a TissueLyser (Qiagen). Plant RNA was extracted using a Qiagen Plant RNeasy Mini Kit following the manufacturer’s protocol, including the recommended on-column DNase I digestion.
Three RNA samples with the best scores (RIN score >= 7) were pooled on two lanes of an Illumina HiSeq 2500 Rapid Run flow cell (v1) and sequenced in a 1x 50-bp single-end format using Rapid SBS reagents.

treatment_protocol: Arabidopsis plants were acclimated at either 23°C (ambient) or 28°C (elevated) for 24h before chemical treatment and/or 48 h before infiltration. Plants were infiltrated with 1 to 2 x 10e6 Colony Forming Units (CFU) mL of Pst DC3000 (OD600=0.0005), as described previously (Huot et al., 2017 Nature Commun). Plants were returned to the growth chamber at the appropriate temperature and 60% relative humidity.

tag: ecotype

value: 4 weeks

tag: treatment

tag: temperature

value: leaves


title: Leaves, Col-0, 30C, DC3000 Rep 3


title: ChIP-seq against CTCF in ES-cells clone with the F-ALL-INV genotype

city: Berlin

first: Rafael

middle: Domínguez

last: Acemel

state: Berlin

address: Hannoversche Str. 28

department: Berlin Institute of Medical Systems Biology (BIMSB)

institute: Max Delbrück Center for Molecular Medicine (MDC)

library_source: genomic

data_processing:
Base calling with standard Illumina Software
Single-end reads were mapped to the same custom reference genomes as specified in the Capture-C section using Bowtie (Langmead et al. 2009, flags -m1 -S --chunkmbs 500). Reads aligning to more than one location were filtered out by bowtie due to the -m1 flag.
Resulting alignments in SAM format were then converted to bam, sorted and deduplicated using Samtools (https://github.com/samtools/samtools).
Then, deduplicated bam files were converted to bed including a 300 base pairs extension and subsequently bedGraph files containing the genome coverage were computed using BEDTools (Quinlan et al. 2010, bamToBed and genomeCoverageBed respectively).
Finally, bedGraph files were converted to bigWig files for visualization in UCSC genome browser (https://genome.ucsc.edu) using UCSC KentUtils (https://github.com/ucscGenomeBrowser/kent).
Genome_build: Custom genome based on the mm9 assembly.
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

source_name: mouse ES-cells

growth_protocol: G4 mESC (George S.H. et al, 2007) were cultured on inactive CD1- feeders using a media containing the following components: ES cell tested fetal calf serum (FCS), 100x non-essential amino acids, 100x glutamine 200nM, 100X Nucleosides, 10mM β-mercaptoethanol, 100x penicillin (5000U/mL)/streptomycin (5000mg/mL).

extract_protocol:
Fixed nuclei were extracted adding 5 mL of ice-cold custom-made lysis buffer containing the following components: 10mM Tris HCl pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, Protease Inhibitor in Milliwater. Extracted nuclei were then collected, snap frozen and stored at -80 °C or further processed using iDeal ChIP for Transcriptional Factors (Diagenode) (Cat. N. C01010055). Chromatin was shared using Diagenode Bioruptor in order to get a fragment size of 200-500 bp. Immunoprecipitation was done using 15-20 mg of chromatin and 1 μg of CTCF Ab (Diagenode:C15410210).
ChIP-seq libraries were prepared using the NEBNext Ultra II Library Prep Kit for Illumina. Library prep was entered with 500pg-1μg of immunoprecipited DNA and processed according to the kit guidelines (NEBNext End Prep, Adaptor Ligation, PCR enrichment of Adaptor-Ligated DNA using NEBNext Multiplex Oligos for Illumina). Clean up and size selection with AMPure beads (NEB). Library was sequenced with single end read of 75 nt.

treatment_protocol: G4 mESC (5.000.000) were 2 times washed with 1X PBS, treated with Trypsin and pelleted for 5 minutes at 1100 rpm at room temperature. Cell pellet was resuspended in 11.7 mL of 10% FCS and successively fixed by adding 325 μL of 37% Formaldehyde (Sigma-Aldrich) (1% fixation) and incubated for 10 minutes at room temperature. To stop the fixation process, the sample was quenched on ice and 1 mL of 1.425M Glycine was added.

value: F-ALL-INV

value: mouse ES-cells

tag: antibody

value: CTCF


title: ChIP-seq against CTCF in ES-cells clone with the R3 genotype


title: ChIP-seq against CTCF in ES-cells clone with the R4 genotype


title: NB01 (RNA-seq)

value: Low

value: Primary


title: HC65, small RNA


title: ChIP-seq against CTCF in ES-cells clone with the R1 genotype


title: Leaves, Col-0, 23C, DC3000 Rep 3


title: WT_6h_rep2

description: count.gene.lifetime.csv

value: mESC

value: nuclear total RNA


title: WT_6h_rep1

description: count.gene.lifetime.csv


title: HC64, small RNA

value: Peripheral blood


title: Leaves, Col-0, 30C, DC3000 Rep 2


title: HC60, small RNA

value: Female


title: ChIP-seq against CTCF in ES-cells clone with the F2 genotype


title: ChIP-seq against CTCF in ES-cells clone with the F-ALL genotype

value: F-ALL


title: HC58, small RNA


title: WT_0h_rep1

description: count.gene.lifetime.csv


title: FtoKO_InputMP_rep2

data_processing:
Base-calling was performed using CASAVA.
sequencing data were sent to trimmomatic to remove low quality bases and adaptor sequence contaminants under default parameters except for “–length 50”
Remaining reads were then aligned to the mouse transcriptome annotation based on mm10 assembly using Bowtie2 with the options ‘ --very-sensitive --no-unal --end-to-end --no-mixed -X 2000’.
Peaks were called for each samples by MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: txt; peaks

extract_protocol:
Chromatin immunoprecipitation was performed using iDeal ChIP-seq kit for Transcription Factors (Diagenode), respectively, following the manufacturer’s protocols. S
Library preparation was performed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocols.

value: Fto Knockout

value: Input

value: cDNA


title: Capture-C in E11.5 distal-limbs from ΔF-all mutant embryos

data_processing:
Base calling with standard Illumina Software
Paired-end reads from all the Capture-C experiments were aligned using bwa mem local aligner (Li et al. 2009) to a custom reference genome encompassing the captured-region (chr1:71-81Mb of the mm9 assembly) with the region corresponding to the baseline DelBs mutation deleted (chr1:76,388,978-77,858,974). There was one exception, the ΔF-all-Inv mutant Capture-C, in which a different version of the genome was used to account for the inverted coordinates (chr1:77,861,422-78,062,382). The rest of chromosomes, including the remaining chr1, were kept in the custom reference genome to be able to distinguish not-uniquely mapped reads.
Then, following the 4DN consortium recommendations, the resulting bam files were parsed with the pairtools suite (https://github.com/mirnylab/pairtools) to produce 4DN format files containing pairwise interactions. Briefly, bam files were parsed using pairtools parse. Then, not-uniquely mapped reads were filtered out using pairtools select (selecting UU, UR and RU pairs). Subsequently, pairs of reads were sorted and duplicated pairs were removed using pairtools sort and pairtools dedup respectively. Finally, dangling-ends were filtered out using a custom python script.
Filtered 4DN formatted pairs of interactions were then used to construct Knight-Ruiz (KR) normalized Hi-C matrices in hic format with Juicer (Durand et al. 2016).
Genome_build: Custom genome based on the mm9 assembly.
Supplementary_files_format_and_content: multiresolution hic files

source_name: E11.5 distal limb buds

growth_protocol: E11.5 mouse limbs were microdissected in 1X PBS and the distal parts of the limb buds were collected and further processed.

extract_protocol:
Fixed nuclei were extracted adding ice-cold custom-made lysis buffer containing the following components: 50mM Tris HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1.15% Triton X-100, 25X Protease Inhibitor in Milliwater. Extracted nuclei were then collected, snap frozen and stored at -80 °C or further processed with the following steps: digestion with DpnII RE, re-ligation of the digested fragments, de-crosslinking and DNA purification (3C fragments).
The 3C library was further processed using SureSelectXT Target Enrichment System for the Illumina Platform (Agilent Technology). 200 ng or 3 μg of sample was shared using Covaris sonicator and the following parameters; duty cycle: 10%, intensity: 5, cycle per burst:200, time: 6 minutes, temperature: 4°C. Shared sample was then treated following the kit guidelines (end repair, dA-tailing, adaptor ligation, PCR enrichment of Adaptor ligated DNA, DNA purification, hybridization and capture). The hybridization was performed using SureSelect XT Custom RNA probes (Cat # 5190-4836) and the capture with Streptavidin-Coated Beads (Invitrogen). PCR enrichment and sample indexing were done following Agilent instructions. Capture libraries were sequenced with 75bp paired-end reads.

