title: lib18838: CAT-EEC 230160

tag: barcode

tag: randomized treatment

value: Group A (NAC followed by EEC)

tag: age

value: Black or African American


title: siControl#2

status: Public on Mar 12 2020

type: SRA

city: tianjin

first: Yongqiang

last: Hou

address: No. 22 Qixiangtai Road, Heping District, Tianjin

country: China

institute: Tianjin Medical University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads were aligned to the reference genome using Tophat v2.1.1
Transcript abundance was quantified using the htseq-count script in the Python package HTSeq v0.6.0.
Genome_build: GRCh37

molecule: total RNA

organism: Homo sapiens

growth_protocol: MDA-MB-231 cells were cultured in L-15 medium supplemented with 10% FBS and without CO2.

extract_protocol:
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Library Prep Kit with standard Illumina protocols

treatment_protocol: Transfections with siRNA against PHF20L1 were performed using Lipofectamine 2000® or Lipofectamine RNAiMAX® Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions

tag: cell line

tag: genotype/variation

value: control


title: siControl#1


title: Vehicle_Rep3

city: Ann Arbor

first: Jacqueline

last: Larouche

state: MI

address: 2800 Plymouth Rd, Building 20 Room 316WB

department: Biomedical Engineering

country: USA

institute: University of Michigan

data_processing:
Sequencing reads were mapped to the mm10 genome using the STAR algorithm (STAR_2.5.0a) using default parameters
Transcript abundances were quantified using RSEM
Genome_build: mm10

organism: Mus musculus

source_name: Tibialis Anterior

extract_protocol:
Tibalis anterior muscles were removed, digested using collagenase II and dispase, and muscle stem cells (Ter119-CD31-CD45-Sca1-CD11b-CXCR4+B1int+) were sorted on a BD FACS Aria III into tryzol. Qiagen mRNeasy Micro kit was used to extract RNA according to manufacturer's instructions. Integrity was determined using an Aligent Bioanalyzer, and samples with a RIN value below 0.9 were discarded.
Takera Bio SMARTseq v4 cDNA synthesis kit was used with 1ng of RNA according to manufacturer's instructions. Libraries were prepared using the Nextera XT DNA Library Preparation Kit according to manufacturer's instructions.

tag: strain

tag: tissue

value: Tibialis Anterior

tag: cell type

value: muscle stem cell

tag: treatment

value: Vehicle


title: lib18839: CAT-EEC 391195

city: Bethesda

first: Tielin

last: Qin

state: MD

address: 7500 Old Georgetown Road, Suite 800

institute: Immune Tolerance Network

description: processed data file: P197-1_CB7GFANXX_170912_combined_counts.csv

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38 release 77
Supplementary_files_format_and_content: P197-1_CB7GFANXX_170912_combined_counts.csv is a comma separated value file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.
Supplementary_files_format_and_content: P197-1_CB6GMANXX_171009_combined_counts.csv is a comma separated value file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

molecule: polyA RNA

source_name: Nasal RNA

extract_protocol:
RNA easy kit, Thaw samples at RT. Vortex. Pass 700ul through Qiashredder. Most tubes contain 2x 700ul, collect flow through in  5ml Eppendorf tubes. Add equal volume of 70% EtOH, mix, transfer 700ul to elute columns.
sequencing libraries were constructed from total RNA using TruSeq stranded mRNA library kit

value: Nasal RNA

tag: participantid

tag: visitnumber

value: Group B (EEC followed by NAC)

tag: Sex

value: Male

tag: race

value: White/Caucasian


title: siPHF20L1#1

value: PHF20L1 knockdown


title: Sample35 Human Fetal retina Location:whole Cultured:Explant H27139

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Illumina protocol

molecule: genomic DNA

source_name: Human fetal retina

label_protocol: Bisulfite conversion was performed on 500 ng of DNA using the llumina Infinium Methylation Assay protocol in the EZ DNA Methylation kit (Zymo Research). Following the desulphonation and wash steps, converted DNA was eluted in 12 μl of the M-Elution buffer and then loaded onto the Infinium Human Methylation 450K BeadChip kit (Illumina, #WG-314-1003)

extract_protocol: Genomic DNA of the retinas was precipitated from the interphase and phenol  phase of the TRIzol solution using 100% ethanol. The DNA pellet was washed 3 times  with 0.1 M sodium citrate/10% ethanol solution and once with 75% ethanol. The pellet  was then resuspended in 8 mM NaOH buffer or concentrated using gDNA Clean and  Concentrator kit (Zymo Research, Irvine, CA).

tag: batch

tag: basename

tag: detailed location retina

value: whole

tag: culture method

value: Explant

tag: externalsampleid

value: SampleDay94 + 42 DIVExplantsInPairsH27139 F

tag: humanid

value: Female

tag: gestational day

tag: days in vitro

tag: human expected days


title: lib18837: CAT-EEC 605830

tag: barcode

tag: randomized treatment

tag: age


title: Vehicle_Rep2

tag: strain

tag: tissue

tag: cell type

tag: treatment


title: Vehicle_Rep1


title: lib18836: CAT-EEC 820573

tag: participantid

tag: visitnumber

tag: Sex

tag: race


title: lib18835: CAT-EEC 444826


title: ResolvinD1_Rep3

value: Resolvin D1


title: Sample30 Human Fetal retina Location:whole Cultured:Explant H-27175

tag: batch

tag: basename

tag: detailed location retina

tag: culture method

value: SampleDay59 + 42 DIVExplantsInPairsH-27175#2


title: ResolvinD1_Rep2


title: Sample27 Human Fetal retina Location:Fovea Cultured:NotCultured H-26930

value: Fovea

value: NotCultured

tag: externalsampleid

tag: humanid

tag: gestational day

tag: days in vitro


title: lib18842: CAT-EEC 874181

tag: barcode

tag: randomized treatment

tag: age

value: Asian


title: Sample29 Human Fetal retina Location:whole Cultured:Explant H-27175

tag: human expected days


title: Sample32 Human Fetal retina Location:whole Cultured:Explant H-27103


title: lib18833: CAT-EEC 659499

tag: tissue

value: Group A (NAC followed by EEC)

value: Black or African American


title: ResolvinD1_Rep1

tag: strain

value: Tibialis Anterior

tag: cell type

value: muscle stem cell

tag: treatment


title: Sample33 Human Fetal retina Location:whole Cultured:Explant H-27103

value: SampleDay67 + 42 DIVExplantsInPairsH-27103#1

tag: Sex


title: Sample26 Human Fetal retina Location:Periphery Cultured:NotCultured H26922

tag: batch

value: Periphery

value: Unknown


title: Sample28 Human Fetal retina Location:NasalCentral Cultured:NotCultured H-26930

tag: basename

value: NasalCentral


title: AB6601

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: metadata2.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Mice were housed under specific-pathogen-free conditions at the Animal Breeding Center of the Weizmann Institute of Science, and were used at 6 to 8 weeks of age. All animals were handled according to the regulations formulated by the Institutional Animal Care and Use Committee.
For the in vitro co-culture experiment, cells were isolated from spleens of C57BL/6 8 week old mice. DC derived from spleen tissues were enriched from the single cell suspension first by negative magnetic selection for CD19, and second by positive magnetic selection for CD11c. 2x106 DC were seeded in 6-well plate for 2h activation with 100ng/ml lipopolysaccharide (LPS; Sigma-Aldrich) and 2ug/ml OVA 323-339 (InvivoGen), at 37oC. In parallel, we isolated CD4+ T cells from spleens of OT-II mice. T cells were enriched by the CD4+ T cell Isolation Kit. For culture experiments CD11c+ DC and CD4+ T cells were plated on 96-well U-shape bottom, tissue culture plates. Co-cultured and mono-cultured cells were seeded in concentration of 1×106 cells/ml (1:1 ration in co-cultures), and harvested at different time points following cell plating (3h, 20h, 44h).
For the in vivo infection experiment, N. brasiliensis (Nb) infective L3 larvae were prepared, washed in sterile PBS and killed by three freeze-thaw cycles. Mice were anesthetized and antigen was administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals. Experiments were performed 48h following antigen injection.  To achieve single cell suspensions, auricular LN were digested in IMDM (Sigma-Aldrich) containing Liberase-TL (100μg/ml, Roche) and DNase-I (100μg/ml, Roche), and incubated with frequent agitation at 37oC for 20 min. Cells were washed with IMDM, filtered through a 100μm cell strainer, and centrifuged at 380g, 5min, 4oC.
In both experiments, prior to sorting, cells were stained with DAPI for evaluation of live/dead cells. For the sorting of T-DC PIC samples were gated for TCRβ+CD11c+, for sorting of T cells samples were gated for TCRβ+, and for the isolation of DC, samples were gated for CD11c+, after exclusion of dead cells (DAPI-), erythrocytes (TER119-) and B cells (CD19-).
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Mice were sacrified by CO2

tag: organ

value: LN

tag: selection marker

value: Ag+ TCRb+ CD11c+

value: Nb

tag: time point

tag: replicate id

value: 6-8 weeks


title: lib18834: CAT-EEC 766908

value: Nasal RNA

tag: participantid

tag: visitnumber

value: Group B (EEC followed by NAC)

value: Male

tag: race

value: White/Caucasian


title: lib18832: CAT-EEC 659506

tag: barcode

tag: randomized treatment

value: Female


title: AB6570

value: CD160+ Trbc+

tag: age


title: lib18831: CAT-EEC 444861

tag: tissue

value: Group A (NAC followed by EEC)


title: lib18830: CAT-EEC 122944


title: M-CTRL 4

city: New York City

first: Jun

last: Wang

address: 1 Gustave L. Levy Pl, New York

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
STAR(2.6.1d) maps the reads to the genome
samtools(1.9) indexes BAM files
featureCounts(subread/1.6.3) counts reads to genomic features
Data were filtered using sum(counts) in all samples >= 20
edgeR package to generate normalized expression data
Genome_build: mm10(Mus_musculus.GRCm38.83.gtf)
Supplementary_files_format_and_content: tab-delimited text file includes expression values for each Sample (row:genes, column:samples, first column is gene id)

source_name: M-CTRL

extract_protocol:
Total RNA was isolated using the Qiagen RNA-easy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were treated with vehicle or dihydrocaffeic acid/malvidin-glucoside two weeks prior to and throughout the social defeat paradigm

tag: strain

value: male

value: PFC

value: 10 weeks

tag: genotype

value: wild type

tag: stress

value: CTRL


title: Sample9 Human Fetal retina Location:whole Cultured:Explant H-26937

tag: detailed location retina

value: whole

tag: culture method

value: Explant

tag: externalsampleid

value: 59d + 0 DIV (RNAseq)

tag: humanid

tag: Sex

value: Unknown

tag: gestational day

tag: days in vitro

tag: human expected days


title: Sample20 Human Fetal retina Location:whole Cultured:NotCultured H-26565

tag: batch

tag: basename

value: NotCultured

value: SampleDay136WholeRetinaH-26565 Used for RNAseq1#2


title: Sample23 Human Fetal retina Location:Periphery Cultured:NotCultured H-26994

value: Periphery

value: SampleDay57 PeripherySubdividedRetinaH-26994 Replicate 2


title: AB6569

tag: organ

value: LN

tag: selection marker

value: TCRb+ CD11c+

tag: treatment

value: Nb

tag: time point

tag: replicate id

value: 6-8 weeks


title: Sample13 Human Fetal retina Location:whole Cultured:NotCultured H-26814

value: Male


title: Sample8 Human Fetal retina Location:whole Cultured:NotCultured H-26802


title: lib18829: CAT-EEC 713238

tag: tissue

value: Nasal RNA

tag: participantid

tag: visitnumber

tag: barcode

tag: randomized treatment

value: Group A (NAC followed by EEC)

tag: age

value: Female

tag: race

value: White/Caucasian


title: Sample12 Human Fetal retina Location:whole Cultured:Explant H-26973

tag: detailed location retina

value: whole

tag: culture method

tag: externalsampleid

value: 105d + 0 DIV (RNAseq)

tag: humanid

tag: Sex

tag: gestational day


title: Sample16 Human Fetal retina Location:whole Cultured:NotCultured H-26163

tag: batch

tag: basename

value: SampleDay94.1WholeRetinaH-26163 Used for RNAseq1#13

tag: days in vitro

tag: human expected days


title: Sample15 Human Fetal retina Location:whole Cultured:Explant H-26946

value: Explant

value: 134d + 0DIV (RNAseq)


