title: YL2_Glu_2_2

city: Vienna

first: Michael

last: Egermeier

address: Muthgasse 18

country: Austria

institute: University of Natural Resources and Life Sciences

description:
Sample L2
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

data_processing:
Base calling was performed by using Illumina’s HCS 2.2.58 and RTA 1.18.64 software.
Reads filtered by default Illumina ﬁlter procedure (chastity ﬁlter).
Mapping of reads to reference sequences was performed using BWA-MEM (version 0.7.12-r1039).
Raw read counts were created using featureCounts (version 1.5.1). Only reads with unique mapping positions and a mapping quality score of at least 1 were considered for read counting.
Raw transcriptomic data were filtered, normalized and differential expression analysis were carried out using the R software, the edgeR package and the GeTMM methods (Gene Length Corrected Trimmed Mean of M-values). The normalized expression data generated were transformed using the function log2 (x+1).
Genome_build: Yarrowia_lipolytica.GCA_000002525.1
Supplementary_files_format_and_content: Raw_Counts.txt: Text file containing raw read counts for all reference features and samples.
Supplementary_files_format_and_content: log2-FPKM.txt: Text file containing GeTMM normalized log2-FPKM values for all reference features and samples.

organism: Yarrowia lipolytica

source_name: Wet biomass from bioreactor

growth_protocol: Cells were cultivated in bioreactors according to the protocol in Egermeier et al. 2017 (doi: 10.3389/fmicb.2017.00049). Glucose or glycerol used as sole carbon source, pH conditions of 3.5 or 5.5 were applied. First sample was taken during growth phase after 12 h (glucose) and 8 hours (glycerol) respectively, only at pH 5.5. Second sample was taken during nitrogen-limited stationary phase 32 hours for all tested conditions.

extract_protocol:
Total RNA extraction was performed according to the manual of RNeasy Midi Kit from Qiagen.
Preparation of strand-specific cDNA libraries, RNA selection using polyA selection, using standard Illumina protocols.

treatment_protocol: Samples were treated by mechanical disruption, using a Bead Ruptor from OMNI International.

tag: carbon source

value: Glucose

tag: ph conditions

tag: timepoint

value: 32 hours post inoculation


title: MU01-0361-GS7

status: Public on Oct 08 2020

type: RNA

city: Rensselaer

first: Martin

last: Tenniswood

address: 1 Discovery Drive

country: USA

institute: miR Scientific LLC

hyb_protocol: Following labeling, 21.5uL of biotin-labeled samples were hybridized for 16 hr at 48C on GeneChip miRNA4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 7G with AGCC software.

data_processing: CEL files were analyzed for quality using Affymetrix Transcriptome Analysis Console 4.0 software, and the RMA-DBAG was used for summarization

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Urine

label_protocol: Standard Affymetrix microRNA labeling protocol

extract_protocol: Standard urine exosome RNA isolation method by Norgen Biotek Corp.

tag: tissue

value: Urine

tag: histopathology

value: Gleason Score 7


title: miRNA_Sample 3 from KC 1 day after partial hepatoctomy

city: Moscow

first: Polina

last: Vishnyakova

address: Oparina 4

country: Russia

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

description: NS_M_miR_v1.5.rlf was used as Reporter Library File

hyb_protocol: Samples were  hybridized for 18 h at 65C according to the instructions at nCounter® miRNA Expression Assay User Manual (NanoString tecnology)

scan_protocol: After hybridization samples were placed in the prep station of nCounter FLEX analysis system, there hybridized samples were purified and immobilized in a sample cartridge (cartridge ID 207911410919) according to standard protocol. Then the sample cartridge was scanned on the nCounter FLEX digital analyzer (Scanner ID 1410C0216)

data_processing: The raw data were processed in nSolver Analysis Software 4.0. We used CodeSetContent(Housekeeping) standard normalization

label: NanoString Reporter CodeSet  and Capture ProbeSet

organism: Mus musculus

source_name: Kupffer cells

label_protocol: 100 ng of  total RNA was used for the miRNA Sample Preparation Protocol according to the instructions at nCounter® miRNA Expression Assay User Manual. Then prepared samples were labed with  Reporter CodeSet and Capture ProbeSet from Mouse miRNA V 1.5 panel according to the instructions at nCounter® miRNA Expression Assay User Manual(NanoString tecnology)

extract_protocol: Sorted cells from 5 animals were pooled. The total RNA was isolated from cells by using RNeasy Plus Mini Kit (Qiagen) with additional purification and concentration with RNA Clean& Concentrator (Zymo Research).

tag: strain

value: Balb/C

tag: cell type

value: Kupffer

tag: days after hepatoctomy


title: BC#8

type: SRA

city: Nanjing

first: Shui

last: Wang

state: Jiangsu

address: 300 Guangzhou Road

country: China

institute: The First Affiliated Hospital with Nanjing Medical University

description: tRNA-derived small RNAs (tsRNAs)

library_source: transcriptomic

data_processing:
Solexa pipeline v1.8 software used for basecalling.
Trimmed reads are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
The expression profiling of tRNA-derived small RNAs (tsRNAs) were calculated based on counts of reads mapped.
Genome_build: hg18
Supplementary_files_format_and_content: The file includes the counts per million mapped reads for each sample.
Supplementary_files_format_and_content: tsRNAs_ID represents the ID of tsRNAs; p_value represents the p-value of the exact test by negative binomial distribution;  q_value represents the FDR adjusted p-value; Group CPM represents the average of log scaled CPM of in groups; CPM represents the counts per million mapped reads.

source_name: Plasma

extract_protocol:
Total RNAs from plasmas were isolated by mirVana PARIS Kit (Invitrogen, Lithuania), and modifications in tsRNAs were removed by rtStar™ tRF&tiRNA Pretreatment Kit (Arraystar, USA). The completed libraries were quantified by Agilent 2100 Bioanalyzer (Agilent, USA), and then sequenced on Illumina NextSeq 500 system (Illumina, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: Sex

value: Female

tag: age

tag: subtype

value: Triple-negative


title: YL2_Glu_2_1

description:
Sample L1
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: MU01-0337-GS5

value: Gleason Score 5


title: YL2_Glu_2_3

description:
Sample L3
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: MU01-0325-GS8

value: Gleason Score 8


title: BC#6

description: tRNA-derived small RNAs (tsRNAs)


title: HD+LPS

city: Kalyani

first: Partho

middle: Sarothi

last: Ray

state: West Bengal

address: Mohanpur

department: Department of Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Kolkata

data_processing:
Paired-end sequence data was geretated from sample using Illumina HiSeq and quality was checked using FastQC software.
Adapter sequences, low quality reads and small fragmented reads(read size below 50 bp) were removed using fastp. Sequence reads were mapped to mouse reference geneome(GRCm38.98) using TopHat2 and sebsequently Cufflink and Cuffmerge package were used for transcript assembly and quantification of gene expression in FPKM. For diffrential gene expression analysis, we used Cuffdiff package.
adapter sequence for read1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
adapter sequence for read2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Genome_build: mm10
Supplementary_files_format_and_content: excel files include FPKM values for each Sample.

source_name: Abelson murine leukemia virus-induced tumor; ascites

growth_protocol: Mouse macrophage cell line RAW264.7 cells was maintained in RPMI 1640 media supplemented with 10% heat-inactivated fetal bovine serum 100 U/ml penicillin and streptomycin, 4 mM L-Glutamine in a humidified incubator at 37degree celsius and 5% CO2.

extract_protocol:
Total RNA was isolated using RNAiso Plus (Takara Bio Inc., Japan) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Post 24h of seeding, HD cells were stimulated or not stimulated with LPS (500ng/ml) for another 24h. After completion of designated time point LD,HD and HD+LPS cells were harvested for  total RNA extraction.

tag: cell line

value: macrophage cell line

tag: density

value: high dense cells (HD)

tag: treatment

value: LPS (500ng/ml) for 24hrs


title: miRNA_Sample 2 from KC 1 day after partial hepatoctomy


title: miRNA_Sample 2 from KC 3 day after partial hepatoctomy


title: MU01-0322-GS6

value: Gleason Score 6


title: MU01-0315-GS6


title: YL2_Gly_2_3

description:
Sample K3
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

value: Glycerol


title: miRNA_Sample 1 from KC 1 day after partial hepatoctomy


title: BC#5

description: tRNA-derived small RNAs (tsRNAs)


title: miRNA_Sample 3 from KC before partial hepatoctomy


title: YL2_Gly_2_2

description:
Sample K2
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: miRNA_Sample 2 from KC before partial hepatoctomy


title: BC#4

description: tRNA-derived small RNAs (tsRNAs)

value: Luminal


title: BC#7

description: tRNA-derived small RNAs (tsRNAs)


title: YL2_Gly_2_1

description:
Sample K1
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: MU01-0297-GS7


title: MU01-0290-GS6


title: YL2_Glu_1_2

description:
Sample J2
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: miRNA_Sample 1 from KC before partial hepatoctomy


title: YL2_Glu_1_3

description:
Sample J3
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: YL2_Glu_1_1

description:
Sample J1
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: BC#1

description: tRNA-derived small RNAs (tsRNAs)

value: In situ


title: NC#4

description: tRNA-derived small RNAs (tsRNAs)


title: BC#2

description: tRNA-derived small RNAs (tsRNAs)


title: JUVSI

city: Plymouth, Devon

first: vengamanaidu

last: modepalli

address: The Laboratory,Citadel Hill

department: Cell and Molecular

country: United Kingdom

institute: Marine Biological Association of the UK

data_processing:
A minimum of 20 million 2x150bp sequencing reads were collected from each sample. The data were pre-processed to remove the adapters using Trimmomatic v0.36
pre-processed reads were mapped to the Sycon ciliatum genome using HISAT2 and the mapped reads were passed to StringTie for transcript assembly
All assembled transcripts were merged by using StringTie's merge module.
The BAM file and GFT file were fed into featureCounts to extract the reads counts per transcript.
Differential expression analyses were performed using DESeq2
Genome_build: The Sycon ciliatum genome is acquired from (https://datadryad.org/stash/dataset/doi:10.5061/dryad.tn0f3) and indexed using bowtie2
Supplementary_files_format_and_content: tab-delimited text files include read counts generated using featureCounts tool

organism: Sycon ciliatum

source_name: Regenerating structures

extract_protocol:
Total RNA was extracted using Trizol (Life technologies, USA) as instructed in manual.
RNA-seq libraries were constructed using SENSE mRNA-Seq Library Prep Kit (Lexogen GmbH). Each library was indexed in order to multiplex samples on the Illumina.