treatment_protocol: Embryonic tissue was resuspended in Trypsin, dissociated to make a single-cell-suspension using a cell-strainer and finally pelleted. Tissue pellet was then fixed in a 2% PFA/FCS/PBS solution by incubation at room temperature for 10 minutes while tumbling. To stop the fixation process, the sample was quenched on ice and 1.425M Glycine was added.

value: [delta]F-all

value: distal limb buds


title: HC55, small RNA

value: Healthy control


title: ChIP-seq against CTCF in ES-cells clone with the F1 genotype


title: HC54, small RNA

value: Male


title: HC57, small RNA


title: Leaves, Col-0, 23C, DC3000 Rep 2

value: 4 weeks

value: leaves


title: FtoKO_Mettl3_rep2


title: Leaves, Col-0, 23C, DC3000 Rep 1


title: HC59, small RNA


title: HC56, small RNA


title: FtoKO_PolII_rep2

value: POLII


title: mouse_OM_scSeq

first: Matthew

middle: Joseph

last: Zunitch

address: 150 Harrison Ave

institute: Tufts University

description: Cells from six animals were pooled then divided to generate four single cell transcriptomic libraries, which were mixed in equimolar ratios prior to sequencing. Results were normalized to library depth and aggregated.

data_processing:
Single cell gene expression quantification was performed using 10X Cell Ranger v2.1.1
Alignment of bulk RNAseq reads was performed using STAR v2.5.2 and --quantMode=GeneCounts
Genome_build: hg19 (bulk RNAseq) or mm10 (scRNAseq)
Supplementary_files_format_and_content: Bulk RNAseq: tab-delimited text file containing raw counts per sample. Single cell RNAseq: counts matrix plus barcode and feature information required for constructing a Seurat object.

source_name: mouse olfactory mucosa

extract_protocol:
Olfactory mucosa was dissected from respiratory tissue and underlying bone. Enzymatic digestion with collagenase, hyaluronidase, dispase, and trypsin released the cells. Neurons and sustentacular cells were selected against using surface marker staining and FACS. Library construction proceeded immediately.
Constructed using 10X Genomics Single Cell Gene Expression kit following manufacturer's instructions.

value: olfactory mucosa

tag: strain

value: CD-1 (Charles River #022)

value: 12 weeks

tag: Sex

value: male and female


title: FtoKO_PolII_rep1

value: mESC


title: Leaves, Col-0, 30C, mock Rep 2

value: mock


title: HC53, small RNA

value: Female

value: Peripheral blood


title: FtoKO_Mettl3_rep1

value: Fto Knockout


title: Leaves, Col-0, 30C, mock Rep 1


title: WT_InputMP_rep2

value: wild type

value: Input

value: cDNA


title: ChIP-seq against CTCF in ES-cells clone with the DelBs genotype

value: DelBs

value: mouse ES-cells

value: CTCF


title: FtoKO_InputMP_rep1


title: HC50, small RNA

value: Male

value: Healthy control


title: HC51, small RNA


title: wt_9h_87

city: Barcelona

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

country: Spain

institute: IRB

data_processing:
FastQ files were aligned against the mm10 genome with the STAR software v2.3.0e and default parameters
Aligned BAM files were sorted and indexed using Sambamba v0.5.9
Per-gene counts were generated with featureCounts function from the Rsubread R package
Differential expression was performed with DESeq2 with processing batch as covariate.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized expression matrix (DESeq2 rlog function)

source_name: BMDMs_wild type_9h

growth_protocol: BMDMs were isolated from the femurs of adult mice as previously described (Celada et al. 1996). Bone marrow cells were differentiated for 7 days on bacteria-grade plastic dishes (Nirco, Ref. 140298) in DMEM supplemented with 20% (vol/vol) FBS, penicillin (100 units/ml), streptomycin (100 mg/ml), L-glutamine (5mg/ml) and 20% L-cell conditioned medium as a source of M-CSF; changing its media on day 5 when BMDMs were plated for the experiment. On day 7, media was changed to DMEM containing 10% FBS, penicillin (100 units/ml), streptomycin (100 mg/ml), L-glutamine (5mg/ml).

extract_protocol:
RNA was extracted using Maxwell following manufacturers instructions (Maxwell 16 LEV SimplyRNA Cells Kit, Promega).
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (Cat#E7770), following manufacturer´s instructions and 8 cycles of amplification.

treatment_protocol: BMDMs were left untreated or stimulated with LPS for 1, 3, 6 or 9 h (10 ng/ml, E. coli 0111:B4, Santa Cruz SC-3535)

tag: strain background

value: mixed C57BL/6J and 129

tag: genotype/variation

value: male

tag: biological replicate

tag: cage

value: Bone Marrow Derived Macrophages (BMDMs)

value: stimulated with LPS

tag: time

tag: batch

tag: barcode

value: ATTCCT


title: Leaves, Col-0, 23C, mock Rep 1

tag: age

value: 4 weeks

value: mock

value: leaves


title: HC48, small RNA

tag: gender

tag: infection

tag: disease symptom

tag: disease state

value: Peripheral blood


title: WT_InputMP_rep1

tag: cell type

value: mESC

tag: genotype

value: wild type

tag: molecule subtype


title: HC49, small RNA

tag: tissue


title: wt_6h_87

source_name: BMDMs_wild type_6h

tag: Sex

tag: treatment

value: ACTGAT


title: Leaves, Col-0, 30C, mock Rep 3

tag: ecotype

tag: temperature


title: Leaves, Col-0, 23C, mock Rep 2


title: Leaves, Col-0, 23C, mock Rep 3


title: HC52, small RNA


title: WT_Mettl3_rep2

tag: antibody

value: cDNA


title: HC45, small RNA


title: WT_PolII_rep1

value: POLII


title: WT_PolII_rep2


title: HC46, small RNA


title: HC42, small RNA

value: Female


title: HC43, small RNA


title: HC41, small RNA


title: HC40, small RNA

value: Male


title: HC39, small RNA

value: Healthy control


title: HC44, small RNA


title: ko_9h_55

tag: strain background

value: mixed C57BL/6J and 129

tag: genotype/variation

tag: biological replicate

tag: cage

tag: time

value: TAGCTT


title: wt_3h_87

source_name: BMDMs_wild type_3h

value: male

value: Bone Marrow Derived Macrophages (BMDMs)

tag: batch

tag: barcode

value: GAGTGG


title: wt_9h_69

value: stimulated with LPS

value: GTCCGC


title: wt_1h_87

source_name: BMDMs_wild type_1h

value: CGTACG


title: wt_un_87

source_name: BMDMs_wild type_un

value: none; unstimulated

value: un

value: GTGAAA


title: wt_6h_69

value: wild type

value: CCGTCC


title: wt_1h_69

value: CTTGTA


title: HC38, small RNA

source_name: Peripheral blood

tag: age

tag: gender

tag: infection

tag: disease symptom

tag: disease state

value: Peripheral blood


title: wt_3h_69

tag: Sex

tag: cell type

value: AGTTCC


title: WT_TFInputEY_rep2

value: mESC

tag: genotype

value: Input

tag: molecule subtype

value: cDNA


title: WT_TFInputEY_rep1

tag: antibody


title: FtoKO_YY1_rep2

value: Fto Knockout


title: WT_Mettl3_rep1


title: FtoKO_EP300_rep2


title: FtoKO_TFInputEY_rep1


title: FtoKO_TFInputEY_rep2


title: ko_3h_55

tag: strain background

value: mixed C57BL/6J and 129

value: male

value: Bone Marrow Derived Macrophages (BMDMs)

tag: treatment

value: GATCAG


title: FtoKO_EP300_rep1


title: HC36, small RNA

value: Female

value: Healthy control

tag: tissue


title: HC37, small RNA


title: ko_6h_55

tag: genotype/variation

tag: biological replicate

tag: cage

value: stimulated with LPS

value: ACTTGA


title: WT_EP300_rep2

value: wild type


title: wt_un_69

value: none; unstimulated

tag: time

value: un

tag: batch

tag: barcode

value: GGCTAC


title: FtoKO_YY1_rep1


title: Enza_rep3

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

country: France

institute: Centre de recherche en transplantation et immunologie

data_processing:
read quality control (fastp)
read mapping (STAR)
expression quantification (RsubRead
Normalization of expression (DESeq2)
Differential expression (DESeq2)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: count files of raw expression per gene

growth_protocol: 3.75 x 105 LAPC4 cells/well in 6-well plate were plated for 48 h in RPMI medium, supplemented with 10%FCS and 1nM DHT.