title: Sample25 Human Fetal retina Location:Fovea Cultured:NotCultured H-26877

value: Fovea

value: NotCultured

value: Unknown


title: M-CTRL 2

tag: strain

value: male

tag: tissue

value: PFC

value: 10 weeks

tag: genotype

value: wild type

tag: stress

value: CTRL

tag: treatment


title: Sample10 Human Fetal retina Location:whole Cultured:NotCultured H-26977


title: Sample19 Human Fetal retina Location:whole Cultured:NotCultured H-25444

value: SampleDay87WholeRetinaH-25444 Used for RNAseq1#7


title: Sample24 Human Fetal retina Location:Periphery Cultured:NotCultured H-27019

value: Periphery

value: Male


title: Sample18 Human Fetal retina Location:whole Cultured:NotCultured H-26563

value: SampleDay57WholeRetinaH-26563 Used for RNAseq1#3


title: Sample11 Human Fetal retina Location:whole Cultured:NotCultured H-26976

value: whole

value: Female


title: Sample17 Human Fetal retina Location:whole Cultured:NotCultured H-26178

value: SampleDay57WholeRetinaH-26178 used for RNAseq1#16


title: Sample14 Human Fetal retina Location:whole Cultured:NotCultured H-26779


title: M-CTRL 1

tag: age


title: Sample6 Human Fetal retina Location:whole Cultured:NotCultured H-26723


title: Sample21 Human Fetal retina Location:whole Cultured:NotCultured H-26562

value: SampleDay80WholeRetinaH-26562 Used for RNAseq1#4


title: Sample7 Human Fetal retina Location:whole Cultured:NotCultured H-25699


title: lib18827: CAT-EEC 391193

value: Nasal RNA

tag: participantid

tag: visitnumber

tag: barcode

tag: randomized treatment

value: Group A (NAC followed by EEC)

tag: race

value: White/Caucasian


title: M-CTRL 3

tag: Sex


title: lib18809: CAT-EEC 283858

value: Group B (EEC followed by NAC)


title: Sample1 Human Fetal retina Location:whole Cultured:NotCultured H-26669

tag: detailed location retina

tag: culture method

value: NotCultured

tag: externalsampleid

tag: humanid

tag: gestational day


title: M-stress/vehicle  3

source_name: M-stress/vehicle

tag: strain

value: male

value: PFC

value: social defeat stress

value: vehicle


title: Sample5 Human Fetal retina Location:whole Cultured:NotCultured H-26765

tag: batch

tag: basename

tag: days in vitro

tag: human expected days


title: AB6568

tag: organ

value: LN

tag: selection marker

value: Ag+ TCRb+ CD11c+

tag: treatment

value: Nb

tag: time point

tag: replicate id

tag: age

value: 6-8 weeks


title: lib18828: CAT-EEC 766906

tag: tissue

tag: participantid

tag: visitnumber

tag: barcode

tag: randomized treatment

tag: Sex

tag: race


title: lib18808: CAT-EEC 820540

value: Black or African American


title: AB6515

tag: strain


title: Sample3 Human Fetal retina Location:whole Cultured:NotCultured H-26779

tag: batch

tag: basename

tag: detailed location retina

value: whole

tag: culture method

tag: externalsampleid

tag: humanid

value: Female

tag: gestational day


title: lib18807: CAT-EEC 498494


title: AB6566

tag: organ

tag: selection marker

tag: treatment

tag: time point

tag: replicate id


title: M-stress/vehicle  1

tag: tissue

tag: age

value: 10 weeks

tag: genotype

value: wild type

tag: stress


title: AB6517

tag: strain

value: Trbc+


title: F-CTRL 3

source_name: F-CTRL

tag: Sex

value: female

value: CTRL


title: M-stress/vehicle  4


title: Sample22 Human Fetal retina Location:whole Cultured:NotCultured H-26658

tag: batch

tag: basename

value: NotCultured

value: SampleDay105WholeRetinaH-26658 Used for RNAseq1#17

value: Male

tag: days in vitro

tag: human expected days


title: AB6516


title: F-CTRL 2

value: PFC


title: lib18806: CAT-EEC 713236

value: Nasal RNA

tag: participantid

tag: visitnumber

tag: barcode

tag: randomized treatment

value: Group A (NAC followed by EEC)

tag: race


title: F-CTRL 4

tag: treatment


title: lib18805: CAT-EEC 820503

value: White/Caucasian


title: AB6513

tag: organ

value: LN

tag: selection marker

value: TCRb+ CD11c+

value: Nb

tag: time point

tag: replicate id


title: F-stress/treatment 3

source_name: F-stress/treatment

tag: tissue

tag: age

tag: genotype

tag: stress

value: social defeat stress

value: dihydrocaffeic acid/malvidin-glucoside


title: F-stress/treatment 2

tag: strain

tag: Sex

value: 10 weeks


title: F-CTRL 1

value: wild type


title: lib18804: CAT-EEC 713174

value: Female


title: AB6512

value: 6-8 weeks


title: F-stress/treatment 1

value: female


title: F-stress/vehicle  4

source_name: F-stress/vehicle

value: vehicle


title: AB6510

value: Ag+ Cd11c+


title: F-stress/vehicle  3


title: F-stress/vehicle  1


title: F-stress/vehicle  2


title: F-stress/treatment 4


title: AB6511


title: lib18803: CAT-EEC 176492


title: lib18801: CAT-EEC 820576

value: Group B (EEC followed by NAC)

value: Male


title: lib18802: CAT-EEC 391158

value: Nasal RNA


title: AB6509

value: Ag+ TCRb+ CD11c+


title: RCF2_3

city: Tai’an

first: Feng

last: Shouqian

state: Shandong

address: 61 Daizong Avenue

department: College of Horticulture Sciences

institute: Shandong Agricultural University

description:
Pyrus communis cv. ‘Red Clapp Favorit'
processed data file: Genes_FPKM.xls

data_processing:
The sequencing data were first filtered to remove adaptors, low-quality data, and contamination using Trimmomatic v 0.38.
Filtered high quality reads were then mapped to Pyrus communis reference genome using default parameter with HISAT2 v 2.1.0.
The transcript sequence assembly and abundance calculation were performed using StringTie v1.3.4d with default parameter.
Differentially expressed genes (DEGs) were analyzed by DESeq2 method (v 1.26.0). The genes with fold change ≥ 2.0 and pvalue ≤ 0.05 were defined as DEGs.
Genome_build: Pyrus communis Genome v1.0 from GDR (https://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0).
Supplementary_files_format_and_content: Genes_FPKM.xls: Excel file includes FPKM values.

organism: Pyrus communis

source_name: the skins collected from pear cultivar 'Red Clapp Favorite’ at 5 DAFB on 22 April 2017

growth_protocol: The pear cultivars ‘CF’ and ‘RCF’ were cultivated in the experimental orchard of Yantai Academy of Agricultural Science, Shandong province, Yantai, China (37°5′N, 122°1′W). The fruits of ‘CF’ and ‘RCF’ were collected in 2017 from 6-year-old trees grafted onto Pyrus betulaefolia rootstocks.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA).
The mRNA was purified from high-quality total RNAs using oligo (dT) magnetic beads and then broken into short fragments with fragmentation buffer. The cDNA was synthesized using a cDNA Synthesis Kit (TaKaRa, Dalian, China) and linked to sequencing adapters at both ends.

treatment_protocol: Fruits of ‘CF’ and ‘RCF’ with a similar green color were first sampled on 19 April 2017; these samples were collected at 2 DAFB, and were named ‘CF1’ and ‘RCF1’, respectively. Fruits with significant differences in color between ‘CF’ and ‘RCF’ were sampled on 22 April 2017; these samples collected at 5 DAFB were named ‘CF2’ and ‘RCF2’, respectively.

tag: cultivar

value: Red Clapp Favorit

value: Skins

tag: developmental stage

value: 5 DAFB


title: RCF2_2


title: Sample2 Human Fetal retina Location:whole Cultured:NotCultured H-25971

tag: batch

tag: basename

tag: detailed location retina

value: whole

tag: culture method

value: NotCultured

tag: externalsampleid

tag: humanid

tag: gestational day

tag: days in vitro

tag: human expected days


title: Sample4 Human Fetal retina Location:whole Cultured:NotCultured H-26724


title: AB6508

tag: organ

value: LN

tag: selection marker

value: Trbc+

tag: treatment

value: PBS

tag: time point

tag: replicate id


title: RCF2_1

tag: tissue


title: AB6507

tag: strain

tag: age


title: CF2_2

description:
Pyrus communis cv. ‘Clapp Favorit'
processed data file: Genes_FPKM.xls

source_name: the skins collected from pear cultivar ‘Clapp Favorite’ at 5 DAFB on 22 April 2017

tag: cultivar

value: Clapp Favorit

tag: developmental stage


title: lib18800: CAT-EEC 283820

tag: participantid

tag: visitnumber

tag: barcode

tag: randomized treatment

tag: Sex

value: Female

tag: race

value: Mixed Race


title: CF2_1


title: RCF1_2

source_name: the skins collected from pear cultivar 'Red Clapp Favorite’ at 2 DAFB on 19 April 2017

value: 2 DAFB


title: AB6506

value: 6-8 weeks


title: AB6514

value: Nb


title: AB6505


title: CF2_3


title: lib18797: CAT-EEC 391230

value: Group B (EEC followed by NAC)

value: Black or African American


title: RCF1_3


title: RCF1_1


title: CF1_3

source_name: the skins collected from pear cultivar ‘Clapp Favorite’ at 2 DAFB on 19 April 2017


title: lib18798: CAT-EEC 605868

value: Nasal RNA


title: CF1_2


title: CF1_1


title: M-S-2

city: Marseille Cedex 9

first: Michaël

last: Pierrelée

address: Case 907 - Parc Scientifique de Luminy

country: France

institute: Aix-Marseille University, CNRS, IBDM

description:
Cultivated in marine inorganic growth medium supplemented with 3% (w/v) sea salt; sampled 6 days after inoculation.
TN1610R1293-1

data_processing:
De novo transcriptome assembly. Trinity v2.8.5. Parameters: paired-end files.
Gene count quantification. RSEM v1.3.2. Parameters: paired-end files, estimation method RSEM, alignment method bowtie.
Differential expression analysis. Normalization with SVCD v0.1.0, statistical tests with DESeq2 v1.20.0. Tests of M-E vs. F-E, F-S vs. F-S and interaction term between both comparisons, using GLM models.
Annotation of isoforms. Only isoforms related to differentially expressed genes were annotated. Trinotate v3.2.0 with Blast+ v2.9.0 BLASTX and in parallel TransDecoder v5.5.0, combined with HMMER v3.2.1 and BLASTP, followed by SignalP v5.0b. BLAST was run by DIAMOND v0.8.36. Databases: SwissProt (release 31-JUL-2019), PFAM (release 30-AUG-2018). BLAST parameters: max-target-seq=1, e-value threshold=1e-5. TransDecoder predicts coding regions using predicted long ORF (m>=100) with BLAST and PFAM homology searches. Trinotate parameter: e-value <= 1e-10 (i.e., in subsequent steps, only BLAST e-values <= 1e-10 were retained).
Extraction of gene orthologies. House-made script to aggregate annotations of isoforms and to get dysregulated KEGG orthologies. Database: KEGG (release 92.0 01-OCT 2019).
In parallel, annotation of supertranscripts (consensus sequences of isoforms). SuperTranscripts (script from Trinity v2.8.5) followed by BLAST2GO v5.2.5. BLAST search parameters: e-value <= 1e-10 against Swissprot (31-JUL-2019).
Functional enrichment. GSEAPY v0.9.15. Databases: Gene-ontology OBO file (release 07-OCT-2019), KEGG (release 92.0 01-OCT 2019).
[Gitlab repository (scripts and data)]  https://gitlab.com/habermann_lab/yun2019_hs2
Supplementary_files_format_and_content: RSEM_raw_gene_count_matrix.tsv: tab-separated table of raw gene counts from RSEM, without any processing (on gitlab, named as “Trinity_genes.gene.counts.matrix”).
DEA_all_results.xlsx: excel file (on gitlab, named as “synthesis_dea_results.xlsx”). The first sheet containing all results of differential expression analysis (i.e., mean counts per condition, log2-fold change and adjusted p-value for the 3 comparisons (M-E vs. F-E, F-S vs. F-S and interaction term), variation of LFC in % between both growth phases, and strenght of variation (significant LFC of interaction term categorized into 4 groups depending on their value)).
Trinotate_annotation_report.tsv: tab-separated table of isoforms and predicted coding-region annotations synthesized by Trinotate (on gitlab, its extension is .csv).
Synthesis.xlsx: user-friendly excel file. 1st sheet joins together results of aggregated isoform annotations from Trinotate into gene annotations, as well as the results of differential expression analysis for these genes. Each row is a differentially expressed gene. 2nd and 3rd sheets gives KEGG PATHWAY and KEGG BRITE annotations per gene, respectively.
BLAST2GO_table.tsv: tab-separated table of the annotated supertranscripts obtained with BLAST2GO, with BLASTX results and gene-ontology mapping (on gitlab, named as “blast2go_go_table.txt”).
trinity_chlorella_hs2_transcriptome.fasta: transcriptome generated by Trinity (on gitlab, named as “Trinity.fasta”). This version is the one used in the downstream steps and differs from the one submitted to TSA database, as it is not contamination-free.

