title: H3K36me3-ChipSeq BK4

data_processing:
read quality was accessed using FastQC 0.11.8
fastq files were trimmed of Illumina adapters with Trimgalore Version 0.6.4 using Illumina parameters
fastq files were aligned to mouse genome GRCm38 mm10 patch release 6 using STAR 2.7.0 using default parameters
fastq files were aligned to Drosophila BDGP R5/dm3 using STAR 2.7.0 using default parameters
bam files were sorted and selected for primary reads using Samtools view 1.9 with the following parameters: -F 256, -@ 5
PCR duplicates were removed from bam files using Picard Tools 2.20.2 using default parameters
read totals were determined and scaling factors were determined using Samtools Flagstat 1.9
coverage for each bam file was calculated using Deeptools bamCoverage 2.0 using the appropriate scaling factor and output as bigwig file
matrices were calculated using Deeptools computeMatrix 2.0 using the parameters ----referencePoint TSS, -S (appropriate .bw files), --sortUsing region_length, --sortUsingSamples 1, -b (appropriate upstream starting position), -a (appropriate downstream ending position), o- (appropriate .gz file)
heatmaps were plotted using Deeptools plotHeatmap 2.0
Tag counts between DMSO controls and EZH2i treated samples were then determined across the entire mouse genome using Bedtools multicov bedtools v2.26.0 and log2 fold change and percent change (i.e. decrease or increase) was calculated.
Genome_build: GRCm38 mm10 patch release 6

source_name: Activated CD8+ T Cells

growth_protocol: unknown

extract_protocol:
For H3K27me3 and H3K36me3 ChIP-Seq, 40 million of cells were cross-linked with 1% formaldehyde for 10 minutes, followed by addition of glycine to stop crosslinking. After washing, cell lysis and sonication, the chromatin samples were incubated with antibody-conjugated Dynabeads (Invitrogen) at 4 degrees Celsius. Beads bound with chromatin were then subject to extensive washing and elution. Eluted chromatin was de-crosslinked overnight at 65 degrees, followed by protein digestion with proteinase K and DNA purification with Qiagen PCR purification kit.
The obtained ChIP DNA samples were submitted to the UNC-Chapel Hill High-Throughput Sequencing Facility (HTSF) for preparation of multiplexed libraries and deep sequencing with an Illumina High-Seq platform according to the manufacturer’s instructions.

treatment_protocol: We performed H3K27me3 and H3K36me3 ChIP-Seq on control and EZH2 inhibited T cells.

tag: chip antibody


title: H3K27me3-ChipSeq BK1

status: Public on Dec 31 2020

type: SRA

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

country: USA

institute: University of Arkansas for Medical Sciences

library_source: genomic

molecule: genomic DNA

organism: Mus musculus


title: H3K27me3-ChipSeq BK3


title: H3K36me3-ChipSeq BK2


title: SC002_T1_N_AMR_R2

city: Chicago

first: Ziyou

last: Ren

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

description: Bisulfite-Seq (reduced representation) of TR-AM

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

source_name: CD45.2+ lung AM cells

growth_protocol: Male and female C57BL/6NJ mice received bone marrow chimeras and myeloablative agent busulfan. Bone marrow chimeras with thoracic shielding were used to assess the origin of pulmonary macrophages (TRAMs vs. Mo-AMs).

extract_protocol:
All groups were euthanized for isolation of CD45.1/2 AM cells by magnetic bead pre-enrichment and fluorescence-activated cell sorting. RNA and genomic DNA were obtained using the AllPrep DNA/RNA Micro Kit (Qiagen).
Genomic DNA was quantified with a Qubit 3.0 instrument. ~50-200 ng of genomic DNA was then digested with the restriction endonuclease MspI (New England BioLabs). Resulting fragments underwent size selection for fragments ~100-250-bp in length using SPRI beads (MagBio Genomics) and subsequent bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Bisulfite conversion efficiency averaged 99.6% as estimated by the measured percent of unmethylated CpGs in λ-bacteriophage DNA (New England BioLabs N3013S) added at a 1:200 ratio to each sample. Libraries for Illumina-based sequencing were prepared with the Pico Methyl-Seq Library Prep Kit (Zymo Research) using Illumina TruSeq DNA methylation barcodes. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and four pooled libraries per run were sequenced on an Illumina Illumina NextSeq 500 instrument using the Illumina NextSeq 500/550 V2 High Output reagent kit (1 x 75 cycles).

treatment_protocol: Mice were not under any special treatment other than bone marrow chimeras

tag: strain

tag: cell type

value: CD45.2+ lung AM cells

tag: exposure

value: naïve


title: SC002_T1_N_AMD_R2

description: Bisulfite-Seq (reduced representation) of Mo-AM

source_name: CD45.1+ lung AM cells

value: CD45.1+ lung AM cells


title: EZH2i_rep5

library_source: transcriptomic

data_processing:
read quality was assessed using FastQC v0.11.7.
adaptors and low-quality bases (Q < 20) were trimmed using Trimmomatic v0.38 (minimum read length: 35 base pairs)
fastq files were aligned to the mouse reference genome (GRCm38 / mm10) using TopHat 2.1.1 with the following parameters:  -p 10 --library-type=fr-firststrand --no-novel-juncs -G genes.gtf --transcriptome-index=transcriptome_data/known genome.
bam files were sorted using samtools v1.9
gene level expression counts based on known gene annotation were quantified using featureCounts
genes with at least 1 CPM in a minimum of 6 libraries were retained for further analysis.
filtered counts were TMM normalized to correct for compositional bias.
Genome_build: GRCm38 / mm10
Supplementary_files_format_and_content: tab-delimited text file of gene level counts for each sample

molecule: polyA RNA

source_name: CD8+ T cells_EZH2 inhibitor

extract_protocol: cDNA libraries were prepared from 500 ng of total RNA using Illumina’s (San Diego, CA) TruSeq stranded mRNA Sample Preparation Kit v2 following the manufacturer’s protocol. Library fragment sizes were validated using a Fragment Analyzer and quantified by a Qubit fluorometer. Equal amounts of each library were pooled for sequencing on the NextSeq 500 platform using a high output flow cell to generate approximately 25 million 75bp SE reads per sample.

treatment_protocol: We performed RNA-seq on DMSO control and EZH2 inhibited CD8+ T cells.

value: spleenocytes

tag: cell subtype

value: CD8+ T cells

tag: treatment

value: EZH2 inhibitor


title: SC005_T1_N_AMD_R5


title: EZH2i_rep4


title: SC001_T1_N_AMR_R1


title: RNA kiPSC-iCD1-JNKi-D2-rp3

city: Guangzhou

first: dongwei

last: Li

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
RNAseq reads were aligned to the mm10 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results and merged together to get a big table
RNAseq data was normalized by EDAseq
Genome_build: mm10
Supplementary_files_format_and_content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data

molecule: total RNA

source_name: reprogramming cells

growth_protocol: EpiSCs were maintained in serum coated well. FN medium which comprised F12 (Ham’s F12, Gibco )/ Neurobasal ( Gibco ) (1:1) with N2 (200×, Gibco), B27 (100×, Gibco), NEAA (100×,Gibco), GlutaMAX(100×, Gibco), BSA (1mg/ml, Gibco), 100 mM 2-mercaptoethanol, 20 ng/ml ActivinA and 20 ng/ml bFGF was used for feeder-free EpiSC culture.

extract_protocol:
Total RNA was prepared with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo-dT (Takara), and then analyzed by qPCR with Premix Ex Taq (Takara).
For RNA-seq, TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina) was used for library construction and the sequencing was done using a NextSeq 500 High Output Kit v2 (75 cycles) (FC-404-1005, Illumina), according to the manufacturers instructions.

value: reprogramming cells

tag: day of reprogramming


title: RNA kiPSC-iCD1-JNKi-D3-rp3


title: RNA kiPSC-rp2

source_name: iPSCs

value: iPSCs


title: RNA kiPSC-iCD1-JNKi-D3-rp2


title: RNA kiPSC-rp1


title: RNA kiPSC-iCD1-JNKi-D2-rp1


title: RNA kiPSC-iCD1-JNKi-D1-rp2


title: RNA kiPSC-iCD1-D3-rp2


title: RNA kiPSC-iCD1-D3-rp1


title: RNA kiPSC-iCD1-D2-rp1


title: RNA kiPSC-iCD1-JNKi-D2-rp2


title: RNA kiPSC-iCD1-JNKi-D1-rp1


title: RNA kiPSC-iCD1-D2-rp2


title: RNA kEpiSC_rp2

source_name: overexpression Klf4 EpiSC stable line

value: overexpression Klf4 EpiSC stable line


title: RNA kiPSC-iCD1-D1-rp2


title: RNA kEpiSC_rp1


title: RNA WT-kiEpiSC-rp1


title: RNA kiPSC-iCD1-D1-rp1


title: RNA WT-kiEpiSC-iCD1-rp2


title: RNA WT-kiEpiSC-iCD1-rp1


title: RNA WT-kiEpiSC-JNKi-rp2


title: RNA WT-kiEpiSC-JNKi-rp1


title: RNA WT-iEpiSC-rp1

source_name: wt ESCs induced EpiSCs

value: wt ESCs induced EpiSCs


title: RNA JunKO-kiEpiSC-rp1


title: RNA JunKO-kiEpiSC-iCD1-rp1


title: RNA JunKO-kiEpiSC-JNKi-rp2


title: RNA JunKO-iEpiSC-rp1

source_name: c-Jun-/- ESCs induced EpiSCs

value: c-Jun-/- ESCs induced EpiSCs


title: RNA JunKO-kiEpiSC-iCD1-rp2


title: RNA JunKO-kiEpiSC-JNKi-rp1


title: RNA EpiSC-rp2

source_name: Epibast stem cells

value: Epibast stem cells


title: RNA EpiSC-rp3


title: RNA ESC-rp5

source_name: Embryonic stem cells

value: Embryonic stem cells


title: RNA EpiSC-rp1


title: 104_SZ_A

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

description: pooled RNA from leaf, shoot tip, flower, tendril

data_processing:
The quality check of the sequenced small RNA libraries was done by FastQC Program and CLC Genomic Workbench 11
Trimming of raw reads was performed using the CLC Genomic Workbench 11
Removing redundant reads using the CLC Genomic Workbench 11
Supplementary_files_format_and_content: trimmed redundant list, each read with its number of repeats

organism: Vitis vinifera

source_name: leaf, shoot tip, flower, tendril samples

extract_protocol:
CTAB method (Gambino, 2008: https://doi.org/10.1002/pca.1078 )
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9

tag: cultivar

value: Sziren 1

tag: tissue

value: mother plant,  leaf, shoot tip, flower, tendril


title: RNA ESC-rp4


title: RNA ESC-rp3


title: RNA ESC-rp2

value: CBA/CaJ X C57BL/6J


title: 110_SZ_M

description: pooled RNA from in vitro meristem culture plantlets

source_name: whole in vitro plantlets

value: in vitro meristem culture plantlets


title: 3_h_after_exercise_6

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

data_processing:
Adapter sequences and low quality reads were trimmed using the Timmomatic tool (v0.36) (options:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35), also 5’-guanine was clipped.
Reads were aligned using STAR (v2.7.0a) with mismatch rate threshold 0.06
rRNA reads and reads from mitochondrial genome excluded using split_bam.py script (RSEQC) with combined annotation (RefSeq and Ensembl rRNA genes and mt genome). Only uniquely mapped reads were used for further analysis.
TSS tag clusters were identified using DPI (Decomposition-based peak identification) for unique mapped filtered reads (50 samples)
TSS tag clusters were annotated using consistently Ensembl (GRCh38.101), Refseq (08/15/2020) and Cufflinks-based annotation (stranded RNA-Seq data, GSE120862).
Genome_build: GRCh38.p13 primary assembly genome
Supplementary_files_format_and_content: Robust DPI TSS clusters (.bed file) and its annotation (tab-delimited .txt)

organism: Homo sapiens

source_name: muscle vastus lateralis

extract_protocol:
RNA was extracted from the frozen samples (~20 mg) using an RNeasy mini kit (Qiagen, Germany) with DNase I treatment (Fermentas, Lithuania). The RNA concentration and integrity were evaluated in a fluorimeter (Qubit 3.0; Thermo Scientific) and by capillary electrophoresis (Bioanalyzer 2100, Agilent, USA), respectively; all samples were at least 7 in RIN.
Libraries were constructed from 2.5-3 mg of RNA according to nAnT-iCAGE (non-Amplified non-Tagging Illumina Cap Analysis of Gene Expression) protocol  using nAnT-iCAGE Library Preparation kit (DNAform, Japan) and SuperScript III Reverse Transcriptase (Invitrogen, USA). The concentration of the obtained libraries was measured on a Qubit 3.0 fluorimeter (Thermo Scintific, USA); the quality of the libraries was checked using an Agilent Bioanalyzer 2100 (Agilent Technologies, USA). The libraries were then validated using real-time PCR (KAPA Library Quantification Kits Illumina, KAPA Biosystems, South Africa) and sequenced

treatment_protocol: Amateur endurance-trained athletes (10 long distance runners, cyclists and cross country skiers, median age, 32 years [interquartile range, 30–36 years]; weight, 75 kg [71–78 kg]; V’O2max/kg [maximal pulmonary O2 consumption rate], 58 ml/min/kg [54–60 ml/min/kg of body mass]) were involved in our study. An intermittent exercise induces greater molecular response compare to a continuous exercise with the same average power. Hence, each subject carried out an intermittent exercise (60 min, [3 min, 50% LT4 [power at lactate threshold at 4 mmol/l] + 2 min, 100% LT4]  12) on a cycle ergometer (Ergoselect 200, Ergoline, Germany) 2 h after a standardized breakfast (3582 kJ; 22 g protein, 154 g carbohydrates and 16 g fat). The LT as well as V’O2max – markers of aerobic performance, were evaluated in a preliminary test session in the incremental cycling test till exhaustion using a Biosen C line analyzer (EKF Diagnostics, Germany) and a medical gas mass-spectrometer AMIS 2000 with a mixing chamber (Innovision, Denmark), as describe elsewhere. Subjects ate a standardized lunch (3714 kJ; 45 g protein, 183 g carbohydrates and 27 g fat) 1 h 15 min after an intermittent exercise. Biopsy samples were taken under local anesthesia (2 mL 2% lidocaine) using a Bergstrome needle with aspiration from the m. vastus lateralis prior to, 2 min, 1 h, 3 h, and 6 h after an intermittent exercise (1st, 2d, and 3d from the one leg, 4st and 5st from another leg) (Figure 1). The muscle samples were quickly blotted with gauze to remove superficial blood, frozen in liquid nitrogen, and stored at -80°C until required.