extract_protocol:
RNA was extracted using innuPREP RNA mini Kit 2.0 (Analytic Jena, Berlin, Germany). 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: Cells were treated with vehicle (DMSO), BAG1L inhibitor (A4B17) (5 µM) or AR inhibitor (Enzalutamide) (5 µM) for 16 h.

tag: cell line

value: prostate cancer cells

value: Enza


title: ko_1h_55

value: GCCAAT


title: Enza_rep2


title: HC35, small RNA

tag: age

tag: gender

tag: infection

tag: disease symptom

value: Peripheral blood


title: WT_YY1_rep2

tag: cell type

value: mESC

tag: genotype

value: cDNA


title: WT_YY1_rep1

tag: antibody

tag: molecule subtype


title: WT_EP300_rep1


title: HC34, small RNA

tag: disease state


title: ko_9h_02

tag: strain background

value: mixed C57BL/6J and 129

tag: Sex

value: male

tag: treatment

value: ACAGTG


title: A4B17_rep3


title: Enza_rep1


title: ko_un_55

tag: genotype/variation

tag: biological replicate

tag: cage

value: Bone Marrow Derived Macrophages (BMDMs)

value: CAGATC


title: FtoKO_Input_rep2

extract_protocol:
Chromatin immunoprecipitation was performed using iDeal ChIP-seq kit for Histone marks (Diagenode), following the manufacturer’s protocols.
Library preparation was performed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocols.

value: Fto Knockout

value: Input


title: A4B17_rep2


title: HC33, small RNA

value: Female

value: Healthy control

tag: tissue


title: FtoKO_Input_rep1


title: ko_un_02

value: none; unstimulated

tag: time

value: un

tag: batch

tag: barcode

value: ATCACG


title: HC30, small RNA

tag: age

tag: gender

tag: infection


title: HC31, small RNA

value: Male

tag: disease symptom


title: HC32, small RNA


title: HC29, small RNA


title: Vehicle_rep3

tag: cell line

tag: cell type

value: prostate cancer cells

value: Vehicle Control


title: Vehicle_rep2


title: ko_1h_02

value: stimulated with LPS

value: CGATGT


title: FtoKO_H3K9me3_rep1

value: mESC

tag: genotype

tag: antibody

tag: molecule subtype

value: cDNA


title: FtoKO_H3K4me3_rep2


title: HC28, small RNA

tag: disease state

value: Peripheral blood


title: wt_9h_88

tag: strain background

value: mixed C57BL/6J and 129

tag: genotype/variation

value: wild type

tag: Sex

value: male

value: Bone Marrow Derived Macrophages (BMDMs)

tag: treatment

value: ATTCCT


title: FtoKO_H3K4me3_rep1

value: Fto Knockout


title: wt_6h_88

tag: biological replicate

tag: cage

tag: time

value: ACTGAT


title: ko_3h_02

tag: batch

tag: barcode

value: TTAGGC


title: Vehicle_rep1


title: ko_6h_02

value: TGACCA


title: HC27, small RNA

tag: age

tag: gender

value: Female

tag: infection

value: Healthy control

tag: tissue


title: A4B17_rep1

tag: cell line

tag: cell type

value: prostate cancer cells


title: FtoKO_H3K4me1_rep2

tag: genotype

tag: antibody

tag: molecule subtype


title: FtoKO_H3K9me3_rep2


title: FtoKO_H3K27ac_rep2


title: HTS-STB06

city: Beijing

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
The paired-end reads Smart-seq2 data was processed using the standard pipeline of Drop-seq_tools-2.0.0 (http://mccarrolllab.com/dropseq/) with modifications.
For read2, bases 1 to 8 were tagged with cell-barcode “XC,”and bases 9 to 16 were tagged with UMI “XM”.
Read1 was trimmed at the 5' end to remove adaptor and TSO sequence, and the 3' end was trimmed to remove poly(A) sequences of length 6 or more and then aligned to hg38 genome reference using STAR aligner.
Gene expression matrix for each cell was then generated with DigitalExpression command.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: trophoblast cells

growth_protocol: hTSCs were cultured in hTSCs medium (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS,  0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 1.5 mg/ml L-ascorbic acid, 50 ng/ml EGF, 2 mM CHIR99021, 0.5 mM A83-01, 1 mM SB431542, 0.8 mM VPA and 5 mM Y27632)

extract_protocol:
Cells in the Petri dish were incubated with TrypLE Express reagent for 10-15 min at 37°C, and dissociated into single cells. Single cells were randomly picked with a mouth pipette in 0.1% BSA and then transferred to 2.5 μl lysis buffer.
The linearized RNA molecules were releasein a thermocycler at 72 °C for 3 min at first. Then, transfer the reactions immediately on ice. Add 2.85 µl RT mixture into every reaction with component as SuperScript II reverse transcriptase, RNase Inhibitor, 5× Superscript II first-strand buffer, dithiothreitol (DTT), betaine, MgCl2, and template switch oligo (TSO) primer. Spin down the 5.4 µl samples in the thermocycler at 25 °C for 5 min, 42 °C for 60 min, 50 °C for 30 min, and then 70 °C for 10 min, 4 °C hold. Prepare 7.5 µl PCR mixture (6.25 μL 2× KAPA HiFi HotStart ReadyMix, ISPCR oligo, and 3′ Anchored oligo) to add in every tube reaction, and amplify samples for 19 cycles. Pool together samples with different barcodes (up to 96 barcodes) and purify DNA. Then prepare the second round of amplification with bio-tinylated index primer and ISPCR oligo for an additional five cycles. Subsequently, purify the biotinylated cDNAs further with 0.8× Ampure XP beads and elute cDNA in 50 µl EB. Next, shear the cDNAs into approximately 300-bp fragments with sonicator.Enrich the cDNA fragments  by Dynabeads® MyOneTM Streptavi- din C1. Libraries were prepared with KAPA Hyper Prep Kits. Use the NEB U-shaped adapter for ligation. Finally, amplify the adapter-ligated fragments using an Illumina QP2 primer and a short universal primer for 9 cycles.

treatment_protocol: STB were cultured in STB medium (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 2.5 mM Y27632, 2 mM forskolin, and 4% KSR)

value: STB

tag: cell treated

value: Cells cultured in STB medium were collected on in vitro day 6

tag: Stage


title: FtoKO_H3K27ac_rep1

value: mESC


title: HTS-STB03

value: Cells cultured in STB medium were collected on in vitro day 3


title: ko_9h_62

tag: strain background

tag: genotype/variation

tag: Sex

tag: treatment

value: stimulated with LPS

value: GTCCGC


title: HTS-STB05

value: Cells cultured in STB medium were collected on in vitro day 5


title: HTS-STB04

value: Cells cultured in STB medium were collected on in vitro day 4


title: wt_3h_88

value: mixed C57BL/6J and 129

value: wild type

value: male

tag: biological replicate

tag: cage

value: Bone Marrow Derived Macrophages (BMDMs)

tag: time

tag: batch

value: GAGTGG


title: HC26, small RNA

tag: age

tag: gender

value: Male

tag: infection

tag: disease symptom

tag: disease state

value: Peripheral blood


title: HTS-STB01

tag: cell type

value: Cells cultured in STB medium were collected on in vitro day 1


title: FtoKO_H3K20me3_rep2

tag: genotype

value: Fto Knockout

tag: antibody

tag: molecule subtype

value: cDNA


title: HC25, small RNA

value: Female

value: Healthy control

tag: tissue


title: wt_un_88

tag: strain background

tag: genotype/variation

value: none; unstimulated

value: un

tag: barcode

value: GTGAAA


title: HC24, small RNA


title: wt_1h_88

tag: Sex

tag: biological replicate

tag: treatment

value: stimulated with LPS

value: CGTACG


title: HC21, small RNA


title: FtoKO_H3K20me3_rep1

value: mESC


title: HTS-STB02

value: STB

tag: cell treated

value: Cells cultured in STB medium were collected on in vitro day 2

tag: Stage


title: ko_6h_62

value: mixed C57BL/6J and 129

value: male

tag: cage

value: Bone Marrow Derived Macrophages (BMDMs)

tag: time

tag: batch

value: CCGTCC


title: HTS01

value: TS cells

value: Cells cultured in hTSCs medium


title: FtoKO_H3K4me1_rep1

value: Fto Knockout

value: cDNA


title: ko_1h_62

value: CTTGTA


title: WT_Input_rep1

data_processing:
Base-calling was performed using CASAVA.
sequencing data were sent to trimmomatic to remove low quality bases and adaptor sequence contaminants under default parameters except for “–length 50”
Remaining reads were then aligned to the mouse transcriptome annotation based on mm10 assembly using Bowtie2 with the options ‘ --very-sensitive --no-unal --end-to-end --no-mixed -X 2000’.
Peaks were called for each samples by MACS2.
Genome_build: mm10

value: wild type

value: Input


title: HC23, small RNA

tag: age

tag: gender

value: Male

tag: infection

tag: disease symptom

value: Healthy control

tag: disease state

value: Peripheral blood


title: YF5 scATAC-seq

city: Epalinges

first: Silvia Asuncion

last: Fuertes Marraco

address: Chemin des Boveresses 155

department: Department of Oncology

country: Switzerland

institute: Centre Hospitalier Universitaire Vaudois (CHUV) - University of Lausanne

data_processing:
The CellRanger -atac v1.2.0 was used for primary analysis of the scATACseq data.
Raw base call (BCL) files were converted to FASTQ files and filtered reads were aligned to the human GRCh38 reference genome.
Libraries were merged using CellRanger -atac aggr
Transposase cut sites in each cell were quantified using barcoded UMIs and 10x cell barcode sequences.
Count matrix for accessible chromatin peaks was generated for downstream analysis using the R package Signac (v0.2.4).
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file documenting single cell barcodes and QC information; tsv file for cell barcodes documenting  source  library and cell type; mtx file for peak x cell matrix; tsv file documenting accessible chromatin fragments; h5 file documenting open chromatin peak x cell matrix; and bed file for open chromatin peak regions generated from CellRanger -atac primary analysis of the raw sequencing data.