organism: Chlorella sp. HS2

source_name: Chlorella sp. HS2

growth_protocol: HS2 samples were cultivated in 1-L cylindrical photobioreactors under pre-determined optimal light and temperature conditions with continuous supplementation of 5% CO2 at 0.2 vvm and agitation at 120 rpm. Both autotrophic cultures grown in freshwater inorganic medium and in marine inorganic growth medium supplemented with 3% (w/v) sea salt were sampled at the exponential (4 days after inoculation) and stationary growth phases (6 days after inoculation).

extract_protocol:
Cultures were harvested during exponential and stationary growth phases by centrifugation at 4500 rpm for 10 min. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA, USA), according to manufacturer’s instructions. The RNA samples were treated with DNase I for 30 min at 37 °C to remove genomic DNA; the quantity and integrity of the total RNA were verified using an Agilent 2100 bioanalyzer.
Libraries for RNA-Sequencing were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (catalog #RS-122-2001, Illumina, San Diego, CA). Starting with total RNA, mRNA was first purified using poly (A) selection, then RNA was chemically fragmented and converted into single-stranded cDNA using random hexamer priming; the second strand was generated to create double-stranded cDNA. Library construction began with generation of blunt-end cDNA fragments from ds-cDNA. Thereafter, an A-base was added to the blunt-end in order to make them ready for ligation of sequencing adapters. After size selection, ligated cDNA fragments which contained adapter sequences were amplified via PCR using adapter specific primers. The library was quantified with the KAPA library quantification kit (Kapa biosystems KK4854) following the manufacturer's instructions.

treatment_protocol: HS2 was cultivated in control condition (freshwater) and in salt-stress condition (marine water).

tag: medium

value: marine water

tag: phase

value: stationary growth phase


title: AB6504

tag: organ

tag: selection marker

value: TCRb+ CD11c+


title: lib18796: CAT-EEC 874243

value: Group A (NAC followed by EEC)

value: White/Caucasian


title: M-S-1

description:
Cultivated in marine inorganic growth medium supplemented with 3% (w/v) sea salt; sampling 6 days after inoculation.
TN1610R1293


title: AB6503

value: LN

tag: treatment

tag: time point


title: AB6502

tag: replicate id


title: F-E-2

description:
Cultivated in freshwater inorganic growth medium; sampled 4 days after inoculation.
TN1610R1302

value: freshwater

value: exponential growth phase


title: M-stress/vehicle  2

tag: strain

value: male

tag: tissue

value: PFC

value: 10 weeks

tag: genotype

value: wild type

tag: stress

value: social defeat stress

value: vehicle


title: lib18794: CAT-EEC 337617

tag: participantid

tag: age

value: Female


title: lib18799: CAT-EEC 605950

tag: visitnumber

tag: barcode

value: Group B (EEC followed by NAC)

value: Black or African American


title: F-E-3

description:
Cultivated in freshwater inorganic growth medium; sampled 4 days after inoculation.
TN1610R1303


title: M-S-3

description:
Cultivated in marine inorganic growth medium supplemented with 3% (w/v) sea salt; sampled 6 days after inoculation.
TN1610R1294

value: marine water


title: AB6423

value: Trbc+

value: Nb

value: 6-8 weeks


title: lib18793: CAT-EEC 122852

value: Nasal RNA

tag: randomized treatment

value: Group A (NAC followed by EEC)

tag: Sex

value: Male


title: AB6422

value: LN

value: Icos+ Trbc+


title: F-S-1

description:
Cultivated in freshwater inorganic growth medium; sampled 6 days after inoculation.
TN1610R1295

tag: medium

value: freshwater

value: stationary growth phase


title: M-E-2

description:
Cultivated in marine inorganic growth medium supplemented with 3% (w/v) sea salt; sampled 4 days after inoculation.
TN1610R1299-1

tag: phase

value: exponential growth phase


title: F-S-3

description:
Cultivated in freshwater inorganic growth medium; sampled 6 days after inoculation.
TN1610R1297


title: F-S-2

description:
Cultivated in freshwater inorganic growth medium; sampled 6 days after inoculation.
TN1610R1296


title: lib18792: CAT-EEC 337488

tag: race


title: AB6420

tag: organ

tag: selection marker

value: CD160+ Trbc+


title: Input_Mixed

city: St Lucia

first: Mikael

last: Boden

state: Queensland

address: Cooper Rd

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie 2 version 2.2.6
BAM files were merged with samtools version 1.4.1
Peaks were called using MACS2 version 2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: Narrow peak files were generated with MACS2

source_name: Cerebellum neural progenitor cells

extract_protocol:
Lysates were clarifed from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed using the standard protocol for the NEBNext Ultra II DNA Library Prep kit from Illumina (Part#E6240). Briefly, DNA was end-repaired and the blunt, phosphorylated ends were then treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adaptors which have a single 'T' base overhang at the 3' end. AMPure XP beads were used for size selection of the dA-tailed DNA and then the DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~275bp were purified using the AMPure XP beads. Libraries were sequenced on the Illumina HiSeq2000 according to the manufacturer's instructions. Paired-end sequencing was not used.

treatment_protocol: Granule neuron progenitors were isolated using the Papain Dissociation kit (Worthington Biochemical Corporation) to obtain a single cell suspension according to Fraser et al 2019 (Brain Struct Funct 224(2):811-827)

tag: cell type

value: Cerebellum granule neuron progenitor cells

value: Postnatal Day 7

value: Mixed background similar to an outbred CD1 strain

tag: chip antibody

value: Input


title: lib18790: CAT-EEC 230190

value: Group B (EEC followed by NAC)

value: Female

value: Black or African American


title: M-E-3

description:
Cultivated in marine inorganic growth medium supplemented with 3% (w/v) sea salt; sampled 4 days after inoculation.
TN1610R1299-2

value: marine water


title: lib18789: CAT-EEC 122887

value: Nasal RNA


title: AB6419

tag: strain

tag: treatment

value: Nb

tag: time point

tag: replicate id

value: 6-8 weeks


title: lib18788: CAT-EEC 552162

tag: tissue

tag: participantid

value: Group A (NAC followed by EEC)


title: AB6413

value: LN

tag: age


title: NfiX_ChIP-seq_Mixed

value: NfiX (Sigma Aldrich, SAB1401263)


title: NfiB_ChIP-seq_Mixed

value: NfiB (Novus Biologicals, NBP1-81000)


title: F-E-1

description:
Cultivated in freshwater inorganic growth medium; sampled 4 days after inoculation.
TN1610R1301

value: freshwater

value: exponential growth phase


title: AB6412


title: lib18787: CAT-EEC 659568

tag: visitnumber

tag: barcode


title: AB6411

value: Tigit+ Trbc+


title: NfiX_ChIP-seq_CD1

value: Cerebellum granule neuron progenitor cells

value: Postnatal Day 7


title: AB6421

value: Icos+ Trbc+


title: NfiB_ChIP-seq_CD1


title: HC-trt_7DAT_rep3

city: Lake Alfred

first: Lisa

last: Tang

state: FL

address: 700 Experiment Station Rd.

department: Citrus Research and Education Center

institute: University of Florida

description:
31-P15-i708-i507_S47
T7_3.genes.results
processed data file: 7DAT.txt, genes.rawmatrix.txt

data_processing:
Sequenced reads were trimmed using Trimmomatic, removing readers shorter than 50 bp and with a quality score lower than 40 (minimum average quality = 30)
Reads were aligned to the transcriptome using STAR_2.5.2a
Gene expression values (FPKM) were quantified and differential gene expression was analyzed using RSEM v1.2.31
Genome_build: Prunus_persica_NCBIv2; GCF_000346465.2
Supplementary_files_format_and_content: Tab-delimited text files include normalized expression values of all genes for all samples in each contrast (3 and 7 DAT)

organism: Prunus persica

source_name: HC-trt_7DAT_peach buds

growth_protocol: Five-year-old low-chill peach cultivar TropicBeauty, which has the chilling requirment of 150 chilling hours, grafted on 'Floridaguard' peach rootstock were grown in an experimental orchard in Citra, Florida, USA.

extract_protocol:
Total RNA was extracted using Plant/Fungi Total RNA Purification Kit (Norgen Biotek, Thorold, Ontario, Canada). The quality and quantity of RNA was evaluated using a spectrophotometer and with denaturing formaldehyde 1.2% agarose gels.
RNA libraries were prepared for sequencing using the Illumina TruSeq mRNA protocol.

treatment_protocol: On 16 December 2015 (with 11 chilling hours fulfilled), four trees, representing four biological replicates, were sprayed with 1% (v/v) hydrogen cyanamide containing 0.15% (v/v) non-ionic surfactant. The other four trees remained not treated with hydrogen cyanamide as control group.

tag: cultivar

value: TropicBeauty

value: Hydrogen cyanamide-treated

tag: day after treatment

value: 7 days after treatment

value: peach buds

tag: biological replicate

value: Biological replicate 3


title: lib18786: CAT-EEC 713167

value: Nasal RNA

tag: randomized treatment

value: Group B (EEC followed by NAC)

tag: Sex

value: Male

tag: race

value: Mixed Race


title: lib18791: CAT-EEC 122885

value: Group A (NAC followed by EEC)

value: Black or African American


title: HC-trt_7DAT_rep4

description:
32-P16-i705-i508_S48
T7_4.genes.results
processed data file: 7DAT.txt, genes.rawmatrix.txt

value: Biological replicate 4


title: lib18785: CAT-EEC 605831

value: Female


title: AB6360

tag: organ

value: LN

tag: selection marker

value: TCRb+ CD11c+

value: PBS

value: 6-8 weeks


title: AB6409

tag: strain

value: Tigit+ Trbc+

value: Nb


title: HC-trt_7DAT_rep1

description:
29-P13-i706-i505_S45
T7_1.genes.results
processed data file: 7DAT.txt, genes.rawmatrix.txt

value: TropicBeauty

tag: treatment

value: Hydrogen cyanamide-treated

value: 7 days after treatment

value: Biological replicate 1


title: M-E-1

description:
Cultivated in marine inorganic growth medium supplemented with 3% (w/v) sea salt; sampled 4 days after inoculation.
TN1610R1299

tag: medium

value: marine water

tag: phase

value: exponential growth phase


title: HC-trt_7DAT_rep2

description:
30-P14-i707-i506_S46
T7_2.genes.results
processed data file: 7DAT.txt, genes.rawmatrix.txt

tag: tissue

value: peach buds

value: Biological replicate 2


title: Control_7DAT_rep4

description:
28-P12-i705-i504_S44
C7_4.genes.results
processed data file: 7DAT.txt, genes.rawmatrix.txt

source_name: Control_7DAT_peach buds

value: Control


title: Murine pancreatic cancer cell line KPC-NC_LoF3

city: New York

first: Xiaoli

last: Mi

state: NY

address: 1275 York Ave

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description: Murine pancreatic cancer cell line non-silencing shRNA Repetition 3

data_processing:
RNA-seq read mapping. For a robust analysis of subtle expression and splicing effects, alignment-based and alignment-free methods were combined. Reads were aligned to Gencode annotation v25 for human or vM12 for mouse using STAR v2.4.1d and quantified by QoRTs v1.1.8, while alignment-free quantification was performed by Kallisto v0.43.0 accounting for hexamer bias and using 100 bootstrap iterations to quantify the technical uncertainty.
Differential gene expression and isoform expression measurements. Differentially expressed genes were then identified from aligned data by DESeq2 v1.10.18 and from alignment-free data by Sleuth v0.28.1. Isoform expression measurements were identified from aligned data by MISO v0.5.3 and from alignment-free data by SUPPA v1. These two algorithms take complementary approaches. While MISO uses the number of split reads aligning to nearby exon junctions to calculate the percent spliced in (PSI) value and a Bayes factor for each splicing event (cassette exon etc.). SUPPA extracts the PSI values for known splicing defects from transcript quantification. Statistical significance is then calculated using a Kolmogorov-Smirnov test to compare the PSI distributions of two conditions as a function of the expression of the transcripts defining the events. To further validate the significance of the splicing defects, the empirical version of the SUPPA algorithm was applied to samples permuted in such to eliminate any biological effect.
Genome_build: Reads were aligned to Gencode annotation v25 for human or vM12 for mouse using STAR v2.4.1d and quantified by QoRTs v1.1.8, while alignment-free quantification was performed by Kallisto v0.43.0 accounting for hexamer bias and using 100 bootstrap iterations to quantify the technical uncertainty.