value: skeletal muscle

tag: individual

tag: time point

value: + 3 h after exrecuse

tag: training status

value: endurance trained amateur athlete

tag: Sex

value: male

tag: age

tag: weight

tag: height

tag: bmi


title: 1_h_after_exercise_5

value: + 1 h after exrecuse


title: 6_h_after_exercise_5

value: + 6 h after exrecuse


title: 3_h_after_exercise_5


title: 1_h_after_exercise_2


title: 1_h_after_exercise_6


title: prior_5

value: prior


title: prior_6


title: 6_h_after_exercise_2


title: 6_h_after_exercise_6


title: 1_h_after_exercise_1


title: Sclera_CoV2_3

city: New York

first: Rasmus

last: Moeller

state: NY

address: 1 Gustave L. Levy Place

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
automated base-calling performed with bcl2fastq (Illumina)
fastq files were aligned using RNA-Seq Alignment application (Basespace, Illumina).
total counts were extracted and comiled in .csv files
Genome_build: hg19
Supplementary_files_format_and_content: .csv file containining total counts of each gene after alignment.

source_name: cadaver donor eye tissue

extract_protocol:
Samples were lysed in 300µl TRIzol reagent (Invitrogen) and total RNA was extracted by phenol/chloroform extraction following manufacturer's protocol.
All libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. Starting material: 1µg total RNA

value: sclera

tag: infection

value: SARS-CoV-2, MOI = 1.0

value: 24 hours


title: RNA ESC-rp1

tag: strain


title: 3_h_after_exercise_1


title: prior_2


title: 108_SZ_SZ

description: pooled RNA from in vitro somatic embryogenesis plantlets


title: prior_1


title: RNA EpiSC-rp4

tag: cell type


title: Sclera_CoV2_2


title: Sclera_CoV2_1


title: Sclera_mock_3

value: mock


title: Sclera_mock_2


title: Limbus_CoV2_2

value: limbus


title: 3_h_after_exercise_2


title: Limbus_CoV2_1


title: Limbus_mock_3


title: Limbus_mock_2


title: Limbus_mock_1


title: Cornea_CoV2_1

value: cornea


title: Cornea_CoV2_3


title: Cornea_CoV2_2


title: Cornea_mock_3


title: Cornea_mock_2


title: Cornea_mock_1


title: Sclera_mock_1


title: RLN2-1

city: Toronto

first: Rob

last: Rottapel

state: ON

address: 101 College Street, Room 12-704

department: Medical Biophysics

country: Canada

institute: University Health Network

data_processing:
Filtered FASTQ files were aligned to Gencode v25 gene annotations and hg38 genome build using the STAR short-read aligner (v2.4.2a)
Read count files generated by STAR were merged with gene annotations in R
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text read counts

source_name: Ovarian cancer cell line (OVCAR8)

growth_protocol: OVCAR8 cells were plated in 6-well format (300,000 cells/well) in RPMI + 10%FBS. 24 hours later, cells were starved in FBS-free RPMI for 16 hours.

extract_protocol:
RNA was extracted using TRIzol™ Reagent (Invitrogen) according to the manufacturer's instructions.
Libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation Kit

treatment_protocol: Following the 16 hour starvation period, cells were either untreated or treated with human recombinant RLN2 (50ng/mL, Phoenix Pharmaceuticals 035-62) in triplicate for 8 hours.

tag: cell line

value: RLN2 (Phoenix Pharmaceuticals 035-62). 50ng/mL. 8h


title: RLN2-2


title: CON4

value: Untreated control


title: Riva pooled input

city: Columbus

first: Hatice Gulcin

last: Ozer

state: OH

address: 1800 Cannon Dr

department: Biomedical Informatics

institute: The Ohio State University

description:
chromatin
RIVA_pooled_Input

data_processing:
75bp single-end read aligned to reference genome with bwa-0.7.12
Alignment results are sorted, indexed, dulicates were removed, and high mapping quality alignments (mapq>30) were selected using samtools v1.3
Genome coverage files were generated using deepTools v3.0.2 using following parameters:
--binSize 20 --smoothLength 60 --normalizeUsing CPM --ignoreForNormalization chrX chrM
Heatmaps depicting genome-wide enrichment of the ChIP signal around transcription start site were generated using computeMatrix and plotHeatmap functions of deepTools.
Genome_build: GRCh38
Supplementary_files_format_and_content: Genome coverage files in bigwig format

source_name: human DLBCL cell line

growth_protocol: Pfeiffer and Riva cells were grown in standard RPMI-1640 medium supplemented with 10% FBS, 1 mM sodium pyruvate and 1% Penicillin-Streptomycin (5,000 U/mL).

extract_protocol:
Cell pellets were snap frozen and shipped on dry ice to Active Motif where subsequent steps were performed according to previously published pipeline (de Almeida Nagata DE et al. Cell Rep 2019;27(1):269-81)
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.
Chip-Seq: After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: 5 million of Pfeiffer and Riva cells were treated with either vehicle control or tegavivint for 12 hours

tag: lymphoma cell line

value: Riva

value: DLBCL cell line

tag: chip antibody

value: none (input)


title: Sample_PPM1G_KO_3_S6

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

institute: UT Southwestern Medical Center

description:
ERCC spike-in RNA added
processed data file: RNAseq_countTable.txt

data_processing:
Quality of reads from all experiments was determined with FASTQC v0.11.2 using default parameters.
4sU-/RNA-seq: Reads were aligned to hg38 with hisat2 version 2.1.0-intel.
4sU-/RNA-seq: Sorted by coordinate BAM files were created by SAMtools v1.3.
4sU-/RNA-seq: ERCC spike-ins were similarly aligned to an ERCC fasta file.
4sU-/RNA-seq: Reads for protein coding genes were counted using the Gencode v27 annotation and featureCounts.
4sU-/RNA-seq: Differential expression analysis was performed using RUVseq v1.14.0 R package.
Genome_build: hg38
Supplementary_files_format_and_content: 4sU-/RNA-seq: Bigwig files were scaled by the ERCC spike-in
Supplementary_files_format_and_content: 4sU-/RNA-seq: Tab-delimited file containing raw transcript counts

growth_protocol: All HCT116 cell lines were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum and 1% Pen/Strep at 37°C with 5% CO2.

extract_protocol:
For 4sU-seq, HCT116 Ctrl and PPM1G KO cells were seeded into 6-well dishes per biological replicate and grown to 70% confluency. Cells were pulsed for 10 min with DMEM + 500 µM 4sU (Sigma-Aldrich, T4509). At the 9 min mark the DMEM + 4sU media was removed and cells were washed one time with 1X PBS. The PBS was removed, and cells were lysed on-plate using the standard TRizol protocol (ThermoFisher Scientific, 15596026). RNA samples were DNase treated (NEB, M0303) and then extracted with acid:phenol chloroform (ThermoFisher Scientific, AM9720) followed by an additional chloroform extraction. RNA was then precipitated with 1/10 volume of NaCl (5M), 1 µL glycoblue, and 2.5 volumes of 100% EtOH. RNA pellets were washed with 1 mL of 75% EtOH and air dried and then resuspended in RNase-free water. RNA (300 µg) was brought to a final concentration of 0.4 mg/mL with RNase-free water. A separate aqueous master mix (20 mM NaOAC pH 5.2, 1 mM EDTA pH 8.0, 0.1% SDS) was added to the diluted RNA mix followed by the addition of 0.2 mg/mL Biotin-HPDP (ThermoFisher Scientific 21341) in dimethylformamide. The biotinylation reaction was incubated at room temperature for 2 hrs followed by acid:phenol chloroform extraction. Biotinylated RNA pellets were resuspended in 500 µL RNA Prurification Beads (RPB) buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 300 mM NaCl). Dyna MyOne Strepavidin T1 beads (200 uL/sample; ThermoFisher Scientific, 65601) were blocked at room temperature in beads wash buffer + 1% polyvinylpyrrolidone for 10 min. After blocking, beads were washed 1X with 1 mL beads wash buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 50 mM NaCl) and then resuspended in RPB buffer. Biotinylated, 4sU RNA was denatured at 65°C for 5 min and then placed on ice for 2 min. 200 µL of blocked beads were added to each sample and incubated for 30 min with rotation at room temperature. Beads were washed 5X with 4sU wash buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 1 M NaCl, 0.1% Tween-20). Biotinylated, 4sU RNA was eluted from beads 2 times in 75 µL of 0.1 M DTT for 15 min at room temperature with rotation, giving a final elution volume of 150 µL. 4sU-RNA was further purified using the Zymo RNA Clean and Concentrator Kit (Zymo Reasearch, R1013). RNA concentration was measured using the Qubit RNA high sensitivity assay (ThermoFisher Scientific, Q32852) and quality was determined using the Agilent Tapestation RNA ScreenTape (Agilent, 5067-5576).  For RNA-seq, HCT116 Ctrl and PPM1G KO cells were grown in 6-well dishes and total RNA extracted using the Zymo Quick-RNA Miniprep Kit (R1055) according to manufacturer instructions.
For 4sU-seq and RNA-seq, the KAPA Stranded RNA-seq kit with RiboErase (HMR) (KAPA Biosystems, KK8483) was used to prepare libraries according to manufacturer’s instructions. Briefly, 200 ng of 4sU RNA and 1 µg of total RNA was used to prepare 4sU-seq and RNA-seq libraries, respectively. Libraries were rRNA depleted followed by DNase treatment. RNA was fragmented and primed followed by 1st strand cDNA synthesis. 2nd strand synthesis was then performed with the incorporation of dUTP. Libraries were then A-tailed, adapter ligated, and amplified. All libraries were quantified using the Qubit 2.0 fluorometer and library size verified using the Agilent Tapestation DNA D1000 ScreenTape (Agilent, 5067-5582). All libraries were submitted to the McDermott Center Sequencing Core at UT Southwestern. 75 bp paired-end reads were generated for all libraries.
Stranded Whole Transcriptome RNA-seq

value: Colorectal Carcinoma Cell Line

tag: genotype/variation

value: PPM1G KO

tag: passages

value: Under 15


title: Pfeiffer no treatment control

description:
chromatin
PFEIF-UNTR_TBL1

value: Pfeiffer


title: Pfeiffer pooled input

description:
chromatin
PFEIF_pooled_Input


title: CON2

tag: treatment


title: Pfeiffer tegavivint

description:
chromatin
PFEIF-BC2059_TBL1


title: Limbus_CoV2_3

tag: tissue


title: Sample_PPM1G_KO_2_S5


title: RLN2-3


title: Riva no treatment control

description:
chromatin
RIVA-UNTR_TBL1


title: Riva tegavivint

description:
chromatin
RIVA-BC2059_TBL1


title: Sample_PPM1G_KO_1_S4


title: Sample_Ctrl_KO_3_S3

value: Ctrl


title: Sample_Ctrl_KO_2_S2


title: Sample_Ctrl_KO_1_S1


title: Sample_4su_PPM1G_KO_2_S3

description:
ERCC spike-in RNA added
processed data file: 4sUseq_countTable.txt

tag: molecule subtype

value: nascent 4sU RNA


title: CON3


title: Strand-specific RNA-seq in circANRIL e16-e5 siRNA #2 treated cells- Replicate #2

city: Toulouse

first: Estelle

last: Nicolas

address: 118 route de Narbonne

country: France

institute: INSERM

data_processing:
Strand-specific RNA-sequencing in senescent cells treated with siRNAs was performed paired-end by Illumina’s NextSeq 500 technology  at EMBL-GeneCore (stranded rRNA-minus RNA-seq). The 8 samples were barcoded and sequenced paired-end in one lane with ~400 millions paired end reads in total. After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2, datasets were processed (sorting and indexing) with samtools. Aligned reads to the rDNA locus were removed for further analysis.
Raw reads were counted, per gene_id, using HT-seq Version 0.6.1 on the NCBI refseq annotation gtf file from UCSC in a strand specific mode with default parameters (files : htseqCount20191029_refSeq_unionRefseq.txt)
Differential analysis (circANRIL e16-e5 siRNAs vs control siRNAs, considering the 2 replicates) was done with DESeq2 Bioconductor R package, version 1.22.1 with default parameters but using normalization by the total hg38 aligned read number per sample ((paired read number *2)/100 000 000). Genes with a mean of less than one read count for all the samples were eliminated for the analysis.
Genome_build: hg38
Supplementary_files_format_and_content: .csv and .txt files contain the output from DESeq2 and the raw counts of sequencing reads for the features from HT-seq, respectively.