source_name: CD8 T cells

extract_protocol:
Nuclei extraction from sorted cells with lysis buffer (10 mM Tris-HCl (pH 7.4), 5 mM MgCl2, 5 mM NaCl, 1% BSA, 0.1% Tween-20, 0.1% NP-40, 0.01 % Digitonin. Wash with buffer (10 mM Tris-HCl (pH 7.4), 5 mM MgCl2, 5 mM NaCl, 1% BSA, 0.1% Tween-20) then wash with Nuclei buffer (10x Genomics), and resuspension in Nuclei buffer (10x Genomics)
Loading was setup to target the recovery of 5'000 nuclei. The library preparation was performed using the Chromium Single Cell ATAC kit (v1.0 Chemistry) strictly following the 10X guidelines (CG000168, revB) running 12 cycles for the GEM incubation step (linear amplification) and  12 PCR cycles for the sample index PCR step.

treatment_protocol: Not applicable; total CD8 T cells were enriched (StemCell negative enrichment) from frozen PBMC and sorted for CD8 T cell populations by flow cytometry

tag: tissue

tag: cell type

value: CD8 T cells


title: YF4 scATAC-seq


title: HC20, small RNA

extract_protocol:
The peripheral blood was collected into standard EDTA blood tubes and stored on ice until processed. The time of centrifugation should be as fast as possible. The upper plasma was separated after centrifuged at 2500 rpm with 20 minutes and frozen in the -80 refrigerator for standby procession. After all plasma samples were collected, the samples were randomly divided into three groups, and RNA was extracted within 3 days. The volume of plasma for RNA extraction was 2-3 ml by Norgen Plasma/Serum Circulating and Exosomal RNA Purification Kit (Slurry Format) (Cat. 42800) kit in a biosafety level 2 (BSL 2) laboratory at the department of inspection, east Hospital, people's Hospital of Wuhan University. 3 μL total RNA was used as input for miRNA library preparation by using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Catalog NO. E7300, New England Biolabs) following the manufacturer’s instruction with modification, which labeled the pre-amplified small RNA molecules with unique molecular identifier (UMI)（LC-Bio Technology Co., LTD）. UMI reduces duplication bias in PCR and sequencing steps. The DNA library was purified by using 6 % PAGE gel, quantified by using QubitTM3 fluorometer (Invitrogen™, Cat. No. Q33216) with Qubit™ dsDNA HS Assay Kit (Invitrogen™, Cat. No. Q32854), examined by using Qsep100TM bio-fragment analyzer (Bioptic Inc., Taiwan, China), and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: ko_un_62

tag: strain background

tag: genotype/variation

value: none; unstimulated

value: un

value: GGCTAC


title: HC22, small RNA


title: HC19, small RNA


title: WT_H3K9me3_rep2

source_name: mESC

value: mESC

tag: genotype

tag: antibody

tag: molecule subtype


title: YF3 scATAC-seq


title: ko_3h_62

value: mixed C57BL/6J and 129

tag: Sex

value: male

tag: biological replicate

value: Bone Marrow Derived Macrophages (BMDMs)

tag: treatment

value: stimulated with LPS

tag: barcode

value: AGTTCC


title: HC18, small RNA


title: WT_Input_rep2

value: cDNA


title: wt_9h_25

tag: cage

tag: time

tag: batch

value: TAGCTT


title: wt_6h_25

value: wild type

value: GATCAG


title: WT_H3K9me3_rep1


title: HC17, small RNA

tag: age

tag: gender

value: Male

tag: infection


title: wt_3h_25

value: ACTTGA


title: HC16, small RNA

tag: disease symptom

value: Healthy control

tag: disease state

tag: tissue

value: Peripheral blood


title: wt_1h_25

tag: strain background

tag: genotype/variation

tag: cell type

value: CAGATC


title: WT_H3K4me3_rep1

tag: genotype

tag: antibody

tag: molecule subtype


title: WT_H3K4me1_rep2


title: WT_H3K4me3_rep2


title: wt_un_25

tag: Sex

tag: biological replicate

tag: treatment

value: none; unstimulated

value: un

value: GCCAAT


title: WT_H3K4me1_rep1

value: mESC


title: HC13, small RNA

value: Female

tag: repeated samples


title: organoid_FH535_3

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

institute: Peking University

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling
Paired-end sequencing data were first applied to a quality control pipeline to remove low quality and adapter-contaminated reads. Then, the cleaned reads were mapped with TopHat and quantified with cuffquant (Trapnell et al., 2009). By running cuffnorm software, we obtained an FPKM (fragments per kilobase of transcript per million mapped reads) expression matrix, and genes with average expression levels of less than 1 were filtered.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19

source_name: tumor derived organoid, treated with FH535

extract_protocol: Population cell RNA was extracted using the RNeasy Mini Kit (Qiagen). Approximately –ng of RNA was then used to perform library construction. Following the instruction that the NEBNest® poly(A) mRNA Magnetic Isolation Module kit (NEB, E7490L) provided, the prepared libraries were sequenced on an Illumina HiSeq 4000 system.

tag: patient diagnosis

value: colorectal cancer

value: tumor derived organoid


title: organoid_FH535_2


title: WT_H3K27ac_rep2


title: ko_9h_03

value: mixed C57BL/6J and 129

value: male

tag: cage

value: Bone Marrow Derived Macrophages (BMDMs)

value: stimulated with LPS

tag: time

tag: batch

tag: barcode

value: ACAGTG


title: ko_3h_03

value: TTAGGC


title: HC12, small RNA

data_processing:
Raw sequencing data was firstly filtered by fastx_toolkit (version: 0.0.13.2, http://hannonlab.cshl.edu/fastx_toolkit/) for discarding the low-quality reads and adaptor sequences were trimmed by cutadapt (version: 1.15) (version: 1.15)
Clean Reads were further treated to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with 100% sequence identity were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-cluster.
Then, the reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA), to remove common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18-26 nucleotide were mapped to human precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’and 5’ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to human mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known human precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p- derived miRNA candidates. For novel miRNAs, the criterion is that the total expression level in 233 samples were >100.The unmapped sequences were BLASTed against the human genomes (ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/), and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi).  The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (<=12); (2) number of base pairs in the stem region of the predicted hairpin (>=16); (3) cutoff of free energy (kCal/mol <=﹣15); (4) length of hairpin (up and down stems + terminal loop >=50); (5) length of hairpin loop (<=20); (6) number of nucleotides in one bulge in mature region (<=8); (7) number of biased errors in one bulge in mature region(<=4); (8) number of biased bulges in mature region (<=2); (9) number of errors in mature region (<=7); (10) number of base pairs in the mature region of the predicted hairpin (>=12); (11) percent of mature in stem (>=80).
Student’t test and paired t-test were used to calculate the differentially expressed miRNAs in different compared groups. P<0.05 and fold changes >1.50 or < 0.67 were selected as the significant level. Low expression of miRNAs was excluded.
Genome_build: GRCh38_v96
Supplementary_files_format_and_content: normalized counts

tag: age

tag: gender

value: Male

tag: infection

tag: disease symptom

tag: disease state


title: HC11, small RNA

value: Healthy control

tag: tissue


title: YF2 scATAC-seq

value: Peripheral blood

tag: cell type

value: CD8 T cells


title: ko_6h_03

tag: strain background

tag: genotype/variation

value: TGACCA


title: WT_H3K27ac_rep1

tag: genotype

value: wild type

tag: antibody

tag: molecule subtype

value: cDNA


title: HC15, small RNA

tag: repeated samples


title: HC14, small RNA


title: YF1 scATAC-seq


title: HC10, small RNA


title: ko_1h_03

tag: Sex

tag: biological replicate

tag: cage

tag: treatment

value: CGATGT


title: organoid_DMSO_2

source_name: tumor derived organoid, control

tag: patient diagnosis


title: organoid_DMSO_1


title: HC08, small RNA

tag: age

tag: gender

value: Female


title: WT_H3K20me3_rep2

value: mESC


title: organoid_FH535_1

value: colorectal cancer

value: tumor derived organoid


title: S7-T-rep1

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling
scRNA-Seq:Read 2 was used to abtain the cell barcodes to further split the reads according to the cell IDs(barcode) and the same time recorded the UMI sequences;Read 1 was picked in each cell according to the cell ID in read2 and the UMI information was aligned to it,and then these raw reads were trimmed to remove TSO or polyA sequence;Adaptor contamination and low-quality reads were discarded from the trimmed Read 1 raw data;TopHat(version 2.0.14) with default settings were used for sequence alignment and uniquely mapped reads were kept.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each single cell RNA samples
Supplementary_files_format_and_content: *Info.txt files include the barcode sequence for each cell ID.