tag: days post dissociation

value: Day 21 to 24

tag: sample set

value: Set I

tag: barcode

value: AATCCG


title: ADULT

source_name: Dissociated cells from whole animal

value: Dissociated cells from whole animal

value: TATGTC


title: JUVSII

value: Set II

value: TACCTT


title: NC#3

description: tRNA-derived small RNAs (tsRNAs)

value: Female


title: MU01-0269-GS6

value: Urine


title: PJUVSIII

value: Day 16 to 18

value: Set III

value: CCTAAG


title: YL2_Gly_1_3

description:
Sample I3
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

tag: carbon source

value: 32 hours post inoculation


title: YL2_Gly_1_2

description:
Sample I2
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

tag: ph conditions


title: MU01-0214-GS6

value: Gleason Score 6


title: PJUVSII

value: ATGAAC


title: MU01-0211-GS6


title: YL2_Gly_1_1

description:
Sample I1
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

value: Glycerol

tag: timepoint


title: NC#2

description: tRNA-derived small RNAs (tsRNAs)


title: NC#1

description: tRNA-derived small RNAs (tsRNAs)


title: PJUVSI

value: TTAACT


title: MU01-0259-GS6

tag: tissue


title: BC#3

description: tRNA-derived small RNAs (tsRNAs)

value: Luminal


title: YL2_Glu_0_3

description:
Sample H3
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

value: Glucose

value: 12 hours post inoculation


title: MU01-0205-GS6

tag: histopathology


title: MU01-0275-GS6


title: D10-14SV

value: Day 10 to 14

value: Set IV

value: CGGTTA


title: YL2_Glu_0_2

description:
Sample H2
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

tag: strain


title: YL2_Glu_0_1

description:
Sample H1
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: D10-14SIV

value: TCAGGA


title: Sample 1 from KC 7 day after partial hepatoctomy

description: NS_Infl_Mm_v2_C2537.rlf was used as Reporter Library File

hyb_protocol: Samples were  hybridized for 18 h at 65C according to the instructions at nCounter® XT Assay User Manual (NanoString tecnology)

scan_protocol: After hybridization samples were placed in the prep station of nCounter FLEX analysis system, there hybridized samples were purified and immobilized in a sample cartridge (cartridge ID 207911400919) according to standard protocol. Then the sample cartridge was scanned on the nCounter FLEX digital analyzer (Scanner ID 1410C0216)

label_protocol: 100 ng of  total RNA was mixed with Reporter CodeSet and Capture ProbeSet from nCounter Mouse Inflammation V2 panel according to the instructions at nCounter® XT Assay User Manual (NanoString tecnology)  User Manual

value: Balb/C

tag: cell type

value: Kupffer


title: D6-8SVI

value: Day 6 to 8

value: Set VI

value: TGTGCA


title: WT_HCT116_R1

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
ChIP-seq reads were trimmed from the 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
For ChIP-seq analysis, H3K27me3 peaks were called with the MACS  v2.1.0 software (Zhang et al. 2008) using default parameters (--broad, q=0.01), while narrow  peaks were called with MACS v1.4.2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: Gene counts table was constructed using HTSeq (Anders et al. 2015) generated counts, we  utilized RUVSeq v1.20.0 (supp. ref: Risso et al. 2014) package to correct for unwanted batch  effects. To remove batch effects and estimate the factors of unwanted variation we applied RUVs protocol, using all  expressed genes grouped by sample replicates, with parameter k=3. Counts data were filtered and visualized using R scripts.

molecule: polyA RNA

growth_protocol: HCT116 cells (ATCC CCL-247), GFP-MLL4-HMG-USD cells (TET-ON, T/O) were grown at 37 °C in DMEM supplemented with 10% FBS (Fisher Scientific, 35-015-CV).

extract_protocol:
For ChIPseq, cells were harvested and washed with ice-cold PBS for two times, and fixed with paraformaldehyde (1% final) for 10 min at RT. Then quench the paraformaldehyde with 2.5M (1/20) glycine and wash the cell pellets twice with PBS. Sonication: the cell pellet was resuspended with lysis buffer 1 (50 mM HEPES, pH=7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, 1 X protease inhibitors) and incubated on nutator at 4 °C for 10 min. Spin down at 500 g for 5 min and discard supernatant. The pellet was washed with lysis buffer 2 (10 mM Tris-HCl, pH=8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1 X protease inhibitors) and resuspended with lysis buffer 3 (10 mM Tris-HCl, pH=8.0, 1 mM EDTA, 0.1% SDS, 1 X protease inhibitors). Adjust the final volume to be 10 times of the pellet with lysis buffer 3. Sonication with 1 ml Covaris tubes at 10% duty cycle, 175 peak intensity power, 200 cycles per burst for 60-1200s. Sonicated DNA size was checked on a 2% agarose gel. We next added 10% of 10X ChIP Dilution Buffer (10% Triton x-100, 1 M NaCl, 1% Na-Deoxycholate, 5% N- Dauroylsarcosine, 5 mM EGTA) to the lysate and spun at 20,000 g for 15 min at 4 °C to pellet debris. Supernatant was collected and the concentration measured by nanodrop. A small aliquot was saved as input. Antibody was added (~ 10 ug per antibody) to each cell lysate and incubated at 4 °C on nutator overnight. The next morning, protein A/G agarose beads (Santa Cruz) were washed in RIPA buffer (50 mM HEPES, pH=7.5, 500 mM LiCl, 1 mM EDTA, 1.0% NP-40, 0.7% Na-Deoxycholate) before being incubated with chromatin/antibody solution at 4 °C on nutator for 4 hours. Samples were next spun down in 15 ml conical tubes at 200g for 5 min at 4 °C and supernatant was discarded. Beads were pelleted in 15 ml conical tubes at 200g for 5 min at 4 °C and washed in RIPA Buffer 4 times at 4 °C on nutator for 10 min each time. Beads were washed once with 1 ml of cold TE + 50 mM NaCl and spun at 1000 g for 3 min at 4 °C and remove any residual buffer. Beads were resuspended in 200μl Elution Buffer (50 mM Tris-HCl, pH=8.0, 10 mM EDTA, 1.0% SDS) and incubated in 65 °C water bath for 30 min, vortexing gently twice in between. Beads were spun down at 1000 g for 3 min at RT and supernatant was transferred to a new tube. To reverse crosslinks, a 50μl aliquot was diluted in 150 μl (3 volumes) Elution Buffer and incubated at 65 °C for 6-15 h. We added 4 μl of 20 mg/ml Protease K and incubated at 55 °C for 2 h to degrade protein. DNA was purified using Qiagen PCR Purification columns.
For RNA-seq, polyA strategy, we use the NEBNext PolyA mRNA Magnetic Isolation Module along with the NEBNext Ultra II Directional RNA Library Prep Kit.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit

treatment_protocol:
For ChIP-seq, MLLKO-TET/ON HMG-USD HCT116 cells were treated with doxycycline for 2 and 4 days. Briefly, about 5M of (TET-ON, T/O) GFP-MLL4-HMG-USD cells were plated in Dulbecco s Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS) using 15 cm dish. The next day, media was removed and replaced with fresh DMEM containing 1mg/ml of Doxycycline. Cells were collected 2 and 4 days following the treatment.
For RNA-seq, MLLKO-TET/ON HCT116 cells were treated with doxycycline for 2, 4 and 8 days, HCT116 WT cells were not treated.

value: colorectal carcinoma

value: untreated

tag: genotype/variant

value: WT


title: HCT116_MLLKO_DOX_Day8_R2

value: treated with doxycycline for 8 days

value: MLLKO-TET/ON


title: MU01-0183-GS6

value: Urine

value: Gleason Score 6


title: YL2_Gly_0_2

description:
Sample G2
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

value: Glycerol

value: 8 hours post inoculation


title: HCT116_MLLKO_DOX_Day8_R1


title: MU01-0181-GS6


title: MU01-0125-GS6


title: MU01-0116-GS7

value: Gleason Score 7


title: HCT116_MLLKO_DOX_Day4_R2

value: treated with doxycycline for 4 days


title: WT_HCT116_R2


title: YL2_Gly_0_1

description:
Sample G1
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: D6-8SII

value: Set II

value: ACATTA


title: HCT116_MLLKO_DOX_Day4_R1


title: YL1_Glu_2_3

description:
Sample F3
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

value: Glucose

value: 32 hours post inoculation


title: MU01-0060-GS6


title: YL1_Glu_2_2

description:
Sample F2
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: YL1_Glu_2_1

description:
Sample F1
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: D6-8SV

value: Day 6 to 8

value: Set V

value: CTAGTC


title: MU01-0143-GS7


title: YL2_Gly_0_3

description:
Sample G3
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: D3-4SII

value: Day 3 to 4

value: TGCACG


title: YL1_Gly_2_3

description:
Sample E3
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: D6-8SIII

value: Set III

value: ATACTG


title: HCT116_MLLKO_noDox_R1

value: colorectal carcinoma

value: untreated

value: MLLKO-TET/ON


title: MU01-0040-Ctrl

value: Urine

value: Control


title: D3-4SI

value: Set I

value: ACCAGT


title: YL1_Gly_2_2

description:
Sample E2
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

value: Glycerol


title: HMG-USD_DOX_Day4

library_source: genomic

molecule: genomic DNA

value: treated with doxycycline for 4 days

tag: chip antibody

value: anti-GFP (Santa Cruz, B-2)


title: MU01-0039-Ctrl


title: HCT116_MLLKO_DOX_Day2_R2

value: treated with doxycycline for 2 days


title: YL1_Gly_2_1

description:
Sample E1
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

value: 32 hours post inoculation


title: MU01-0041-Ctrl


title: D3-4SVI

value: Set VI

value: GTGTAG


title: MU01-0103-GS6

value: Gleason Score 6


title: T83 Scrb IL13

city: Denver

first: Satria

last: Sajuthi

state: Colorado

address: 1400 Jackson St.

institute: National Jewish Health

description: 10X scRNA-seq

data_processing:
Raw FASTQ files were trimmed with skewer
Trimmed reads were aligned to human transcriptome iGenomes hg38 with GSNAP
Gene counting were performed with HTSEQ-count
Individual count table were combined with R statistical software to create a raw count matrix
Raw count matrix was then normalized by size factor with DESEQ2
Genome_build: Hg38
Supplementary_files_format_and_content: Raw gene count matrix and normalized gene count matrix in tab separated value file format

source_name: Tracheal biopsy

extract_protocol:
RNA was purified from sample lysates using the Quick-RNATM MiniPrep kit (Zymo Research). Lysates were centrifuged at 16,000xg for 2 minutes in a QIAshredder (Qiagen) to homogenize sample and remove insoluble debris before beginning standard manufacturer protocol with inclusion of optional DNase step. RNA was eluted in 30 mL of DNase/RNase free water and eluent was passed through the column one additional time to ensure maximum RNA recovery from filter.
KAPA Biosystems mRNA HyperPrep whole transcriptome libraries (Roche) were constructed with 250 ng RNA per sample and 12 cycles of library amplification. Libraries were barcoded using Illumina Dual-Index adapters (Integrated DNA Technologies) and paired-end sequenced using the Illumina NovaSeq® 6000 system.

value: Tracheal airway epithelium


title: MU01-0037-Ctrl


title: Nasal Brush SC

description: 10X scRNA-seq

source_name: Nasal brush

value: Nasal airway epithelium


title: MU01-0044-Ctrl


title: HCT116_MLLKO_DOX_Day2_R1

value: colorectal carcinoma


title: YL1_Glu_1_3

description:
Sample D3
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

value: Glucose


title: D3-4SV

value: Day 3 to 4

value: Set V

value: CAGCGT


title: HMG-USD_noDox

value: untreated

value: MLLKO-TET/ON


title: HCT116_MLLKO_noDox_R2


title: T83 Scrb BSA

description: 10X scRNA-seq

value: BSA


title: MU01-0036-Ctrl

value: Urine

value: Control


title: MU01-0032-Ctrl


title: H3k27me3_DOX_Day4

value: treated with doxycycline for 4 days

value: anti-H3k27me3 (Homemade)


title: 72hr IL13 - 5686

description: RNA-seq

value: 72hr IL13


title: YL1_Gly_1_3

description:
Sample C3
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

value: Glycerol

value: 32 hours post inoculation


title: MU01-0031-Ctrl


title: H3k27me3_DOX_Day2

value: treated with doxycycline for 2 days


title: HMG-USD_DOX_Day2

value: anti-GFP (Santa Cruz, B-2)


title: YL1_Gly_1_2

description:
Sample C2
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: MU01-0030-Ctrl


title: YL1_Gly_1_1

description:
Sample C1
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: YL1_Glu_1_1

description:
Sample D1
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: Control - 5398

description: RNA-seq

value: Nasal airway epithelium


title: UTX_DOX_Day4

value: colorectal carcinoma

value: anti-UTX (Homemade)


title: 24hr HRVA - 5681

description: RNA-seq

value: 24hr HRVA


title: YL1_Glu_0_3

description:
Sample B3
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

value: Glucose

value: 12 hours post inoculation


title: 72hr IL13 - 5681

description: RNA-seq


title: YL1_Glu_0_2

description:
Sample B2
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: MU01-0027-Ctrl


title: YL1_Glu_0_1

description:
Sample B1
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: UTX_noDox

