title: CD14+ monocytes, T1D patient, replicate 11

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.52.0).

source_name: CD14+ monocytes, isolated from peripheral blood mononuclear cells obtained from a patient with type 1 diabetes

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: For this transcriptome profiling study, 12 patients with T1D and 12 healthy nondiabetic control subjects carefully matched for age, sex and BMI were included. Patients included in the study were diagnosed with T1D at least 10 years ago and were recruited from the outpatient clinic of the Radboud University Medical Center (Radboudumc) Nijmegen. HbA1c levels were averaged from the last ten visits. Ethical approval for this study was obtained from the Institutional Review Board of the Radboud University Medical Center (NL62200.091.17 2017-3555), and registered at ClinicalTrials.gov (NCT03441919). The study was conducted according to the principles expressed in the Declaration of Helsinki. All participants gave written informed consent before participation.

extract_protocol: RNA was isolated using Qiagen RNeasy Micro Kit (Qiagen), quantified using NanoDrop, and quality was checked with the Agilent 2100 bioanalyzer (Agilent Technologies). Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by dilution of blood with pyrogen-free PBS and differential density centrifugation over Ficoll-Plaque gradient media (GE Healthcare, Eindhoven, The Netherlands). PBMCs were purified to CD14+ monocytes using indirect magnetic labelling (Miltenyi Biotec B.V., Leiden, The Netherlands), and used for RNA isolation.

value: type 1 diabetes

tag: subjectid

tag: sex (female=0, male=1)

tag: bmi

tag: age (yrs)

tag: hba1c (mmol/mol)

value: CD14+ monocytes


title: CD14+ monocytes, T1D patient, replicate 9

status: Public on Oct 09 2020

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: disease state

tag: cell type


title: CD14+ monocytes, T1D patient, replicate 10


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A7_ad002

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: CA

tag: Sex

value: male

tag: age

tag: strain


title: CD14+ monocytes, T1D patient, replicate 7


title: CD14+ monocytes, T1D patient, replicate 6


title: CD14+ monocytes, T1D patient, replicate 12


title: gRNA library1 HeLa in vitro D30 replicate1

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
gRNA enrichment and deep sequencing datasets were removed adapters by cutadapt (1.16) using the following adapter sequences (R1: -a TTTTTTAAGCTTGGCGTAACTAGATCT -m 15, -g CCCTACCAACTGGTCGGGGTTTGAAAC -m 15; R2: -a GTTTCAAACCCCGACCAGTTGGTAGGG -m 15, -g AGATCTAGTTACGCCAAGCTTAAAAAA -m 15).
After removing adapters at 3' and 5' ends, processed reads were aligned to gRNA library sequences with Bowtie (v1.1.2, parameters: -v 3 -m 1 -k 1), and only uniquely-mapped reads were obtained for gRNA enrichment.
Uniquely-mapped reads for each unique gRNA were normalized to RPM.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: txt file (RPM of gRNA enrichment and deep sequencing datasets)

source_name: gRNA library1 HeLa in vitro D30

growth_protocol: HT29, HeLa and 293FT cells were purchased from the American Type Culture Collection (ATCC; http://www.atcc.org) or ThermoFisher, respectively, and were originally authenticated using STR profiling. HT29 cells were maintained in RPMI 1640, HeLa (human female origin) and 293FT cells (human fetus origin) were maintained in DMEM, and all supplemented with 10% Fetal Bovine Serum (FBS) and 0.1% penicillin/streptomycin. We maintained cell lines at 37°C in a 5% CO2 cell culture incubator and tested all cell lines routinely to exclude mycoplasma contamination.