source_name: Patient 7 normal tissue in vivo

growth_protocol: Organoid culture was performed as previously described (Chua et al., 2014), with minor modifications to the tissue dissociation protocol to improve cell viability. In brief, crypts from normal tissues were isolated through gently scraping from washed tissues. Then crypts were mixed with Matrigel (Biosciences) and cultured in 24-well plates (50μL Matrigel/well). As for tumor tissues, the supernatant contained cells were first centrifuged at 400g for 5 minutes at 4°C. Then the cell pellet was resuspend with Matrigel and cultured in 24-well plates (50μL Matrigel/well).The composition of normal colonic organoid culture medium:Advanced DMEM/F12 , 100 U/ml penicillin/streptomycin, 2 mM GlutaMAX, 10 mM HEPES, 0.5 μM A83-01 (Tocris), 1x B27 (Invitrogen), 3 μM SB202190 (SIGMA), 10 nM prostaglandin E2(SIGMA), 0.5μg/ml R-spondin(Nuvelo) , 10mM nicotinamide (SIGMA), 1 mM N-acetylcysteine (Sigma) , 10 nM gastrin I (Sigma),50 ng/ml EGF (Invitrogen), 100 ng/ml Noggin (Peprotech), 100 ng/mlWnt-3A(Millipore) .10μM Y-27632(Tocris BioScience) was supplemented to the medium in the first week. Tumor organoid medium contain all of the above without Wnt-3A. Medium were changed every 2 days.

extract_protocol:
Single cells were manually-picked into lysis buffer of single cell RNA-seq carefully. Single cell RNA was released by vortexed for about 45 secs and further incubated at 72℃ for 3 min, which were further proceed to transcription process.
Single cell RNA sequencing protocol: Single cell RNA-seq libraries were prepared using a method developed based on the STRT-seq. The primer designed for transcription was modified: 8bp barcodes was added to label different cells, 8bp UMIs were used to eliminate duplication. After total 19 cycles of PCR amplification, about 300ng of cDNA was acoustic sheared into 300bp. Dynabeads MyOne Streptavidin C1 beads were further used to capture the biotin modified cDNA. Kapa Hyper Prep Kit (Kapa Biosystems) were applied for libraries construction. The libraries were sequenced on Illumina HiSeq 4000.

treatment_protocol: The tumor and adjacent normal colon tissue that derived from biopsies of CRC patients were isolated and dissected into small pieces using surgical scissors separately. After washed by cold PBS at least three times, the tissue was further digested at 37℃ for about 40 to 60 min with 2mg/ml Collagenase/Dispase(Roche). The digested cell suspension was then collected by centrifuging at 800g for 5min and re-suspended. As for the organoid cultures, each cell cluster was picked out and digested in a about 200μl drop of TrypLE Express (Invitrogen) on a 3.5mm dish at 37℃ for 20-30 min, which were prepared for further cell-picking.

tag: patient id

value: Patient 7

value: normal tissue


title: ko_un_03

value: mixed C57BL/6J and 129

value: male

value: Bone Marrow Derived Macrophages (BMDMs)

value: none; unstimulated

tag: time

value: un

tag: batch

tag: barcode

value: ATCACG


title: XCR1-DTR DTx + aPD-L1 (D11_3)

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing: The sequencing data was processed using CellRanger software.

source_name: CD8+, PD-1+ CD8 T cell from spleen

extract_protocol: Not provided

treatment_protocol: B/6 Mice were infected with 2x10^6 IU LCMV clone13 after 2 times CD4 T cell depletion (d-2 and d0) with 300µg GK1.5 antibody. At the chronic infection phase (> d24), splenocytes were isolated and CD8+, PD-1+, Tim-3 low (F7 + C1_2) or  CD8+, PD-1+ (D11_3 + D12_3) cells were sorted using FACS AriaIII. Treated mice were injected i.p. 200µg aPD-L1 antibody (clone 10F.9G2) 2h before cell isolation or  2 times  with 200µg aPD-L1 antibody (clone 10F.9G2) and 500ng DTX before cell isolation. Cells were pooled form 3-4 mice per group.

tag: strain

value: XCR1-DTR (Xcr1tm2(HBEGF/Venus)Ksho)

tag: tissue

value: spleen

value: XCR1-DTR heterozygous

value: DTx + aPD-L1 (96h)


title: HC09, small RNA

tag: infection

tag: disease symptom

value: Healthy control

tag: disease state

value: Peripheral blood


title: organoid_DMSO_3


title: S7-T-O-rep1

source_name: Patient 7 normal derived organoid

value: normal derived organoid


title: SLG_DAM_2

description: Expression_Profile_Organoid.mm10.gene.xlsx

data_processing:
fastq files were aligned to version 108 of mouse reference genome GRCm38 using the HISAT2 aligner.
Results from the alignments were annotated to genes and normalized using the StringTie program.
Differentially expressed genes (³2-fold and £ 0.05 p-value) were identified by DESeq2 in R package.
Differentially expressed genes were clustered with clusterProfiler in R package.
Genome_build: version 108 of mouse reference genome GRCm38
Supplementary_files_format_and_content: excel files include raw read counts, FPKM, and TPM values for each Sample

source_name: salivary gland epithelial cells

growth_protocol: Murine salivary gland organoids were embedded in matrigel and maintained in culture plate for suspension culture and placed in a 5% CO2 37 °C incubator throughout the culture.

extract_protocol:
RNA was isolated using the Trizol (Thermo) and processed as manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit, according to the manufacturer’s instructions.

treatment_protocol: Organoids were maintained in growth media or in differentiation media for 3 days.

tag: background strain

value: sublingual gland organoid

tag: genotype

value: wild-type

value: cultured in differentiation media


title: HC07, small RNA

value: Female


title: veg2.2

city: Valencia

first: Marcos

last: Serra

state: Comunidad Valenciana

address: Carrer de l'Enginyer Fausto Elio

institute: Instituto de Biología Molecular y Celular de Plantas Primo Yúfera (IBMCP) CSIC

data_processing:
For RNA-seq analyses, ribosomal RNA sequences were filtered out using SortMeRNA (Kopylova et al., 2012)
Sequences of adapters were trimmed from the remaining reads using Trimmomatic (Bolger et al., 2014)
The trimmed sequences were then aligned against the Pea transcriptome using STAR (Dobin et al., 2013) and reads were counted with HTSeqCount (Anders et al., 2015)
DESeq2 with default parameters was used to perform differential expression analysis (Love et al., 2014)
Identification of genes with opposite expression patterns was performed by constructing Venn Diagrams with the online tool Venny (Oliveros, 2007-2015). Genes with opposite expression pattern in veg1 and pim samples were visualized in a heatmap created with the tool ClustVis (Metsalu et al., 2015).
Genome_build: PsUniLowCopy database, Ps Cameor database
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Lathyrus oleraceus

growth_protocol: Plants were grown in a greenhouse at 21 ºC day 16 ºC night and under long-day (LD) photoperiod (16h light / 8h darkness). When needed to maintain LD photoperiod conditions natural light was supplemented with supplementary lighting (400W Phillips HDK/400 HPI (R)(N)). Plants were irrigated periodically using Hoagland Nº1 solution supplemented with oligoelements.

extract_protocol:
For RNA-seq experiments, inflorescence apex samples (three biological replicates) from pea wild type, NGB5839 line, and veg1, pim and veg2 mutants plants were collected at floral transition, when the primary stem plant had formed 10 nodes (approximately 4 weeks after germination). Each biological replicate consisted of 3-4 inflorescence apices. Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and treated with DNaseI (Turbo DNA-free kit INVITROGEN; Ref-AM1907) following the manufacturer’s instructions. The quality of the RNA was checked on an Agilent 2100 Bioanalyzer instrument using the RNA6000 nano kit.
Strand-specific RNA libraries were constructed using the TruSeq stranded mRNA kit (Illumina). Libraries were sequenced in a Illumina HiSeq 2500 to produce 50-nucleotide single-end reads.