source_name: Murine pancreatic cancer cell line KPC

growth_protocol: Primary patient derived and murine PanIN organoids were culture following the protocols previously described5. Murine PDAC cells (KrasG12D; p53R172H/null; Pdx1-Cre [KPC cells]) and 293T cells, were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS) and 1% Pen Strep (Gibco). All cell lines were incubated at 37°C and 5% CO2. Primary patient derived organoids were generated at Memorial Sloan Kettering Cancer Center (MSKCC) using primary patient samples from tumor resection under Institutional Review Boards approval and in accordance to the Declaration of Helsinki protocol. Informed consents were obtained from all human subjects. Murine PanIN organoids were generated using the Mist1:CreERT2 (CiMist1) Lox-Stop-Lox (LSL)-KrasG12D/+ mice6 with td Tomato tracer and following the protocol from Boj et al., 20155. Murine PDAC cells were obtained from Dr. Robert Vonderheide, generated from the PDX-1-Cre; LSL-KrasG12D/+; LSL-Trp53R172H/+7. All cells are tested yearly for mycoplasma contamination.

extract_protocol:
For all cells, RNA was extracted using Qiagen RNeasy columns.
poly(A)-selected, unstranded Illumina libraries were prepared with a modified TruSeq protocol. 0.5× AMPure XP beads were added to the sample library to select for fragments <400 bp, followed by 1× beads to select for fragments >100 bp. These fragments were then amplified with PCR (15 cycles) and separated by gel electrophoresis (2% agarose). 300 bp DNA fragments were isolated and sequenced on the Illumina HiSeq 2000 (~100M 2×49 bp reads per sample).

tag: cell line

value: KPC

value: Murine pancreatic cancer cell line

value: non-silencing shRNA


title: lib18795: CAT-EEC 283856

description: processed data file: P197-1_CB7GFANXX_170912_combined_counts.csv

value: Nasal RNA

tag: participantid

value: Group A (NAC followed by EEC)

tag: age

value: Female

value: White/Caucasian


title: lib18783: CAT-EEC 391166

tag: visitnumber

tag: barcode

value: Group B (EEC followed by NAC)

value: Male

value: Mixed Race


title: Control_7DAT_rep3

description:
27-P11-i704-i503_S43
C7_3.genes.results
processed data file: 7DAT.txt, genes.rawmatrix.txt

tag: cultivar

value: TropicBeauty

tag: day after treatment

value: 7 days after treatment

value: Biological replicate 3


title: lib18782: CAT-EEC 176493

tag: randomized treatment


title: AB6358

value: LN

value: Trbc+

value: Nb

tag: time point

tag: replicate id

value: 6-8 weeks


title: Control_7DAT_rep2

description:
26-P10-i703-i502_S42
C7_2.genes.results
processed data file: 7DAT.txt, genes.rawmatrix.txt

value: Control

value: peach buds

tag: biological replicate

value: Biological replicate 2


title: AB6356

tag: organ

tag: selection marker

value: TCRb+ CD11c+


title: NfiA_ChIP-seq_Mixed

tag: cell type

value: Cerebellum granule neuron progenitor cells

value: Postnatal Day 7

tag: strain

value: Mixed background similar to an outbred CD1 strain

tag: chip antibody

value: NfiA (Abcam, ab41851)


title: Control_7DAT_rep1

description:
25-P9-i702-i501_S41
C7_1.genes.results
processed data file: 7DAT.txt, genes.rawmatrix.txt

tag: treatment

tag: tissue

value: Biological replicate 1


title: lib18780: CAT-EEC 713176

value: Nasal RNA

tag: participantid

value: Group B (EEC followed by NAC)

tag: Sex

value: Female

tag: race

value: Black or African American


title: NfiA_ChIP-seq_CD1

tag: age


title: Murine pancreatic cancer cell line KPC-NC_LoF1

description: Murine pancreatic cancer cell line non-silencing shRNA Repetition 1

tag: cell line

value: KPC

value: Murine pancreatic cancer cell line

value: non-silencing shRNA


title: AB6355

value: LN

value: PBS

value: 6-8 weeks


title: Murine pancreatic cancer cell line KPC-Hnrnpksh4-3

description: Murine pancreatic cancer cell line Hnrnpk sh4 Repetition 3

value: Hnrnpk sh4


title: AB6359

value: Trbc+


title: lib18784: CAT-EEC 874245

tag: visitnumber

tag: barcode


title: Murine pancreatic cancer cell line KPC-NC_LoF2

description: Murine pancreatic cancer cell line non-silencing shRNA Repetition 2


title: Murine pancreatic cancer cell line KPC-Hnrnpksh4-2

description: Murine pancreatic cancer cell line Hnrnpk sh4 Repetition 2


title: lib18779: CAT-EEC 283893

tag: randomized treatment


title: AB6354

tag: time point

tag: replicate id


title: Murine pancreatic cancer cell line KPC-Hnrnpksh4-1

description: Murine pancreatic cancer cell line Hnrnpk sh4 Repetition 1


title: AB6357

tag: organ

value: Nb


title: HC-trt_3DAT_rep3

description:
23-P7-i711-i507_S39
T3_3.genes.results
processed data file: 3DAT.txt, genes.rawmatrix.txt

source_name: HC-trt_3DAT_peach buds

tag: cultivar

value: TropicBeauty

value: Hydrogen cyanamide-treated

tag: day after treatment

value: 3 days after treatment

value: peach buds

tag: biological replicate

value: Biological replicate 3


title: HC-trt_3DAT_rep2

description:
22-P6-i712-i506_S38
T3_2.genes.results
processed data file: 3DAT.txt, genes.rawmatrix.txt

value: Biological replicate 2


title: Murine pancreatic cancer cell line KPC-Hnrnpksh1-3

description: Murine pancreatic cancer cell line Hnrnpk sh1 Repetition 3

value: Hnrnpk sh1


title: Murine pancreatic cancer cell line KPC-Hnrnpksh1-2

description: Murine pancreatic cancer cell line Hnrnpk sh1 Repetition 2


title: RNA-Seq_PAH9_female_wild type_2

city: Heidelberg

first: Judith

middle: B

last: Zaugg

state: Heidelberg

address: Meyerhofstraße 1

country: Germany

institute: European Molecular Biology Laboratory (EMBL)

data_processing:
Sequenced reads were trimmed using Trimmomatic V0.33 using paired-end mode and these parameters ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
RNA-seq data in fastq format were aligned using STAR v.2.5.2b to hg19/GRCh37 assembly from ENSEMBL release 75 and raw read abundances were estimated internally in STAR using the algorithm of HT-Seq.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts per gene for each Sample.

source_name: pulmonary arterial endothelial cells

extract_protocol:
RNA samples were extracted using the Qiagen All-Prep kit per manufacturer instructions
Libraries were prepared from total RNA using the TruSeq Stranded Total RNA Library Prep Kit per manufacturer instructions

tag: condition

value: PAH

tag: gender

value: female

value: wild type

tag: batch

tag: barcodes


title: RNA-Seq_PAH8_male_wild type_1

value: male

value: CTGAAGCT-TAATCTTA


title: AB6353

tag: strain

value: LN

tag: selection marker

tag: treatment

value: PBS


title: HC-trt_3DAT_rep1

description:
21-P5-i711-i505_S37
T3_1.genes.results
processed data file: 3DAT.txt, genes.rawmatrix.txt

tag: tissue

value: Biological replicate 1


title: lib18826: CAT-EEC 391285

source_name: Nasal RNA

value: Nasal RNA

tag: participantid

tag: visitnumber

value: Group A (NAC followed by EEC)

tag: age

tag: Sex

value: Female

tag: race

value: White/Caucasian


title: AB6351

tag: organ

value: TCRb+ CD11c+

tag: time point

tag: replicate id

value: 6-8 weeks


title: RNA-Seq_PAH6_female_wild type_1

value: TCTCGCGC-AGGCGAAG


title: Murine pancreatic cancer cell line KPC-Hnrnpksh1-1

description: Murine pancreatic cancer cell line Hnrnpk sh1 Repetition 1

tag: cell line

value: KPC

value: Murine pancreatic cancer cell line


title: Control_3DAT_rep4

description:
20-P4-i708-i504_S36
C3_4.genes.results
processed data file: 3DAT.txt, genes.rawmatrix.txt

source_name: Control_3DAT_peach buds

tag: cultivar

value: TropicBeauty

value: Control

tag: day after treatment

value: 3 days after treatment

value: peach buds

tag: biological replicate

value: Biological replicate 4


title: RNA-Seq_PAH5_male_wild type_1

tag: condition

value: PAH

tag: gender

value: male

value: wild type

tag: batch

tag: barcodes

value: ATTACTCG-AGGCGAAG


title: AB6350

tag: strain

value: LN

tag: selection marker

value: Trbc+

tag: treatment

value: Nb


title: Murine pancreatic intraepithelial neoplasia organoid p53 Heterozygous R172H Replicate 3

source_name: organoids

tag: cell type

value: organoids


title: Control_3DAT_rep3

description:
19-P3-i707-i503_S35
C3_3.genes.results
processed data file: 3DAT.txt, genes.rawmatrix.txt

tag: tissue

value: Biological replicate 3


title: AB6352

value: TCRb+ CD11c+

value: PBS

tag: age

value: 6-8 weeks


title: AB6349

tag: organ


title: Control_3DAT_rep2

description:
18-P2-i706-i502_S34
C3_2.genes.results
processed data file: 3DAT.txt, genes.rawmatrix.txt

value: TropicBeauty

value: Biological replicate 2


title: Murine pancreatic intraepithelial neoplasia organoid p53 Heterozygous R172H Replicate 2


title: RNA-Seq_PAH3_female_BMPR2_1

value: female

value: GAGATTCC-AGGCGAAG


title: AB6567

tag: time point


title: RNA-Seq_PAH2_male_BMPR2_1

value: CGCTCATT-TAATCTTA


title: AB6347

tag: replicate id


title: AB6346


title: HC-trt_3DAT_rep4

description:
24-P8-i712-i508_S40
T3_4.genes.results
processed data file: 3DAT.txt, genes.rawmatrix.txt

value: Hydrogen cyanamide-treated

value: 3 days after treatment

value: peach buds

value: Biological replicate 4


title: 36007

city: Columbia

first: Youwen

last: Zhang

state: South Carolina

address: 715 Sumter Street CLS109

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina (Columbia)

data_processing:
Sequences were aligned to the P. maniculatus genome (HU_Pman_2.1 (GCA_003704035.1)) in ensembl.org using STAR v2.7.2.
Reads were counted using the featureCounts function of the R Subreads package using Ensembl GTF and summarized at exon, transcript, or gene level.
Genome_build: HU_Pman_2.1
Supplementary_files_format_and_content: comma-separated values file with gene counts for each sample

organism: Peromyscus maniculatus

source_name: Liver

growth_protocol: Deer mice, P. maniculatus were obtained from the Peromyscus Genetic Stock Center (PGSC), University of South Carolina (USC), Columbia, SC (RRID:SCR_002769). Deer mouse, P. maniculatus bairdii (BW Stock), was closed colony bred in captivity since 1948 and descended from 40 ancestors wild-caught near Ann Arbor, Michigan. Sonoran deer mouse, P. maniculatus sonoriensis (SM2 Stock), was derived from about 50 animals wild-caught by Jack Hayes in 1995 near White Mountain Research Station, CA (1).