extract_protocol:
Genomic DNA of screening cell samples were extracted with DNA EXTRACTION Kit (Tiangen)according to the manufacturer’s protocol.
For gRNA library analysis, genomic DNAs from HT29, 293FT and HeLa cells for screens were extracted. gRNA library was enriched by PCR amplification. Deep sequencing of amplified PCR products containing gRNA sequences was conducted by Illumina NextSeq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: To infect HeLa, 293FT or HT29 cells with lentivirus, cells were incubated with culture medium containing 10 μL concentrated lentivirus and 5 mg/mL polybrene (Sigma). Infected cells were treated with puromycin to increase knockdown efficiency.

tag: cell line

value: HeLa cells

tag: treatment

value: lentiviral gRNA library infection

tag: time


title: PO_IMVD_002_Precision_antiMYC_Purified_orfEnd_3p

city: New York

first: Panos

last: Oikonomou

state: New York

address: 1150 St. Nicholas Ave

department: Biological Sciences

institute: Columbia University

description:
3' ORF Reads
inVivoDisplay_PO_Supplementary_Table_2_Precision.xlsx

library_source: transcriptomic

data_processing:
Library strategy: in vivo mRNA display
clip 3' universal adapter sequence with cutadapt
clip  5' custom index sequence and demultiplex with cutadapt
Reads aligned with bowtie2  version 2.2.6 to the 5’ and 5’ ends of S. Cerevisiae ORFs
Final matrix of log2(Counts) generated with a custom script in python 2.7.15
Genome_build: SGD genome version R64-1-1
Supplementary_files_format_and_content: xlsx

organism: Saccharomyces cerevisiae

source_name: Precision: antiMYC Purification: Purified Sample

growth_protocol: Cell were induced in SC -URA -MET dropout media at OD660 ~0.05-0.1 and grown for 6-8 hours to OD ~0.75

extract_protocol:
RNA was extracted using Trizol
in vivo mRNA display libraries were subjected to RT, 2nd Strand Synthesis with construct specific primers, followed by RE digestion, y-Linker ligation and amplification with flanking illumina sequences

tag: tissue

value: Liquid Culture

tag: protocol

value: in vivo mRNA display

tag: growth stage

value: Exponential

tag: fixed

value: No

tag: sequenced molecule

value: cDNA


title: gRNA library2 HT29 in vivo D1 replicate1

source_name: gRNA library2 HT29 in vivo D1

value: HT29 cells


title: PO_IMVD_002_Precision_antiMYC_Input_Lysate_orfEnd_5p

description:
5' ORF Reads
inVivoDisplay_PO_Supplementary_Table_2_Precision.xlsx

source_name: Precision: antiMYC Purification: Input Lysate Sample


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A6_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A6_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A7_ad008


title: gRNA library1 HeLa in vitro D1 replicate1

source_name: gRNA library1 HeLa in vitro D1


title: gRNA library1 HeLa in vitro D1 replicate2


title: gRNA library1 293FT in vitro D30 replicate2

source_name: gRNA library1 293FT in vitro D30

value: 293FT cells


title: PO_IMVD_001_Precision_antiHIS_Purified_orfEnd_5p

source_name: Precision: antiHIS Purification: Purified Sample


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A6_ad010


title: PO_IMVD_002_Precision_antiMYC_Input_Lysate_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A7_ad004


title: CD14+ monocytes, T1D patient, replicate 4

tag: subjectid

tag: sex (female=0, male=1)

tag: bmi


title: CD14+ monocytes, T1D patient, replicate 2

tag: disease state

tag: age (yrs)

tag: hba1c (mmol/mol)


title: CD14+ monocytes, T1D patient, replicate 8

tag: cell type


title: CD14+ monocytes, T1D patient, replicate 5


title: gRNA library1 293FT in vitro D30 replicate1


title: CD14+ monocytes, T1D patient, replicate 1


title: CD14+ monocytes, T1D patient, replicate 3


title: gRNA library1 293FT in vitro D1 replicate2

source_name: gRNA library1 293FT in vitro D1


title: PO_IMVD_001_Precision_antiHIS_Purified_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A6_ad002