value: untreated

value: MLLKO-TET/ON


title: UTX_DOX_Day2


title: MU01-0029-Ctrl

value: Urine


title: 24hr HRVA - 5148

description: RNA-seq


title: MU01-0026-Ctrl

value: Control


title: Control - 1723

description: RNA-seq


title: YL1_Gly_0_3

description:
Sample A3
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

value: 8 hours post inoculation


title: Input_DOX_Day4

value: treated with doxycycline for 4 days


title: Input_DOX_Day2


title: Control - 5686

description: RNA-seq


title: 72hr IL13 - 5148

description: RNA-seq

value: 72hr IL13


title: H3k27me3_noDox

value: anti-H3k27me3 (Homemade)


title: Input_noDox


title: MU01-0024-Ctrl


title: YL1_Gly_0_2

description:
Sample A2
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt

value: Glycerol


title: MU01-0023-Ctrl


title: YL1_Gly_0_1

description:
Sample A1
processed data file: Raw_Counts.txt
processed data file: Normalized_CPM.txt


title: Control - 5148

description: RNA-seq


title: 72hr IL13 - 5398

description: RNA-seq


title: D10-14SIII

value: Day 10 to 14

value: Set II

value: TGTGCA


title: BC10

city: New York

first: Matthew

last: Bendall

state: NY

address: Belfer Research Building, Room BB-528, 413 East 69th Street

institute: Weill Cornell Medicine

data_processing:
BCL2FastQ2 Conversion Software (version 2.20, Illumina Inc.) was used to demultiplex data and convert the sequencing files to reads in FASTQ format
Paired-end reads were trimmed for adaptors with Trimmomatic and filtered by quality (phred =>30) and length (=> 35)
Filtered paired-end reads were then aligned to the reference human genome (hg38) using Bowtie2 (--score-min L,0,1.6 -k 200 --very-sensitive-local)
The bowtie2 output was used as input for Telescope and Htseq-count software
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each sample

source_name: Breast cancer tumor

extract_protocol:
RNA extraction and purification from FFPE tissue sections were carried out using the RNeasy FFPE Kit (Qiagen, cat. no. 73504). The RNeasy MinElute spin columns were incubated for 5 minutes with RNase-free water before centrifugation. Samples were eluted in 20uL RNase-free water. A DNase treatment was added using HL-dsDNase kit (ArticZymes, cat. no. 70800-201 250U), with additive MgCl2 (ThermoFisher Scientific, cat. no. AB0359) and DTT, Molecular Grade (Promega, cat. no. P117A). RNA samples were DNase-treated at room temperature for 15 minutes, followed by a 55°C 10-minute incubation to complete enzyme activity.  RNA was stored at -80°C.
RNA samples were prepared with Ovation® Human FFPE RNA-Seq Library Systems (Nugen, cat. no. 0340, 0341). Clean-up steps, including magnetic bead purifications, were performed with freshly made 70% EtOH from 100% proof Absolute Ethanol (Fisher BioReagents™, cat. no. BP2818-500), nuclease-free water (Ambion®, cat. no. AM9939), and DynaMag™-96 Side magnetic plates (Invitrogen, cat. no. 12331D). As a rule, each library was amplified for 18 PCR cycles.
Libraries were pooled in 8 sample sets, and sequenced in a paired-end mode for 75 cycles, Mid-Output platform on an Illumina NextSeq 2000 Sequencing System.

value: FFPE blocks of breast tissue

tag: subject id

tag: hiv

value: positive

tag: tumor stage

tag: molecular subtype

tag: age at diagnosis

tag: ffpe date


title: D10-14SII

tag: days post dissociation

tag: sample set

value: Set I

value: CCGCAA


title: BC09

value: Luminal


title: 24hr HRVA - 5686

description: RNA-seq

value: Nasal airway epithelium

tag: treatment

value: 24hr HRVA


title: MU01-0020-Ctrl

value: Urine


title: 24hr_HRVA - 1723

description: RNA-seq


title: BC07


title: D3-4SIV

value: Day 3 to 4

value: Set IV

tag: barcode

value: CTAGTC


title: BC06

value: negative


title: BC08

value: Triple-negative


title: 24hr HRVA - 5398

description: RNA-seq


title: MU01-0019-Ctrl

value: Control


title: BC05


title: MU01-0017-Ctrl


title: Control - 5681

description: RNA-seq


title: MU01-0021-Ctrl


title: MU01-0014-GS6

value: Gleason Score 6


title: BC04


title: MU01-0010-Ctrl


title: MU01-0012-Ctrl


title: D2_SII

value: Day 2

value: Set II

value: TATGTC


title: MU01-0005-GS6


title: 72hr IL13 - 1723

description: RNA-seq

value: 72hr IL13


title: BC03

value: FFPE blocks of breast tissue

value: positive


title: siYTHDF2-2

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

description: transfected with YTHDF2 siRNA-2

data_processing:
All samples were sequenced by NovaSeq 6000 sequencer with single end 100 bp read length. The deep sequencing data were mapped to human genome version 38(GRCh38.87).
After reads were mapped with HISAT2 version 2.1.0, StringTie v2.1.1 was used to calculate the read counts of each gene which represent their transcriptional expression level. Then we performed DEseq2 v1.26.0 to calculate normalized reads counts in each gene and detect enriched transcripts with a double threshold on the fold change (>1.5) and the correspondent statistical significance (P-adjust < 0.05).
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file containing read count and processed Fold change (siYTHDF2 vs siControl) for each gene

source_name: human cell line

growth_protocol: GSC11 cells were cultured as tumorspheres in DMEM/F12 medium supplemented with B27 supplement (Life Technologies), bFGF and EGF (20 ng/mL each). Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
Total RNA was isolated from YTHDF2 knockdown (siYTHDF2) or control (siControl) GSC11 cells using Trizol reagent (Thermo Fisher).
The RNA-Seq library was generated using TruSeq Stranded mRNA Library Prep Kit (illumina).

treatment_protocol: GSC11 cells were transfected with control or YTHDF2 siRNAs (siControl-1, siControl-2, siYTHDF2-1, and siYTHDF2-2)

tag: cell line

value: Glioblastoma-derived stem cells

tag: transfection

value: YTHDF2 siRNA-2


title: siYTHDF2-1

description: transfected with YTHDF2 siRNA-1

value: YTHDF2 siRNA-1


title: D2_SI

value: Set I

value: GTCAGG


title: D6-8SIV

value: Day 6 to 8

value: Set IV

value: CACACT


title: BC02

tag: tissue

value: negative

value: Luminal


title: D6-8SI

value: GGAGGT


title: MU01-0003-Ctrl

value: Urine

tag: histopathology

value: Control


title: MU01-0004-Ctrl


title: siControl-2

description: transfected with control siRNA-2

tag: cell type

value: control siRNA-2


title: D1_SII

value: Day 1

value: Set II

value: ATACTG


title: siControl-1

description: transfected with control siRNA-1

value: Glioblastoma-derived stem cells

value: control siRNA-1


title: D1_SI

value: TCTTAA


title: KO, Sedentary, replicate 3

status: Public on Oct 07 2020

city: Albany

first: Sneha

last: Damal Villivalam

state: CA

address: 485 Ohlone Ave, Apt 210

department: NST

institute: UC Berkeley

data_processing:
RNA-seq reads were aligned to UCSC mm10 using STAR aligner and uniquely aligned reads were retained for downstream analysis. After filtering rRNA mad mitochondrial reads, gene expression levels were measured using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing raw read count and RPKM-normalized count for each gene

source_name: Soleus muscle tissue

growth_protocol: Dnmt3a floxed mice or Dnmt3a KO mice were maintained on chow diet

extract_protocol:
BGI Library Preparation Kit,
Tissues were removed, flash frozen on liquid nitrogen. For RNA seq,  RNA was harvested using Trizol reagent. Qiagen Rneasy mini kit Sample Prep Kit (Cat#74106) was used with 1 ug of total RNA for the construction of sequencing libraries.  The sequencing was performed on the BGISEQ.
Libraries were prepared by the genome sequencing facility following manufacturers instructions for BGILibrary prep kit for RNA seq.

treatment_protocol: Mice at either sedentary or after exercise in wild-type and MCK-Dnmt3a KO mice.

tag: strain

tag: genotype

value: MCK-Dnmt3a KO

tag: group

value: Sedentary


title: WT, Sedentary, replicate 3

value: Dnmt3a floxed, WT


title: KO, Sedentary, replicate 1


title: WT, Sedentary, replicate 2


title: WT, Sedentary, replicate 1


title: WT, Exercise, replicate 3

value: Exercise


title: KO, Exercise, replicate 2


title: MU01-0002-Ctrl


title: WT, Exercise, replicate 2


title: KO, Sedentary, replicate 2


title: KO, Exercise, replicate 3


title: TNBC, NT4h (RNA-seq)

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Prinseq-lite-0.20.4 to remove reads size < 35b
Mapping with STAR_2.4.0a then bowtie2-2.2.4 versus canFam3 build + vaccina virus NC_006998 sequence
Bam files merging using MergeSamFiles.jar (picard-tools-1.119) then counting with HTSeq-0.6.1 "--minaqual=0 --mode=intersection-nonempty" parameters
Raw counts were coverted to counts per million (CPM) and log-transformed
Genome_build: CanFam3
Supplementary_files_format_and_content: tab-delimited text file including log2 counts per million for each sample.

organism: Canis lupus familiaris

source_name: TNBC, NT4h

extract_protocol:
Poly(A) RNAs were purified using a Dynabeads mRNA purification kit (Invitrogen) and fragmented for 7 min at 95 °C.
Libraries were then generated with the Ion Total RNA seq kit V2 (life technologies) and sequenced on the Ion Proton system with P1 chip V3 following the manufacturer’s instructions.
instrument model: AB Ion Proton

value: TNBC

tag: infection

value: control

tag: time


title: TNBC, NT0 (RNA-seq)

source_name: TNBC, NT0


title: KO, Exercise, replicate 1


title: TNBC, NT2h (RNA-seq)

source_name: TNBC, NT2h


title: WT, Exercise, replicate 1


title: TNBC, NT8h (RNA-seq)

source_name: TNBC, NT8h


title: TNBC, T8h (RNA-seq)

source_name: TNBC, T8h

value: vaccinia infected


title: TNBC, T4h (RNA-seq)

source_name: TNBC, T4h


title: BC01

value: FFPE blocks of breast tissue

tag: subject id

tag: hiv

value: negative

tag: tumor stage

tag: molecular subtype

value: Luminal


title: TNBC, T2h (RNA-seq)

source_name: TNBC, T2h


title: D3-4SIII

tag: days post dissociation

value: Day 3 to 4

tag: sample set

value: Set III

value: GAGTCC


title: TNBC, T0 (RNA-seq)

source_name: TNBC, T0


title: enp1-1 + Pab1GFP vector 90 minutes replicate 1

city: Davis

first: Ben

last: Montpetit

address: One Shields Ave

department: Viticulture and Enology

institute: University of California, Davis

description:
tag_seq_counts.csv
BM_enp1_1_pBM766_1

data_processing:
All code related to RNA-seq analyses has been deposited  at: https://github.com/montpetitlab/Aguilar_and_Paul_et_al_2020
Genome and transcriptome preparation: For transcript quantification, all libraries were quantified against the same transcriptome using Salmon (version 0.12.0). The custom transcriptome was prepared using a bed file that contained coordinates for pervasive transcripts, ribosomal RNAs, and mRNAs to obtain transcript fasta sequences using bedtools getfasta command (version 2.29.2) against the UCSC sacCer3 genome.
The first 12 reads were trimmed per manufacturer instructions using Trimmomatic (version 0.38). Poly(A) tails and adapters were removed using the bbMap command bbduk.sh (version 38.20). Trimmed reads were quantified against the custom transcriptome using Salmon quant. A count matrix was generated using the tximport R package (version 1.14.0), and by selection the counts dataframe from the tximport object, as 3’Tag-seq data should not be normalized for transcript length given that reads originate from the 3’ end of the transcript.
Genome_build: S. cerevisiae R64 GCA_000146045.2_R64_rna_from_genomic file
Supplementary_files_format_and_content: CSV file with count data for each feature

organism: Saccharomyces cerevisiae

source_name: vegetative cells

growth_protocol: Cells were grown at permissive temperature (25°C) until an OD600 of ~0. 8 before cultures were shifted to non-permissive temperature (37°C) for 90 minutes prior to being harvested. Harvested cells were rapidly frozen in liquid nitrogen .