extract_protocol:
Animals were sacrificed using isoflurane as an anesthetic followed by cervical dislocation, and the livers were collected. RNAs were extracted with a Qiagen RNeasy Plus Mini kit as per manufacturer’s recommendations (Qiagen, Valencia, CA)
RNA integrity was assessed using the Agilent Bioanalyzer and samples had a quality score ≥ 8.6. RNA libraries were prepared using established protocol with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Lynn, MA). Each library was made with one of the TruSeq barcode index sequences and pooled together into one sample to be sequenced on the HiSeq 2x150bp pair-ended sequencing platform (Genewiz).

treatment_protocol: Cohorts of 16 deer mice with 6 males (5 BWs and 1 SM2) on a regular diet, 7 males (5 BWs and 2 SM2s) and 3 females (all BWs) on HFD were used in this study. Deer mice were fed either a regular chow diet or a high fat diet (HFD, 58 kcal% fat and sucrose, Research Diets D12331) for 28 weeks, starting at 3-4 months of age. Body weight was measured every two weeks.

tag: stock

value: BW

tag: diet

value: Chow Diet

tag: age of animal at termination

value: 10 months

tag: steatosis

value: No

tag: Sex

value: Male


title: Murine pancreatic intraepithelial neoplasia organoid p53 Wildtype Replicate 2

value: organoids


title: 36001


title: RNA-Seq_PAH10_female_wild type_1

tag: condition

value: PAH

tag: gender

value: wild type

value: TAATGCGC-AGGCGAAG


title: AB6345

value: LN

value: TCRb+ CD11c+

value: Nb

value: 6-8 weeks


title: 35990

value: High Fat Diet

value: Yes

value: Female


title: Murine pancreatic intraepithelial neoplasia organoid p53 Wildtype Replicate 1


title: RNA-Seq_PAH4_male_wild type_1

value: male

tag: batch

tag: barcodes

value: TCCGCGAA-AGGCGAAG


title: AB6223

tag: strain

value: in vitro

tag: selection marker

value: Mono-culture


title: Murine pancreatic cancer cell line p53R172H ON Replicate 6

source_name: 2D cell line

tag: cell type

value: Murine pancreatic cancer cell line

value: 2D cell line


title: AB6348

tag: treatment


title: RNA-Seq_CTRL8_female_wild type_1

value: CTRL

value: female

value: CGGCTATG-TAATCTTA


title: 35975

value: BW

value: Chow Diet

value: 10 months

value: No

value: Male


title: Murine pancreatic intraepithelial neoplasia organoid p53 Heterozygous R172H Replicate 1

value: organoids


title: Control_3DAT_rep1

description:
17-P1-i705-i501_S33
C3_1.genes.results
processed data file: 3DAT.txt, genes.rawmatrix.txt

tag: cultivar

value: TropicBeauty

value: Control

tag: day after treatment

value: 3 days after treatment

tag: tissue

value: peach buds

tag: biological replicate

value: Biological replicate 1


title: AB6222

tag: organ

value: in vitro

value: Mono-culture

tag: time point

tag: replicate id

tag: age

value: 6-8 weeks


title: Murine pancreatic intraepithelial neoplasia organoid p53 Wildtype Replicate 3


title: AB6221

value: Trbc+


title: Murine pancreatic cancer cell line p53R172H ON Replicate 5

value: Murine pancreatic cancer cell line

value: 2D cell line


title: 35972

tag: stock

value: BW

tag: diet

tag: age of animal at termination

tag: steatosis

tag: Sex


title: Murine pancreatic cancer cell line p53R172H ON Replicate 4

tag: strain


title: 35955

value: High Fat Diet

value: Yes

value: Female


title: Murine pancreatic cancer cell line p53R172H shshRNA2 OFF Replicate 3


title: RNA-Seq_CTRL6_male_wild type_1

tag: condition

value: CTRL

tag: gender

value: male

value: wild type

tag: batch

tag: barcodes

value: GAGATTCC-TAATCTTA


title: RNA-Seq_PAH1_female_wild type_1

value: PAH

value: female

value: CGGCTATG-AGGCGAAG


title: RNA-Seq_CTRL5_male_wild type_1

value: ATTCAGAA-TAATCTTA


title: Murine pancreatic cancer cell line p53R172H shshRNA2 OFF Replicate 2

tag: cell type


title: AB6219

value: in vitro

tag: selection marker

tag: treatment

value: Co-culture


title: AB6220

tag: organ

value: Trbc+

value: Mono-culture

value: 6-8 weeks


title: 35930

value: BW

value: 10 months

value: No

value: Male


title: RNA-Seq_CTRL4_female_wild type_1

value: CTRL

value: TCCGGAGA-AGGCGAAG


title: 35937

value: High Fat Diet


title: AB6218

tag: time point


title: Murine pancreatic cancer cell line p53R172H shshRNA2 OFF Replicate 1

value: Murine pancreatic cancer cell line

value: 2D cell line


title: RNA-Seq_CTRL7_female_wild type_1

value: female

value: wild type

value: CGCTCATT-AGGCGAAG


title: 35998

value: Chow Diet


title: Murine pancreatic cancer cell line p53R172H ON Replicate 3


title: 36016

value: Yes


title: AB6217

value: in vitro

value: Co-culture

tag: replicate id


title: RNA-Seq_CTRL3_male_wild type_1

value: male

value: ATTCAGAA-AGGCGAAG


title: Murine pancreatic cancer cell line p53R172H ON Replicate 2


title: AB6216

value: TCRb+ CD11c+

tag: age

value: 6-8 weeks


title: Murine pancreatic cancer cell line p53R172H ON Replicate 1


title: RNA-Seq_CTRL2_female_wild type_1

value: GAATTCGT-AGGCGAAG


title: RNA-Seq_CTRL1_male_wild type_1

value: CTRL

value: TCTCGCGC-TAATCTTA


title: 35987

tag: stock

value: BW

value: High Fat Diet

value: 10 months

value: No

value: Male


title: RNA-Seq_CTRL10_male_wild type_1

value: wild type

value: ATTACTCG-TAATCTTA


title: AB6215


title: Murine pancreatic cancer cell line p53R172H shRNA1 OFF Replicate 3

value: Murine pancreatic cancer cell line

value: 2D cell line


title: 10880

tag: diet

value: Yes


title: 35982

tag: age of animal at termination

value: Female


title: 35963

tag: steatosis


title: AB6213

value: in vitro

value: Mono-culture


title: Murine pancreatic cancer cell line p53R172H shRNA1 OFF Replicate 2


title: AB6212

value: 6-8 weeks


title: 10876

value: Chow Diet

tag: Sex


title: AB6211

tag: strain

value: Trbc+


title: Tet2 WT2(Wild-type2)

city: Charlottesville

first: Anupreet

last: Kour

state: Virginia

address: 415 Lane road

department: CVRC

institute: University of Virginia

data_processing:
Adapter trimming of raw data files was done using trimgalore/0.6.4.
Alignment of the reads was done with kallisto (Version 0.44.0)
Further analysis was done using different packages in R
Genome_build: GRCm38.cdna.all.fa.gz from Ensembl
Supplementary_files_format_and_content: tsv files with Estimated counts and Transcript per million (TPM) values

source_name: derived from donor Hematopoietic progenitor cells

extract_protocol:
Heart tissue was digested from mice and cardiac macrophages were sorted. From these sorted cells RNA was isolated.
The sorted cells were sent to Genewiz company and library construction was done by the company.

value: Tet2 sufficient cardiac macrophages

tag: genotype/variation

value: Tet2 WT


title: Tet2 WT3(Wild-type3)


title: Tet2 WT1(Wild-type1)


title: 10865

value: High Fat Diet


title: AB6209

value: Co-culture


title: AB6214


title: Tet2 KO1(Knock-out1)

value: Tet2 deficient cardiac macrophages

value: Tet2 KO


title: AB6210


title: Tet2 KO2(Knock-out2)


title: scRNA-seq_DRG_699

city: Davis

first: Carrie

middle: Jacqueline

last: Finno

address: Room 4206 Vet Med 3A

department: Vet Med: PHR

institute: UC Davis

data_processing:
Cellranger v.2.0.1 and bcl2fastq v.2.17.1.14 commands mkfastq and count were used to generate fastq files per sample, align to mm10, filter, and perform barcode and UMI counting
Normalization, clustering, and calculation of TSNE (van der Maaten and Hinton, 2008) coordinates were conducted using Seurat, version 2.3.0 (Satija et al., 2018).
Differential expression analyses between treatments, adjusting for sample and sex, were conducted on the filtered and normalized data using limma, version 3.32.10 (Ritchie et al., 2015).
Gene ontology enrichment analyses were conducted using Kolmogorov-Smirnov tests, as implemented in topGO, version 2.28.0 (Alexa and Rahnenfuhrer, 2016).
Genome_build: mm10

extract_protocol: Barcoded 3' single cell libraries were prepared from single cell suspensions using the Chromium Single Cell 3' Library and Gel b ead kit v2 (10X Genoics, Pleasanton, California). Libraries were pooled and sequenced on an Illumina HiSeq4000 with pair-end 100 bp reads.

value: Ttpa+/+

value: male

value: 5 months

value: dorsal root ganglia neurons


title: AB6208


title: Murine pancreatic cancer cell line p53R172H shRNA1 OFF Replicate 1

value: Murine pancreatic cancer cell line

value: 2D cell line


title: Input_CD1

value: Cerebellum granule neuron progenitor cells

value: Postnatal Day 7

tag: chip antibody

value: Input


title: scRNA-seq_DRG_698

value: female


title: Tet2 KO3(Knock-out3)


title: AB6207

value: in vitro

value: 6-8 weeks


title: AB6206

value: TCRb+ CD11c+


title: scRNA-seq_DRG_670

value: Ttpa-/-

value: 6 months


title: scRNA-seq_DRG_671


title: pax6_72hpa_rep3

city: Seattle

first: Anneke

middle: Dixie

last: Kakebeen

state: WA

address: 5611 9th Ave NW

department: Biochemistry

institute: University of Washington

description:
P723
peaks_counts.txt
ALL_merged_summits.bed

data_processing:
Trim Galore!. Trim sequencing adaptors from fastq files. trim_galore --paired --phred33 --trim1 --nextera ${fastqDIR}${file}_R1_001.fastq.gz ${fastqDIR}${file}_R2_001.fastq.gz --output_dir
Bowtie2. align reads to the genome. bowtie2 --very-sensitive -x ${GenomeDIR} -X 2000 2>> ${BAMDIR}bowtie_log.txt -p 1 -1 ${fastqDIR}trimmed/${file}_R1_001_val_1.fq.gz -2 ${fastqDIR}trimmed/${file}_R2_001_val_2.fq.gz | samtools view -Sb - | samtools sort - -o ${BAMDIR}${file}.bam
MACS2. call peaks on aligned reads. macs2 callpeak -t ${BAMDIR}${file}.bam --nomodel --shift -100 --extsize 200 -g 1.7e9 -f BAM -n ${file} --outdir ${MACSDIR}${file}
GenomicRanges. annotated peaks to nearest transcription start site. used:  Xtropicalisv9.0.Named.primaryTrs.gff3 for annotation
Rsubread. make counts matrix for all samples. featureCounts(isPairedEnd=TRUE, maxFragLength=2000)
Genome_build: Xtropicalis9.0

organism: Xenopus tropicalis

source_name: tadpole spinal cord neural progenitor cells

growth_protocol: Xenopus were reared in 1/9 Modified Ringers solution at 23C.

extract_protocol: The regenerated tail was isolated from the tadpole and cells were dissociated into single cell suspension using Liberase, washed in PBS and sorted for fluoresence through an Aria III cell sorter.