tag: brain region

tag: Sex

tag: age


title: PO_IMVD_001_Precision_antiHIS_Input_Lysate_orfEnd_5p

source_name: Precision: antiHIS Purification: Input Lysate Sample


title: gRNA library1 293FT in vitro D1 replicate1

tag: cell line

tag: treatment


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A5_ad012

tag: strain


title: gRNA library1 HT29 in vitro D30 replicate1

source_name: gRNA library1 HT29 in vitro D30

tag: time


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A5_ad008


title: gRNA library1 HT29 in vitro D30 replicate2


title: gRNA library1 HT29 in vitro D1 replicate2

source_name: gRNA library1 HT29 in vitro D1


title: CD14+ monocytes, healthy nondiabetic control, replicate 10

source_name: CD14+ monocytes, isolated from peripheral blood mononuclear cells obtained from a healthy nondiabetic control subject

value: control


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A5_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A6_ad004


title: gRNA library1 HT29 in vitro D1 replicate1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A5_ad004


title: HeLa ribo– RNA-seq replicate2

description: HeLa ribo– RNA-seq replicate2

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
RNA-seq sequencing read quality was evaluated by FastQC (v0.11.5), and then mapped by using TopHat (TopHat v2.0.12, parameters: –microexon-search -g 1 -a 6 -m 2) to GRCh37/hg19 human reference genome with the UCSC Genes annotation (Human: hg19 knownGene.txt updated at 2013/06/30). The TopHat2-mapped sam files were transferred to bam format by samtools (version 0.1.19).
Bam to Bedgraph using genomeCoverageBed (v2.28.0)  Bedgraph to bigwig using UCSC bedGraphToBigWig (v4)
bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigwig file

source_name: HeLa cells

extract_protocol:
Total RNAs from HT29, 293FT and HeLa cells were extracted with Trizol (Life Technologies) according to the manufacturer’s protocol.
For circRNA expression analysis, total RNAs from HT29, 293FT and HeLa WT cells was processed with the RiboMinus kit (Human/Mouse Module, Invitrogen) to deplete ribosomal RNAs for sequencing. Ribo– RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA LT Sample Prep Kit. All libraries were size-selected with AmpureXP beads (Agencourt) and quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Size-selected libraries were subjected to deep sequencing with Illumina HiSeq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.
ribo– RNA-seq

treatment_protocol: HT29, 293FT and HeLa cells were collected for total RNAs extraction.

value: untreated


title: PO_IMVD_001_Precision_antiHIS_Input_Lysate_orfEnd_3p

tag: tissue

tag: protocol

tag: growth stage


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A5_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A5_ad001


title: 293FT ribo– RNA-seq replicate2

description: 293FT ribo– RNA-seq replicate2

source_name: 293FT cells


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A4_ad012


title: CD14+ monocytes, healthy nondiabetic control, replicate 9

tag: subjectid


title: 293FT ribo– RNA-seq replicate1

description: 293FT ribo– RNA-seq replicate1


title: CD14+ monocytes, healthy nondiabetic control, replicate 8

tag: sex (female=0, male=1)


title: CHD patients after treatment, biological rep8

city: Tianjin

first: Ya-dong

last: Fan

address: No.10 PoYangHu Road, JingHai, District,

institute: Tianjin university of TCM

description: Expression data from eight patients with coronary heart disease after Tongmai Yangxin Pills treatment for eight weeks.

hyb_protocol: In vitro transcription synthesizes aRNA and incorporates a biotin-congugated nucleotide (cRNA is also known as amplified RNA or aRNA). The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays. GeneChip® HT Hybridization, Wash, and Stain Kit for GeneTitan: Affymetrix, P/N 901406.

scan_protocol: GeneChips were scanned using  GeneChip Scanner 3000 (Affymetrix).

data_processing: AGCC software (Affymetrix GeneChip Command Console version4.0) was used to extract the data from the scan image in .CEL format. This data can be opened by the Expression Console software. The original data were imported into Genespring software (version 13.1,Agilent), and the RMA method was used to standardize the results, including the original signal value, the standardized signal value and detailed annotation information.