source_name: total RNA (ribosomal RNA depleted) from circANRIL e16-e5 siRNA #2-treated senescent WI38 hTERT RAF1-ER cells

extract_protocol:
Total RNAs were prepared using the MasterPure RNA Purification Kit (Epicentre Biotechnologies) supplemented with Baseline-ZERO DNAse (Epicentre). EMBL-GeneCore performed the ribosomal RNA depletions.
Library construction (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®) was performed by EMBL GeneCore (Heidelberg, Germany) (stranded rRNA-minus RNA-seq). The 8 samples were barcoded, sequenced paired-end in one lane by Next Seq 500 Illumina device and demultiplexed.

treatment_protocol: Senescent  WI38 hTERT RAF1-ER cells were transfected by siRNAs for 3 days.

value: WI38 hTERT RAF1-ER

value: induced in senescence for 3 days and then transfected with circANRIL e16-e5 siRNA #2 for 3 days


title: Sample_4su_Ctrl_KO_1_S3


title: Sample_4su_Ctrl_KO_2_S1


title: Sample_4su_PPM1G_KO_1_S4


title: Strand-specific RNA-seq in control Pool siRNA treated cells- Replicate #2

source_name: total RNA (ribosomal RNA depleted) from Control Pool siRNA-treated senescent WI38 hTERT RAF1-ER cells

value: induced in senescence for 3 days and then transfected with control Pool siRNA for 3 days


title: Strand-specific RNA-seq in circANRIL e16-e5 siRNA #1 treated cells- Replicate #2

source_name: total RNA (ribosomal RNA depleted) from circANRIL e16-e5 siRNA #1-treated senescent WI38 hTERT RAF1-ER cells

value: induced in senescence for 3 days and then transfected with circANRIL e16-e5 siRNA #1 for 3 days


title: Strand-specific RNA-seq in control Scramble #2 siRNA treated cells- Replicate #2

source_name: total RNA (ribosomal RNA depleted) from Control Scramble #2 siRNA-treated senescent WI38 hTERT RAF1-ER cells

value: induced in senescence for 3 days and then transfected with control Scramble #2 siRNA for 3 days


title: Strand-specific RNA-seq in circANRIL e16-e5 siRNA #2 treated cells- Replicate #1


title: Strand-specific RNA-seq in control Scramble #2 siRNA treated cells- Replicate #1


title: Strand-specific RNA-seq in circANRIL e16-e5 siRNA #1 treated cells- Replicate #1


title: Sample_4su_PPM1G_KO_3_S4


title: SPANX KD 86 Rep3

city: Rockville

first: Tongwu

last: Zhang

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standstard illumina base calling pipeline and stored in illumina cloud service BaseSpace. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned with the STAR aligner
FeatureCounts implemented in Subread will be used to count the sequencing reads from mapped BAM files. Analyses of differentially expressed genes (DEGs) were subsequently performed using a negative binomial test method (edgeR)10 implemented using SARTools R Package
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read count for each annoted gene.

source_name: Melanoma cell line A375

extract_protocol:
RNA was prepared 7 days following SPANX knockdown, and triplicates were used for RNAseq analysis. Libraries were prepared from isolated total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen, (Vienna, Austria). Barcoded libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Melanoma Cell Line

value: SPANX KD


title: SPANX KD 86 Rep1


title: EV Rep2

value: EV control


title: EV Rep3


title: SPANX KD 87 Rep2


title: 6_h_after_exercise_1

value: skeletal muscle

tag: individual

tag: time point

value: + 6 h after exrecuse

tag: training status

value: endurance trained amateur athlete

value: male


title: ATACseq_rep2_HepG2

city: Charlestown

first: Keith

last: Joung

state: MA

institute: MGH

data_processing:
ATAC-seq Reads aligned to hg19 using BWA. Properly aligned reads were filtered to exclude PCR duplicates and processed as previously described (PMC3959825). Read start positions were shifted towards the 3’ end by 4 bp in for reads aligning to plus strand and 5 bp towards the 5’ end for reads aligning to minus strand.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for visualization on igv

source_name: Human liver cancer cell-line HepG2

growth_protocol: U2OS cells and HEK293 cells were grown in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin until 80% confluent. HepG2 cells  were grown in EMEM with 10% FBS and 1% penicillin and streptomycin. K562 cells were grown in RPMI supplemented with 10% heat-inactivated FBS, 2 mM GlutaMax, and 1% penicillin and streptomycin.

extract_protocol:
For ATAC-seq, cells (5 x 104) were incubated with DNase I (Worthington cat# LS002007) to remove DNA from dead cells, washed with PBS, resuspended in lysis buffer, and treated with transposase from Nextera DNA sample Prep Kit (Illumina, cat# FC-121-1030).
Libraries were made through adding adpators on purified tagmented DNA, followed by double-sided bead purification. Purified products were sequenced with PE 150 cycles on an Illumina Nextseq500 system

tag: cell status

value: native cells


title: ATACseq_rep2_K562

source_name: Human immortalised myelogenous leukemia cell line K562


title: EV Rep1


title: SPANX KD 86 Rep2


title: ATACseq_rep2_HEK293

source_name: Human embryonic kidney cell-line 293


title: ATACseq_rep1_K562


title: SPANX KD 87 Rep3


title: ATACseq_rep1_HepG2


title: ATACseq_rep1_HEK293


title: Strand-specific RNA-seq in control Pool siRNA treated cells- Replicate #1


title: Sample_4su_Ctrl_KO_3_S2

value: Colorectal Carcinoma Cell Line

value: Under 15


title: SPANX KD 87 Rep1


title: ATACseq_rep2_U2OS

source_name: Human bone osteosarcoma epithelial cells-U2OS


title: Input_rep1_HepG2_ChIPseq

data_processing:
ChIP-seq reads were aligned to human reference genome hg19 using Burrows-Wheeler Alignment (BWA) tool (PMC2705234). Genome-wide coverage was calculated after extending to 200 bases(approximate fragment size) and averaged over 25 bp windows using igvtools (https://doi.org/10.1093/bib/bbs017). Coverage was then normalized and scaled using RSeqC (http://rseqc.sourceforge.net/#normalize-bigwig-py)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for visualization on igv

extract_protocol:
For ChIP-seq, chromatin from 1% formaldehyde-fixed cells were fragmented to 200-500 bps by sonication for 5-6 mins using the Branson sonifer SFX250
Sequencing libraries were prepared with 3 ng of each H3K27Ac ChIP DNA and input sample using SMARTer ThruPLEX DNA-seq kit (Takara, Cat# R400675). Libraries were sequenced with single-end (SE) 75 cycles on an Illumina Nextseq 500 system


title: ATACseq_rep1_U2OS


title: Input_rep1_HEK293_ChIPseq


title: Input_rep1_K562_ChIPseq


title: Input_rep1_U2OS_ChIPseq


title: H3K27Ac_rep1_K562_ChIPsep

value: H3K27Ac antibody (Active motif, cat#, lot#10918010)


title: H3K27Ac_rep2_HepG2_ChIPsep


title: H3K27Ac_rep2_HEK293_ChIPsep


title: H3K27Ac_rep1_HepG2_ChIPsep


title: H3K27Ac_rep2_U2OS_ChIPsep


title: RNAseq_rep2_HepG2

data_processing:
RNA-seq reads were aligned to hg19 using STAR(doi: 10.1093/bioinformatics/bts635) and PCR duplicates were removed using Picard tools(http://broadinstitute.github.io/picard/). Reads aligning to ribosomal RNA were then filtered out of the alignment. Genomic coverage from filtered alignments were calculated by normalizing to sequencing depth using bedtools(https://doi.org/10.1093/bioinformatics/btq033). FPKMs were calculated using Cufflinks(https://doi.org/10.1038/nbt.1621)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files that include FPKM values for each gene

extract_protocol:
For RNA-seq, total RNA was extracted from native cells using the NucleoSpin RNA Plus Kit (Clontech, cat# 740984.250)
Single-end libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit (Illumina) and TruSeq RNA Single Indexes, pooled, and sequenced using an NextSeq500.


title: H3K27Ac_rep1_HEK293_ChIPsep


title: RNAseq_rep1_HEK293


title: H3K27Ac_rep1_U2OS_ChIPsep


title: RNAseq_rep2_K562


title: RNAseq_rep1_HepG2


title: RNAseq_rep2_U2OS


title: RNAseq_rep1_U2OS


title: H3K27Ac_rep2_K562_ChIPsep


title: RNAseq_rep2_HEK293


title: RNAseq_rep1_K562


title: Patient_14T008890

type: RNA

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

institute: IUCT-ONCOPOLE

description: Gene expression data from patient n°14T008890, frozen FL biopsy

hyb_protocol: Labeled complementary RNA (cRNA)  from these samples was then fragmented and hybridized to Affymetrix GeneChip™ Human Transcriptome Array 2.0

scan_protocol: The chips were then washed, scanned on the Affymetrix Fluidics Station 400, and controlled for quality, before analysis.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, and then RMA normalized on Expression Console version 1.4.1 (Affymetrix).

label: biotin

source_name: Patient n°14T008890, woman, 62 yrs, frozen FL biopsy

label_protocol: RNAs were amplified, prepared and labelled from 15 µg total RNA, with the GeneChip® WT PLUS Reagent Kit (Affymetrix)

growth_protocol: No culture was performed, frozen tissues were used for RNA extraction.

extract_protocol: Extraction of total RNA from frozen samples was performed according to the manufacturer's instructions. RNA samples were qualified using RNA 6000 Nano Chip on Bioanalyzer 2100 (Agilent)

treatment_protocol: No treatment

value: FL biopsy (inguinal lymph node)

tag: gender

value: female

tag: age

value: 62 yrs


title: Patient_15T006443

description: Gene expression data from patient n°15T006443, frozen FL biopsy

source_name: Patient n°15T006443, woman, 60 yrs, frozen FL biopsy

value: FL biopsy (mesenteric lymph node)

value: 60 yrs


title: Patient_13P20764

description: Gene expression data from patient n°13P20764, frozen FL biopsy

source_name: Patient n°13P20764, man, 68 yrs, frozen FL biopsy

value: FL biopsy (supraclavicular lymph node)

value: 68 yrs


title: Patient_12P354

description: Gene expression data from patient n°12P354, frozen FL biopsy

source_name: Patient n°12P354, man, 41 yrs, frozen FL biopsy

value: 41 yrs


title: Patient_14T016770

description: Gene expression data from patient n°14T016770, frozen FL biopsy

source_name: Patient n°14T016770, woman, 75 yrs, frozen FL biopsy

value: FL biopsy (cervical lymph node)

value: 75 yrs


title: Patient_10P11727

description: Gene expression data from patient n°10P11727, frozen FL biopsy

source_name: Patient n°10P11727, man, 65 yrs, frozen FL biopsy

value: 65 yrs


title: Patient_14P6455

description: Gene expression data from patient n°14P6455, frozen FL biopsy

source_name: Patient n°14P6455, man, 76 yrs, frozen FL biopsy

value: 76 yrs


title: Patient_14T002913

description: Gene expression data from patient n°14T002913, frozen FL biopsy

source_name: Patient n°14T002913, woman, 55 yrs, frozen FL biopsy

value: 55 yrs


title: Patient_12P10674

description: Gene expression data from patient n°12P10674, frozen FL biopsy

source_name: Patient n°12P10674, man, 73 yrs, frozen FL biopsy

value: FL biopsy (retrocrural lymph node)

value: male

value: 73 yrs


title: Patient_10P13853

description: Gene expression data from patient n°10P13853, frozen FL biopsy

source_name: Patient n°10P13853, man, 73 yrs, frozen FL biopsy


title: Patient_11R12248

description: Gene expression data from patient n°11R12248, frozen FL biopsy

source_name: Patient n°11R12248, man, 83 yrs, frozen FL biopsy

value: FL biopsy (axillary lymph node)

value: 83 yrs


title: Patient_13P8769

description: Gene expression data from patient n°13P8769, frozen FL biopsy

source_name: Patient n°13P8769, man, 69 yrs, frozen FL biopsy

value: 69 yrs


title: Patient_12P13774

description: Gene expression data from patient n°12P13774, frozen FL biopsy

source_name: Patient n°12P13774, man, 45 yrs, frozen FL biopsy

value: 45 yrs


title: Patient_13P16129

description: Gene expression data from patient n°13P16129, frozen FL biopsy

source_name: Patient n°13P16129, man, 75 yrs, frozen FL biopsy

value: FL biopsy (inguinal lymph node)


title: Patient_11P9156

description: Gene expression data from patient n°11P9156, frozen FL biopsy

source_name: Patient n°11P9156, man, 78 yrs, frozen FL biopsy

value: 78 yrs


title: Patient_11P12260

description: Gene expression data from patient n°11P12260, frozen FL biopsy

source_name: Patient n°11P12260, man, 63 yrs, frozen FL biopsy

value: FL biopsy (spinal lymph node)

value: 63 yrs


title: Patient_10P2554

description: Gene expression data from patient n°10P2554, frozen FL biopsy

source_name: Patient n°10P2554, man, 61 yrs, frozen FL biopsy

value: 61 yrs


title: Patient_13R20900

description: Gene expression data from patient n°13R20900, frozen FL biopsy

source_name: Patient n°13R20900, man, 67 yrs, frozen FL biopsy

value: FL biopsy (supraclavicular lymph node)