treatment_protocol: The posterior third of an anestitized tadpole tail was amputated at NF stage 41. Tadpoles were replaced in media without anesthetiz and allowed to regenerated until desired collection timepoint.

tag: regeneration timepoint

value: 72 hours post amputation

tag: stage amputated

value: NF Stage 41 (3 days post fertilization)

tag: genotype


title: pax6_72hpa_rep1

description:
P721
peaks_counts.txt
ALL_merged_summits.bed

tag: cell type

value: tadpole spinal cord neural progenitor cells


title: 24hpa_tail

description:
Data collected from GPF positive cells that were FAC sorted from single cell suspensions of cells from 24hpa regenerated tail tissue. tadpole tail.
pax.combined_metadata.txt
pax.neural_metadata.txt

data_processing:
Expression matrix files and BAM files were generated using cellranger (10X genomics) version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries.
Genome_build: GRCz11
Supplementary_files_format_and_content: Expression matrix files and BAM files were generated using cellranger (10X genomics) version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.

source_name: tadpole tail tissue

extract_protocol:
10X genomics single cell gene expression V2 protocol following manufacturer recommendations.
10X genomics single cell gene expression V2 protocol following manufacturer recommendations.

treatment_protocol: The posterior third of an anesthetized tadpole tail was amputated at NF stage 41. Tadpoles were replaced in media without anesthetic and allowed to regenerated until desired collection timepoint.

tag: tissue

value: tadpole tail

value: 24 hours post amputation


title: pax6_24hpa_rep3

description:
P243
peaks_counts.txt
ALL_merged_summits.bed


title: uninjured_tail

description:
Data collected from GPF positive cells that were FAC sorted from single cell suspensions of cells from uninjured tail tips. tadpole tail.
pax.combined_metadata.txt
pax.neural_metadata.txt

value: uninjured


title: pax6_72hpa_rep2

description:
P722
peaks_counts.txt
ALL_merged_summits.bed


title: AB6205

tag: organ

tag: selection marker

tag: treatment

value: Co-culture


title: AB6204

tag: time point

tag: replicate id

tag: age


title: pax6_24hpa_rep1

description:
P241
peaks_counts.txt
ALL_merged_summits.bed


title: scRNA-seq_DRG_657

value: male

value: dorsal root ganglia neurons


title: pax6_24hpa_rep2

description:
P242
peaks_counts.txt
ALL_merged_summits.bed


title: pax6_6hpa_rep3

description:
P63
peaks_counts.txt
ALL_merged_summits.bed

value: 6 hours post amputation


title: AB6203


title: lib18781: CAT-EEC 337489

description: processed data file: P197-1_CB7GFANXX_170912_combined_counts.csv

value: Nasal RNA

tag: participantid

tag: visitnumber

tag: barcode

tag: randomized treatment

value: Group A (NAC followed by EEC)

value: Male

tag: race

value: Black or African American


title: scRNA-seq_DRG_654

tag: genotype/variation

tag: Sex

value: female


title: pax6_6hpa_rep2

description:
P62
peaks_counts.txt
ALL_merged_summits.bed

tag: regeneration timepoint

tag: stage amputated


title: pax6_6hpa_rep1

description:
P61
peaks_counts.txt
ALL_merged_summits.bed

tag: cell type

tag: genotype


title: AB6202

tag: strain

tag: organ

value: in vitro

value: TCRb+ CD11c+

value: 6-8 weeks


title: AB6200

tag: selection marker

value: Trbc+

tag: treatment

value: Mono-culture


title: lib18778: CAT-EEC 176612

tag: tissue

value: Group B (EEC followed by NAC)

value: Female


title: AB6199

tag: time point

tag: replicate id

tag: age


title: NB tetramers

first: Peter

last: Smibert

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
10x data (TCR data) processed using cellranger vdj pipeline
tetramer data were mapped to a 12 base reference tetramer list using CITE-seq-Count (v1.4.1)
DMF5 data was mapped to its reference using CITE-seq-Count with 5 mismatches, 1000 cells
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files onsisting of tetramer data, TCR data, and DMF5 receptor data

source_name: Jurkat/MA cells, neuroblastoma cells

extract_protocol: ‘Stained’ and washed cells were loaded into 10x Genomics single cell 5’ system and processed according to manufacturer’s instructions, and the ECCITE-seq protocols (Mimitou et al, 2019).

treatment_protocol: cells stained with tetramers, sorted for tetramer positive cells

value: neuroblastoma

tag: library type

value: 10x Genomics Single Cell V(D)J

tag: sample type

value: tetramer


title: AB6198


title: pax6_0hpa_rep3

description:
P03
peaks_counts.txt
ALL_merged_summits.bed

value: tadpole spinal cord neural progenitor cells

value: 0 hours post amputation

value: NF Stage 41 (3 days post fertilization)


title: pax6_0hpa_rep2

description:
P02
peaks_counts.txt
ALL_merged_summits.bed


title: Jurkat receptor

source_name: Jurkat/MA cells

value: Jurkat

value: TCR transcript


title: AB6197


title: AB6201

value: Co-culture


title: Comparison LOG2ratio

type: RNA

city: Tsu

first: Naohiro

last: Seo

state: Mie

address: 2-174 Edobashi

department: Immuno-Gene Therpy

country: Japan

institute: Mie University Graduate School of Medicine

hyb_protocol: Hybridization was performed with hybridyzation chamber (Takara Bio #TX711)

scan_protocol: 3D-Gene Scanner 3000 (Toray) was used in this study.

data_processing: After the image was acquired with the optimal PMT value (laser-100%), it was digitized with digitizing software.

source_name: CTL culture sup.

label_protocol: miRNA was labeled with Amersham Cy3 or Cy5 mono-reactive dye

growth_protocol: Murine CTL was cultured for 7days, and culture supernatant was collected.

extract_protocol: Total RNA was extracted, and subjected to AP treatment (3D-gene miRNA Labeling kit).

treatment_protocol: Murine CTL culture supernatant was subjected to DEAE column chromatograpy after concentration of deproteinization of 750 kDa MWCO ultrafiltration.

value: BALB/c

value: CTL culture sup.

value: 0.3 M NaCl eluted Exo and 0.5 M NaCl eluted Exo

value: 0.5 M NaCl eluted Exo


title: spleen tetramer

source_name: spleen - CD8+ T-cells

value: spleen


title: spleen TCR


title: pax6_uninjured_rep3

description:
PW3
peaks_counts.txt
ALL_merged_summits.bed

value: uninjured


title: AB6196

value: in vitro

value: Trbc+

value: 6-8 weeks


title: pax6_uninjured_rep2

description:
PW2
peaks_counts.txt
ALL_merged_summits.bed


title: pax6_0hpa_rep1

description:
P01
peaks_counts.txt
ALL_merged_summits.bed


title: H3_rep1

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

institute: Hubei university

data_processing:
Fastq files for chip-seq samples were generated with bcl2fastq 1.8.3 from Illumina.
ChIP-seq data was aligned to sacCer3 genome from UCSC with bowtie2 (2.2.0) using -k 1
bigWig files were created in R (3.2.2) by reading in bam files, normalizing to reads per kilomillion by multiplying by 1 kilomillion and dividing by the total number of alignments for each sample.
Genome_build: sacCer3

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD until mid-log phase, then culture media were shifted to YPD 2 hours.

extract_protocol:
Lysates were clarified from sonicated yeast cell pellets and histone-DNA complexes were isolated with antibody against H3pT11 (ab5168, Abcam) or H3 (ab1791, Abcam)
Libraries were prepared using the HTP KAPA kit

value: wild type

tag: mediam

value: YPD

tag: chip antibody

value: H3 (ab1791, Abcam)


title: H3_rep2


title: pax6_uninjured_rep1

description:
PW1
peaks_counts.txt
ALL_merged_summits.bed

value: tadpole spinal cord neural progenitor cells


title: H3T11p_rep2

value: H3pT11 (ab5168, Abcam)


title: All-tissue_72hpa_rep1.1

description:
W7212
peaks_counts.txt
ALL_merged_summits.bed

value: tadpole tail

value: 72 hours post amputation

value: NF Stage 41 (3 days post fertilization)


title: H3T11p_rep1


title: All-tissue_72hpa_rep3

description:
W723
peaks_counts.txt
ALL_merged_summits.bed


title: D7 P10-2

city: nottingham

first: Sutham

last: Suthaporn

state: UK

address: Derby road

department: Ob&Gyn

country: United Kingdom

institute: University of Nottingham

description: HESCs treated with progesterone 10 μM for 7 days

hyb_protocol: A mixture of purified, and fragmented biotinylated and labelled sscDNA, and hybridisation controls (Affymetrix) was hybridised on Affymetrix' Clariom S array followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: Detection was performed using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Gene expression data were analysed using Partek Genomics Suite 6.6 software (Partek). The raw CEL files were normalized using the robust multiarray average (RMA) background correction with quantile normalization, log base 2 transformation and mean probe-set summarization with adjustment for guanine-cytosine content

label: biotin

source_name: HESCs,  progesterone 10 μM, 7 days

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip WT Plus Reagent Kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from human endometrium by using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.

treatment_protocol: HESCs were treated with differential medium containing 10 nM β-oestradiol and 0.5 mM 8-Br-cAMP. HESCs were treated with different concentrations of progesterone: 0.1, 1 and 10 μM.

value: HESCs

tag: agent

value: progesterone 10 microM

value: 7 days


title: D7 P10-1


title: All-tissue_72hpa_rep2

description:
W722
peaks_counts.txt
ALL_merged_summits.bed

tag: regeneration timepoint


title: D7 P0.1_3

description: HESCs treated with progesterone 0.1 μM for 7 days

source_name: HESCs,  progesterone 0.1 μM, 7 days

value: progesterone 0.1 microM


title: D7 P10-3


title: AB6195

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: metadata2.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts

extract_protocol:
Mice were housed under specific-pathogen-free conditions at the Animal Breeding Center of the Weizmann Institute of Science, and were used at 6 to 8 weeks of age. All animals were handled according to the regulations formulated by the Institutional Animal Care and Use Committee.
For the in vitro co-culture experiment, cells were isolated from spleens of C57BL/6 8 week old mice. DC derived from spleen tissues were enriched from the single cell suspension first by negative magnetic selection for CD19, and second by positive magnetic selection for CD11c. 2x106 DC were seeded in 6-well plate for 2h activation with 100ng/ml lipopolysaccharide (LPS; Sigma-Aldrich) and 2ug/ml OVA 323-339 (InvivoGen), at 37oC. In parallel, we isolated CD4+ T cells from spleens of OT-II mice. T cells were enriched by the CD4+ T cell Isolation Kit. For culture experiments CD11c+ DC and CD4+ T cells were plated on 96-well U-shape bottom, tissue culture plates. Co-cultured and mono-cultured cells were seeded in concentration of 1×106 cells/ml (1:1 ration in co-cultures), and harvested at different time points following cell plating (3h, 20h, 44h).
For the in vivo infection experiment, N. brasiliensis (Nb) infective L3 larvae were prepared, washed in sterile PBS and killed by three freeze-thaw cycles. Mice were anesthetized and antigen was administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals. Experiments were performed 48h following antigen injection.  To achieve single cell suspensions, auricular LN were digested in IMDM (Sigma-Aldrich) containing Liberase-TL (100μg/ml, Roche) and DNase-I (100μg/ml, Roche), and incubated with frequent agitation at 37oC for 20 min. Cells were washed with IMDM, filtered through a 100μm cell strainer, and centrifuged at 380g, 5min, 4oC.
In both experiments, prior to sorting, cells were stained with DAPI for evaluation of live/dead cells. For the sorting of T-DC PIC samples were gated for TCRβ+CD11c+, for sorting of T cells samples were gated for TCRβ+, and for the isolation of DC, samples were gated for CD11c+, after exclusion of dead cells (DAPI-), erythrocytes (TER119-) and B cells (CD19-).
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