source_name: CHD patients withTMYX treament for eight weeks

label_protocol: In the GeneChip® 3’ IVT Express Protocol total RNA undergoes reverse transcription to synthesize first-strand cDNA. This cDNA is then converted into a double-stranded DNA template for transcription.

growth_protocol: All patients received TMYX (40 pills/time, 2 times/day) for eight weeks. Blood samples for further study were obtained from the antecubital vein of patients on the day of enrollment and eight-week administration of TMYX.

extract_protocol: Total RNA was isolated with mirVana™ PARIS™ Kit (Ambion-1556, United States) according to the manufacturers’ instructions. Total RNA was isolated with mirVana™ PARIS™ Kit (Ambion-1556, United States) according to the manufacturers’ instructions. To improve RNA purity for further analysis, RNasey Mini Kit (Qiagen p/n 74104, Germany) was used for total RNA clean-up. Total RNA concentration and purity were estimated with NanoDrop1000 (Thermo Scientific, United States). RNA integrity was assessed using the Agilent 2100 bioanalyzer (Agilent Technologies), RNA LabChip® kits and RNA Integrity Number software.

treatment_protocol: Peripheral blood samples (2.5ml) of each patient were collected with PAX gene Vacutainer Tube (BD Biosciences, New York, United States) in the morning, before breakfast.

value: peripheral blood mononuclear cells

tag: disease

value: coronary heart disease

tag: agent

value: Tongmai Yangxin

tag: gender


title: CD14+ monocytes, healthy nondiabetic control, replicate 6

tag: disease state

tag: bmi

tag: age (yrs)

tag: hba1c (mmol/mol)

value: CD14+ monocytes


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A4_ad010

tag: brain region

value: CA

tag: Sex

tag: age


title: CD14+ monocytes, healthy nondiabetic control, replicate 11

tag: cell type


title: CHD patients after treatment, biological rep7

value: female


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A5_ad002

value: male

tag: strain


title: CHD patients after treatment, biological rep6

tag: tissue


title: HeLa ribo– RNA-seq replicate1

description: HeLa ribo– RNA-seq replicate1

tag: cell line

value: HeLa cells

tag: treatment


title: CD14+ monocytes, healthy nondiabetic control, replicate 7

tag: subjectid


title: CD14+ monocytes, healthy nondiabetic control, replicate 5

tag: sex (female=0, male=1)


title: CHD patients after treatment, biological rep4

tag: disease


title: CD14+ monocytes, healthy nondiabetic control, replicate 4


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A4_ad008


title: CD14+ monocytes, healthy nondiabetic control, replicate 3


title: WDFL_rep2

city: Hyderabad

first: Divya Tej

last: Sowpati

state: Telangana

address: Habsiguda

country: India

institute: CSIR Centre for Cellular and Molecular biology

data_processing:
Base-calling was performed using bcl2fastq of Illumina
Quality control was performed on the FASTQ read files using FastQC v0.11.7.
The reads were aligned to the reference genome using STAR-2.5.2 with the parameters STAR --runThreadN 16 --runMode alignReads --readFilesCommand zcat --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM
Abundance estimates were calculated using RSEM-1.3.1 using the parameters  rsem-calculate-expression --bam --no-bam-output -p
Differential expression across the three conditions were performed using EBSeq module from RSEM-1.3.1
Genome_build: danRer10
Supplementary_files_format_and_content: Files containing TPM values for both tissues

organism: Danio rerio

source_name: Withdrawal Female Liver 2

growth_protocol: Zebrafish were maintained at CSIR-CCMB zebrafish facility as per standard practices.One-hundred twenty naïve wild-type (short fin,‘AB’strain)D. rerio(60 males, 60 females) were separated into four groups,representing male control,male alcohol-exposed,female control,and female alcohol-exposed groups.Thus, each group was composed of 30 fish, exclusively either male or female, maintained in a 20-L water tank.