tag: ecotype

tag: genotype/variation

value: inflorescence apex


title: S7-C-rep3

source_name: Patient 7 tumor tissues in vivo

value: Patient 7

value: colorectal cancer

value: tumor tissue


title: veg2.3


title: veg2.1


title: WT_H3K20me3_rep1

first: Chuan

address: 929 E 57th Street

institute: University of Chicago

tag: cell type

value: mESC

value: wild type

tag: antibody

tag: molecule subtype

value: cDNA


title: HC06, small RNA

tag: age

tag: gender


title: HC05, small RNA


title: pim.3


title: SLG_DAM_1

tag: treatment


title: S7-C-rep2

tag: patient id

tag: patient diagnosis


title: SMG_DAM_2

value: submandibular gland organoid


title: pim.2


title: S7-C-rep1


title: SMG_DAM_1


title: HC04, small RNA

value: Male


title: PG_DAM_2

value: parotid gland organoid


title: pim.1


title: HC03, small RNA

value: Healthy control


title: veg1.3


title: S7-C-O-rep1

source_name: Patient 7 tumor derived organoid

value: tumor derived organoid


title: S7-C-O-rep2


title: S7-C-O-rep3


title: WT DTx + aPD-L1 (D12_3)

tag: strain

value: spleen

value: DTx + aPD-L1 (96h)


title: PG_DAM_1

tag: tissue

value: wild-type


title: veg1.2


title: HC02, small RNA

tag: infection

value: Peripheral blood


title: SMG_GEM_2

value: cultured in growth media


title: S6-T-rep1

source_name: Patient 6 normal tissue in vivo

value: Patient 6

value: normal tissue


title: 22Rv1-shpICln-BR3-Dox+

city: West Lafayette

first: Chang-Deng

last: Hu

state: IN

address: 201. S. University St, HANS 401A

department: Department of Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
fastq files quality were checked by using fastqc and MultiQC tools
raw fastq files were aligned by using STAR tool with paired-end function to UCSC hg38 regerence genome
bam files were filtered by using samtools view function with cutoff of MAPQ10
feature counts were done by using featureCounts tool with MAPQ10 filtered bam files
differential expression analysis was done by using edgeR package
Genome_build: UCSC hg38
Supplementary_files_format_and_content: excel file include logFC, p-value of each comparison and RPKM, raw counts of each sample

source_name: Human castration-resistant prostate cancer cells 22Rv1

growth_protocol: 22Rv1-shPRMT5, -shMEP50, -shpICln cells were cultured in RPMI1640 medium with 10% fetal bovine serum

extract_protocol:
Trizol reagent (Ambion, Carlsbad, CA, USA) was used for total RNA isolation. RNA integrity and purity were confirmed using agarose gel (no degradation or contamination) and Agilent 2100 (RNA integrity number ≥ 6.8).
At least 1 μg of total RNA was used for DNA library preparation with NEB Next Ultra II kit (New England Biolabs, Ipswich, MA, US).

treatment_protocol: 22Rv1-shPRMT5, -shMEP50, -shpICln cells were seeded on 10 cm dishes and Doxycyline (Dox) was applied at the final concentration of 1 µg/mL every 48 hours to establish and maintain the knockdown.

tag: knockdown

value: shpICln

tag: agent

value: Dox +

tag: biological replicates


title: WT.3

value: inflorescence apex


title: veg1.1


title: SMG_GEM_1

tag: background strain

tag: genotype


title: S6-T-O-rep1

source_name: Patient 6 normal derived organoid

value: colorectal cancer

value: normal derived organoid


title: SLG_tissue_2

description: Expression_Profile_Tissue.mm10.gene.xlsx

value: sublingual gland

value: untreated


title: HC01, small RNA

first: chengsheng

address: 277 West Yanta Road, Xi'an, Shaanxi, P.R.China

institute: First Affiliated Hospital of Xi 'an Jiaotong University

value: Female

tag: disease symptom

tag: disease state


title: S6-T-O-2m-rep1

source_name: Patient 6 normal derived organoid cultured for 2 month


title: WT.2

tag: ecotype

tag: genotype/variation


title: 22Rv1-shpICln-BR2-Dox+


title: WT.1


title: SLG_tissue_1


title: 22Rv1-shpICln-BR3-Dox-

value: Dox -


title: 22Rv1-shpICln-BR2-Dox-


title: S6-C-rep3

source_name: Patient 6 tumor tissues in vivo

value: tumor tissue


title: SMG_tissue_2

value: submandibular gland


title: 22Rv1-shpICln-BR1-Dox+


title: S6-C-rep1


title: SMG_tissue_1


title: 22Rv1-shpICln-BR1-Dox-


title: PG_tissue_2

value: parotid gland


title: S6-C-O-rep3

source_name: Patient 6 tumor derived organoid

value: tumor derived organoid


title: 22Rv1-shMEP50-BR3-Dox-


title: MAD4

first: yihan

last: liu

address: No.10 Xitoutiao, Youanmen, Fengtai District

institute: Capital Medical University

data_processing:
Illumina sequencing is used to obtain the original off-machine sequences (Raw Reads), and high-quality sequences (Clean Reads) are obtained through a series of data processing processes such as removing low-quality sequences, removing adapter contamination, and removing rRNA. All subsequent analyses are based on Clean Reads.
Remove the Reads contaminated by the adaptor (the number of bases contaminated by the adaptor in the Reads is greater than 5bp). Remove low-quality reads (bases with a quality value of Q≤19 in Reads account for more than 50% of the total bases). Remove reads with N ratio greater than 5% (for paired-end sequencing, if one-end sequencing does not meet the above requirements, remove the reads at both ends). Reads matching ribosomal RNA were removed.
We used HiSAT2 to compare and analyze the filtered RNA-seq data of each sample with the genome. HiSAT2 is an upgraded version of Tophat2 and HiSAT. It uses HGFM (Hierarchical Graph FM index) as the core retrieval method, which enables faster and more accurate comparison.
When performing novel lncRNA screening, it mainly targets three types of screening: lincRNA, intronic lncRNA, and anti-sense lncRNA. The basic screening conditions are as follows: (1) The length of the transcript is greater than or equal to 200bp, and the number of exons is greater than or equal to 2; (2) The reads coverage of each transcript is calculated, and the transcripts that are less than 5 in all samples are screened out; ( 3) Use gffcompare to compare with the annotation file of the species, and screen out the known mRNA and other non-coding RNAs (rRNA, tRNA, snoRNA, snRNA, etc.) in the species; (4) According to the class_code information in the comparison result ("u ","i","x") to screen potential lincRNAs, intronic lncRNAs, and anti-sense lncRNAs.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: blood serum

growth_protocol: The blood samples were collected from DMC parients, then leaved at room temperature for half an hour. The serum were separated by centrifugation at 3500-4000 rpm for 5-10 minutes

extract_protocol:
The RNA samples were extracted from GC tissues and cells using RNA Isolation TRIzol Reagent. Complementary DNA (cDNA) were synthesized from RNA sample using 5X All-In-One RT MasterMix. The amplification reaction volume was 20 μL and contained 10 μL EvaGreen 2X qPCR MasterMix, 1 μL cDNA, 2 μL amplification primers, and 7 μL ddH2O.
The lncRNA library was constructed by taking 3 μg of total RNA for each sample as the starting amount. Use Ribo-Zero™ GoldKits to remove rRNA in the sample, and select different index tags to build the library according to the instructions of NEB Next Ultra Directional RNA LibraryPrep Kit for Illumina.