value: Co-culture


title: AB6193

value: TCRb+ CD11c+


title: AB6192

value: in vitro


title: AB6194


title: AB6046

value: Trbc+

value: Transwell


title: AB6045

value: 6-8 weeks


title: D7 P1_1

description: HESCs treated with progesterone 1 μM for 7 days

source_name: HESCs,  progesterone 1 μM, 7 days

value: progesterone 1 microM


title: All-tissue_72hpa_rep1

description:
W721
peaks_counts.txt
ALL_merged_summits.bed

tag: stage amputated


title: All-tissue_24hpa_rep3

description:
W243
peaks_counts.txt
ALL_merged_summits.bed

value: 24 hours post amputation


title: NSC: neural stem cells

city: Beijing

first: Jian

address: 28 Fuxing

department: neurosurgery

institute: Chinese People's Liberation Army of China(PLA) General Hospital

data_processing:
Base-calling  performed with Cell Ranger Single-Cell Software (10×Genomics, version 2.0.2).
The data was aligned and quantified with Cell Ranger Single-Cell Software (10×Genomics, version 2.0.2).
The processed data were then loaded in Seurat software for normalization, dimensionality reduction (tSNE) and downstream analysis
Genome_build: hg19
Supplementary_files_format_and_content: Table-separated values files and Matrix Market format files

source_name: NSC: neural stem cells

growth_protocol:
E3 cells were cultured in NSC-medium with addition of EVs(extracellular vesicles) extracted from CM(contioned medium) of Ln229 cells every two days at 37 ℃ in a 5 % CO2 incubator for 6 weeks (EVs concentration was 10 µg/ml )
T0 cells were cultured in Dulbecco`s modified Eagle`s medium (DMEM) supplemented with 10 % FBS at 37 ℃ in a 5 % CO2 incubator.
NSC cells were cultured in the NSC-medium comprised of a neurobasal medium supplemented with B27 (20 µl/ml), Recombinant human Epidermal Growth Factor (Hu EGF, 20 ng/ml), Recombinant human Fibroblast Growth Factor-basic (FGFb, 20 ng/ml), Penicillin Streptomycin solution (Penicillin, 100 U/ml, Streptomycin, 100 µg/ml) and GlutaMAX (10 µl/ml), at 37 ℃ in a 5 % CO2 incubator.

extract_protocol:
Cells of the samples were harvested and filtered with 40 µm strainers to form single-cell suspension
The single-cell RNA-seq libraries were generated with the Chromium Single Cell 3` Reagent Kit (10×Genomics), and the single-cell suspension and real-time polymerase chain reaction (RT-PCR) Master Mix were loaded together with Single Cell 3` Gel Beads and Partitioning Oil into a Single Cell 3` chip (10×Genomics) according to the manufacture`s protocol. RNA transcripts from single cells were barcoded and reverse-transcribed within droplets, followed by construction of complementary DNAs (cDNAs) libraries of single cells according to the manufacture`s protocol

tag: cell type

value: human embryo neural stem cells

tag: passages

value: brain(normal)


title: AB6043

first: Ido

address: 234 Herzl st.

institute: Weizmann Institute of Science

tag: strain


title: Sample65 hESC derived RetinalOrganoid

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

institute: University of California, Los Angeles

data_processing: Noob normalization using preprocessNoob in the minfi R package

label: cy3, cy5

source_name: Human fetal retina

extract_protocol: Genomic DNA of the retinas was precipitated from the interphase and phenol  phase of the TRIzol solution using 100% ethanol. The DNA pellet was washed 3 times  with 0.1 M sodium citrate/10% ethanol solution and once with 75% ethanol. The pellet  was then resuspended in 8 mM NaOH buffer or concentrated using gDNA Clean and  Concentrator kit (Zymo Research, Irvine, CA).

tag: batch

tag: basename

tag: detailed location retina

value: whole but could be disorganized

tag: culture method

value: RetinalOrganoid

tag: externalsampleid

tag: humanid

tag: Sex

value: Female

tag: gestational day

tag: days in vitro

tag: human expected days


title: D7 P0.1_2

value: HESCs

tag: time point


title: D7 P1_3

tag: agent


title: All-tissue_24hpa_rep2

description:
W242
peaks_counts.txt
ALL_merged_summits.bed

tag: tissue

value: tadpole tail

tag: regeneration timepoint

value: NF Stage 41 (3 days post fertilization)

tag: genotype


title: QM84C21

hyb_protocol: Hybridization was performed with hybridyzation chamber (Takara Bio #TX711

source_name: 0.5 M NaCl eluted Exo

label_protocol: Amplified aRNA was labeled with Amersham Cy5 mono-reactive dye (GE #PA25001)

extract_protocol: Total RNA was extracted, and amplified with Ambion Amino Allyl aRNA kit.

tag: sample type

value: CTL culture supernatant


title: T0: glioblastoma cells

source_name: T0: glioblastoma cells

treatment_protocol: E3 cells were cultured in NSC-medium with addition of EVs(extracellular vesicles) extracted from CM(contioned medium) of Ln229 cells every two days at 37 ℃ in a 5 % CO2 incubator for 6 weeks (EVs concentration was 10 µg/ml )

tag: cell type

value: primary culture glioblastoma cells

tag: passages

value: brain(tumor)


title: AB6044

city: Rehovot

last: Amit

tag: strain

tag: organ

value: in vitro

tag: selection marker

tag: treatment

tag: replicate id

tag: age


title: AB6042


title: All-tissue_24hpa_rep1

description:
W241
peaks_counts.txt
ALL_merged_summits.bed

tag: stage amputated


title: viral bulk tetramers

data_processing:
CITE-seq-Count for tetramer data
Supplementary_files_format_and_content: csv files consisting of bulk tetramer data

organism: synthetic construct

source_name: tetramers

extract_protocol:
‘Stained’ and washed cells were loaded into 10x Genomics single cell 5’ system and processed according to manufacturer’s instructions, and the ECCITE-seq protocols (Mimitou et al, 2019).
bulk 10x PCR

value: tetramer

tag: library type

value: bulk 10x style library


title: QM84C20

source_name: 0.3 M NaCl eluted Exo


title: AB6041

value: Transwell

value: 6-8 weeks


title: D7 P0.1_1

value: progesterone 0.1 microM

value: 7 days


title: E3: induced neural stem cells

last: Wang

source_name: E3: induced neural stem cells

value: induced human embryo neural stem cells

value: brain(normal)


title: Sample55 Human Fetal retina Location:whole Cultured: Explant

tag: batch

tag: basename

tag: detailed location retina

value: whole

tag: culture method

value: Explant

tag: externalsampleid

value: 54d Control #5

tag: humanid

tag: gestational day

tag: days in vitro

tag: human expected days


title: All-tissue_6hpa_rep3

description:
W63
peaks_counts.txt
ALL_merged_summits.bed

tag: tissue

value: tadpole tail

tag: regeneration timepoint

value: 6 hours post amputation

tag: genotype


title: D11 P1_3

description: HESCs treated with progesterone 1 μM for 11 days

source_name: HESCs,  progesterone 1 μM, 11 days

tag: cell type

value: HESCs

tag: agent

value: progesterone 1 microM

tag: time point

value: 11 days


title: Sample61 Human Fetal hESC Location:whole Cultured: Explant

value: 113d Control #10

tag: Sex

value: Female


title: Sample63 hESC derived RetinalOrganoid

value: whole but could be disorganized

value: RetinalOrganoid


title: All-tissue_6hpa_rep2

description:
W62
peaks_counts.txt
ALL_merged_summits.bed

tag: stage amputated

value: NF Stage 41 (3 days post fertilization)


title: D11 P1_2


title: Sample66 hESC derived RetinalOrganoid

tag: batch


title: AB6039

tag: strain

tag: organ

value: in vitro

tag: selection marker

value: Trbc+

tag: treatment

value: Mono-culture

tag: replicate id

tag: age

value: 6-8 weeks


title: UC Exo 3

type: other

description: Evanescent-wave fluorescence excitation method

hyb_protocol: Labeled EVs were incubated for o/n on Rexxam (96) lectin array chip.

scan_protocol: Fluorescence images were acquired using an evanescent field-activated fluorescence scanner (GlycoStationTM reader 1200; GP BioSciences).

data_processing: The fluorescence signal of each spot was quantified using Array Pro Analyzer version 4.5 (Media Cybernetics, Bethesda), and the background value was subtracted. The background value was obtained from the area without lectin immobilization.

molecule: other

label_protocol: Hydrophobic fraction was labeled with Cy3 NHS ester (GE Healthcare).

extract_protocol: Without extraction process, 2 x 10^9 particles/mL EVs were labeled and subjected lectin maicroarray.

value: UC prepared Exo


title: All-tissue_0hpa_rep3

description:
W03
peaks_counts.txt
ALL_merged_summits.bed

value: 0 hours post amputation


title: AB6038


title: UC Exo 1


title: AB6037


title: Sample62 hESC

tag: basename

tag: externalsampleid

tag: humanid

tag: gestational day

tag: days in vitro


title: 0.5 M Exo 3

value: 0.5 M NaCl eluted Exo


title: All-tissue_0hpa_rep1

description:
W01
peaks_counts.txt
ALL_merged_summits.bed

tag: tissue

value: tadpole tail

tag: regeneration timepoint

tag: genotype


title: UC Exo 2


title: All-tissue_6hpa_rep1

description:
W61
peaks_counts.txt
ALL_merged_summits.bed

value: 6 hours post amputation


title: AB6036

value: Co-culture

tag: time point


title: C11-3

description: HESCs without progesterone

source_name: HESCs, control

tag: cell type

value: HESCs

tag: agent


title: D3 P1_1

description: HESCs treated with progesterone 1 μM for 3 days

source_name: HESCs,  progesterone 1 μM, 3 days

value: progesterone 1 microM

value: 3 days


title: 0.5 M Exo 2


title: Sample58 Human Fetal retina Location:whole Cultured: Explant

tag: batch

tag: detailed location retina

value: whole

tag: culture method

value: Explant

value: 103d Control #8

tag: human expected days


title: All-tissue_uninjured_rep1.1

description:
WW11
peaks_counts.txt
ALL_merged_summits.bed

source_name: tadpole tail tissue

value: uninjured

tag: stage amputated

value: NF Stage 41 (3 days post fertilization)


title: C7_2

description: HESCs without progesterone


title: D3 P1_2


title: D11 P1_1

value: 11 days


title: D7 P1_2

value: 7 days


title: D3 P1_3


title: C11-2

description: HESCs without progesterone


title: C7_3

description: HESCs without progesterone


title: C11-1

description: HESCs without progesterone


title: AB6035

tag: strain

tag: organ

value: in vitro

tag: selection marker

tag: treatment

tag: replicate id

tag: age

value: 6-8 weeks


title: C7_1

description: HESCs without progesterone


title: 0.5 M Exo 1


title: All-tissue_uninjured_rep3

description:
WW3
peaks_counts.txt
ALL_merged_summits.bed

tag: tissue


title: AB6034

value: Trbc+


title: 0.3 M Exo 3

value: 0.3 M NaCl eluted Exo


title: All-tissue_uninjured_rep2

description:
WW2
peaks_counts.txt
ALL_merged_summits.bed

value: tadpole tail

tag: regeneration timepoint


title: C3_3

description: HESCs without progesterone


title: AB6033

value: TCRb+ CD11c+


title: 0.3 M Exo 2


title: AB6032

value: Co-culture


title: LSC_MSI2-ADA_C

status: Public on Mar 11 2020

first: Diu

middle: Thi Thanh

last: Nguyen

state: New York

address: 417 East 68th street

data_processing:
The paired-end RNA-seq reads to mouse (mm10) genome using STAR aligner (Dobin et al., 2013)
All mutations (SNP) were identified for each RNA-seq library using the GATK (Van der Auwera et al., 2013) workflow for calling variants in RNA-seq
The mutations were then restricted to annotated mRNA transcripts, as well as restricted to A-to-G mutations in transcripts encoded by the forward strand and T-to-C mutations in transcripts encoded by the reverse strand.
Data were then filtered using mutations found in the dbSNP database since they are most likely DNA-level mutations.
The filtered sets of RNA editing events from all RNA-seq libraries of the same experiment were combined, and counted the number of reads containing reference (A/T) and alternative (G/C) alleles from each library at each site
Genome_build: mm10
Supplementary_files_format_and_content: "mouse_lsk_snp_counts_dedupped.xlsx" and "mouse_lsc_snp_counts_dedupped.xlsx" files include coordinates of the editing sites, strand, entrez id, gene symbol, annotation, reference nucleotide, alternative nucleotide (edited nucleotide) for each RNA-seq library. "Mouse_lsk_snp_counts_dedupped_significant.csv" and "mouse_lsc_snp_counts_dedupped_significant.csv" files include also difference frequency (editing frequency of a site in MSI2_ADA sample subtracted to the average of editing frequency of the site in MSI2_DCD sample and MIG sample), p value, adjusted p value, number of edit sites per gene, fpkm in each sample for edited genes. "lsk_rnaseq_read_count_entrez_id.csv" and lsc_rnaseq_read_count_entrez_id.csv" files contain read counts for all genes mapped to the reference genome in lsk and lsc, respectively.