extract_protocol:
RNA extractions were performed using 5 OD yeast cell pellets. RNA was extracted using the Quick-RNA Fungal/Bacterial prep kit (Zymo Research).
Library preparation and sequencing was carried out by UC Davis Genome Center following the 3´-Tag Sequencing method (QuantSeq 3´ mRNA-Seq kits).
Sequencing used an Illumina HiSeq 4000 with single end 90 bp reads. The adapters, polyA tails, and the first 12 bases of each read were trimmed according to manufacturer instructions (https://www.lexogen.com/quantseq-data-analysis/).

treatment_protocol: 37 degrees celcius for 90 minutes

tag: genetic background


title: enp1-1 + Pab1GFP vector 90 minutes replicate 3

description:
tag_seq_counts.csv
BM_enp1_1_pBM766_3


title: enp1-1 + empty vector 90 minutes replicate 3

description:
tag_seq_counts.csv
BM_enp1_1_pBM5_3


title: enp1-1 + empty vector 90 minutes replicate 1

description:
tag_seq_counts.csv
BM_enp1_1_pBM5_1


title: enp1-1 + empty vector 90 minutes replicate 2

description:
tag_seq_counts.csv
BM_enp1_1_pBM5_2


title: csl4-ph + empty vector 90 minutes replicate 2

description:
tag_seq_counts.csv
BM_csl4ph_pBM5_2


title: control + Pab1GFP vector 90 minutes replicate 3

description:
tag_seq_counts.csv
BM_WT_pBM766_3


title: csl4-ph + empty vector 90 minutes replicate 1

description:
tag_seq_counts.csv
BM_csl4ph_pBM5_1


title: csl4-ph + Pab1GFP vector 90 minutes replicate 3

description:
tag_seq_counts.csv
BM_csl4ph_pBM766_3


title: csl4-ph + Pab1GFP vector 90 minutes replicate 1

description:
tag_seq_counts.csv
BM_csl4ph_pBM766_1


title: control + Pab1GFP vector 90 minutes replicate 2

description:
tag_seq_counts.csv
BM_WT_pBM766_2


title: control + empty vector 90 minutes replicate 3

description:
tag_seq_counts.csv
BM_WT_pBM5_3


title: control + empty vector 90 minutes replicate 2

description:
tag_seq_counts.csv
BM_WT_pBM5_2


title: control + Pab1GFP vector 90 minutes replicate 1

description:
tag_seq_counts.csv
BM_WT_pBM766_1


title: control + empty vector 90 minutes replicate 1

description:
tag_seq_counts.csv
BM_WT_pBM5_1


title: csl4-ph + Pab1GFP vector 90 minutes replicate 2

description:
tag_seq_counts.csv
BM_csl4ph_pBM766_2


title: 201InputHipp

city: Oklahoma City

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

data_processing:
Following sequencing, reads were trimmed, aligned, differential expression statistics and correlation analyses were performed in Strand NGS software package (Agilent)
Reads were aligned against the Mm10 build of the mouse genome (2014.11.26). Alignment and filtering criteria included: adapter trimming, fixed 2bp trim from 5’ and 6bp from 3’ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum of 5% gap, trimming of 3’ end with Q<30.
Alignment was performed directionally with Read 1 aligned in reverse and Read 2 in forward orientation. Reads were filtered based on the mapping status and only those reads that aligned normally (in the appropriate direction) were retained.
Quantitation was performed with the DESeq algorithm and samples were normalized to input.
Transcripts with an average read count value >20 in at least 100% of the samples in at least one group were considered expressed at a level sufficient for quantitation per tissue and those transcripts below this level were considered not detected/not expressed and excluded, as these low levels of reads are close to background and are highly variable.
Genome_build: mm10
Supplementary_files_format_and_content: txt file, raw read counts and normalized read counts for all expressed genes

source_name: Brain (hippocampus)

extract_protocol:
The purification of cell-specific RNA from brain tissue from Tam-induced Cx3cr1-cre/ERT2+; NuTRAP+ mice was achieved by following an established protocol, with slight modifications. For each mouse, hippocampi were minced into small pieces and homogenized in 2 ml ice-cold homogenization buffer (50 mM Tris, pH 7.4; 12 mM MgCl2; 100 mM KCl; 1% NP-40; 1 mg/mL sodium heparin; 1 mM DTT) supplemented with 100 ug/mL cycloheximide (#C4859-1ML, Millipore Sigma), 200 units/mL RNaseOUT™ Recombinant Ribonuclease Inhibitor (#10777019; Thermofisher), and 1X cOmplete™, EDTA-free Protease Inhibitor Cocktail (#11836170001; Millipore Sigma) with a glass dounce tissue grinder set (#D8938; 10 times with pestle A and 10 times with pestle B). Homogenate was transferred to a 2 mL round-bottom tube and centrifuged at 12,000 x g for 10 minutes at 4°C. After centrifugation, 100 uL of the supernatant was saved as input. The remaining supernatant was transferred to a 2 mL round-bottom tube and incubated with 5 ug/uL of anti-GFP antibody (ab290; Abcam) at 4°C with end-over-end rotation for one hour. Dynabeads™ Protein G for Immunoprecipitation (#10003D; Thermofisher) were washed three times in 1 mL ice-cold low-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 100mM KCl; 1% NP-40; 100μg/ml cycloheximide; 1mM DTT). After removal of the last wash, the homogenate/antibody mixture was transferred to the 2 mL round-bottom tube containing the washed Protein-G Dynabeads and incubated at 4°C with end-over-end rotation for an additional two hours. Magnetic beads were collected using a DynaMag-2 magnet and the unbound- ribosomes and associated RNA saved as the “negative” fraction. Beads were then washed three times with 1 mL of high-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 300mM KCl; 1% NP-40; 100μg/ml cycloheximide; 2mM DTT). Following the last wash, 350 uL of Buffer RLT (Qiagen) supplemented with 3.5 uL 2-β mercaptoethanol was added directly to the beads and incubated with mixing on a ThermoMixer (Eppendorf) for 10 minutes at room temperature. The beads were magnetically separated and the supernatant containing the target bead-bound ribosomes and associated RNA was transferred to a new tube. 350 uL of 100% ethanol was added to the tube (“positive” fraction) and then loaded onto an RNeasy MinElute column. RNA was isolated using RNeasy Mini Kit (#74104, Qiagen), according to manufacturer’s instructions. RNA was quantified with a Nanodrop 2000c spectrophotometer (Thermofisher Scientific) and its quality assessed by HSRNA screentape with a 2200 Tapestation analyzer (Agilent Technologies).
The NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L; New England Biolabs Inc., Ipswich, MA) was used on 25 ng of total RNA for the preparation of strand-specific sequencing libraries from each TRAP-isolated RNA sample (input and positive fraction) and from conventionally isolated RNA samples from brain (tissue), according to manufacturer's instructions. Briefly, polyA containing mRNA was purified using oligo-dT attached magnetic beads. mRNA was chemically fragmented and cDNA synthesized. For strand-specificity, the incorporation of dUTP instead of dTTP in the second strand cDNA synthesis does not allow amplification past this dUTP with the polymerase. Following cDNA synthesis, each product underwent end repair process, the addition of a single ‘A’ base, and finally ligation of adapters. The cDNA products were further purified and enriched using PCR to make the final library for sequencing. Library sizing was performed with HS RNA ScreenTape (#5067-5579; Agilent Technologies).

value: Cx3cr1-Cre/Ert2+; NuTRAP+

tag: fraction

value: Input

tag: animal number

tag: library prep kit

value: NEBNext Ultra II Directional RNA Library Prep Kit for Illumina


title: 207InputHipp


title: csl4-ph + empty vector 90 minutes replicate 3

description:
tag_seq_counts.csv
BM_csl4ph_pBM5_3


title: scRNA-seq, olfactory epithelium, UNO - open (R)

city: Aurora

first: Stephen

middle: William

last: Santoro

department: Department of Pediatrics, Section of Developmental Biology

institute: University of Colorado Denver - Anschutz Medical Campus

description:
aggregation_barcodes.tsv.gz
aggregation_features.tsv.gz
aggregation_matrix.mtx.gz
aggregation_cloupe.cloupe

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq 6000 was converted into FASTQ files and de-multiplexed using the 10X Genomics’ Cell Ranger software (3.0.2).
UMI and cell barcode de-convolution and mapping to the genome were performed using 10X Genomics’ Cell Ranger software package (3.0.2) to generate the final digital gene expression matrices and .cloupe files.
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files contain the aggregated filtered feature barcode matrix
Supplementary_files_format_and_content: The cloupe file contains gene expression information for cells in the sample; gene expression-based clustering information for the cells, including t-SNE and UMAP projections and differentail gene expression; and gene annotation information from the transcriptome reference.

source_name: Olfactory epithelium

extract_protocol:
Frozen dissociated cells from half-OEs were used for library preparation using the Chromium Single Cell 3’ v3 Kit (10X Genomics) following dead cell removal.
Single cell RNA libraries were generated using the Chromium Single Cell 3’ Kit (10X Genomics) following Dead Cell Removal (Miltenyi). Cells were counted using a trypan blue exclusion count assay with a hemocytometer and diluted for loading onto the Chromium Controller. Loading was performed to target capture of ~10,000 Gel Beads in Emulsion (GEMs) per sample for downstream analysis, and samples were processed through the Chromium Controller following the manufacturer’s specifications. Sequencing libraries were evaluated for quality on the Agilent TapeStation (Agilent Technologies), and quantified using a Qubit 2.0 Fluorometer (ThermoFisher Scientific) and pooled libraries were quantified using qPCR (Applied Biosystems) prior to sequencing.

treatment_protocol: Samples are from the open and closed sides of the olfactory epithelium of a mouse that was UNO-treated at PD14.

tag: age

tag: Sex

value: male

tag: treatment

value: unilateral naris occlusion (PD14)

tag: side

value: open (R)

value: all olfactory epithelial cells


title: HFD+E2 M rep6

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

country: Sweden

institute: Karolinska Institute

description: Sample 127

data_processing:
Clustering was done by 'cBot' and samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.4.0/RTA v3.3.3) with a 2x51 setup using 'NovaSeqXp' workflow in 'S1' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.19.1.403 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+
Sequenced reads were trimmed for adaptor sequence and trimming for low-quality regions using TrimGalore, then mapped to mm10 whole genome using STAR
FeatureCounts were used to generate the raw counts and FPKM and TPM values were generated with StringTie
Genome_build: mm10
Supplementary_files_format_and_content: [gene_abund.txt] tab-delimited text file includes raw counts and TPM values for each Sample
[merged_gene_counts.txt] Gene count table

source_name: Colon

extract_protocol:
Colons were removed, snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent with the RNeasy Mini Kit (Qiagen). Illumuna TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero was used with total RNA for the construction of the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were fed a control diet or high fat diet for 13-weeks and treated with vehicle or estrogen for the last three weeks prior to sacrifice (9 I.P injcections). E2 concentration (0.5mg/kg BW)

tag: strain

value: Male

tag: tissue

value: Colon

tag: diet

value: High fat diet HFD

value: Estrogen


title: 201posHipp

tag: genotype

value: Positive


title: HFD+E2 M rep4

description: Sample 123


title: 207posHipp


title: 208InputHipp


title: 208posHipp


title: HFD+E2 M rep3

description: Sample 118


title: enp1-1 + Pab1GFP vector 90 minutes replicate 2

description:
tag_seq_counts.csv
BM_enp1_1_pBM766_2


title: HFD+E2 M rep2

description: Sample 116


title: scRNA-seq, olfactory epithelium, UNO - closed (L)

value: closed (L)

tag: cell type


title: HFD M rep5

description: Sample 121

value: Vehicle


title: Adult Intact and Castrated Mouse Prostate Run 2

city: Macclesfield

first: Renaud

last: Mevel

address: Cancer Research UK, Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Alderley Edge

description:
GL60_04
Individually sorted populations (RFP+ / RFP-) from each lobe were multiplexed using MULTI-seq lipid-tagged indices. Lobes from intact and castrated mice were kept separated. Each lobe had a RFP+ and RFP- fraction, comprising basal and luminal cells.