value: 67 yrs


title: Patient_14T024886

description: Gene expression data from patient n°14T024886, frozen FL biopsy

source_name: Patient n°14T024886, man, 44 yrs, frozen FL biopsy

value: FL biopsy (cervical lymph node)

value: 44 yrs


title: Patient_15T026729

description: Gene expression data from patient n°15T026729, frozen FL biopsy

source_name: Patient n°15T026729, man, 73 yrs, frozen FL biopsy


title: Patient_11P17002

description: Gene expression data from patient n°11P17002, frozen FL biopsy

source_name: Patient n°11P17002, woman, 68 yrs, frozen FL biopsy

value: female

value: 68 yrs


title: Patient_10P17074

description: Gene expression data from patient n°10P17074, frozen FL biopsy

source_name: Patient n°10P17074, woman, 53 yrs, frozen FL biopsy

value: 53 yrs


title: Patient_15T031604

description: Gene expression data from patient n°15T031604, frozen FL biopsy

source_name: Patient n°15T031604, woman, 61 yrs, frozen FL biopsy


title: Patient_12P14585

description: Gene expression data from patient n°12P14585, frozen FL biopsy

source_name: Patient n°12P14585, woman, 58 yrs, frozen FL biopsy

value: 58 yrs


title: Patient_12R14960

description: Gene expression data from patient n°12R14960, frozen FL biopsy

source_name: Patient n°12R14960, man, 55 yrs, frozen FL biopsy

value: FL biopsy (epidural mass)

value: male

value: 55 yrs


title: Patient_10P6884

description: Gene expression data from patient n°10P6884, frozen FL biopsy

source_name: Patient n°10P6884, woman, 79 yrs, frozen FL biopsy

value: 79 yrs


title: Patient_16T029507

description: Gene expression data from patient n°16T029507, frozen FL biopsy

source_name: Patient n°16T029507, man, 28 yrs, frozen FL biopsy

value: FL biopsy (inguinal lymph node)

value: 28 yrs


title: Patient_15T006944

description: Gene expression data from patient n°15T006944, frozen FL biopsy

source_name: Patient n°15T006944, man, 73 yrs, frozen FL biopsy

value: 73 yrs


title: Patient_10P7213

description: Gene expression data from patient n°10P7213, frozen FL biopsy

source_name: Patient n°10P7213, man, 69 yrs, frozen FL biopsy

value: FL biopsy (axillary lymph node)

value: 69 yrs


title: Patient_14T026127

description: Gene expression data from patient n°14T026127, frozen FL biopsy

source_name: Patient n°14T026127, man, 68 yrs, frozen FL biopsy

value: FL biopsy (supraclavicular lymph node)


title: Patient_12P5669

description: Gene expression data from patient n°12P5669, frozen FL biopsy

source_name: Patient n°12P5669, man, 68 yrs, frozen FL biopsy


title: Patient_13R13781

description: Gene expression data from patient n°13R13781, frozen FL biopsy

source_name: Patient n°13R13781, woman, 77 yrs, frozen FL biopsy

value: FL biopsy (mediastinal lymph node)

value: 77 yrs


title: Control littermate mouse at 2wk, biological rep1

city: PARIS

first: laurent

last: SCHIBLER

address: 24 Boulevard du Montparnasse

department: Imagine Institute, UMR 1163

description: Gene expression data from control fgfr3+/+ mouse at 1wk

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data were analysed in BioConductor2.5, intensities were normalized using the gcrma package and log2-transformed

source_name: fgfr3+/+ mouse at 1wk, biological rep1

label_protocol: standard Affymetrix protocol

extract_protocol: Samples were crushed in liquid nitrogen using a mortar and pestle and RNA extraction was ensured using Qiagen RNeasy Mini kit, following the animal tissue protocol. Total RNA quality was checked with an Agilent2100 Bioanalyzer using RNA 6000 Nano Kits. All RNA samples had an RNA integrity number (RIN) above 8

treatment_protocol: Femoral heads of each mice were collected at slaughter and immediately frozen in liquid nitrogen

value: femoral head

tag: genotype

value: 14 days


title: Patient_13P1678

description: Gene expression data from patient n°13P1678, frozen FL biopsy

source_name: Patient n°13P1678, man, 52 yrs, frozen FL biopsy

value: 52 yrs


title: Patient_12P12434

description: Gene expression data from patient n°12P12434, frozen FL biopsy

source_name: Patient n°12P12434, man, 73 yrs, frozen FL biopsy


title: Control littermate mouse at 3wk, biological rep1

tag: strain

value: female

value: 21 days


title: Patient_13P19788

description: Gene expression data from patient n°13P19788, frozen FL biopsy

source_name: Patient n°13P19788, man, 70 yrs, frozen FL biopsy

value: FL biopsy (cervical lymph node)

value: 70 yrs


title: Patient_15T038384

description: Gene expression data from patient n°15T038384, frozen FL biopsy

source_name: Patient n°15T038384, man, 53  yrs, frozen FL biopsy

value: male

value: 53 yrs


title: Mutant mouse at 4wk, biological rep2

description: Gene expression data from mutant fgfr3Y367C/+  mouse at 1wk

source_name: fgfr3Y367C/+  mouse at 1wk, biological rep1

value: 28 days


title: Patient_14T021716

description: Gene expression data from patient n°14T021716, frozen FL biopsy

source_name: Patient n°14T021716, woman, 60 yrs, frozen FL biopsy

value: FL biopsy (inguinal lymph node)

value: 60 yrs


title: Control littermate mouse at 4wk, biological rep2


title: Control littermate mouse at 4wk, biological rep1


title: Control littermate mouse at 4wk, biological rep3


title: Control littermate mouse at 1wk, biological rep3

value: 7 days


title: Patient_12P5877

description: Gene expression data from patient n°12P5877, frozen FL biopsy

source_name: Patient n°12P5877, man, 76 yrs, frozen FL biopsy

value: 76 yrs


title: Control littermate mouse at 2wk, biological rep3


title: Control littermate mouse at 1wk, biological rep2


title: Control littermate mouse at 3wk, biological rep2


title: Control littermate mouse at 2wk, biological rep2


title: Control littermate mouse at 3wk, biological rep3


title: Mutant mouse at 3wk, biological rep1


title: Mutant mouse at 3wk, biological rep2


title: Mutant mouse at 2wk, biological rep3


title: Mutant mouse at 4wk, biological rep3


title: Mutant mouse at 3wk, biological rep3


title: Patient_12P6659

description: Gene expression data from patient n°12P6659, frozen FL biopsy

source_name: Patient n°12P6659, man, 62 yrs, frozen FL biopsy

value: 62 yrs


title: Mutant mouse at 4wk, biological rep1


title: Control littermate mouse at 1wk, biological rep1


title: Mutant mouse at 2wk, biological rep2


title: Mutant mouse at 1wk, biological rep3


title: lymphoma: 5043_ADR_outgrowth_rep1

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

country: Germany

institute: Charite University Medicine, Berlin

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice in C57/Bl6 bacground
This sample did not pass quality control and was not included in the final analysis

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip® Mouse Gene 1,0 ST Array (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing: Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization). Sample 5043_NS was removed from the data matrix, as it didn't pass quality control.

source_name: primary Eµ-myc;Suv39h1-null lymphoma cells, transduced with Suv39h1-ERT2 and Bcl2; 14 days after terminating ADR treatment

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 3 ug total RNA.

growth_protocol: Primary Emu-myc lymphoma cells explated from lymph nodes of transgenic Emu-myc;Suv39h1-null mice, retrovirally transduced with Suv39h1-ERT2 and Bcl2

extract_protocol: The total RNA from the cells treated as described was prepared using an RNeasy Mini kit (QIAGEN, Valencia, California) according to the manufacturer's instruction.

treatment_protocol: Each lymphomas was treated either with ADR alone or ADR+4-OHT for 5 days in vitro. After 5 days, the cells were plated in ADR/4-OHT-free medium and cultivated for another 14 days.

value: C57/Bl6 bacground

value: Emu-myc B-cell lymphoma


title: Mutant mouse at 1wk, biological rep2

value: femoral head


title: lymphoma: 5043_ADR_rep1

description: Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice in C57/Bl6 bacground

source_name: primary Eµ-myc;Suv39h1-null lymphoma cells, transduced with Suv39h1-ERT2 and Bcl2, ADR-treated for 5 days


title: lymphoma: 5043_ADR+OHT_outgrowth_small_rep1

source_name: primary Eµ-myc;Suv39h1-null lymphoma cells, transduced with Suv39h1-ERT2 and Bcl2; 14 days after terminating ADR+OHT treatment; morphologically small cells FACS-sorted


title: Patient_12P7541

description: Gene expression data from patient n°12P7541, frozen FL biopsy

source_name: Patient n°12P7541, woman, 42 yrs, frozen FL biopsy

value: 42 yrs


title: lymphoma: 5043_ADR+OHT_outgrowth_big_rep1

source_name: primary Eµ-myc;Suv39h1-null lymphoma cells, transduced with Suv39h1-ERT2 and Bcl2; 14 days after terminating ADR+OHT treatment; morphologically big cells FACS-sorted


title: lymphoma: 5043_untreated_rep1

source_name: primary Eµ-myc;Suv39h1-null lymphoma cells, transduced with Suv39h1-ERT2 and Bcl2; untreated


title: lymphoma: 4146_ADR_outgrowth_rep1


title: lymphoma: 4146_ADR+OHT_outgrowth_small_rep1


title: lymphoma: 4936_ADR+OHT_outgrowth_big_rep1


title: lymphoma: 4146_ADR_rep1


title: lymphoma: 4146_untreated_rep1


title: prior_10

source_name: muscle vastus lateralis

value: skeletal muscle

value: prior

value: endurance trained amateur athlete

tag: Sex

tag: weight

tag: height

tag: bmi


title: 1_h_after_exercise_10

value: + 1 h after exrecuse


title: 3_h_after_exercise_10

value: + 3 h after exrecuse


title: lymphoma: 4146_ADR+OHT_rep1

source_name: primary Eµ-myc;Suv39h1-null lymphoma cells, transduced with Suv39h1-ERT2 and Bcl2, ADR+4-OHT-treated for 5 days


title: Mutant mouse at 1wk, biological rep1

value: female


title: Mutant mouse at 2wk, biological rep1

value: 14 days


title: lymphoma: 4936_ADR_outgrowth_rep1


title: lymphoma: 4936_untreated_rep1


title: lymphoma: 4936_ADR+OHT_rep1


title: 6_h_after_exercise_9

value: + 6 h after exrecuse

value: male


title: lymphoma: 4936_ADR+OHT_outgrowth_small_rep1


title: lymphoma: 5043_ADR+OHT_rep1


title: lymphoma: 4936_ADR_rep1


title: 6_h_after_exercise_10


title: 3_h_after_exercise_9


title: lymphoma: 4146_ADR+OHT_outgrowth_big_rep1


title: E14.5 ureters, Gata2cKO vs. control, rep2

city: Hannover

first: Andreas

last: Kispert

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the 'Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7' (Agilent Technologies), except that 1000ng of each labeled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing:
Data extraction, processing and intra-array normalization of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE2_107_Sep09.xml’.  Measurements of on-chip replicates were averaged using the geometric mean of ProcessedSignal (PS) values (for each channel independently) to retrieve one resulting value per probe, sample, and channel. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per feature that exceeded 0.5.
For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500) by the 75th Percentile of the microarray dataset to be normalized. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:
normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)
Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized PS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

label: Alexa Fluor 647

source_name: Control

label_protocol: Synthesis of AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA was performed with the 'Amino Allyl MessageAmp™ II aRNA Amplification Kit' (#AM1753, Life Technologies) according to the manufacturer's recommendations, except that reaction volumes were halved.

extract_protocol: Total RNA was extracted using peqGOLD RNAPure™ (VWR) according to the manufacturer's recommendations.

tag: strain/background

value: NMRI

tag: genotype/variation

value: Male

tag: developmental stage

value: Ureter

label: Alexa Fluor 555

tag: strain/variation


title: E14.5 ureters, Gata2cKO vs. control, rep1

value: Female

tag: tissue


title: 6_h_after_exercise_8

tag: individual


title: prior_9

tag: time point


title: 6_h_after_exercise_7

tag: training status


title: 1_h_after_exercise_7


title: 3_h_after_exercise_7


title: 3_h_after_exercise_8


title: prior_8


title: prior_7


title: 1_h_after_exercise_8


title: 1_h_after_exercise_4


title: prior_3


title: 6_h_after_exercise_3


title: 1_h_after_exercise_3


title: 3_h_after_exercise_3


title: 1_h_after_exercise_9


title: 6_h_after_exercise_4


title: 3_h_after_exercise_4


title: prior_4


title: Female TCDD 100 ng/kg rep6

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

institute: Ontario Institute for Cancer Research

hyb_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

data_processing: Raw array data (CEL files) were loaded into the R statistical environment using the affy package (v1.48.0) of the BioConductor library. Data was investigated for distributional homogeneity, then pre-processed using the RMA algorithm. The custom Probe to Entrez Gene ID map, ragene20strnentrezgcdf (v21.0.0) was used for annotation.

organism: Rattus norvegicus

source_name: liver_female_TCDD treated F0_100 ng/kg

growth_protocol: Upon weaning, same-sex littermates were housed in stainless steel, wire-mesh bottom cages with pelleted rat feed (R36, Lactamin, Stockholm, Sweden) and tap water available ad libitum. The housing environment was maintained at 21±0.2°C and relative humidity at 50±3%, with a 12/12h artificial light/dark cycle.