value: blood serum

value: diabetic macrovascular disease


title: MAD5


title: MAD3


title: MAD6


title: S6-C-O-rep2

value: Patient 6


title: 22Rv1-shMEP50-BR3-Dox+


title: PG_tissue_1

value: wild-type


title: S6-C-O-rep1


title: wl17m2

city: pittsburgh

first: Huabo

last: Wang

state: Pennsylvania

address: 4401 Penn Avenue

department: Pediatrics

institute: Children hospital of pittsburgh

description: Expression_Browser_Old_Liver_vs _MlxKO_adenoma.xlsx

data_processing:
CLC Genomics Workbench v21.0
Genome_build: Reference sequence = Mus_musculus_ensembl_v80_Sequence Gene track = mus_musculus_refseq_GRCm38.p6_Genes  mRNA track = mus_musculus_refseq_GRCm38.p6_mRNA

source_name: WT Liver 17 months old

extract_protocol:
RNA purification from five representative tumors of each group was performed using Qiagen RNAeasy columns (Qiagen, Inc., Valencia, CA) followed by DNase digestion. Sample integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Foster City, CA).  All samples had RIN values of 8.5-10 prior to any further processing.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: All mice have been treatment by Tamoxifen( 75 mg/kg) ip injection daily for 5 days

value: Liver

value: M

tag: age on tamoxifen ip injection

value: 28 days

tag: feed

tag: age

value: 17 month

value: WT


title: 22Rv1-shMEP50-BR2-Dox+

value: Dox +


title: 22Rv1-shMEP50-BR2-Dox-


title: C6

value: healthy control


title: MAD1


title: wl17f2

tag: gender

value: F


title: 22Rv1-shMEP50-BR1-Dox+


title: S6-C-O-2m-rep1

source_name: Patient 6 tumor derived organoid cultured for 2 month

tag: patient id

tag: patient diagnosis

value: colorectal cancer


title: wl17m1

tag: tissue

tag: strain


title: S6-C-rep2

value: tumor tissue


title: wl17f1


title: C5


title: 22Rv1-shMEP50-BR1-Dox-

tag: knockdown

value: Dox -


title: C4


title: S5-T-O-rep1

source_name: Patient 5 normal derived organoid

value: Patient 5

value: normal derived organoid


title: 22Rv1-shPRMT5-BR3-Dox+

tag: agent


title: MAD2

value: blood serum


title: S6-C-O-2m-rep2

value: tumor derived organoid


title: T9805

source_name: MLXKO Liver Adenoma

value: Alb_CreERT2 + Mlxloxp/loxp

value: 15 month

value: MLXKO


title: T3621

value: Liver


title: C3


title: C2


title: 22Rv1-shPRMT5-BR2-Dox+

tag: biological replicates


title: S5-C-rep3

source_name: Patient 5 tumor tissues in vivo


title: wl17_4282

value: M

value: 28 days


title: T3608

value: 17 month


title: 22Rv1-shPRMT5-BR2-Dox-


title: S5-C-rep1


title: C1


title: S5-T-rep1

source_name: Patient 5 normal tissue in vivo

value: normal tissue


title: S5-C-rep2


title: T3686

value: 14 month


title: S5-C-O-rep3

source_name: Patient 5 tumor derived organoid


title: X5L5239

source_name: MlxKO liver_5_months_old

value: B6.129-Gt(ROSA)26Sor tm1(cre/ERT2)Tyj /J + Mlxloxp/loxp

value: fast for 14 hour

value: MlxKO


title: S5-C-O-rep2

value: colorectal cancer


title: T3606

value: F


title: S5-C-O-rep1

value: Patient 5


title: PAIP1_input_2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of PAIP1 on genome using “ABLIRC” strategy.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

source_name: HeLa cell

growth_protocol: HeLa cells were first lysed in ice-cold lysis buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 10 mM DTT) with 200 U/ml RNase inhibitor (Promega) and a protease inhibitor (Roche) on ice for 5 min

extract_protocol:
The beads were washed 6 times with lysis buffer and then divided into two groups, one for RNA isolation from PAIP1-RNA complexes and another for the western blotting assay for PAIP1 immunoprecipitation.The PAIP1-bound RNAs were isolated from the immunoprecipitate of monoclonal Flag antibody (Sigma), followed by the preparation of the Illumina Truseq pair-end libraries.
The reverse transcription was performed with RT primers harboring 3′ adaptor sequence and random hexamer. The generated cDNAs were PCR-amplified and the 200–500 bp products were purified

treatment_protocol: The supernatant was pre-cleared with 100 μl of DynaBeads protein G (Life Technologies) at 4 °C for 30 min. The pre-cleared supernatant was incubated with DynaBeads protein G conjugated with monoclonal Flag antibody (Sigma) or Input at 4℃ for 30 min.

tag: antibody

value: input


title: PAIP1_IP_1

value: anit-Flag


title: X5L5238

tag: genotype


title: PAIP1_IP_2


title: S4_T_rep2

source_name: Patient 4 normal tissue in vivo

value: Patient 4


title: 22Rv1-shPRMT5-BR3-Dox-

value: Dox -


title: X5L5001


title: S4_T_rep1


title: shPAIP1_2nd

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 16 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Pvalue <= 0.01
Genome_build: GRCH38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: HeLa

growth_protocol: HeLa cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
The HeLa cells were ground into fine powder before RNA extraction. Total RNA was extracted by the hot phenol method. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 10μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.  For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. Illumina HiSeq 4000 was used to collect data from 150-bp pair-end sequencing (ABlife Inc., Wuhan, China).

treatment_protocol: shRNA plasmid transfection of HeLa cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for q-PCR analysis.

tag: treatment

value: shPAIP


title: X5L4299

value: Liver


title: dk5L5649

source_name: DKO_ Liver 5 months old

value: M

value: B6.129-Gt(ROSA)26Sor tm1(cre/ERT2)Tyj /J + Mlxloxp/loxp+Mycloxp/loxp

value: DKO


title: S4_C_O_rep1

source_name: Patient 4 tumor derived organoid

value: tumor derived organoid


title: dk5L5648

value: 28 days


title: S4_C_rep2

source_name: Patient 4 tumor tissues in vivo

value: tumor tissue


title: S4_C_rep1


title: shCtrl_2nd (PAIP1 control)

value: control


title: dk5L5620

value: fast for 14 hour


title: dk5L5647


title: S4_C_O_rep2

value: colorectal cancer


title: S3_T_O_rep1

source_name: Patient 3 normal derived organoid

value: Patient 3

value: normal derived organoid


title: S3_T_rep2

source_name: Patient 3 normal tissue in vivo

value: normal tissue


title: S3_T_rep1


title: PAIP1_input_1

value: input


title: YFP+ (indomethacin treated) replicate 3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

data_processing:
reads were trimmed from adapters using cutadapt 3.4
reads were mapped to the genome assembly GRCm38 from Ensembl using STAR 2.7.3a
Genes were counted using FeatureCounts 2.0.1
Differential expression testing was conducted using DESeq2 library 1.24.0.The normalization and dispersion estimation were performed with DESeq2 using the default parameters; statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between conditions. Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Assembly: mm10 (GRCm38) from Ensembl
Supplementary files format and content: tab-delimited text files from DESeq2 include raw and norm values for each Sample

source_name: Small intestine

extract_protocol: Cells were isolated by FACS from the small intestine and collected in lysis buffer + 1% ß-mercaptoethanol. Librairies were prepared from total mRNA using the SMARTer® Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara Bio) and sequenced using Illumina NextSeq 500/550 High Output kit v2.5.

value: Small intestine

tag: cell type

value: CD45-CD31- Stromal cells

value: YFP+

value: Indomethacin


title: YFP+ (indomethacin treated) replicate 1


title: shCtrl_1st (PAIP1 control)