data_processing:
Raw sequencing reads were processed using CellRanger v3.1.0.
The mm10 Mus musculus genome was used for mapping the reads.
MULTI-seq barcode libraries were processed using the ‘deMULTIplex’ (v1.0.2) R package.
For adult runs 1, 2, 3, sample integration was performed using Seurat (v3.1.5).
MULTI-seq sample barcodes were demultiplexed using the HTODemux function implemented in Seurat.
Genome_build: Mus musculus mm10 GRCm38 Ensembl 93
Supplementary_files_format_and_content: UMI_matrix_raw: Gene-by-cell matrix containing raw counts for each cell.
Supplementary_files_format_and_content: multiseq_matrix: Cell-by-barcode matrix of MULTI-seq barcode counts for each cell used for sample demultiplexing.
Supplementary_files_format_and_content: sample_metadata: Table of correspondance between samples and MULTI-seq barcodes for each run.
Supplementary_files_format_and_content: gene_ids: Table of correspondance between ensembl gene id and gene symbol for each run.

source_name: prostate

extract_protocol:
Cells were lysed in droplets in the 10x Genomics Chromium system. cDNA synthesis and library construction was performed using the 3' scRNA-seq Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v3 (10x Genomics). Gene expression (cDNA) libraries were prepared according to the manufacturer’s protocol. MULTI-seq barcode libraries were separated from the cDNA libraries during the first round of size selection, and PCR amplified prior to sequencing according to the MULTI-seq library preparation protocol (McGinnis et al., 2019).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Adult (> 8 weeks old)

value: Intact and Castrated (> 4 weeks)

value: ICR (CD-1)

tag: model

value: prostate


title: Adult Intact and Castrated Mouse Prostate Run 1

institute: Cancer Research UK Manchester Institute, The University of Manchester

description:
GL60_01
Individually sorted populations (RFP+ / RFP-) from each lobe were multiplexed using MULTI-seq lipid-tagged indices. Lobes from intact mice were kept separated. Lobes from castrated mice were pooled. Each lobe had a RFP+ and RFP- fraction, comprising basal and luminal cells.


title: HFD M rep4

description: Sample 114


title: HFD+E2 M rep1

description: Sample 103


title: HFD M rep2

description: Sample 108


title: HFD+E2 M rep5

description: Sample 125


title: HFD M rep1

description: Sample 101


title: HFD M rep6

description: Sample 128


title: HFD F rep4

description: Sample 115

value: Female


title: HFD M rep3

description: Sample 109


title: CD M rep5

description: Sample 126

value: Control diet CD


title: CD M rep4

description: Sample 124


title: HFD F rep1

description: Sample 105


title: HFD F rep3

description: Sample 113


title: CD M rep6

description: Sample 130


title: HFD F rep2

description: Sample 107


title: MU01-0025-Ctrl

source_name: Urine

value: Urine

tag: histopathology

value: Control


title: CD M rep2

description: Sample 111


title: CD F rep6

description: Sample 129


title: CD F rep3

description: Sample 110


title: CD F rep4

description: Sample 112


title: CD F rep5

description: Sample 119


title: CD M rep1

description: Sample 106


title: CD M rep3

description: Sample 117


title: CD F rep1

description: Sample 102


title: HFD F rep5

description: Sample 120


title: Female 2

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
FASTQ files for 10X V2 samples were generated and demultiplexed using Illumina bcl2fastq 2.18.0.12, and V3 samples were processed with bcl2fastq 2.20.0.422.
In V2 samples, R1 (26p) corresponds to a 16bp cell barcode + 10bp UMI barcode and R2 (98bp) contains the biological read.  For V3 samples, R1 (28bp) contains a 16bp cell barcode + 12bp UMI barcode, and R2 is only 91bp.
A filtered digital gene expression matrix was generated for each gene expression library against the 10X Genomics mm10 reference build (version 3.0.0, GRCm38.93) using 10X Genomics Cellranger count version 3.0.2
Genome_build: GRCm38.93
Supplementary_files_format_and_content: Counts matrices are in Matrix Market CSR format and gzipped.  Rows correspond to genes in the associated features.tsv.gz and columns correspond to cell-barcodes in associated barcodes.tsv.gz

source_name: Ventroposterior hypothalamus

extract_protocol: Suspensions of dissociated cells were washed and suspended in PBS containing 0.04% BSA, and each suspension was processed as follows.  Cells were counted on Countess II automated cell counter (ThermoFisher), and 12,000 cells were loaded for capture onto an individual lane of a Chromium Controller (10X Genomics). Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform according to the manufacturer’s protocol (#CG00052) using version 2 (V2) chemistry for the first set of male and female samples and version 3 (V3) chemistry for the second set. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR.

value: Ventroposterior hypothalamus

value: female

tag: 10x chemistry

tag: harvest


title: CD F rep2

description: Sample 104


title: Mouse_PDGFRab_Sham

city: Aachen

first: Mahmoud

middle: M

last: Ibrahim

address: Pauwelsstraße 30

department: Faculty of Medicine

country: Germany

institute: RWTH Aachen University

description: 10x chromium version 2

data_processing:
Fastq files were processed using Alevin and Salmon (salmon version 0.13.1), setting the number of expected cells to 3x the number predicted by the knee of the read count per barcode curve. Resulting UMI-barcode count matrices are provided as processed data files.
Genome_build: mm10
Supplementary_files_format_and_content: raw UMI barcode count matrices produced by Alevin in csv files and corresponding row (gene) and column (cell barcode)  information

extract_protocol:
Kidneys were removed and kidney tissue was digested using Liberase TL and DNAse for 30 min 37°C and apllied to GentleMACs program spleen 4 after 15 minutes and after 30 minutes.
10X 3' scRNA-seq libaries were generated using the compnay's protocol.
single-cell RNA Seq. Read 1 constitutes the cell barcodes and transcript UMIs. Read 2 is the RNA transcript read for alignment (10x Chromium)

tag: days after uuo

value: sham

value: kidney

value: FVBN


title: Mouse_PDGFRab_UUO

description: 10x chromium version 2

value: kidney (UUO, unilateral urether obstruction)


title: Male 2

value: male


title: embryonic day 6.5 Mullerian duct [cs10_S10]

city: Clayton

first: Kirill

last: Tsyganov

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

data_processing:
Raw fastq files have been analysed with RNAsik pipeline (Tsyganov et al. 2018) to produce raw genes count matrix and various quality control metrics.
For this analysis RNAsik pipeline (Tsyganov et al. 2018) ran with STAR aligner option (Dobin et al. 2013) and reads were quantified with featureCounts (Liao, Smyth, and Shi 2014).
The reference GFF and FASTA files were downloaded from RefSeq database (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002315.6)
Raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical conts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000002315.6
Supplementary_files_format_and_content: ReverseStrandedCounts.txt: raw gene counts, featureCounts
Supplementary_files_format_and_content: ReverseStrandedCounts.txt.summary: summary QC metrics
Supplementary_files_format_and_content: ReverseStrandedCounts-withNames.txt: raw gene counts, all features, annotated with gene symbols
Supplementary_files_format_and_content: ReverseStrandedCounts-withNames-proteinCoding.txt: raw gene counts, proteing coding features only, annotated with gene symbols

organism: Gallus gallus

source_name: kidney cells

extract_protocol:
libraries were prepared in triplicate from 300ng of total RNA using the Illumina TruSeq Stranded mRNA kit using single indexing according to the manufacturer's recommendation
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic day 6.5 Mullerian duct

tag: cell types

value: Müllerian duct cells


title: embryonic day 5.5 Mullerian duct [cs9_S9]

value: embryonic day 5.5 Mullerian duct


title: embryonic day 4.5 posterior region kidney only (negative control) [cs6_S6]

value: Posterior half of mesonephric kidney


title: embryonic day 5.5 Mullerian duct [cs7_S7]


title: embryonic day 4.5 posterior region kidney only (negative control) [cs5_S5]


title: embryonic day 4.5 anterior region kidney + duct [cs3_S3]

value: Anterior half of mesonephric cells and  Müllerian anlagen


title: embryonic day 4.5 anterior region kidney + duct [cs2_S2]


title: embryonic day 4.5 posterior region kidney only (negative control) [cs4_S4]


title: Lung Sacrodosis Tissue Rep5

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

institute: institution of microbology

data_processing:
The adaptors and low quality bases assessed using FASTQC 0.11.3 were trimmed by Trimmomatic 0.39 using the following options: TRAILING:20, MINLEN:235 and CROP:235
Trimmed reads were then aligned to the ensembl 79 (GRCh38.p2) reference genome using STAR 2.4.2a
FeatureCounts 1.6.2 was subsequently employed to convert aligned short reads into read counts for each sample
The data were then analyzed using R 3.4.4 and DEseq2 1.18.1. Differentially expressed genes of each disease group were identified using Wald statistics test, with fold-change > 2 and Benjamini–Hochberg (BH)-adjusted P < 0.1 as compared to NC group
Genome_build: ensembl 79 (GRCh38.p2)
Supplementary_files_format_and_content: tab-delimited text files include raw count values

extract_protocol:
Human lung tissues were used for total RNA extraction with RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed using a Nanodrop ND-2000 (Thermo Scientific), and each RNA sample had an A260:A280 ratio above 1.8 and an A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies), and each sample had the RNA Integrity Number (RIN) above 7.0. The ribosomal RNAs (rRNAs) were removed using Ribo-Zero rRNA Removal Kits (Illumina).
RNA libraries were then constructed by NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) and evaluated using the Agilent 2200 TapeStation and Qubit® 2.0 (Life Technologies). Sequencing was performed by RiboBio Co., Ltd. on an Illumina HiSeq 3000 machine with paired-end 150-bp reads.

value: Lung

tag: disease

value: Sacrodosis


title: Lung Sacrodosis Tissue Rep3

tag: age

value: Male


title: Lung Sacrodosis Tissue Rep4

tag: Sex

value: Female


title: Lung Sacrodosis Tissue Rep1


title: Lung Sacrodosis Tissue Rep2


title: Lung Adenocarcinoma Tissue Rep5

value: Adenocarcinoma


title: Lung Adenocarcinoma Tissue Rep4


title: Lung Adenocarcinoma Tissue Rep1


title: Lung Tuberculosis Tissue Rep5

value: Tuberculosis


title: embryonic day 6.5 Mullerian duct [cs12_S12]


title: Lung Adenocarcinoma Tissue Rep3


title: Lung Adenocarcinoma Tissue Rep2


title: embryonic day 6.5 Mullerian duct [cs11_S11]


title: Lung Tuberculosis Tissue Rep1


title: HFD F rep6

description: Sample 122

value: Colon

value: High fat diet HFD

tag: treatment

value: Vehicle


title: Lung Tuberculosis Tissue Rep3


title: Lung Tuberculosis Tissue Rep2


title: embryonic day 5.5 Mullerian duct [cs8_S8]


title: Normal Lung Tissue Rep5

value: Normal


title: Normal Lung Tissue Rep4


title: Lung Tuberculosis Tissue Rep4


title: Normal Lung Tissue Rep3


title: Normal Lung Tissue Rep1


title: Normal Lung Tissue Rep2


title: embryonic day 4.5 anterior region kidney + duct [cs1_S1]


title: Rv-C-6_1

city: Bronx

first: Erik

middle: James

last: Hasenoehrl

state: New York

address: 1301 Morris Park Ave. Price 569

department: Microbiology & Immunology

institute: Albert Einstein College of Medicine

data_processing:
Illumina reads were mapped to reference genome using bowtie2, which generated SAM files
SAM files were converted to coordinate-sorted BAM files using samtools
Reads per gene were countedusing featureCounts
Differential gene expression analysis was performed using DeSeq2
Data analysis protocol can be found in more detail in Benjak, et. Al., Methods Mol Biol, 2015
Genome_build: NC_000962.3
Supplementary_files_format_and_content: count files were produced from illumina fastq readfiles using fetureCounts and contain a raw count of reads per gene; DGE Analysis files were generated using DeSeq2 and contain analyzed read count comparisons between samples at time of starvation compared to time 0 (before starvation), these include p-values.