extract_protocol:
Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine (Sigma, USA). Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater (~200 μl in total volume; Sigma) for storage in RNase-free microcentrifuge tubes (Ambion). Tissues were later stored at -80 °C. Total RNA was prepared using NucleoSpin® RNA kit (Macherey-Nagel, REF # 740955.50) as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer (from RNA kit) using a hand-held microtube homogenizer. On-column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water (Sigma). After purification, the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis, respectively. All RNA samples were stored at -80 °C.
TruSeq RNA Library Prep Kit (v2 LT) Non-stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.

treatment_protocol: For the chronic alcohol exposure program,fish were transferred every afternoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle (14/10 h),temperature of 28C, water salinity of 3 g of sea salt per liter, and aeration by air bubbling were maintained. This way,fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each afternoon to a new tank but without ethanol in the medium. From the 5th week of alcohol treatment to the 9th week,fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations - both partners control,only male alcohol-exposed, only female alcohol-exposed, and both sexes alcohol-exposed. Because alcohol-exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding, we kept male and female fish in the same breeding tank a night before the breeding. The next morning, breeding was stimulated by white light and eggs were collected after 1 h. Eggs were counted manually and maintained further to look for developmental defects.

value: short fin, 'AB' strain

tag: condition

value: Withdrawal

value: Female

value: Liver


title: CD14+ monocytes, healthy nondiabetic control, replicate 1


title: CHD patients after treatment, biological rep2

tag: agent

tag: gender


title: CHD patients after treatment, biological rep5


title: WDFL_rep1

source_name: Withdrawal Female Liver 1


title: CD14+ monocytes, healthy nondiabetic control, replicate 2

tag: disease state

tag: bmi


title: HT29 ribo– RNA-seq replicate2

description: HT29 ribo– RNA-seq replicate2

source_name: HT29 cells


title: HT29 ribo– RNA-seq replicate1

description: HT29 ribo– RNA-seq replicate1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A4_ad007

source_name: C57BL/6J Male P56 Mouse Brain


title: Human1_3_CNCCs

city: Jerusalem

first: David

last: Gokhman

address: Givat Ram, Safra Campus

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Remove sequencing adapters with SeqPrep version 1.2
Map reads to GRCh38 and PanTro5 with STAR version 2.5.1b
Remove duplicate reads with Picard 2.18.27
Remove reads which exhibit mapping bias with WASP (Hornet)
Count allele specific and total reads
Genome_build: Human: GRCh38; Chimpanzee: PanTro5
Supplementary_files_format_and_content: Counts matrix with total and allele-specific raw read counts (rows are genes, there are 4 columns per sample: ref counts (aligned to reference genome), alt counts (aligned to alternative genome), no ASE (no segregating SNPs) and ambiguous (SNPs from both genome); matrix text files are provided for samples mapped on both the human and chimpanzee genomes; text files with sample meta data are also included for each data set
Supplementary_files_format_and_content: GRCh38 (1st sheet), panTro5 (2nd sheet)
Supplementary_files_format_and_content: Raw read counts per gene across all samples