extract_protocol: Total hepatic RNA was isolated for analysis on microarrays. Briefly, 20 mg hepatic tissue was ground to a powder in liquid nitrogen using a mortar and pestle, followed by rapid homogenization using a Brinkmann Polytron (Polytron PT1600E with a PT-DA 1607 generator). RNA was extracted using an RNeasy Mini Plus Kit following the manufacturer’s recommended protocol (Qiagen, Mississauga, Canada).

treatment_protocol: Pregnant F0 dams were treated by oral gavage with a single bolus of either TCDD (30, 100, 300 or 1000 ng/kg) dissolved in corn oil vehicle or vehicle alone (5mL/kg) on gestational day 11.

value: Sprague-Dawley

tag: lineage (f0 dam, f1 male, f2 male, f3)

tag: tcdd dose (f0)

value: 100 ng/kg

value: liver


title: Male TCDD 100 ng/kg rep6

scan_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

source_name: liver_male_TCDD treated F0_100 ng/kg


title: Male TCDD 300 ng/kg rep6

source_name: liver_male_TCDD treated F0_300 ng/kg

label_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

value: 300 ng/kg


title: Male TCDD 300 ng/kg rep5


title: Female TCDD 30 ng/kg rep8

source_name: liver_female_TCDD treated F0_30 ng/kg

value: 30 ng/kg


title: Female TCDD 1000 ng/kg rep7

source_name: liver_female_TCDD treated F0_1000 ng/kg


title: Female TCDD 300 ng/kg rep4

source_name: liver_female_TCDD treated F0_300 ng/kg


title: Male TCDD 1000 ng/kg rep8

source_name: liver_male_TCDD treated F0_1000 ng/kg


title: Female TCDD 1000 ng/kg rep8


title: Male TCDD 30 ng/kg rep8

source_name: liver_male_TCDD treated F0_30 ng/kg


title: Male TCDD 1000 ng/kg rep7


title: Female TCDD 300 ng/kg rep5


title: Female TCDD 1000 ng/kg rep6


title: Female TCDD 100 ng/kg rep5


title: Male TCDD 1000 ng/kg rep6


title: Male TCDD 100 ng/kg rep5


title: Female CornOil rep6

source_name: liver_female Sprague-Dawley_corn oil treated F0

value: Corn Oil vehicle


title: Female TCDD 1000 ng/kg rep5


title: Female TCDD 1000 ng/kg rep1


title: Male CornOil rep5

source_name: liver_male Sprague-Dawley_corn oil treated F0


title: Female CornOil rep5


title: Female TCDD 1000 ng/kg rep2


title: Male TCDD 1000 ng/kg rep3


title: Female TCDD 1000 ng/kg rep4


title: Male TCDD 1000 ng/kg rep4


title: Female TCDD 1000 ng/kg rep3


title: Male TCDD 1000 ng/kg rep5


title: Male TCDD 1000 ng/kg rep1


title: Female CornOil rep4


title: Male TCDD 1000 ng/kg rep2


title: Male TCDD 100 ng/kg rep4


title: Female TCDD 30 ng/kg rep6


title: Male CornOil rep3


title: Female TCDD 100 ng/kg rep3


title: Male CornOil rep4


title: Female TCDD 30 ng/kg rep7


title: Female CornOil rep3


title: Male CornOil rep2


title: Male TCDD 30 ng/kg rep7


title: Female TCDD 100 ng/kg rep4


title: Male TCDD 100 ng/kg rep3


title: Female TCDD 30 ng/kg rep4


title: Male TCDD 30 ng/kg rep6


title: Male CornOil rep1


title: Female CornOil rep2


title: Male TCDD 30 ng/kg rep5


title: Female TCDD 30 ng/kg rep5


title: Female CornOil rep1


title: Female TCDD 30 ng/kg rep3


title: Male TCDD 30 ng/kg rep2


title: Male TCDD 300 ng/kg rep4


title: Female TCDD 300 ng/kg rep3


title: Female TCDD 30 ng/kg rep2


title: Male TCDD 30 ng/kg rep4


title: scMNase-seq_EILP_Tcf7KO_GC1428

city: Bethesda

first: Keji

last: Zhao

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

data_processing:
Basecalling by RTA 1.18.66.3, Illumina instrument run time analysis software
Sequencing reads were aligned to mouse genome (mm9) using Bowtie2 with default parameters.
Reads from replicates were merged and redundant reads were removed from further analysis.
For ChIC-seq samples, reads from replicates were merged for peak calling. Peak calling were performed using MACS2 with default parameters.
For scMNase-seq samples, reads with length between 140 and 180 bp were selected as nucleosome reads while reads with length less than 80 bp were selected as subnucleosomal reads.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIC-seq and DNase-seq samples, .wig files contain normalized tag density, which can be uploaded to UCSC genome browser for visulization. For scMNase-seq samples, bed files provide genomic positions on chromosomes for nucleosomes (140-180 bp) and subnucleosomes (<80 bp).

growth_protocol: Samples were isolated by cell sorting from bone marrow single cell suspensions

extract_protocol:
For scMNase-Seq, single live cells for EILP, EILPTcf7-/-, ILCP were sorted by flow cytometer and deposited directly into 96 well plate, which containing 32 μl of cell lysis buffer  (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 2 mM CaCl2, 0.1% Triton X-100). 32 μl of cell lysis buffer. 8 μl diluted MNase (1:3000 in lysis buffer) was added to the sorted cells and incubated at 37 °C for 5 minutes. The reaction was stopped by addition of 80 μl of stop buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EGTA), and 1 μl of 20 mg/ml Proteinase K. Following incubation at 65°C for 2 hours, DNA was purified by Phenol-chloroform extraction and precipitation with ethanol in the presence of glycogen.
For MNase-seq libraries, DNA were end-repaired in 50 μl of reaction volume at RT for 45 minutes using End-It DNA-Repair kit (Epicenter, Cat#ER81050) according to the manufacturer’s instructions. Next, DNA were purified by enzyme reaction clean kit (Qiagen). The blunted DNA fragments were subject to adding 3 end A base using the Klenow fragment (3′ → 5′ exo-) (NEB). The DNA was then ligated with the ‘‘Y’’-shaped Illumina adaptor and amplified for 16 cycles using indexing primers with the PCR condition: 98°C,10”; 67°C, 30”; 72°C, 30”. PCR products between 150-250 bp were isolated on 2% E-gel for sequencing on Illumina Hiseq-3000.