organism: Mycobacterium tuberculosis

source_name: H37Rv at T6, treated with combined, biological rep 1

extract_protocol:
Culure samples were collected and pelleted via centrifugation. Cell pellets were resuspended in Trizol reagent and RNA was harvested via phenol-chloroform extraction. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

tag: time

value: 6 h


title: delcydAB-C-6_3

source_name: H37Rv∆cydAB at T6, treated with combined,biological rep 3


title: delcydAB-C-6_1

source_name: H37Rv∆cydAB at T6, treated with combined,biological rep 1


title: Rv-ND-6_3

source_name: H37Rv at T6, treated with ND-011992, biological rep 3


title: Rv-C-6_3

source_name: H37Rv at T6, treated with combined, biological rep 3


title: delcydAB-ND-6_1

source_name: H37Rv∆cydAB at T6, treated with ND-011992,biological rep 1


title: Rv-C-6_2

source_name: H37Rv at T6, treated with combined, biological rep 2


title: delcydAB-Q-6_3

source_name: H37Rv∆cydAB at T6, treated with Q203,biological rep 3


title: Rv-Q-6_1

source_name: H37Rv at T6, treated with Q203, biological rep 1


title: delcydAB-Q-6_1

source_name: H37Rv∆cydAB at T6, treated with Q203,biological rep 1


title: delcydAB-ND-6_3

source_name: H37Rv∆cydAB at T6, treated with ND-011992,biological rep 3


title: Rv-ND-6_1

source_name: H37Rv at T6, treated with ND-011992, biological rep 1


title: delcydAB-Q-6_2

source_name: H37Rv∆cydAB at T6, treated with Q203,biological rep 2


title: Rv-Q-6_2

source_name: H37Rv at T6, treated with Q203, biological rep 2


title: delcydAB-0_3

source_name: H37Rv∆cydAB at T0, biological rep 3

value: Standard

value: 0 h


title: Rv-0_2

source_name: H37Rv at T0, biological rep 2


title: RNABL2058_CTRL_rep2

city: Protland

first: Joel

middle: T.

last: Nigg

state: Oregon

address: 3181 S.W. Sam Jackson Park Road

department: Department of Psychiatry

institute: Oregon Health & Science University

data_processing:
Raw files were processed with Helisphere software package ver. 1.2.740
Reads aligned to the human genome with indexDPgenomic and filtered with parameters: min_len=25, min_score=4.3, best_only=1, global_ambiguity=all
Raw expression was calculated with a custom script: +1 is added if a read occurs inside an exon and +0.5 if read covers exonic junction
Raw counts were RPKM normalized with a custom script
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT tab-separated file with DGE counts

source_name: Whole blood

extract_protocol:
RNA was extracted with the Qiagen PAXgene blood RNA kit (P/N 762164) using a QIAcube automation system.
Total RNA, rRNA depleted
Ribosomal RNA depletion of approximately 0.5-2 ug of total RNA was performed using the Illumina Ribo-Zero Gold kit (#MRZG12324). First strand cDNA synthesis was carried out by initially incubating 7 µL of sample plus water (~30-50 ng RNA) at 95°C for 5 minutes and chilling on ice for 2 minutes. While on ice, 5 µL of 50 ng/µL random hexamers (Invitrogen #51709) and 1 µL of 10 mM dNTP (Invitrogen #Y02256) mix were added to the RNA and the mixture was incubated at 65°C for 5 minutes. While on ice, 4 µL of 5x buffer and 1 µL of 0.1 M DTT were mixed into the solution and incubated at 15°C for 20 minutes. Finally, 1 µL of RNase Inhibitor and 1 µL of 200 U/µL Superscript III Reverse Transcriptase (Invitrogen #18080-044) were added. The following program was run on the thermal cycler: 25°C for 10 minutes, 40°C for 40 minutes, 55°C for 50 minutes, and 85°C for 5 minutes. Upon completion, 1 µL each of 2 U/µL RNase H (Invitrogen #18021-071) and 50 U/µL RNase If (NEB #MO243) were used to digest the RNA strand at 37°C for 30 minutes and subsequently purified using EdgeBio Performa DTR Gel filtration cartridges (#42453). 3’ Poly A tailing was initiated by addition of 4 µL of 10x TdT buffer and 4 µL of 2.5 mM CoCl2 and water to 10 µL of cDNA, denatured at 95 °C for 5 minutes, and snap cooled. Then 250x dATP and 1 µL of 20 U/µL (diluted to 10 U/µL) Terminal Transferase (NEB #M0315) were added and the solution was incubated for 30 minutes at 37°C. Finally, 2 µL of 200 µM ddATP were spiked into the reaction which was incubated at 37°C for 1 hour, and 70°C for 10 minutes to inactivate the enzyme.
PCR-free RNA-Seq

value: CTRL

tag: twin pair id

tag: tissue

value: Whole blood


title: Rv-0_1

source_name: H37Rv at T0, biological rep 1

tag: genotype


title: delcydAB-0_1

source_name: H37Rv∆cydAB at T0, biological rep 1


title: RNABL2000_CTRL


title: RNABL2044_CTRL_rep3


title: Rv-0_3

source_name: H37Rv at T0, biological rep 3


title: RNABL2050_CTRL_rep3


title: delcydAB-C-6_2

source_name: H37Rv∆cydAB at T6, treated with combined,biological rep 2


title: delcydAB-0_2

source_name: H37Rv∆cydAB at T0, biological rep 2


title: RNABL2040_CTRL_rep2


title: RNABL2057_CTRL_rep3


title: RNABL2034_CTRL_rep4


title: delcydAB-ND-6_2

source_name: H37Rv∆cydAB at T6, treated with ND-011992,biological rep 2


title: Rv-ND-6_2

source_name: H37Rv at T6, treated with ND-011992, biological rep 2


title: RNABL2019_CTRL_rep2


title: RNABL2024_CTRL_rep2


title: RNABL2034_CTRL_rep3


title: RNABL2015_CTRL_rep3


title: RNABL2004_CTRL_rep2


title: RNABL2012_CTRL_rep3


title: RNABL2032_CTRL_rep2


title: RNABL2055_CTRL_rep2


title: RNABL2010_CTRL_rep3


title: RNABL2030_CTRL_rep2


title: RNABL2046_CTRL_rep3


title: RNABL2014_CTRL_rep3


title: RNABL2057_CTRL_rep2


title: RNABL2046_CTRL_rep2


title: RNABL2050_CTRL_rep2


title: RNABL2015_CTRL_rep2


title: RNABL2012_CTRL_rep2


title: RNABL2014_CTRL_rep2


title: RNABL2034_CTRL_rep2


title: RNABL2010_CTRL_rep2


title: RNABL2004_CTRL_rep1


title: RNABL2044_CTRL_rep2


title: RNABL2057_CTRL_rep1


title: RNABL2002_CTRL


title: RNABL2006_CTRL_rep2


title: RNABL2050_CTRL_rep1


title: RNABL2055_CTRL_rep1


title: RNABL2046_CTRL_rep1


title: RNABL2040_CTRL_rep1


title: RNABL2044_CTRL_rep1


title: RNABL2034_CTRL_rep1


title: RNABL2058_CTRL_rep1


title: RNABL2033_CTRL


title: RNABL2032_CTRL_rep1


title: RNABL2030_CTRL_rep1


title: RNABL2012_CTRL_rep1


title: RNABL2019_CTRL_rep1


title: RNABL2014_CTRL_rep1


title: RNABL2010_CTRL_rep1


title: RNABL2001_ADHD_rep3

value: ADHD


title: RNABL2015_CTRL_rep1


title: RNABL2006_CTRL_rep1


title: RNABL2016_ADHD_rep3


title: RNABL2024_CTRL_rep1


title: RNABL2001_ADHD_rep2


title: RNABL2016_ADHD_rep2


title: RNABL2029_ADHD_rep2


title: RNABL2035_ADHD_rep3


title: RNABL2027_ADHD_rep2


title: RNABL2056_ADHD_rep2


title: RNABL2025_ADHD_rep2


title: RNABL2047_ADHD_rep2


title: RNABL2021_ADHD


title: RNABL2054_ADHD_rep3


title: RNABL2016_ADHD_rep1


title: RNABL2018_ADHD_rep2


title: RNABL2013_ADHD_rep3


title: RNABL2011_ADHD_rep2


title: RNABL2049_ADHD_rep2


title: RNABL2007_ADHD_rep3


title: RNABL2054_ADHD_rep2


title: RNABL2009_ADHD_rep3


title: RNABL2031_ADHD_rep3


title: RNABL2031_ADHD_rep2


title: RNABL2003_ADHD


title: RNABL2005_ADHD


title: RNABL2009_ADHD_rep2


title: RNABL2007_ADHD_rep2


title: RNABL2054_ADHD_rep1


title: RNABL2056_ADHD_rep1


title: RNABL2049_ADHD_rep1


title: RNABL2041_ADHD_rep1


title: RNABL2037_ADHD


title: RNABL2047_ADHD_rep1


title: RNABL2031_ADHD_rep1


title: RNABL2029_ADHD_rep1


title: RNABL2027_ADHD_rep1


title: RNABL2025_ADHD_rep1


title: RNABL2023_ADHD


title: RNABL2039_ADHD_rep2


title: RNABL2013_ADHD_rep1


title: RNABL2041_ADHD_rep2


title: RNABL2018_ADHD_rep1


title: RNABL2013_ADHD_rep2


title: RNABL2035_ADHD_rep2


title: RNABL2009_ADHD_rep1


title: RNABL2011_ADHD_rep1


title: RNABL2001_ADHD_rep1


title: RNABL2039_ADHD_rep1


title: RNABL31582_CTRL


title: RNABL31512_ADHD


title: RNABL31581_ADHD


title: RNABL31511_CTRL_rep1


title: RNABL31501_ADHD_rep2


title: RNABL31501_ADHD_rep1


title: RNABL31502_CTRL_rep1


title: RNABL31452_ADHD


title: RNABL31381_ADHD


title: RNABL2035_ADHD_rep1


title: RNABL31451_CTRL


title: RNABL31182_ADHD


title: RNABL31181_CTRL


title: RNABL30922_CTRL_rep3


title: RNABL31511_CTRL_rep2


title: RNABL30922_CTRL_rep1


title: RNABL30921_ADHD_rep2


title: RNABL30921_ADHD_rep1


title: RNABL30922_CTRL_rep2


title: RNABL30832_CTRL


title: RNABL30831_ADHD_rep1


title: RNABL30831_ADHD_rep2


title: RNABL30682_ADHD_rep2


title: RNABL30682_ADHD_rep3


title: RNABL30682_ADHD_rep1


title: RNABL30681_CTRL_rep3


title: RNABL31502_CTRL_rep2


title: RNABL30681_CTRL_rep2


title: RNABL30681_CTRL_rep1


title: RNABL31382_CTRL


title: RNABL30641_CTRL


title: RNABL30671_ADHD_rep2


title: RNABL30392_CTRL_rep2


title: RNABL30672_CTRL_rep3


title: RNABL30672_CTRL_rep2


title: RNABL30642_ADHD


title: RNABL30671_ADHD_rep1


title: RNABL30391_ADHD_rep2


title: RNABL30392_CTRL_rep1


title: RNABL30391_ADHD_rep1


title: RNABL30382_ADHD_rep1


title: RNABL30382_ADHD_rep2


title: RNABL2007_ADHD_rep1


title: Perforin-deficient CAR-T post-activation, biological rep 5

city: bethesda

first: Jack

last: Shern

state: MD

address: 10 Center drive

institute: NCI

description:
homozygous Prf1 knockout
gene expression data from perforin-deficient CD8+ CAR-T cells after activation
P5

hyb_protocol: Microarray core facility in The Frederick National Laboratory for Cancer Research (FNLCR) performed labeling and hybridization on microarray chips according to protocols specified by the manufacturers

data_processing: CEL files were input to the Partek Flow, then use the STAR(2.5.3a) align to the mm10 genome, Counts per million (CPM) were quantified using the Partek E/M model. The file Partek_Kazusa_mouse_microarray_Normalization_Normalized_counts.txt includes the normalized values used for the analysis of this study.