source_name: Sorted c-Kit high (top 10%) from quaternary MLL-AF9 Actin-DsRed mice

growth_protocol: LSK cells were obtained from Flow cytometry sorting and grown in SFEM medium containing 10ng/ml murine IL-3, 10ng/ml IL-6, 50ng/ml SCF, 10ng/ml thrombopoietin (TPO), and 20ng/ml FLT3l. Quaternary MLL-AF9 leukemia model on Actin-dsRed background mice were generated as described before (Puram et al., 2016). Bone marrow cells from these mice were grown in BMT medium (RPMI 10%FBS 1%L-Glutamine PenStrep supplemented with 10ng/mL murine IL-3, 10ng/mL murine IL-6, 10ng/mL murine SCF and 10ng/mL murine GM-CSF).

extract_protocol:
Sorted GFP positive cells were harvested and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2ng total RNA with RNA integrity numbers ranging from 9.3 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification.Subsequently, 10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR.

treatment_protocol: LSKs were spinoculated with retrovirus expressing MSI2-ADA, MSI2-DCD or MIG controls and 4ug/mL polybrene on retronectin-coated plates at 2500rpm for 2 hours at 32oC. Cells were incubated for 48hrs and then sorted by flow cytometry for GFP positive (overexpressing the fusions). Bone marrow cells from MLL-AF9 Actin-DsRed mice were infected with MSI2-HyperTRIBE expressing virus in BMT medium for 48 hrs. LSC-enriched population was isolated by sorting dsRed+, GFP+ and c-Kit-APC-Cy7 high (top 10-12%) for library preparation and RNA-seq.

value: Leukemic stem cells

tag: overexpression

value: Overexpressing MSI2-HyperADAR fusion

value: 48hr after transduction


title: LSC_MIG_C

value: Overexpressing empty vector

tag: time point


title: All-tissue_uninjured_rep1

description:
WW1
peaks_counts.txt
ALL_merged_summits.bed

tag: genotype


title: LSK_MSI2-DCD_C

source_name: Sorted LSKs from normal C57/B6J mice

tag: cell type

value: normal hematopoietic stem and progenitor cells

value: Overexpressing MSI2-HyperADAR catalytic dead fusion


title: LSC_MIG_A


title: LSC_MSI2-DCD_A


title: LSC_MSI2-ADA_A


title: LSC_MSI2-DCD_C


title: Sample57 Human Fetal retina Location:whole Cultured: Explant

tag: batch

tag: basename

value: whole

value: Explant

tag: externalsampleid

value: 105d Control #7

tag: humanid

tag: Sex

value: Male

tag: gestational day

tag: days in vitro


title: LSC_MSI2-DCD_B


title: Sample59 Human Fetal retina Location:whole Cultured: Not cultured

tag: detailed location retina

tag: culture method

value: Not cultured

value: 113d Trisomy 13

tag: human expected days


title: LSK_MIG_C


title: LSC_MSI2-ADA_B


title: LSK_MSI2-ADA_B


title: 0.3 M Exo 1

source_name: CTL culture sup.

tag: treatment


title: LSK_MSI2-ADA_C


title: C3_1

description: HESCs without progesterone

value: HESCs

tag: agent


title: LSK_MSI2-DCD_A


title: H3K27me3_Sox9 rep2

city: Durham

first: Sara

middle: A.

last: Garcia-Moreno

state: North Carolina

address: Nanaline Bldg. Research Drive

institute: Duke University

data_processing:
Files were trimmed for quality using trim_galore with a stringency setting of 5
Reads were aligned to the mm9 genome with bowtie using the parameters -m 1 and --best
Unmapped reads were eliminated with samtools view using -F 4 settings
HOMER was used for calling peaks with the findPeaks function and settings “--style histone”, with a size of 5000 for H3K27me3. The setting “-C 0” was used in MNase ChIP to  disable fold enrichment limit of expected unique tag positions. H3K27me3 was used as treament (-t) and H3 as control (-c)
bigwig files were created from .bdg files using BedGraphToBigWig for visualization on the UCSC genome browser.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain tracks for visualization on the UCSC genome browser.

source_name: FACS-sorted Sertoli cells

extract_protocol:
Embryonic gonads were micro-dissected at according stage, removed from the mesonephros and incubated in 0.05% trypsin for 5 minutes at 37C. Gonads were then mechanically dissasociated in PBS/3% BSA and passed through a filter cap to obtain a single cell suspension. Fluorescently-labeled cells were collected by Fluorescence Activated Cell Sorting (FACS).  For ChIP-seq, ~100K cells were collected per replicate.
ChIP-seq libraries were prepared with no modifications according to Van Galen et al., 2016.

value: FACS-sorted Sertoli cells

tag: strain

value: C57BL/6 x CD1

tag: embryonic stage

value: male

tag: transgenic line

tag: chip antibody

value: H3K27me3 CST 9733S


title: H3K27me3_TESm rep2

source_name: FACS-sorted granulosa cells

tag: cell type

value: FACS-sorted granulosa cells

value: female

value: TESM-CFP


title: H3K27me3_Sox9 rep1


title: C3_2

description: HESCs without progesterone


title: LSK_MSI2-DCD_B

tag: overexpression

tag: time point

value: 48hr after transduction


title: Sample56 Human Fetal retina Location:whole Cultured: Explant

tag: batch

tag: basename

tag: externalsampleid

value: 80d Control #6

value: Female


title: H3Input_Sox9 rep2

tag: Sex

value: H3 Active Motif 39763


title: LSK_MIG_B

value: normal hematopoietic stem and progenitor cells

value: Overexpressing empty vector


title: H3Input_Sox9 rep1


title: LSK_MSI2-ADA_A

value: Overexpressing MSI2-HyperADAR fusion


title: Sample60 Human Fetal retina Location:whole Cultured: Explant

value: whole

value: Explant

value: 72d Control #9

tag: humanid

tag: gestational day

tag: days in vitro


title: Bmal1 -/- Exp 2

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

data_processing:
bcl2fastq v2.18.0.12 used for basecalling
Cutadapt 1.9.1 with parameters -q 20 -m 20 used for quality-trimming sequences
STAR_2.5.2b used for aligning sequences to mm9 reference genome and quantifying genes
Raw counts normalized with TMM method (NOISeq R package)
Genome_build: mm9
Supplementary_files_format_and_content: Text file with TMM-normalized counts for all genes (rows) and the four samples (columns)

source_name: Bmal1 -/- Exp 2

growth_protocol: mESCs were grown in serum-free 2i media: N2B27 supplemented with MEK inhibitor PD0325901 (1µM) (Millipore) and GSK3 inhibitor CHIR99021 (3 µM) (Millipore) in the presence of LIF.  mESCs were cultured feeder-free on 0.1% gelatin-coated dishes at 37 ºC and 5% CO2.

extract_protocol:
Total RNA was extracted from cells grown in monolayer using TRIzol reagent ( Thermofisher 15596026) according to the manufacturer´s protocol.
Libraries were generated from 1ug Total RNA of using the TruSeq Stranded mRNA kit (Illumina  Cat. No. RS-122-2101) according  to manufacturer´s instructions

value: Mouse embryonic stem cells

tag: genotype/variation

value: Bmal1 -/-


title: JM8 wild-type Exp2

source_name: JM8 wild-type Exp2

value: JM8 wild-type


title: JM8 wild-type Exp1

source_name: JM8 wild-type Exp1


title: MPP2-ADA_2

description:
Mouse_HSC_rnaseq_read_count_entrez_id.csv
mouse_hsc_snp_counts_dedupped.xlsx
mouse_hsc_snp_counts_dedupped_significant.csv

data_processing:
The paired-end RNA-seq reads to mouse (mm10) genome using STAR aligner (Dobin et al., 2013)
All mutations (SNP) were identified for each RNA-seq library using the GATK (Van der Auwera et al., 2013) workflow for calling variants in RNA-seq
The mutations were then restricted to annotated mRNA transcripts, as well as restricted to A-to-G mutations in transcripts encoded by the forward strand and T-to-C mutations in transcripts encoded by the reverse strand.
Data were then filtered using mutations found in the dbSNP database since they are most likely DNA-level mutations.
The filtered sets of RNA editing events from all RNA-seq libraries of the same experiment were combined, and counted the number of reads containing reference (A/T) and alternative (G/C) alleles from each library at each site
Genome_build: mm10
Supplementary_files_format_and_content: "mouse_hsc_snp_counts_dedupped.xlsx" file includes coordinates of the editing sites, strand, entrez id, gene symbol, annotation, reference nucleotide, alternative nucleotide (edited nucleotide) for each RNA-seq library. "Mouse_hsc_snp_counts_dedupped_significant.xlsx" file includes also difference frequency (editing frequency of a site in MSI2_ADA sample subtracted to the average of editing frequency of the site in MSI2_DCD sample and MIG sample), p value, adjusted p value, number of edit sites per gene, fpkm in each sample for edited genes. "Mouse_HSC_rnaseq_read_count_entrez_id.csv" contains read counts for all genes that are mapped to the reference genome in each sample.

source_name: Sorted MPP2 from bone marrow of normal C57/B6J mice

growth_protocol: Bone marrow cells from 6-8 week-old C57BL/6 strain were processed for c-Kit enrichment by incubation with 50 μl of MACS CD117/c-Kit beads per mouse and then run on an AutoMACs (Miltenyi Biotec) following the manufacturer’s instructions. Cells were stained with Lineage antibody cocktail (CD3, CD4, CD8, Gr1, B220, CD19, TER119 conjugated with PeCy5), Sca1-Pacific Blue, and c-KIT-APC-Cy7. Lin-Sca+Kit+ cells (LSKs) were sorted using a BD FACS Aria II instrument. Sorted LSKs were grown overnight in SFEM medium containing 10ng/ml murine IL-3, 10ng/ml IL-6, 50ng/ml SCF, 10ng/ml thrombopoietin (TPO), and 20ng/ml FLT3l.

extract_protocol:
360-20,000 sorted cells were used for RNA extraction and sequencing.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2ng total RNA with RNA integrity numbers ranging from 9.3 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification.Subsequently, 10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR.

treatment_protocol: Cells were spinoculated with retrovirus expressing MSI2-ADA, MSI2-DCD or MIG controls and 4ug/mL polybrene on retronectin-coated plates at 2500rpm for 2 hours at 32oC. After 48 hours of transduction, all cells were collected and transplanted into lethally irradiated C57BL/6 mice (15,000 cells per mouse). Engraftment was checked after 6 weeks. After 7 weeks of transplantation, mice were sacrificed and c-Kit enriched bone marrow cells were stained with LSK markers as described above plus CD48-PE and CD150-APC. Cells were sorted into 4 populations GFP positive CD150+ CD48- (LT-HSC), CD150- CD48-  (ST-HSC or MPP1), CD150+ CD48+ (MPP2) and CD150- CD48+ (MPP4).

value: Myeloid-biased multipotent progenitor cells

value: 7 weeks after transplantation


title: LT-HSC-ADA_1

source_name: Sorted LT-HSC from bone marrow of normal C57/B6J mice

value: Long-term hematopoietic stem cells


title: H3Input_TESm rep1

value: FACS-sorted granulosa cells

value: C57BL/6 x CD1

value: female

value: TESM-CFP


title: LSK_MIG_A

value: 48hr after transduction


title: Bmal1 -/- Exp 1

source_name: Bmal1 -/- Exp 1


title: ST-HSC-ADA_2

source_name: Sorted ST-HSC from bone marrow of normal C57/B6J mice

value: Short-term hematopoietic stem cells


title: MPP4-ADA_1

source_name: Sorted MPP4 from bone marrow of normal C57/B6J mice

value: Lymphoid-biased multipotent progenitor cells