molecule: polyA RNA

source_name: iPSC-derived CNCCs

growth_protocol: Three independent CNCC differentiation experiments were performed. In each one, human-chimpanzee hybrid iPSC (Hy1_30), parental human (Hu1), parental chimpanzee (Ch1) iPSC lines, and human embryonic stem cells (hESCs, control) were differentiated into CNCCs. Briefly, iPSCs and hESCs were incubated with 2mg/ml collagenase for ~30-50 min leading to detachment of colonies. Detached cells were plated as clusters of 100-200 cells in low-attachment petri dishes and cultured in the presence of CNCC differentiation medium consisting of 1:1 Neurobasal medium/DMEM F-12 medium (ThermoFisher Scientific), 0.5× B-27 supplement with Vitamin A (50× stock, GeminiBio), 0.5× N-2 supplement (100× stock, GeminiBio), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich), 5 µg/ml bovine insulin (Sigma-Aldrich) and 1× Glutamax-I supplement (100× stock, ThermoFisher Scientific). Cells grown in CNCC differentiation medium grew as neural spheres/rosettes. For the first four days of differentiation, spheres were separated from cell debris by gentle centrifugation and re-plated into new petri dishes in fresh CNCC differentiation medium. After four days, the neural spheres were allowed to settle for three days to promote attachment to the culture plate surface. After the neural spheres began to attach to the plate, media was changed daily, and neural crest cells were allowed to migrate out of the neural rosettes for 4-5 days. Afterwards, neuroectodermal spheres were manually picked and removed from the culture dishes leaving behind emigrated neural crest cells, which were dissociated with 1x Accutase and passaged onto fibronectin (7.5µg/ml) (ThermoFisher Scientific) coated plates. The early migratory CNCCs were cultured in the presence of maintenance medium comprising of 1:1 Neurobasal medium/DMEM F-12 medium (Invitrogen), 0.5× B-27 supplement with Vitamin A (50× stock, GeminiBio), 0.5× N-2 supplement (100× stock, GeminiBio), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich), 1 mg/ml bovine serum albumin, serum replacement grade (Gemini Bio-Products # 700-104P) and 1× Glutamax-I supplement (100× stock, ThermoFisher Scientific). The CNCCs were cultured on fibronectin coated dishes, with passaging every three days with 1x Accutase for additional two passages. Afterwards, medium was changed to BMP/ChIR medium by adding 3µM ChIRON 99021 (Selleck, CHIR-99021) and 50pg/ml BMP2 (Peprotech) to the maintenance medium, which increased cell proliferation and decreased migration.

extract_protocol:
Qiagen Rneasy Mini Kit with on-column DNAse digestion (Qiagen)
Illumina TruSeq Stranded mRNA library prep kit (Illumina)


title: WDML_rep2

source_name: Withdrawal Male Liver 2

value: Male


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A4_ad006


title: Human1_2_CNCCs


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A4_ad004


title: WDML_rep1

source_name: Withdrawal Male Liver 1


title: Human1_1_CNCCs


title: ALFL_rep2

source_name: Alcohol exposed Female Liver 2

value: Alcohol exposed


title: HeLa cells, Mut (sg-SON) m6a rep 2

city: Beijing

first: Zonggui

last: Chen

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: Academy for Advanced Interdisciplinary Studies

institute: Peking University

description:
m6A-seq
m6a_peak_mutFTO_sgSON_rep2.tsv.gz

data_processing:
Adapter sequences were trimmed using Cutadapt(2.5) program.
Potential ribosomal RNA contamination were eliminated by using Bowtie(1.2.2) program to align reads to reference ribosomal RNA sequences.
Reads were mapped to GRCh38 by using STAR(STAR_2.5.0a) program. Only proper-pair and primary alingments were retained.
Fragment counts and FPKM of transcripts were counted by using custom scripts.
Lifetime were calculated by the comparison of the FPKM at different time points.
m6A enriched peaks were identified by comparing the normalized coverage of IP and Input.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include the fragment count and FPKM values for all samples and RNA lifetime calculated by FPKM of different time points. Bed files include the peak regions on BED12 format.