source_name: CD8+ perforin-deficient CAR-T cells after activation

growth_protocol: Mouse splenocytes were isolated and transduced with anti-CD19 chimeric antigen receptor, and enriched for CD8+ fraction.

extract_protocol: RNA were extracted using Qiagen RNA exraction kit (Rneasy Plus Mini Kit) according to manufacturer's instruction

treatment_protocol: CD8+ T cells transduced with anti-CD19 chimeric antigen recepter were co-cultured with CD19+ mouse leukemia cell line (E2aPBx) for 24 hours

tag: cell type

value: CD8+ CAR-T cells

value: homozygous Prf1 knockout

value: after activation with cognate-antigen-positive leukemia cells


title: Perforin-deficient CAR-T post-activation, biological rep 4

description:
homozygous Prf1 knockout
gene expression data from perforin-deficient CD8+ CAR-T cells after activation
P4

scan_protocol: Microarray core facility in The Frederick National Laboratory for Cancer Research (FNLCR) performed labeling and hybridization on microarray chips according to protocols specified by the manufacturers


title: RNABL30381_CTRL_rep2


title: RNABL30672_CTRL_rep1


title: Wild-type CAR-T post-activation, biological rep 2

description:
Wild-type C57BL/6
gene expression data from Wild-type CD8+ CAR-T cells after activation
W2

source_name: CD8+ Wild-type CAR-T cells after activation

label_protocol: Microarray core facility in The Frederick National Laboratory for Cancer Research (FNLCR) performed labeling and hybridization on microarray chips according to protocols specified by the manufacturers

value: Wild-type

tag: background strain


title: Wild-type CAR-T post-activation, biological rep 4

description:
Wild-type C57BL/6
gene expression data from Wild-type CD8+ CAR-T cells after activation
W4


title: Wild-type CAR-T post-activation, biological rep 5

description:
Wild-type C57BL/6
gene expression data from Wild-type CD8+ CAR-T cells after activation
W5


title: RNABL30152_ADHD


title: Perforin-deficient CAR-T post-activation, biological rep 3

description:
homozygous Prf1 knockout
gene expression data from perforin-deficient CD8+ CAR-T cells after activation
P3


title: RNABL30381_CTRL_rep1


title: Perforin-deficient CAR-T post-activation, biological rep 2

description:
homozygous Prf1 knockout
gene expression data from perforin-deficient CD8+ CAR-T cells after activation
P2


title: RNABL30151_CTRL


title: Wild-type CAR-T post-activation, biological rep 3

description:
Wild-type C57BL/6
gene expression data from Wild-type CD8+ CAR-T cells after activation
W3


title: Wild-type CAR-T post-activation, biological rep 1

description:
Wild-type C57BL/6
gene expression data from Wild-type CD8+ CAR-T cells after activation
W1


title: RNABL30382_ADHD_rep3


title: RNABL30052_ADHD_rep1


title: Wild-type CAR-T pre-activation, biological rep 2

description:
Wild-type C57BL/6
gene expression data from Wild-type CD8+ CAR-T cells before activation
PreW2

source_name: CD8+ Wild-type CAR-T cells before activation

value: before activation with cognate-antigen-positive leukemia cells


title: Wild-type CAR-T pre-activation, biological rep 3

description:
Wild-type C57BL/6
gene expression data from Wild-type CD8+ CAR-T cells before activation
PreW3


title: Perforin-deficient CAR-T preactivation, biological rep 3

description:
homozygous Prf1 knockout
gene expression data from perforin-deficient CD8+ CAR-T cells before activation
PreP3

source_name: CD8+ perforin-deficient CAR-T cells before activation


title: Perforin-deficient CAR-T preactivation, biological rep 2

description:
homozygous Prf1 knockout
gene expression data from perforin-deficient CD8+ CAR-T cells before activation
PreP2


title: Wild-type CAR-T pre-activation, biological rep 1

description:
Wild-type C57BL/6
gene expression data from Wild-type CD8+ CAR-T cells before activation
PreW1


title: RNABL30051_CTRL_rep2


title: RNABL30051_CTRL_rep3


title: Perforin-deficient CAR-T post-activation, biological rep 1

description:
homozygous Prf1 knockout
gene expression data from perforin-deficient CD8+ CAR-T cells after activation
P1


title: RNABL30042_CTRL_rep1


title: RNABL30042_CTRL_rep2


title: RNABL30051_CTRL_rep1


title: RNABL30041_ADHD_rep2


title: rrp6 deletion 90 minutes ribo- replicate 2

description: ribo depleted total RNA

data_processing:
All code related to RNA-seq analyses has been deposited  at: https://github.com/montpetitlab/Aguilar_and_Paul_et_al_2020
Genome and transcriptome preparation: For transcript quantification, all libraries were quantified against the same transcriptome using Salmon (version 0.12.0). The custom transcriptome was prepared using a bed file that contained coordinates for pervasive transcripts, ribosomal RNAs, and mRNAs to obtain transcript fasta sequences using bedtools getfasta command (version 2.29.2) against the UCSC sacCer3 genome.
Paired-end reads were trimmed using Trimmomatic (version 0.39) to quality trim and remove adapters. Trimmed reads were quantified against the custom transcriptome using Salmon quant. A count matrix was generated using the tximport R package (version 1.14.0)  Differential expression was performed using the R package DESeq2 (version 1.26.0) using the DESeq function and specifying a wald test.
Genome_build: S. cerevisiae R64 GCA_000146045.2_R64_rna_from_genomic file
Supplementary_files_format_and_content: CSV file with count data for each feature

source_name: vegetative cells

growth_protocol: Cells were grown at permissive temperature (25°C) until an OD600 of ~0. 8 before cultures were shifted to non-permissive temperature (37°C) for 30 or 90 minutes prior to being harvested. Harvested cells were rapidly frozen in liquid nitrogen and cryolysis was performed by solid phase milling in a planetary ball mill (Retsch) producing a fine cell grindate (Oeffinger et al., 2007).

extract_protocol:
RNA extractions were performed using 5 mg of cell powder. Cell grindate was thawed into 500 µL of Trizol. All kits were used as per supplier specifications. The RNA extracts (74104, Qiagen) were enriched via or ribo-depleted (MRZY1324, Epicentre).
cDNA libraries were prepared using the Kapa stranded RNA-seq library preparation kit (Kapa Biosystems).
Paired end 50 (PE50) RNA-sequencing was performed using a Hiseq 2500

tag: genetic background


title: RNABL30041_ADHD_rep1


title: RNABL30052_ADHD_rep2


title: rrp6 deletion 90 minutes ribo- replicate 1

description: ribo depleted total RNA


title: dis3-1 90 minutes ribo- replicate 2

description: ribo depleted total RNA


title: control 90 minutes ribo- replicate 2

description: ribo depleted total RNA


title: stop1_Fe

city: Irapuato

first: Luis

middle: Rafael

last: Herrera-Estrella

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

department: Langebio

country: Mexico

institute: Cinvestav - Langebio

data_processing:
Paired-end reads were aligned to the Arabidopsis genome (TAIR10; Release 46) using HISAT2 (version 2.1.0).
Raw counts per gene/locus were calculated using HTSeq (version 0.11.2).
Normalization of raw counts was carried out in R using edgeR package (version 3.28.0); only genes with at least 3 alligned reads in more than 1 library were kept.
Genome_build: TAIR10; Release 46
Supplementary_files_format_and_content: Tab Separated Text File (.txt) format file count_table.txt contains counts per million reads (cpm) normalized by library size.

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Seedlings were grown 5 days after germination under in petri dishes with 0.1X Modified MS media (1% w/v Sucrose, pH 5.7, and 1% w/v agar) and then transferred to treatment conditions.

extract_protocol:
Total RNA was isolated using the TRIZOL reagent (Invitrogen) according to the manufacturer's instructions and further purificated using the Qiagen RNeasy plant mini kit according to the manufacturer's instructions.
Strand-specific mRNA-seq libraries were generated from 5 μg of total RNA (Plant RNeasy kit) and prepared by using the TruSeq RNA Sample Prep kit (Illumina) according to the manufacturer’s instructions.
RNA-Seq was performed using the HiSeq 2500 Platform (Illumina) strand-specific paired-ends (150 bp).

treatment_protocol: Seedlings were transferred for 16h to a base 0.1X Modified MS liquid media (1% w/v Sucrose, with no phosphate  (KH2PO4; Pi added)) with 6 specific modifications described in the sample section (1 mM, 0.1 mM or 0 mM Pi; pH 5 or pH 6; +AlCl3; +0.1 mM FeSO4)

tag: ecotype

value: 0.1 mM Pi @pH 5 +0.1 mM FeSO4

tag: time point

value: 16 h exposure


title: Perforin-deficient CAR-T preactivation, biological rep 1

description:
homozygous Prf1 knockout
gene expression data from perforin-deficient CD8+ CAR-T cells before activation
PreP1


title: RPE1_single_Foci_MidS_scRepli-seq

city: Tsu

first: Shin-ichiro

last: Takebayashi

state: Mie

address: 2-174, Edobashi

department: Graduate School of Medicine

country: Japan

institute: Mie University

data_processing:
Library strategy: scRepli-seq
Single-cell data (FACS sorted samples): sequence reads were trimmed to remove adapter sequences using the cutadapt program before mapping. We performed a two-step adapter trimming, first removing the Illumina adapter based on the index of each NGS library and then removing the SEQXE adapter. As the SEQXE adapter sequence was not available, we empirically estimated it as the sequence that repeatedly appeared near the 5’ end.  Single-cell data (samples collected by the micromanupitator): sequence reads were trimmed to remove the WGA4 universal sequences using seqtk program ("seqtk trimfq -b 30 -e 30", trimming 30bp of both 5' and 3' ends) before mapping.
Trimmed reads were mapped into hg19 genome by using bwa (ver: 0.7.10-r789, command: bwa aln => bwa samse). Duplicated reads mapped into hg19 were removed by using picard tool and the reads overlapped with hg19 black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered out. The mapped reads with MAQP>10 were used for the further analysis. Sequence reads were saved as a GenomicRanges object (data can be loaded by R program).
For the analysis of single mid-S cell (sample collected by micromanupitator), we counted the reads in sliding windows of 200 kb at 40-kb intervals, and used the correctMappability command in the R package AneuFinder (http://bioconductor.org/packages/release/bioc/html/AneuFinder.html) for normalizing mid-S data based on the M-phase control. From the mappability corrected mid-S read counts, the genome-wide median was obtained and was used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the single-cell mid-S RT score.
For paired-end reads, only "R1" (Fwd) reads were used for the analysis.
Please see our scRepli-seq pipeline (https://github.com/kuzobuta/scRepliseq-Pipeline) for the further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: GenomirRanges object files including the mapped reads (GenomicRange_Format_data_set.zip) and README.txt describes the information of each sample.
Supplementary_files_format_and_content: bedGraph

growth_protocol: hTERT-RPE1 cells were grown in MEM-alpha supplemented with 10% FBS and penicillin/streptomycin.

extract_protocol:
For single-cells samples collected by FACS, cells were sorted with a Sony SH800 cell sorter using the single-cell mode. Sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a SeqPlex kit (Sigma, SEQXE). Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu). For single-cell samples collected by the micromanipulator, sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a WGA4 kit (Sigma, WGA4).
NGS libraries were constructed with a NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions, with slight modifications based on the previous study (Kadota et al., Sci. Rep. 2017). For a multi-plex NGS run, a SeqCap adapter kit A/B (Roche, 07141530001/ 07141548001) and NEXTflex DNA barcode (Bio Scientific, NOVA) were used. The samples were subjected to NGS on an Illumina Hiseq 1500 system (80, 84, 127-bp length, single-read or paired-end read). For NGS on Ion Proton system, libraries were constructed using Ion Plus Core Module for AB Library Builder System (Thermo Fisher Scientific, #4477683) with Ion Xpress Barcode Adapters 1-16 Kit (Thermo Fisher Scientific, #4477683).