title: shPAIP1_1st

value: shPAIP


title: YFP+ (indomethacin treated) replicate 2


title: S3_C_rep2

source_name: Patient 3 tumor tissues in vivo


title: S3_T_O_rep2


title: K5L5248

source_name: MycKO Liver 5 months old

value: Liver

value: M

value: B6.129-Gt(ROSA)26Sor tm1(cre/ERT2)Tyj /J + Mycloxp/loxp

value: MycKO


title: dk5L5619

value: B6.129-Gt(ROSA)26Sor tm1(cre/ERT2)Tyj /J + Mlxloxp/loxp+Mycloxp/loxp

value: 28 days

value: DKO


title: YFP- (indomethacin treated) replicate 4

value: YFP-


title: YFP+ (indomethacin treated) replicate 4


title: K5L5218

value: fast for 14 hour


title: K5L5118

value: F


title: YFP- (indomethacin treated) replicate 1


title: YFP- (indomethacin treated) replicate 2


title: S3_C_O_rep2

source_name: Patient 3 tumor derived organoid

value: Patient 3

value: colorectal cancer

value: tumor derived organoid


title: YFP- (indomethacin treated) replicate 3

value: Small intestine

value: CD45-CD31- Stromal cells


title: S2_T_rep1

source_name: Patient 2 normal tissue in vivo

value: Patient 2

value: normal tissue


title: S2_T_O_rep1

source_name: Patient 2 normal derived organoid

value: normal derived organoid


title: YFP+PDGFRα+ replicate 3

value: YFP+ PDGFRa+


title: W5L5042

source_name: WT Liver 5 months old

value: Liver

value: WT


title: YFP+PDGFRα+ replicate 1


title: S2_C_rep2

source_name: Patient 2 tumor tissues in vivo

value: tumor tissue


title: W5L5041

value: 28 days


title: YFP+PDGFRα+ replicate 4


title: W5L5277

value: M


title: K5L4285

value: B6.129-Gt(ROSA)26Sor tm1(cre/ERT2)Tyj /J + Mycloxp/loxp

value: MycKO


title: S3_C_O_rep1


title: W5L5005

value: fast for 14 hour


title: S2_C_O_rep1

source_name: Patient 2 tumor derived organoid


title: YFP+PDGFRα- replicate 3

value: YFP+ PDGFRa-


title: K5L5116

value: F


title: W5L5004


title: K5L4284


title: W5L5299


title: S2_C_rep1

value: colorectal cancer


title: YFP+PDGFRα- replicate 1

value: Small intestine


title: YFP+PDGFRα+ replicate 2

value: CD45-CD31- Stromal cells


title: S1_T_rep1

source_name: Patient 1 normal tissue in vivo

value: Patient 1


title: S1_C_rep1

source_name: Patient 1 tumor tissues in vivo


title: S3_C_rep1

value: Patient 3


title: YFP+PDGFRα- replicate 2


title: S1_C_O_rep2

source_name: Patient 1 tumor derived organoid

value: tumor derived organoid


title: YFP- replicate 3

value: YFP+


title: YFP+PDGFRα- replicate 4


title: S1_C_O_rep1


title: YFP- replicate 2


title: S1_T_O_rep1

source_name: Patient 1 normal derived organoid

value: normal derived organoid


title: YFP- replicate 4


title: ChIP-seq against CTCF in ES-cells clone with the ALL genotype

data_processing:
Base calling with standard Illumina Software
Single-end reads were mapped to the same custom reference genomes as specified in the Capture-C section using Bowtie (Langmead et al. 2009, flags -m1 -S --chunkmbs 500). Reads aligning to more than one location were filtered out by bowtie due to the -m1 flag.
Resulting alignments in SAM format were then converted to bam, sorted and deduplicated using Samtools (https://github.com/samtools/samtools).
Then, deduplicated bam files were converted to bed including a 300 base pairs extension and subsequently bedGraph files containing the genome coverage were computed using BEDTools (Quinlan et al. 2010, bamToBed and genomeCoverageBed respectively).
Finally, bedGraph files were converted to bigWig files for visualization in UCSC genome browser (https://genome.ucsc.edu) using UCSC KentUtils (https://github.com/ucscGenomeBrowser/kent).
Genome_build: Custom genome based on the mm9 assembly.
Supplementary_files_format_and_content: bigWig

source_name: mouse ES-cells

extract_protocol:
Fixed nuclei were extracted adding 5 mL of ice-cold custom-made lysis buffer containing the following components: 10mM Tris HCl pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, Protease Inhibitor in Milliwater. Extracted nuclei were then collected, snap frozen and stored at -80 °C or further processed using iDeal ChIP for Transcriptional Factors (Diagenode) (Cat. N. C01010055). Chromatin was shared using Diagenode Bioruptor in order to get a fragment size of 200-500 bp. Immunoprecipitation was done using 15-20 mg of chromatin and 1 μg of CTCF Ab (Diagenode:C15410210).
ChIP-seq libraries were prepared using the NEBNext Ultra II Library Prep Kit for Illumina. Library prep was entered with 500pg-1μg of immunoprecipited DNA and processed according to the kit guidelines (NEBNext End Prep, Adaptor Ligation, PCR enrichment of Adaptor-Ligated DNA using NEBNext Multiplex Oligos for Illumina). Clean up and size selection with AMPure beads (NEB). Library was sequenced with single end read of 75 nt.

value: ALL

value: mouse ES-cells

value: CTCF


title: ChIP-seq against CTCF in ES-cells clone with the R2 genotype


title: YFP- replicate 1


title: Capture-C in E11.5 distal-limbs from ΔF-all-Inv mutant embryos

data_processing:
Base calling with standard Illumina Software
Paired-end reads from all the Capture-C experiments were aligned using bwa mem local aligner (Li et al. 2009) to a custom reference genome encompassing the captured-region (chr1:71-81Mb of the mm9 assembly) with the region corresponding to the baseline DelBs mutation deleted (chr1:76,388,978-77,858,974). There was one exception, the ΔF-all-Inv mutant Capture-C, in which a different version of the genome was used to account for the inverted coordinates (chr1:77,861,422-78,062,382). The rest of chromosomes, including the remaining chr1, were kept in the custom reference genome to be able to distinguish not-uniquely mapped reads.
Then, following the 4DN consortium recommendations, the resulting bam files were parsed with the pairtools suite (https://github.com/mirnylab/pairtools) to produce 4DN format files containing pairwise interactions. Briefly, bam files were parsed using pairtools parse. Then, not-uniquely mapped reads were filtered out using pairtools select (selecting UU, UR and RU pairs). Subsequently, pairs of reads were sorted and duplicated pairs were removed using pairtools sort and pairtools dedup respectively. Finally, dangling-ends were filtered out using a custom python script.
Filtered 4DN formatted pairs of interactions were then used to construct Knight-Ruiz (KR) normalized Hi-C matrices in hic format with Juicer (Durand et al. 2016).
Genome_build: Custom genome based on the mm9 assembly.
Supplementary_files_format_and_content: multiresolution hic files

source_name: E11.5 distal limb buds

extract_protocol:
Fixed nuclei were extracted adding ice-cold custom-made lysis buffer containing the following components: 50mM Tris HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1.15% Triton X-100, 25X Protease Inhibitor in Milliwater. Extracted nuclei were then collected, snap frozen and stored at -80 °C or further processed with the following steps: digestion with DpnII RE, re-ligation of the digested fragments, de-crosslinking and DNA purification (3C fragments).
The 3C library was further processed using SureSelectXT Target Enrichment System for the Illumina Platform (Agilent Technology). 200 ng or 3 μg of sample was shared using Covaris sonicator and the following parameters; duty cycle: 10%, intensity: 5, cycle per burst:200, time: 6 minutes, temperature: 4°C. Shared sample was then treated following the kit guidelines (end repair, dA-tailing, adaptor ligation, PCR enrichment of Adaptor ligated DNA, DNA purification, hybridization and capture). The hybridization was performed using SureSelect XT Custom RNA probes (Cat # 5190-4836) and the capture with Streptavidin-Coated Beads (Invitrogen). PCR enrichment and sample indexing were done following Agilent instructions. Capture libraries were sequenced with 75bp paired-end reads.

value: [delta]F-all-Inv

value: distal limb buds


title: Capture-C in E11.5 distal-limbs from ΔR1+F2 mutant embryos


title: S1_C_rep2

value: tumor tissue


title: Capture-C in E11.5 distal-limbs from Δ-All mutant embryos

value: [delta]-All


title: ChIP-seq against CTCF in ES-cells clone with the R-ALL genotype

value: R-ALL


title: T cells_Control_Day 15_rep4

type: RNA

city: Atlanta

first: Jingru

last: Zhu

state: GA

address: 1365 E Clifton Rd NE Building C

department: Hematology/Oncology

institute: Winship Cancer Institute

description:
Control-D15-4
T cells were isolated from the spleen cells of recipient mice using FACS sorter (BD AriaII). Immediately afterwards, they were frozen and stored. Cellular RNA was stabilized using 1/3 RLT buffer (Qiagen). After extraction of RNA using Qiagen RNeasy Micro kit, Nanodrop and Agilent 2100 were used to quantify, and quality check the RNA. RNA analyzed using the nCounter® Myeloid Innate Immunity Panel (Nanostring Technologies, Seattle, WA).

hyb_protocol: Probes and target transcripts were hybridized overnight at 65°C for at least 16 hours.

scan_protocol: Hybridized RNA was then diluted in molecular grade water and loaded into nCounter SPRINT cartridge (NanoString), placed into nCounter SPRINT Profiler, and quantified.

data_processing: Raw NanoString data (n=24) from both batches was exported from NSolver. Data quality was assessed with the help of QC plots using R package NanoStringNorm5. Three potential outlier samples were excluded from the analysis. The remaining 21 samples were imported and analyzed using R package NanoStringClustR6. Data was normalized using quantile normalization after background subtraction of mean2sd, and count thresholding. Differential expression analysis was carried out using NanoStringClustR and genes were identified as significant with an FDR adjusted p-value of less than or equal to 0.05. Functional enrichment and network analysis for the principal comparison of interest was carried out using an ordered query on gProfiler7.

label: codeset probes

source_name: T cells, Control, Day 15

label_protocol: nCounter gene expression assays (NanoString Technologies) were performed for the NanoString innate immunology mouse panel. Samples were labelled with panel-specific codeset probes.

value: male

value: T cells, Control

tag: time point

value: Day 15


title: YFP+ replicate 2

value: Small intestine

value: CD45-CD31- Stromal cells

value: YFP-


title: YFP+ replicate 1


title: YFP+ replicate 4