value: bone marrow

tag: sorting profile

value: Lin- Kit+ 2B4+ a4b7+ GFP+ Thy1-


title: scMNase-seq_EILP_Tcf7KO_GC1426


title: scMNase-seq_EILP_Tcf7KO_GC1427


title: scMNase-seq_EILP_Tcf7KO_GC1425


title: scMNase-seq_EILP_Tcf7KO_GC1424


title: scMNase-seq_EILP_Tcf7KO_GC1421


title: scMNase-seq_EILP_Tcf7KO_GC1423


title: Female TCDD 300 ng/kg rep1


title: Male TCDD 30 ng/kg rep3


title: Male TCDD 300 ng/kg rep2


title: Female TCDD 300 ng/kg rep2


title: scMNase-seq_EILP_Tcf7KO_GC1420


title: Male TCDD 300 ng/kg rep1


title: Male TCDD 300 ng/kg rep3


title: scMNase-seq_EILP_Tcf7KO_GC1418


title: scMNase-seq_EILP_Tcf7KO_GC1417


title: scMNase-seq_EILP_Tcf7KO_GC1404


title: scMNase-seq_EILP_Tcf7KO_GC1402


title: scMNase-seq_EILP_Tcf7KO_GC1419


title: scMNase-seq_EILP_Tcf7KO_GC1401


title: scMNase-seq_EILP_Tcf7KO_GC1396


title: scMNase-seq_EILP_Tcf7KO_GC1393


title: scMNase-seq_EILP_Tcf7KO_GC1397


title: scMNase-seq_EILP_Tcf7KO_GC1385


title: scMNase-seq_EILP_Tcf7KO_GC1389


title: scMNase-seq_EILP_Tcf7KO_GC1391


title: scMNase-seq_EILP_Tcf7KO_GC1387


title: scMNase-seq_EILP_Tcf7KO_GC1395


title: scMNase-seq_EILP_Tcf7KO_GC1340


title: scMNase-seq_EILP_Tcf7KO_GC1342


title: scMNase-seq_EILP_Tcf7KO_GC1341


title: scMNase-seq_EILP_Tcf7KO_GC1392


title: Male TCDD 100 ng/kg rep1


title: Female TCDD 30 ng/kg rep1


title: scMNase-seq_EILP_Tcf7KO_GC1344


title: Female TCDD 100 ng/kg rep2


title: Male TCDD 100 ng/kg rep2


title: Female TCDD 100 ng/kg rep1


title: scMNase-seq_EILP_Tcf7KO_GC1383


title: scMNase-seq_EILP_Tcf7KO_GC1338


title: scMNase-seq_EILP_Tcf7KO_GC1339


title: scMNase-seq_EILP_Tcf7KO_GC1337


title: scMNase-seq_EILP_Tcf7KO_GC1335


title: scMNase-seq_EILP_Tcf7KO_GC1336


title: scMNase-seq_EILP_Tcf7KO_GC1330


title: scMNase-seq_EILP_Tcf7KO_GC1331


title: scMNase-seq_EILP_Tcf7KO_GC1334


title: Male TCDD 30 ng/kg rep1


title: scMNase-seq_EILP_Tcf7KO_GC1333


title: scMNase-seq_EILP_Tcf7KO_GC1303


title: scMNase-seq_EILP_Tcf7KO_GC1332


title: scMNase-seq_EILP_Tcf7KO_GC1301


title: scMNase-seq_EILP_Tcf7KO_GC1298


title: scMNase-seq_EILP_Tcf7KO_GC1327


title: scMNase-seq_EILP_Tcf7KO_GC1305


title: scMNase-seq_EILP_Tcf7KO_GC1328


title: scMNase-seq_EILP_Tcf7KO_GC1295


title: scMNase-seq_EILP_Tcf7KO_GC1302


title: scMNase-seq_EILP_Tcf7KO_GC1296


title: scMNase-seq_EILP_Tcf7KO_GC1300


title: scMNase-seq_EILP_Tcf7KO_GC1294


title: scMNase-seq_EILP_Tcf7KO_GC1292


title: scMNase-seq_EILP_Tcf7KO_GC1291


title: scMNase-seq_EILP_Tcf7KO_GC1289


title: scMNase-seq_EILP_Tcf7KO_GC1285


title: scMNase-seq_EILP_Tcf7KO_GC1287


title: scMNase-seq_EILP_Tcf7KO_GC1248


title: scMNase-seq_EILP_Tcf7KO_GC1247


title: scMNase-seq_EILP_Tcf7KO_GC1243


title: scMNase-seq_EILP_Tcf7KO_GC1241


title: scMNase-seq_EILP_Tcf7KO_GC1245


title: scMNase-seq_EILP_Tcf7KO_GC1242


title: scMNase-seq_EILP_Tcf7KO_GC1304


title: scMNase-seq_EILP_Tcf7KO_GC1240


title: scMNase-seq_EILP_Tcf7KO_GC1234


title: scMNase-seq_EILP_Tcf7KO_GC1232


title: scMNase-seq_EILP_Tcf7KO_GC1238


title: scMNase-seq_EILP_Tcf7KO_GC1230


title: scMNase-seq_EILP_Tcf7KO_GC1229


title: scMNase-seq_EILP_Tcf7KO_GC1236


title: scMNase-seq_EILP_Tcf7KO_GC1227


title: scMNase-seq_EILP_Tcf7KO_GC1228


title: scMNase-seq_EILP_Tcf7KO_GC1202


title: scMNase-seq_EILP_Tcf7KO_GC1204


title: scMNase-seq_EILP_Tcf7KO_GC1210


title: scMNase-seq_EILP_Tcf7KO_GC1201


title: scMNase-seq_EILP_Tcf7KO_GC1206


title: scMNase-seq_EILP_Tcf7KO_GC1208


title: scMNase-seq_EILP_Tcf7KO_GC1188


title: scMNase-seq_EILP_Tcf7KO_GC1209


title: scMNase-seq_EILP_Tcf7KO_GC1212


title: scMNase-seq_EILP_Tcf7KO_GC1190


title: scMNase-seq_EILP_Tcf7KO_GC1189


title: scMNase-seq_EILP_Tcf7KO_GC1184


title: scMNase-seq_EILP_Tcf7KO_GC1187


title: scMNase-seq_EILP_Tcf7KO_GC1183


title: scMNase-seq_EILP_Tcf7KO_GC1181


title: scMNase-seq_EILP_Tcf7KO_GC1235


title: scMNase-seq_EILP_Tcf7KO_GC1178


title: scMNase-seq_EILP_Tcf7KO_GC1177


title: scMNase-seq_EILP_Tcf7KO_GC1176


title: scMNase-seq_EILP_Tcf7KO_GC1168


title: scMNase-seq_EILP_Tcf7KO_GC1173


title: scMNase-seq_EILP_Tcf7KO_GC1162


title: scMNase-seq_EILP_Tcf7KO_GC1164


title: scMNase-seq_EILP_Tcf7KO_GC1207


title: scMNase-seq_EILP_Tcf7KO_GC1199


title: scMNase-seq_EILP_Tcf7KO_GC1160


title: scMNase-seq_EILP_Tcf7KO_GC1157


title: scMNase-seq_EILP_Tcf7KO_GC1156


title: scMNase-seq_EILP_Tcf7KO_GC1151


title: scMNase-seq_EILP_Tcf7KO_GC1149


title: scMNase-seq_EILP_Tcf7KO_GC1148


title: scMNase-seq_EILP_Tcf7KO_GC1145


title: scMNase-seq_EILP_Tcf7KO_GC1155


title: scMNase-seq_EILP_Tcf7KO_GC1142


title: scMNase-seq_EILP_Tcf7KO_GC1154


title: scMNase-seq_EILP_Tcf7KO_GC1138


title: scMNase-seq_EILP_Tcf7KO_GC1150


title: scMNase-seq_EILP_Tcf7KO_GC1134


title: scMNase-seq_EILP_Tcf7KO_GC1147


title: scMNase-seq_EILP_Tcf7KO_GC1133


title: scMNase-seq_EILP_Tcf7KO_GC1132


title: scMNase-seq_EILP_Tcf7KO_GC1140


title: scMNase-seq_EILP_Tcf7KO_GC1106


title: scMNase-seq_EILP_Tcf7KO_GC1114


title: scMNase-seq_EILP_Tcf7KO_GC1159


title: scMNase-seq_EILP_Tcf7KO_GC1104


title: scMNase-seq_EILP_Tcf7KO_GC1113


title: scMNase-seq_EILP_Tcf7KO_GC1103


title: scMNase-seq_EILP_Tcf7KO_GC1093


title: scMNase-seq_EILP_Tcf7KO_GC0995


title: scMNase-seq_EILP_Tcf7KO_GC0994


title: scMNase-seq_EILP_Tcf7KO_GC1099


title: scMNase-seq_EILP_Tcf7KO_GC0988


title: scMNase-seq_EILP_Tcf7KO_GC1115


title: scMNase-seq_EILP_Tcf7KO_GC0987


title: scMNase-seq_EILP_Tcf7KO_GC0986


title: scMNase-seq_EILP_Tcf7KO_GC1144


title: scMNase-seq_EILP_Tcf7KO_GC1107


title: scMNase-seq_EILP_Tcf7KO_GC0979


title: scMNase-seq_EILP_Tcf7KO_GC0978


title: scMNase-seq_EILP_Tcf7KO_GC0973


title: scMNase-seq_EILP_Tcf7KO_GC0970


title: scMNase-seq_EILP_Tcf7KO_GC0971


title: scMNase-seq_EILP_Tcf7KO_GC0966


title: scMNase-seq_EILP_Tcf7KO_GC0672


title: scMNase-seq_EILP_Tcf7KO_GC0963


title: scMNase-seq_EILP_Tcf7KO_GC0961


title: scMNase-seq_EILP_Tcf7KO_GC0962


title: scMNase-seq_EILP_Tcf7KO_GC0671


title: scMNase-seq_EILP_Tcf7KO_GC0669


title: scMNase-seq_EILP_Tcf7KO_GC0670


title: scMNase-seq_EILP_Tcf7KO_GC0666


title: scMNase-seq_EILP_Tcf7KO_GC0668


title: scMNase-seq_EILP_Tcf7KO_GC0665


title: scMNase-seq_EILP_Tcf7KO_GC0664


title: scMNase-seq_EILP_Tcf7KO_GC0661


title: scMNase-seq_EILP_Tcf7KO_GC0658


title: scMNase-seq_EILP_Tcf7KO_GC0660


title: scMNase-seq_EILP_Tcf7KO_GC0980


title: scMNase-seq_EILP_Tcf7KO_GC0655


title: scMNase-seq_EILP_Tcf7KO_GC0656


title: scMNase-seq_EILP_Tcf7KO_GC0652


title: scMNase-seq_EILP_Tcf7KO_GC0974


title: scMNase-seq_EILP_Tcf7KO_GC0653


title: scMNase-seq_EILP_Tcf7KO_GC0967


title: scMNase-seq_EILP_Tcf7KO_GC0651


title: scMNase-seq_EILP_Tcf7KO_GC0643


title: scMNase-seq_EILP_Tcf7KO_GC0632


title: scMNase-seq_EILP_Tcf7KO_GC0633


title: scMNase-seq_EILP_Tcf7KO_GC0631


title: scMNase-seq_EILP_Tcf7KO_GC0630


title: scMNase-seq_EILP_Tcf7KO_GC0629


title: scMNase-seq_EILP_Tcf7KO_GC0628


title: scMNase-seq_EILP_Tcf7KO_GC0626


title: scMNase-seq_EILP_Tcf7KO_GC0627


title: scMNase-seq_EILP_Tcf7KO_GC0663


title: scMNase-seq_EILP_Tcf7KO_GC0659


title: scMNase-seq_EILP_Tcf7KO_GC0622


title: scMNase-seq_EILP_Tcf7KO_GC0625


title: scMNase-seq_EILP_Tcf7KO_GC0621


title: scMNase-seq_EILP_Tcf7KO_GC0624


title: scMNase-seq_EILP_Tcf7KO_GC0623


title: scMNase-seq_EILP_Tcf7KO_GC0618


title: scMNase-seq_EILP_Tcf7KO_GC0614


title: scMNase-seq_EILP_Tcf7KO_GC0616


title: scMNase-seq_EILP_Tcf7KO_GC0613


title: scMNase-seq_EILP_Tcf7KO_GC0607


title: scMNase-seq_EILP_Tcf7KO_GC0645


title: scMNase-seq_EILP_Tcf7KO_GC0606


title: scMNase-seq_EILP_Tcf7KO_GC0600


title: scMNase-seq_EILP_Tcf7KO_GC0599


title: scMNase-seq_EILP_Tcf7KO_GC0598


title: scMNase-seq_EILP_Tcf7KO_GC0597


title: scMNase-seq_EILP_Tcf7KO_GC0596


title: scMNase-seq_EILP_Tcf7KO_GC0583


title: scMNase-seq_EILP_Tcf7KO_GC0581


title: scMNase-seq_EILP_Tcf7KO_GC0585


title: scMNase-seq_EILP_Tcf7KO_GC0594


title: scMNase-seq_EILP_Tcf7KO_GC0595


title: scMNase-seq_EILP_Tcf7KO_GC0589


title: scMNase-seq_EILP_Tcf7KO_GC0586


title: scMNase-seq_EILP_Tcf7KO_GC0590


title: scMNase-seq_EILP_Tcf7KO_GC0593


title: scMNase-seq_EILP_Tcf7KO_GC0580


title: scMNase-seq_EILP_Tcf7KO_GC0185


title: scMNase-seq_EILP_Tcf7KO_GC0579


title: scMNase-seq_EILP_Tcf7KO_GC0187


title: scMNase-seq_EILP_Tcf7KO_GC0184


title: scMNase-seq_EILP_Tcf7KO_GC0186


title: scMNase-seq_EILP_Tcf7KO_GC0578


title: scMNase-seq_EILP_Tcf7KO_GC0189


title: scMNase-seq_EILP_Tcf7KO_GC0178


title: scMNase-seq_EILP_Tcf7KO_GC0183


title: scMNase-seq_EILP_Tcf7KO_GC0173


title: scMNase-seq_EILP_Tcf7KO_GC0162


title: scMNase-seq_EILP_Tcf7KO_GC0169


title: scMNase-seq_EILP_Tcf7KO_GC0161


title: scMNase-seq_EILP_Tcf7KO_GC0168


title: scMNase-seq_EILP_Tcf7KO_GC0160


title: scMNase-seq_EILP_Tcf7KO_GC0592


title: scMNase-seq_EILP_Tcf7KO_GC0164


title: scMNase-seq_EILP_Tcf7KO_GC0175


title: scMNase-seq_EILP_Tcf7KO_GC0587


title: scMNase-seq_EILP_Tcf7KO_GC0156


title: scMNase-seq_EILP_Tcf7KO_GC0155


title: scMNase-seq_EILP_Tcf7KO_GC0157


title: scMNase-seq_EILP_Tcf7KO_GC0177


title: scMNase-seq_EILP_Tcf7KO_GC0144


title: scMNase-seq_EILP_Tcf7KO_GC0153


title: scMNase-seq_EILP_Tcf7KO_GC0151


title: scMNase-seq_EILP_Tcf7KO_GC0138


title: scMNase-seq_EILP_Tcf7KO_GC0139


title: scMNase-seq_EILP_Tcf7KO_GC0140


title: scMNase-seq_EILP_Tcf7KO_GC0128


title: scMNase-seq_EILP_Tcf7KO_GC0143


title: scMNase-seq_EILP_Tcf7KO_GC0134


title: scMNase-seq_EILP_Tcf7KO_GC0133


title: scMNase-seq_EILP_Tcf7KO_GC0152


title: scMNase-seq_EILP_Tcf7KO_GC0136


title: scMNase-seq_EILP_Tcf7KO_GC0142


title: scMNase-seq_EILP_Tcf7KO_GC0125


title: scMNase-seq_EILP_Tcf7KO_GC0122


title: scMNase-seq_EILP_Tcf7KO_GC0126


title: scMNase-seq_EILP_Tcf7KO_GC0123


title: scMNase-seq_EILP_Tcf7KO_GC0124


title: scMNase-seq_EILP_Tcf7KO_GC0121


title: scMNase-seq_EILP_Tcf7KO_GC0115


title: scMNase-seq_EILP_Tcf7KO_GC0114


title: scMNase-seq_EILP_Tcf7KO_GC0116


title: scMNase-seq_EILP_Tcf7KO_GC0158


title: scMNase-seq_EILP_Tcf7KO_GC0147


title: scMNase-seq_EILP_Tcf7KO_GC0111


title: scMNase-seq_EILP_Tcf7KO_GC0110


title: scMNase-seq_EILP_Tcf7KO_GC0107


title: scMNase-seq_EILP_Tcf7KO_GC0105


title: scMNase-seq_EILP_Tcf7KO_GC0106


title: scMNase-seq_EILP_Tcf7KO_GC0101


title: scMNase-seq_EILP_Tcf7KO_GC0099


title: scMNase-seq_ILCP_GC1436

source_name: ILCP

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1+ IL-7Ra+


title: scMNase-seq_ILCP_GC1435


title: scMNase-seq_ILCP_GC1434


title: scMNase-seq_ILCP_GC1431


title: scMNase-seq_ILCP_GC1430


title: scMNase-seq_ILCP_GC1375


title: scMNase-seq_EILP_Tcf7KO_GC0118


title: scMNase-seq_ILCP_GC1432


title: scMNase-seq_ILCP_GC1374


title: scMNase-seq_ILCP_GC1370


title: scMNase-seq_ILCP_GC1369


title: scMNase-seq_ILCP_GC1307


title: scMNase-seq_ILCP_GC1373


title: scMNase-seq_ILCP_GC1372


title: scMNase-seq_ILCP_GC1308


title: scMNase-seq_ILCP_GC1284


title: scMNase-seq_ILCP_GC1278


title: scMNase-seq_ILCP_GC1279


title: scMNase-seq_ILCP_GC1283


title: scMNase-seq_ILCP_GC1277


title: scMNase-seq_EILP_Tcf7KO_GC0103


title: scMNase-seq_ILCP_GC1276