tag: cell line

value: Epithelial cells immortalized with hTERT

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

value: XX

tag: single-cell collection method

value: Micromanipulator

tag: cell cycle phase

value: MidS


title: stop1_Fe_2


title: RPE1_single_Foci_Mphase_scRepli-seq

value: M-phase


title: dis3-1 90 minutes ribo- replicate 1

description: ribo depleted total RNA


title: control 90 minutes ribo- replicate 1

description: ribo depleted total RNA


title: stop1_-Pi_pH5_2

value: 0 mM Pi @pH 5


title: stop1_Al

value: 0 mM Pi @pH 5 +100 µM AlCl3


title: stop1_Al_2


title: stop1_-Pi_pH5


title: srm1-ts 90 minutes ribo- replicate 2

description: ribo depleted total RNA


title: stop1_-Pi_pH6_2

value: 0 mM Pi @pH 6


title: stop1_+Pi_pH5_2

value: 1 mM Pi @pH 5


title: srm1-ts 90 minutes ribo- replicate 1

description: ribo depleted total RNA


title: stop1_+Pi_pH5


title: enp1-1 90 minutes ribo- replicate 2

description: ribo depleted total RNA


title: stop1_+Pi_pH6_2

value: 1 mM Pi @pH 6


title: stop1_-Pi_pH6


title: stop1_+Pi_pH6


title: WT2_Muscle_E18

city: PARIS

first: Pascal

last: Maire

address: 24 Rue du Fg St Jacques

department: Développement Reproduction et Cancer

institute: Institut Cochin. INSERM U1016, CNRS UMR 8104, U.Paris

hyb_protocol: The cDNA was then hybridized to GeneChip® Mouse Gene 1.0 or 2.0 ST (Affymetrix) at 45 °C for 17 h. After overnight hybridization, the ChIPs were washed using the fluidic station FS450 following specific protocols (Affymetrix).

scan_protocol: the ChIPs were  scanned using the GCS3000 7G. The scanned images were then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for quality controls

data_processing: Normalisation with R, by project  Project 1 :   WT1_Muscle_E15,WT2_Muscle_E15,WT3_Muscle_E15,Mut1_Muscle_E15,Mut2_Muscle_E15,Mut3_Muscle_E15 → mogene20st_Mm_ENTREZG from Brainarray, version 20, Matrix 3  WT1_Muscle_E18,WT2_Muscle_E18,Mut1_Muscle_E18,Mut2_Muscle_E18 →  mogene10st_Mm_ENTREZG from Brainarray, version 20, Matrix 2  Then we conserved only common genes between the two lists.    Project 2 :  WT1_PAX7_E15, WT2_PAX7_E15, WT3_PAX7_E15, Mut1_PAX7_E15, Mut2_PAX7_E15, Mut3_PAX7_E15, WT6_PAX7_E18, WT7_PAX7_E18, WT8_PAX7_E18, Mut6_PAX7_E18,Mut7_PAX7_E18,Mut8_PAX7_E18   mogene20st_Mm_ENTREZG from Brainarray, version 19, Matrix 1    We strictly follow the Brainrray recomandations for the normalisation by using the affy package they provide for each version of their custom CDF files.

source_name: whole back muscle

label_protocol: 50 ng (E18.5 whole back muscles), 2 ng (E15.5 FACS-sorted cells and whole back muscles) or 0.21 ng (E18.5 FACS-sorted cells) of total RNA were reverse-transcribed following the Ovation PicoSL or PicoV2 WTA System (Nugen). Briefly, the resulting double-strand cDNA was used for amplification based on SPIA technology. After purification according to Nugen protocol, 5 μg of single strand DNA was used for generation of Sens Target DNA using Ovation Exon Module kit (Nugen). 2.5 μg of Sens Target DNA were fragmented and labelled with biotin using Encore Biotin Module kit (Nugen).

growth_protocol: No growth protocol, the tissue is extracted directly from E15 or E18 embryos

extract_protocol: RNA extraction from Pax7-nGFP+ FACS-sorted cells was performed using the Qiagen RNeasy microkit directly after isolation. Whole back muscles required a tissue lyser lyse step in Trizol solution.

treatment_protocol: no treatment

value: whole back muscle

tag: genotype/variation

value: WT


title: WT1_Muscle_E18


title: Mut1_Muscle_E18

value: SIX1/4 mutant


title: Mut2_Muscle_E18


title: wt_Fe

tag: treatment


title: csl4-ph 90 minutes ribo- replicate 3

description: ribo depleted total RNA


title: csl4-ph 90 minutes ribo- replicate 2

description: ribo depleted total RNA


title: wt_-Pi_pH5_2


title: wt_Al


title: wt_-Pi_pH5


title: wt_+Pi_pH5_2


title: srm1-ts 90 minutes dT replicate 2

description: polyA RNA

extract_protocol:
RNA extractions were performed using 5 mg of cell powder. Cell grindate was thawed into 500 µL of Trizol. All kits were used as per supplier specifications. The RNA extracts (74104, Qiagen) were enriched via oligo d(T) (E7490, NEB).
cDNA libraries were prepared using the Kapa stranded RNA-seq library preparation kit (Kapa Biosystems).
Paired end 50 (PE50) RNA-sequencing was performed using a Hiseq 2500


title: csl4-ph 90 minutes ribo- replicate 1

description: polyA RNA


title: wt_Al_2


title: wt_+Pi_pH5


title: wt_+Pi_pH6_2


title: wt_-Pi_pH6


title: enp1-1 90 minutes dT replicate 1

description: polyA RNA


title: enp1-1 90 minutes dT replicate 2

description: polyA RNA


title: wt_+Pi_pH6


title: enp1-1 90 minutes ribo- replicate 1

description: ribo depleted total RNA


title: wt_Fe_2


title: PA-WIRR

city: Philadelphia

first: yinfei

last: tan

state: PA

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

description:
not cultured
human T-ALL specimen

data_processing:
fastq files was generated at the basespace cloud
fastq files was aligned to hg38 using HISAT2 to generate bam files
Counts aligns reads per gene with HTSeq
Differentially expressed gene list was obtained by using DEseq2
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq-normalized read counts; DEseq2-differentially expressed genes

source_name: Children's Oncology Group

growth_protocol: Primary human T-ALL specimen kept as cryo-preserved

extract_protocol:
RNA was extract with Trizol, and purified via Qiagen RNeasy column
takara pico-input stranded RNA-seq kit was used
total RNA was heat fragmentated, then reverse transcribled to cDNA. crDNA was removed,  Illumina adapters were ligated to the cDNA and PCR was performed to get the final library.

tag: sample type

value: primary tumor

value: T-ALL

tag: tissue preparation

value: cryo-preserved


title: PA-WJKM

description:
not cultured
human T-ALL specimen


title: PA-VWMM

description:
not cultured
human T-ALL specimen


title: control 90 minutes dT replicate 2

description: polyA RNA


title: control 90 minutes dT replicate 3

description: polyA RNA


title: PA-URXZ

description:
not cultured
human T-ALL specimen


title: PA-VKPV

description:
not cultured
human T-ALL specimen


title: control 90 minutes dT replicate 1

description: polyA RNA


title: PA-VSRU

description:
not cultured
human T-ALL specimen


title: csl4-ph 90 minutes dT replicate 3

description: polyA RNA


title: PA-UKIZ

description:
not cultured
human T-ALL specimen


title: srm1-ts 90 minutes dT replicate 1

description: polyA RNA


title: PA-TZXK

description:
not cultured
human T-ALL specimen


title: PA-UTBD

description:
not cultured
human T-ALL specimen


title: PA-TVDU

description:
not cultured
human T-ALL specimen


title: wt_-Pi_pH6_2

value: 16 h exposure


title: PA-TPKZ

description:
not cultured
human T-ALL specimen


title: csl4-ph 90 minutes dT replicate 1

description: polyA RNA


title: PA-SVYP

description:
not cultured
human T-ALL specimen


title: PA-SXLM

description:
not cultured
human T-ALL specimen


title: csl4-ph 90 minutes dT replicate 2

description: polyA RNA


title: PA-TDDT

description:
not cultured
human T-ALL specimen


title: PA-SUHS

description:
not cultured
human T-ALL specimen


title: RPE1_single_MidS_19_scRepli-seq

value: Epithelial cells immortalized with hTERT

value: Single cell

value: FACS


title: PA-RXBR

description:
not cultured
human T-ALL specimen


title: PA-SRPK

description:
not cultured
human T-ALL specimen


title: RPE1_single_MidS_18_scRepli-seq

value: XX

value: MidS


title: PA-SKXP

description:
not cultured
human T-ALL specimen


title: RPE1_single_MidS_17_scRepli-seq


title: PA-RVRF

description:
not cultured
human T-ALL specimen


title: RPE1_single_MidS_16_scRepli-seq


title: PA-RGIR

description:
not cultured
human T-ALL specimen


title: RPE1_single_G1_04_scRepli-seq


title: RPE1_single_G1_05_scRepli-seq


title: UGS Explant

description:
GL60_03
UGS explant cultures were collected at successive time points for scRNA-seq: E15.5 (D0), day 1 (D1), day 3 (D3), and day 6 (D6). Individually sorted populations multiplexed using MULTI-seq lipid-tagged indices.

source_name: urogenital sinus

tag: developmental stage

value: Embryonic (E15.5)

value: Urogenital sinuses (UGS) were isolated from E15.5 embryos and cultured using a Durapore Membrane Filter 0.65 μm placed on a stainless-steel mesh for up to 7 days in Ham’s F-12/DMEM (Gibco) supplemented with Insulin-Transferrin-Sodium Selenite Supplement (Roche) and 10 μM dihydrotestosterone (Sigma). Media were renewed every 2-3 days.

tag: strain

value: ICR (CD-1)

value: urogenital sinus


title: RPE1_single_MidS_13_scRepli-seq


title: 5dpi-1

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

data_processing:
Illumina Casava software used for basecalling.
10x Genomic Chromium mapping and analysis procedure
Cell Ranger v.3.0.2
Genome_build: Mouse GrCm38 genome
Supplementary_files_format_and_content: 10x Genomic Chromium expression files

source_name: Neonatal microglia cells from 5 dpi

extract_protocol:
After a quick PBS perfusion, spinal cords of neonatal mice were rapidly dissected out before (intact), 3 days after or 5 days after the crush. The central 1 mm of the lower thoracic lesion including the lesion core and 0.5 mm rostral and caudal were then rapidly removed after PBS perfusion. Tissues were dissociated using Neural Tissue Dissociation Kit (P) (Miltenyi Biotec) and stained with CD45 and CD11b for 10 min at 4°C. Microglia were then FACS purified using the markers CD45 and CD11b. The sequencing followed10X genomics chromium protocols.
Single cell suspension from FACS-sorted microglia cells was prepared using 10x Genomics Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics, Pleasanton, CA) according to manufacture’s protocol. Quantity and quality of cDNA were assessed by Agilent 2100 expert High Sensitivity DNA Assay. cDNA samples were sequenced on 1 lane of NovaSeq 6000 S2 flowcell at UCLA Technology Center for Genomics and Bioinformatics.

tag: age

value: Postnatal day 7

tag: geneotype

value: Wild-type


title: RPE1_single_MidS_12_scRepli-seq

tag: cell type


title: Adult Intact Mouse Prostate Run 3

description:
GL64
Individually sorted populations (RFP+ / RFP-) from each lobe were multiplexed using MULTI-seq lipid-tagged indices. Lobes from intact mice were kept separated. No castrated sample were included in this run. Each lobe had a RFP+ and RFP- fraction, comprising basal and luminal cells.

source_name: prostate

value: Adult (> 8 weeks old)

value: Intact

tag: model

tag: tissue

value: prostate


title: 3dpi-2

source_name: Neonatal microglia cells from 3 dpi

value: Postnatal day 5


title: 3dpi-1


title: RPE1_single_MidS_14_scRepli-seq


title: RPE1_single_MidS_11_scRepli-seq


title: Ctr

source_name: Neonatal microglia cells from 0 dpi

value: Postnatal day 2


title: 5dpi-2