growth_protocol: HeLa (ATCC) cells were maintained using DMEM (high glucose) supplemented with 10% fetal bovine serum, and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was isolated by TRIzol reagent (Invitrogen). PolyA-RNA was isolated by two rounds of ployA selection with Oligo d(T)25 Magnetic Beads (NEB, S1419S) from total RNA and followed by additional TURBO DNase treatment. mRNA were purified by RNA Clean & Concentrator Kits and then fragmented to about 100 nt using RNA Fragmentation Reagents (Invitrogen, AM8740). The fragmented mRNA were purified by using RNA Clean & Concentrator Kits. For m6A-seq, while 100 ng mRNA was saved as input sample, the rest mRNA was used for m6A-immunoprecipitation. Briefly, nearly 5 ug mRNA was incubated with m6A antibody (Synaptic Systems, 202 003) and diluted into 500 uL IP buffer (150 mM NaCl, 0.1% Igepal CA-630, 10 mM Tris, pH 7.4, 100 U RNase inhibitor). The mixture was rotated at 4°C for 2 hours, following Dynabeads® Protein A (Invitrogen, 10002D) was added into the solution and rotated for another 2 hours at 4 °C. After four times washing by IP buffer, the m6A IP portion was eluted twice by 100 uL m6A-elute buffer (IP buffer, 6.7mM m6A, 30 U RNase inhibitor) with incubating and shaking at 4°C for 1 hour. Finally, m6A IP mRNA was recovered by RNA Clean & Concentrator Kits and the RNA concentration was measured with Qubit® RNA HS Assay Kit (Invitrogen, Q32855).
Sequencing libraries of input and ip samples were prepared using NEBNext Ultra II RNA Library Prep Kit.

treatment_protocol: The co-transfection ratio of GCN4-GGS6-dCas13b, scFv-effector protein-GB1 and sgRNA-expressing plasmid is 1:1:2. For m6A-seq, cells were transfeced by identical plasmids for overall 48 hours. For RNA lifetime profiling, cells were transfected by identical plasmids for overall 48 hours. And actinomycin D was added to 5 ug/mL at 6 hours, 3 hours and 0 hour before cell scraping collection.

tag: genotype

value: mutant FTO

value: HeLa

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTOH201A D233A-GB1 and sg-SON for overall 48 hours.

tag: rip antibody


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A4_ad002

tag: brain region

tag: Sex


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A3_ad012

tag: age


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A3_ad010

tag: strain


title: HeLa cells, WT (sg-Control) m6a rep 2

description:
m6A-seq
m6a_peak_wildtype_sgControl_rep2.tsv.gz

value: WT

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTO-GB1 and sg-Control for overall 48 hours.

value: m6A antibody (Synaptic Systems, 202 003)


title: CHD patients before treatment, biological rep8

description: Expression data from eight patients with coronary heart disease before  Tongmai Yangxin Pills treatment.

source_name: CHD patients without TMYX treament

tag: tissue

value: peripheral blood mononuclear cells

value: coronary heart disease


title: ALFL_rep1

source_name: Alcohol exposed Female Liver 1


title: ALML_rep1

source_name: Alcohol exposed Male Liver 1


title: ALML_rep2

source_name: Alcohol exposed Male Liver 2


title: HeLa cells, WT (sg-SON) m6a rep 2

description:
m6A-seq
m6a_peak_wildtype_sgSON_rep2.tsv.gz

tag: cell line

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTO-GB1 and sg-SON for overall 48 hours.


title: CHD patients after treatment, biological rep3

value: Tongmai Yangxin

value: female


title: CHD patients before treatment, biological rep5


title: CTFL_rep2

source_name: Control Female Liver 2

value: short fin, 'AB' strain

value: Control


title: CHD patients before treatment, biological rep3


title: CHD patients before treatment, biological rep6

value: male


title: CHD patients before treatment, biological rep7


title: CHD patients before treatment, biological rep4


title: CHD patients before treatment, biological rep2


title: CHD patients after treatment, biological rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A3_ad006

value: CA


title: tgs1KO-2L-Rep2

city: Guangzhou

first: Lin

last: Cheng

state: Guangdong

address: No.132, East Outer Ring Road, Guangzhou University City

institute: Sun Yat-sen University

description:
CRISPR/Cas9 mediated knock out of tgs1
Larvae GeneFPKM.txt

data_processing:
data processing step
Supplementary_files_format_and_content: FPKM

organism: Drosophila melanogaster

source_name: Second instar larvae

growth_protocol: All of the fly stocks were cultured at 25℃.