title: scMNase-seq_ILCP_GC1437


title: scMNase-seq_ILCP_GC1429


title: scMNase-seq_ILCP_GC0959


title: scMNase-seq_ILCP_GC0958


title: scMNase-seq_ILCP_GC0957


title: scMNase-seq_ILCP_GC0954


title: scMNase-seq_ILCP_GC0955


title: scMNase-seq_ILCP_GC0951


title: scMNase-seq_ILCP_GC0950


title: scMNase-seq_ILCP_GC0948


title: scMNase-seq_ILCP_GC0949


title: scMNase-seq_ILCP_GC0947


title: scMNase-seq_ILCP_GC0946


title: scMNase-seq_ILCP_GC0944


title: scMNase-seq_ILCP_GC0945


title: scMNase-seq_ILCP_GC0943


title: scMNase-seq_ILCP_GC0941


title: scMNase-seq_ILCP_GC1274


title: scMNase-seq_ILCP_GC0942


title: scMNase-seq_ILCP_GC0939


title: scMNase-seq_ILCP_GC0937


title: scMNase-seq_ILCP_GC0938


title: scMNase-seq_ILCP_GC0936


title: scMNase-seq_ILCP_GC0960


title: scMNase-seq_ILCP_GC0933


title: scMNase-seq_ILCP_GC0953


title: scMNase-seq_ILCP_GC0934


title: scMNase-seq_ILCP_GC0931


title: scMNase-seq_ILCP_GC0956


title: scMNase-seq_ILCP_GC0932


title: scMNase-seq_ILCP_GC0952


title: scMNase-seq_ILCP_GC0918


title: scMNase-seq_ILCP_GC0924


title: scMNase-seq_ILCP_GC0923


title: scMNase-seq_ILCP_GC0922


title: scMNase-seq_ILCP_GC0940


title: scMNase-seq_ILCP_GC0920


title: scMNase-seq_ILCP_GC0915


title: scMNase-seq_ILCP_GC0921


title: scMNase-seq_ILCP_GC0917


title: scMNase-seq_ILCP_GC0916


title: scMNase-seq_ILCP_GC0919


title: scMNase-seq_ILCP_GC0914


title: scMNase-seq_ILCP_GC0911


title: scMNase-seq_ILCP_GC0909


title: scMNase-seq_ILCP_GC0906


title: scMNase-seq_ILCP_GC0908


title: scMNase-seq_ILCP_GC0910


title: scMNase-seq_ILCP_GC0905


title: scMNase-seq_ILCP_GC0904


title: scMNase-seq_ILCP_GC0912


title: scMNase-seq_ILCP_GC0907


title: scMNase-seq_ILCP_GC0903


title: scMNase-seq_ILCP_GC0899


title: scMNase-seq_ILCP_GC0902


title: scMNase-seq_ILCP_GC0900


title: scMNase-seq_ILCP_GC0894


title: scMNase-seq_ILCP_GC0896


title: scMNase-seq_ILCP_GC0898


title: scMNase-seq_ILCP_GC0893


title: scMNase-seq_ILCP_GC0913


title: scMNase-seq_ILCP_GC0892


title: scMNase-seq_ILCP_GC0889


title: scMNase-seq_ILCP_GC0891


title: scMNase-seq_ILCP_GC0885


title: scMNase-seq_ILCP_GC0883


title: scMNase-seq_ILCP_GC0884


title: scMNase-seq_ILCP_GC0886


title: scMNase-seq_ILCP_GC0887


title: scMNase-seq_ILCP_GC0888


title: scMNase-seq_ILCP_GC0880


title: scMNase-seq_ILCP_GC0879


title: scMNase-seq_ILCP_GC0878


title: scMNase-seq_ILCP_GC0881


title: scMNase-seq_ILCP_GC0876


title: scMNase-seq_ILCP_GC0877


title: scMNase-seq_ILCP_GC0872


title: scMNase-seq_ILCP_GC0875


title: scMNase-seq_ILCP_GC0874


title: scMNase-seq_ILCP_GC0873


title: scMNase-seq_ILCP_GC0871


title: scMNase-seq_ILCP_GC0870


title: scMNase-seq_ILCP_GC0890


title: scMNase-seq_ILCP_GC0869


title: scMNase-seq_ILCP_GC0868


title: scMNase-seq_ILCP_GC0865


title: scMNase-seq_ILCP_GC0867


title: scMNase-seq_ILCP_GC0766


title: scMNase-seq_ILCP_GC0768


title: scMNase-seq_ILCP_GC0767


title: scMNase-seq_ILCP_GC0765


title: scMNase-seq_ILCP_GC0763


title: scMNase-seq_ILCP_GC0882


title: scMNase-seq_ILCP_GC0764


title: scMNase-seq_ILCP_GC0762


title: scMNase-seq_ILCP_GC0760


title: scMNase-seq_ILCP_GC0761


title: scMNase-seq_ILCP_GC0757


title: scMNase-seq_ILCP_GC0755


title: scMNase-seq_ILCP_GC0754


title: scMNase-seq_ILCP_GC0758


title: scMNase-seq_ILCP_GC0752


title: scMNase-seq_ILCP_GC0753


title: scMNase-seq_ILCP_GC0750


title: scMNase-seq_ILCP_GC0748


title: scMNase-seq_ILCP_GC0749


title: scMNase-seq_ILCP_GC0751


title: scMNase-seq_ILCP_GC0747


title: scMNase-seq_ILCP_GC0744


title: scMNase-seq_ILCP_GC0742


title: scMNase-seq_ILCP_GC0740


title: scMNase-seq_ILCP_GC0738


title: scMNase-seq_ILCP_GC0737


title: scMNase-seq_ILCP_GC0733


title: scMNase-seq_ILCP_GC0731


title: scMNase-seq_ILCP_GC0741


title: scMNase-seq_ILCP_GC0730


title: scMNase-seq_ILCP_GC0739


title: scMNase-seq_ILCP_GC0736


title: scMNase-seq_ILCP_GC0735


title: scMNase-seq_ILCP_GC0759


title: scMNase-seq_ILCP_GC0734


title: scMNase-seq_ILCP_GC0722


title: scMNase-seq_ILCP_GC0728


title: scMNase-seq_ILCP_GC0724


title: scMNase-seq_ILCP_GC0725


title: scMNase-seq_ILCP_GC0727


title: scMNase-seq_ILCP_GC0713


title: scMNase-seq_ILCP_GC0721


title: scMNase-seq_ILCP_GC0726


title: scMNase-seq_ILCP_GC0716


title: scMNase-seq_ILCP_GC0723


title: scMNase-seq_ILCP_GC0718


title: scMNase-seq_ILCP_GC0717


title: scMNase-seq_ILCP_GC0732


title: scMNase-seq_ILCP_GC0711


title: scMNase-seq_ILCP_GC0709


title: scMNase-seq_ILCP_GC0708


title: scMNase-seq_ILCP_GC0707


title: scMNase-seq_ILCP_GC0706


title: scMNase-seq_ILCP_GC0704


title: scMNase-seq_ILCP_GC0702


title: scMNase-seq_ILCP_GC0701


title: scMNase-seq_ILCP_GC0703


title: scMNase-seq_ILCP_GC0699


title: scMNase-seq_ILCP_GC0720


title: scMNase-seq_ILCP_GC0697


title: scMNase-seq_ILCP_GC0694


title: scMNase-seq_ILCP_GC0692


title: scMNase-seq_ILCP_GC0689


title: scMNase-seq_ILCP_GC0688


title: scMNase-seq_ILCP_GC0696


title: scMNase-seq_ILCP_GC0698


title: scMNase-seq_ILCP_GC0687


title: scMNase-seq_ILCP_GC0682


title: scMNase-seq_ILCP_GC0683


title: scMNase-seq_ILCP_GC0681


title: scMNase-seq_ILCP_GC0719


title: scMNase-seq_ILCP_GC0680


title: scMNase-seq_ILCP_GC0690


title: scMNase-seq_ILCP_GC0691


title: scMNase-seq_ILCP_GC0678


title: scMNase-seq_ILCP_GC0677


title: scMNase-seq_ILCP_GC0675


title: scMNase-seq_ILCP_GC0676


title: scMNase-seq_ILCP_GC0673


title: scMNase-seq_ILCP_GC0287


title: scMNase-seq_ILCP_GC0288


title: scMNase-seq_ILCP_GC0286


title: scMNase-seq_ILCP_GC0285


title: scMNase-seq_ILCP_GC0282


title: scMNase-seq_ILCP_GC0283


title: scMNase-seq_ILCP_GC0284


title: scMNase-seq_ILCP_GC0281


title: scMNase-seq_ILCP_GC0686


title: scMNase-seq_ILCP_GC0685


title: scMNase-seq_ILCP_GC0280


title: scMNase-seq_ILCP_GC0252


title: scMNase-seq_ILCP_GC0279


title: scMNase-seq_ILCP_GC0278


title: scMNase-seq_ILCP_GC0277


title: scMNase-seq_ILCP_GC0251


title: scMNase-seq_ILCP_GC0249


title: scMNase-seq_ILCP_GC0250


title: scMNase-seq_ILCP_GC0245


title: scMNase-seq_ILCP_GC0246


title: scMNase-seq_ILCP_GC0239


title: scMNase-seq_ILCP_GC0240


title: scMNase-seq_ILCP_GC0238


title: scMNase-seq_ILCP_GC0243


title: scMNase-seq_ILCP_GC0242


title: scMNase-seq_ILCP_GC0237


title: scMNase-seq_ILCP_GC0235


title: scMNase-seq_ILCP_GC0232


title: scMNase-seq_ILCP_GC0234


title: scMNase-seq_ILCP_GC0231


title: scMNase-seq_ILCP_GC0230


title: scMNase-seq_ILCP_GC0229


title: scMNase-seq_ILCP_GC0226


title: scMNase-seq_ILCP_GC0228


title: scMNase-seq_ILCP_GC0223


title: scMNase-seq_ILCP_GC0227


title: scMNase-seq_ILCP_GC0222


title: scMNase-seq_ILCP_GC0221


title: scMNase-seq_ILCP_GC0220


title: scMNase-seq_ILCP_GC0219


title: scMNase-seq_ILCP_GC0241


title: scMNase-seq_ILCP_GC0215


title: scMNase-seq_ILCP_GC0216


title: scMNase-seq_ILCP_GC0218


title: scMNase-seq_ILCP_GC0214


title: scMNase-seq_ILCP_GC0236


title: scMNase-seq_ILCP_GC0212


title: scMNase-seq_ILCP_GC0210


title: scMNase-seq_ILCP_GC0209


title: scMNase-seq_ILCP_GC0207


title: scMNase-seq_ILCP_GC0205


title: scMNase-seq_ILCP_GC0204


title: scMNase-seq_ILCP_GC0198


title: scMNase-seq_ILCP_GC0203


title: scMNase-seq_ILCP_GC0201


title: scMNase-seq_ILCP_GC0199


title: scMNase-seq_ILCP_GC0202


title: scMNase-seq_ILCP_GC0197


title: scMNase-seq_ILCP_GC0196


title: scMNase-seq_ILCP_GC0195


title: scMNase-seq_ILCP_GC0213


title: scMNase-seq_EILP_GC1422

source_name: EILP

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1-


title: scMNase-seq_ILCP_GC0194


title: scMNase-seq_ILCP_GC0211


title: scMNase-seq_EILP_GC1408


title: scMNase-seq_EILP_GC1405


title: scMNase-seq_EILP_GC1406


title: scMNase-seq_EILP_GC1407


title: scMNase-seq_ILCP_GC0208


title: scMNase-seq_EILP_GC1410


title: scMNase-seq_EILP_GC1409


title: scMNase-seq_ILCP_GC0206


title: scMNase-seq_EILP_GC1353


title: scMNase-seq_EILP_GC1365


title: scMNase-seq_EILP_GC1354


title: scMNase-seq_EILP_GC1366


title: scMNase-seq_EILP_GC1367


title: scMNase-seq_EILP_GC1368


title: scMNase-seq_EILP_GC1364


title: scMNase-seq_EILP_GC1349


title: scMNase-seq_EILP_GC1348


title: scMNase-seq_EILP_GC1350


title: scMNase-seq_EILP_GC1324


title: scMNase-seq_EILP_GC1346


title: scMNase-seq_EILP_GC1347


title: scMNase-seq_EILP_GC1345


title: scMNase-seq_EILP_GC1320


title: scMNase-seq_EILP_GC1321


title: scMNase-seq_EILP_GC1317


title: scMNase-seq_EILP_GC1272


title: scMNase-seq_EILP_GC1306


title: scMNase-seq_EILP_GC1318


title: scMNase-seq_EILP_GC1269


title: scMNase-seq_EILP_GC1316


title: scMNase-seq_EILP_GC1265


title: scMNase-seq_EILP_GC1315


title: scMNase-seq_EILP_GC1267


title: scMNase-seq_EILP_GC1270


title: scMNase-seq_EILP_GC1266


title: scMNase-seq_EILP_GC1351


title: scMNase-seq_EILP_GC1260


title: scMNase-seq_EILP_GC1263


title: scMNase-seq_EILP_GC1264


title: scMNase-seq_EILP_GC1268


title: scMNase-seq_EILP_GC1257


title: scMNase-seq_EILP_GC1323


title: scMNase-seq_EILP_GC1259


title: scMNase-seq_EILP_GC1253


title: scMNase-seq_EILP_GC1254


title: scMNase-seq_EILP_GC1256


title: scMNase-seq_EILP_GC1261


title: scMNase-seq_EILP_GC1252


title: scMNase-seq_EILP_GC1250


title: scMNase-seq_EILP_GC1249


title: scMNase-seq_EILP_GC1092


title: scMNase-seq_EILP_GC1091


title: scMNase-seq_EILP_GC1262


title: scMNase-seq_EILP_GC1086


title: scMNase-seq_EILP_GC1083


title: scMNase-seq_EILP_GC1084


title: scMNase-seq_EILP_GC1087


title: scMNase-seq_EILP_GC1258


title: scMNase-seq_EILP_GC1088


title: scMNase-seq_EILP_GC1080


title: scMNase-seq_EILP_GC1078


title: scMNase-seq_EILP_GC1081


title: scMNase-seq_EILP_GC1082


title: scMNase-seq_EILP_GC1251


title: scMNase-seq_EILP_GC1079


title: scMNase-seq_EILP_GC1076


title: scMNase-seq_EILP_GC1071


title: scMNase-seq_EILP_GC1072


title: scMNase-seq_EILP_GC1077


title: scMNase-seq_EILP_GC1075


title: scMNase-seq_EILP_GC1073


title: scMNase-seq_EILP_GC1070


title: scMNase-seq_EILP_GC1068


title: scMNase-seq_EILP_GC1085


title: scMNase-seq_EILP_GC1062


title: scMNase-seq_EILP_GC1065


title: scMNase-seq_EILP_GC1066


title: scMNase-seq_EILP_GC1064


title: scMNase-seq_EILP_GC1059


title: scMNase-seq_EILP_GC1061


title: scMNase-seq_EILP_GC1060


title: scMNase-seq_EILP_GC1058


title: N1_LPBS2

city: Hangzhou

first: He

middle: Qiu

last: ju

address: Yuhangtang road

institute: Zhejiang University

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

organism: Oryza sativa Japonica Group

source_name: Shoot

extract_protocol:
Total RNA was isolated from the shoots and roots of 7-day-old seedlings treated with 200 μM or 10 μM Pi for 2 weeks using a Total RNA Purification Kit (Machery-Nagel, Germany). The roots and shoots from three seedlings were pooled to represent a single biological replicate and three biological replicates were used per genotype.
The degree of RNA degradation and contamination was monitored on 1% agarose gels and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 3 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. Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s protocols.

value: Japanese rice

value: shoot

tag: age

value: 7-day-old seedlings treated with 10 μM Pi for 2 weeks

tag: genotype

value: wild type


title: s4_HPAS3

tag: strain

value: 21-day-old seedlings grown in 200 μM Pi

value: spx4 T-DNA


title: N1_LPBS3


title: N1_LPBS1


title: s4_HPAS2


title: scMNase-seq_EILP_GC1067


title: Myc-liquid-rep1

city: VILLEURBANNE

first: MATHIAS

last: CHOQUER

address: 10, rue Raphaël Dubois

institute: UNIVERSITE LYON1

description: This sample is of wild-type Botrytis cinerea B05.10, cultured for 44h in liquid PDB medium diluted 1/4 with agitation. It is the first of three mycelium (Myc) biological replicates used in this experiment, each from separate cultures

hyb_protocol: Hybridizations on microarrays were done using the procedures established by Nimblegen (Roche) and the reagents from Invitrogen (Life Technologies, France)

scan_protocol: Scanning was performed using Agilent scanner at 532nm optimized for Nimblegen 4-plex arrays

data_processing: The raw data (.pair files) were subjected to RMA-background correction, quantile normalization, and gene summarization (Irizarry et al., 2003; Bolstad et al., 2003) as implemented in the ANAIS website( http://anais.versailles.inra.fr).

organism: Botrytis cinerea

source_name: Botrytis cinerea B05.10

label_protocol: Synthesis of double-strand cDNA and Cy3-labelling were done following the procedures established by Nimblegen (Roche) and using reagents from Invitrogen (Life Technologies, France)

growth_protocol: Botrytis cinerea conidia were spread onto cellophane sheets placed on PDB 1/4-agar plates and harvested after 44h of culture when infection cushions (IC) represented about 40% of the surface of the plates. For the Mycelium control (Myc), conidia were cultivated in liquid PDB medium diluted 1/4 during 44h with agitation.

extract_protocol: Total RNA was extracted from 4 mg of lyophilized grounded material using the RNeasy Midi kit (Qiagen), and according to the manufacturerʼs instructions. A DNase treatment (Ambion) was performed to remove traces of genomic DNA. RNA profiles were assessed using the Bioanalyzer RNA 6000 Nano kit (Agilent).

value: Wild-type

tag: growth condition

value: liquid PDB medium diluted 1/4


title: IC-cellophane-rep4

description: This sample is of wild-type Botrytis cinerea B05.10, cultured for 44h on PDB medium diluted 1/4, supplemented with agar and covered with a cellophane sheet. It is the fourth of fourth Infection Cushion (IC) biological replicates used in this experiment, each from separate cultures.

value: solid PDB 1/4 covered with cellophane sheets


title: Myc-liquid-rep3

description: This sample is of wild-type Botrytis cinerea B05.10, cultured for 44h in liquid PDB medium diluted 1/4 with agitation. It is the third of three mycelium (Myc) biological replicates used in this experiment, each from separate cultures


title: IC-cellophane-rep3

description: This sample is of wild-type Botrytis cinerea B05.10, cultured for 44h on PDB medium diluted 1/4, supplemented with agar and covered with a cellophane sheet. It is the third of four Infection Cushion (IC) biological replicates used in this experiment, each from separate cultures.


title: IC-cellophane-rep2

description: This sample is of wild-type Botrytis cinerea B05.10, cultured for 44h on PDB medium diluted 1/4, supplemented with agar and covered with a cellophane sheet. It is the second of four Infection Cushion (IC) biological replicates used in this experiment, each from separate cultures.


title: IC-cellophane-rep1

description: This sample is of wild-type Botrytis cinerea B05.10, cultured for 44h on PDB medium diluted 1/4, supplemented with agar and covered with a cellophane sheet. It is the first of four Infection Cushion (IC) biological replicates used in this experiment, each from separate cultures.


title: Myc-liquid-rep2

description: This sample is of wild-type Botrytis cinerea B05.10, cultured for 44h in liquid PDB medium diluted 1/4 with agitation. It is the second of three mycelium (Myc) biological replicates used in this experiment, each from separate cultures


title: scMNase-seq_EILP_GC1043


title: scMNase-seq_EILP_GC1055


title: scMNase-seq_EILP_GC1047


title: o2_HPAS3

value: bHLH6 OV


title: scMNase-seq_EILP_GC1063


title: scMNase-seq_EILP_GC1039


title: scMNase-seq_EILP_GC1040


title: scMNase-seq_EILP_GC1041


title: scMNase-seq_EILP_GC1049


title: scMNase-seq_EILP_GC1037


title: scMNase-seq_EILP_GC1034


title: scMNase-seq_EILP_GC1048


title: scMNase-seq_EILP_GC1038


title: o2_HPAS1


title: s4_HPAS1


title: scMNase-seq_EILP_GC1045


title: N1_HPAS2


title: N1_HPAS1


title: scMNase-seq_EILP_GC1035


title: scMNase-seq_EILP_GC1036


title: scMNase-seq_EILP_GC1033


title: scMNase-seq_EILP_GC1030


title: N1_LPBR3

source_name: Root

value: root


title: scMNase-seq_EILP_GC1017


title: N1_LPBR2


title: scMNase-seq_EILP_GC1019


title: scMNase-seq_EILP_GC1016


title: scMNase-seq_EILP_GC1014


title: N1_LPBR1


title: scMNase-seq_EILP_GC1018


title: scMNase-seq_EILP_GC1013


title: o2_HPAS2


title: scMNase-seq_EILP_GC1012


title: N1_HPAS3


title: s4_HPAR3


title: scMNase-seq_EILP_GC1011


title: scMNase-seq_EILP_GC1010


title: scMNase-seq_EILP_GC1007


title: scMNase-seq_EILP_GC1006


title: scMNase-seq_EILP_GC1020


title: scMNase-seq_EILP_GC1009


title: scMNase-seq_EILP_GC1008


title: s4_HPAR2


title: s4_HPAR1


title: o2_HPAR1


title: o2_HPAR2


title: scMNase-seq_EILP_GC1005


title: scMNase-seq_EILP_GC1001


title: scMNase-seq_EILP_GC0998


title: scMNase-seq_EILP_GC1000


title: scMNase-seq_EILP_GC1003


title: N1_HPAR3


title: scMNase-seq_EILP_GC0863


title: scMNase-seq_EILP_GC0862


title: N1_HPAR1


title: scMNase-seq_EILP_GC0861


title: scMNase-seq_EILP_GC0859


title: scMNase-seq_EILP_GC0860


title: o2_HPAR3


title: scMNase-seq_EILP_GC1002


title: scMNase-seq_EILP_GC0857


title: scMNase-seq_EILP_GC0856


title: scMNase-seq_EILP_GC0854


title: scMNase-seq_EILP_GC0853


title: scMNase-seq_EILP_GC0848


title: scMNase-seq_EILP_GC0850


title: scMNase-seq_EILP_GC0852


title: scMNase-seq_EILP_GC0851


title: scMNase-seq_EILP_GC0855


title: scMNase-seq_EILP_GC0849


title: scMNase-seq_EILP_GC0845


title: N1_HPAR2


title: scMNase-seq_EILP_GC0847


title: scMNase-seq_EILP_GC0828


title: scMNase-seq_EILP_GC0827


title: scMNase-seq_EILP_GC0846


title: scMNase-seq_EILP_GC0842


title: scMNase-seq_EILP_GC0841


title: scMNase-seq_EILP_GC0826


title: scMNase-seq_EILP_GC0844


title: scMNase-seq_EILP_GC0824


title: scMNase-seq_EILP_GC0864


title: scMNase-seq_EILP_GC0823


title: scMNase-seq_EILP_GC0822


title: scMNase-seq_EILP_GC0817


title: scMNase-seq_EILP_GC0819


title: scMNase-seq_EILP_GC0820


title: scMNase-seq_EILP_GC0821


title: scMNase-seq_EILP_GC0858


title: scMNase-seq_EILP_GC0814


title: scMNase-seq_EILP_GC0843


title: scMNase-seq_EILP_GC0813


title: scMNase-seq_EILP_GC0818


title: scMNase-seq_EILP_GC0825


title: scMNase-seq_EILP_GC0810


title: scMNase-seq_EILP_GC0811


title: scMNase-seq_EILP_GC0815


title: scMNase-seq_EILP_GC0816


title: scMNase-seq_EILP_GC0791


title: scMNase-seq_EILP_GC0790


title: scMNase-seq_EILP_GC0806


title: scMNase-seq_EILP_GC0805


title: scMNase-seq_EILP_GC0809


title: scMNase-seq_EILP_GC0792


title: scMNase-seq_EILP_GC0789


title: scMNase-seq_EILP_GC0788


title: scMNase-seq_EILP_GC0787


title: scMNase-seq_EILP_GC0807


title: scMNase-seq_EILP_GC0786


title: scMNase-seq_EILP_GC0785


title: scMNase-seq_EILP_GC0812


title: scMNase-seq_EILP_GC0784


title: scMNase-seq_EILP_GC0783


title: scMNase-seq_EILP_GC0782


title: scMNase-seq_EILP_GC0779


title: scMNase-seq_EILP_GC0778


title: scMNase-seq_EILP_GC0780


title: scMNase-seq_EILP_GC0781


title: scMNase-seq_EILP_GC0776


title: scMNase-seq_EILP_GC0775


title: scMNase-seq_EILP_GC0774


title: scMNase-seq_EILP_GC0773


title: scMNase-seq_EILP_GC0772


title: scMNase-seq_EILP_GC0478


title: scMNase-seq_EILP_GC0475


title: scMNase-seq_EILP_GC0769


title: scMNase-seq_EILP_GC0770


title: scMNase-seq_EILP_GC0771


title: S7_R2

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

data_processing:
Data obtained in FASTQ files were processed to remove adapter sequences using cutadapt (v1.12) and low-quality reads using qrqc package in R.
High-quality filtered identical reads were collapsed into a unique reads to estimate abundance of small RNAs at different stages of seed development and leaf tissue.
Supplementary_files_format_and_content: FASTA files containing non-redundant reads with their read counts.

organism: Cicer arietinum

source_name: Seed

growth_protocol: Plants were grown in natural field conditions and seeds undergoing different stages of development were harvested from the field-grown plants.

extract_protocol:
Total RNA was isolated followed by preparation of small RNA sequencing libraries using TruSeq Small RNA Sample Prep Kit (Illumina Technologies).
Small RNA libraries were prepared for sequencing using Illumina's standard protocols.

value: Himchana 1

value: Seed

tag: development stage

value: Late maturation (S7)


title: scMNase-seq_EILP_GC0473

value: bone marrow


title: scMNase-seq_EILP_GC0474


title: S7_R1


title: scMNase-seq_EILP_GC0472


title: scMNase-seq_EILP_GC0471


title: S6_R2

value: Late maturation (S6)


title: scMNase-seq_EILP_GC0470

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1-


title: scMNase-seq_EILP_GC0469


title: scMNase-seq_EILP_GC0468


title: scMNase-seq_EILP_GC0777


title: scMNase-seq_EILP_GC0467


title: S6_R1

value: Mid maturation (S5)


title: S4_R2

value: Early maturation (S4)


title: S5_R1


title: scMNase-seq_EILP_GC0466


title: scMNase-seq_EILP_GC0477


title: scMNase-seq_EILP_GC0465


title: scMNase-seq_EILP_GC0464


title: scMNase-seq_EILP_GC0463


title: scMNase-seq_EILP_GC0480


title: S4_R1


title: S3_R2

value: Late embryogenesis (S3)


title: scMNase-seq_EILP_GC0443


title: scMNase-seq_EILP_GC0462


title: scMNase-seq_EILP_GC0440


title: scMNase-seq_EILP_GC0442


title: scMNase-seq_EILP_GC0441


title: scMNase-seq_EILP_GC0444


title: S3_R1


title: scMNase-seq_EILP_GC0438


title: scMNase-seq_EILP_GC0437


title: S2_R1

value: Mid embryogenesis (S2)


title: scMNase-seq_EILP_GC0436


title: S1_R2

value: Early embryogenesis (S1)


title: scMNase-seq_EILP_GC0433


title: S1_R1


title: scMNase-seq_EILP_GC0434


title: scMNase-seq_EILP_GC0435


title: scMNase-seq_EILP_GC0432


title: Leaf_R2

source_name: Leaf

value: Leaf


title: scMNase-seq_EILP_GC0429


title: Leaf_R1


title: scMNase-seq_EILP_GC0427


title: scMNase-seq_EILP_GC0430


title: scMNase-seq_EILP_GC0431


title: scMNase-seq_EILP_GC0426


title: S2_R2


title: scMNase-seq_EILP_GC0425


title: scMNase-seq_EILP_GC0457


title: scMNase-seq_EILP_GC0422


title: scMNase-seq_EILP_GC0424


title: scMNase-seq_EILP_GC0419


title: scMNase-seq_EILP_GC0414


title: scMNase-seq_EILP_GC0418


title: scMNase-seq_EILP_GC0413


title: scMNase-seq_EILP_GC0420


title: scMNase-seq_EILP_GC0411


title: scMNase-seq_EILP_GC0412


title: scMNase-seq_EILP_GC0415


title: scMNase-seq_EILP_GC0410


title: scMNase-seq_EILP_GC0416


title: scMNase-seq_EILP_GC0409


title: scMNase-seq_EILP_GC0406


title: scMNase-seq_EILP_GC0405


title: scMNase-seq_EILP_GC0407


title: scMNase-seq_EILP_GC0404


title: scMNase-seq_EILP_GC0400


title: scMNase-seq_EILP_GC0399


title: scMNase-seq_EILP_GC0398


title: scMNase-seq_EILP_GC0396


title: scMNase-seq_EILP_GC0397