extract_protocol:
For RNA sequencing, total RNA was extract from about 100 testes or 80 second instar larvae using TRIzol reagent.
mRNA was enriched by using the NEBNext Poly(A) mRNA Magnetic Isolation Module , then an RNA-Seq library were prepared with the NEBNext Ultra RNA Library Prep Kit for Illumina, the libraries were sequenced with Illumina HiSeq X Ten.

value: Whole larvae

value: Second instar larvae


title: CHD patients before treatment, biological rep1


title: CTFL_rep1

source_name: Control Female Liver 1

value: Female

value: Liver


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A3_ad004


title: tgs1KO-2L-Rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A3_ad007


title: HeLa cells, WT (sg-SON) m6a rep1

description:
m6A-seq
m6a_peak_wildtype_sgSON_rep1.tsv.gz

source_name: HeLa cells

value: HeLa

tag: treatment


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A3_ad002


title: WT-2L-Rep2

description:
The tgs12-4 allele without any mutation in tgs1 or moi ORFs has the most similar genetic background as the Cas9-generate tgs2 and behaves as a wild type allele.
Larvae GeneFPKM.txt


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A3_ad001


title: CTML_rep1

source_name: Control Male Liver 1

value: Male


title: WT-2L-Rep1

description:
The tgs12-4 allele without any mutation in tgs1 or moi ORFs has the most similar genetic background as the Cas9-generate tgs1 and behaves as a wild type allele.
Larvae GeneFPKM.txt


title: WDFB_rep2

source_name: Withdrawal Female Brain 2

value: Withdrawal

value: Brain


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A2_ad008


title: tgs1hypo-testes-Rep2

description:
moi cDNA can't rescue tgs1hypo as mutant
Testes GeneFPKM.txt

source_name: Adult testes

value: Testes

value: Adult


title: HeLa cells, Mut (sg-SON) input rep 2

description:
RNA-seq
m6a_peak_mutFTO_sgSON_rep2.tsv.gz

value: mutant FTO

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTOH201A D233A-GB1 and sg-SON for overall 48 hours.


title: HeLa cells, WT (sg-Control) input rep 2

description:
RNA-seq
m6a_peak_wildtype_sgControl_rep2.tsv.gz

value: WT

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTO-GB1 and sg-Control for overall 48 hours.


title: HeLa cells, WT (sg-Control) m6a rep1

description:
m6A-seq
m6a_peak_wildtype_sgControl_rep1.tsv.gz

value: m6A antibody (Synaptic Systems, 202 003)


title: HeLa cells, WT (sg-SON) input rep 2

description:
RNA-seq
m6a_peak_wildtype_sgSON_rep2.tsv.gz

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTO-GB1 and sg-SON for overall 48 hours.


title: HeLa cells, Mut (sg-SON) input rep1

description:
RNA-seq
m6a_peak_mutFTO_sgSON_rep1.tsv.gz


title: WDFB_rep1

source_name: Withdrawal Female Brain 1

value: short fin, 'AB' strain


title: WDMB_rep3

source_name: Withdrawal Male Brain 3


title: WT-testes-Rep2

description:
tgs1 cDNA can rescue tgs1hypo as wt
Testes GeneFPKM.txt


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A2_ad012

source_name: C57BL/6J Male P56 Mouse Brain

value: CA

value: male


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A2_ad010


title: WDMB_rep2

source_name: Withdrawal Male Brain 2


title: CTML_rep2

source_name: Control Male Liver 2

value: Control


title: WT-testes-Rep1


title: WDMB_rep1

source_name: Withdrawal Male Brain 1


title: HeLa cells, WT (sg-Control) input rep1

description:
RNA-seq
m6a_peak_wildtype_sgControl_rep1.tsv.gz


title: HeLa cells, WT (sg-SON) input rep1

description:
RNA-seq
m6a_peak_wildtype_sgSON_rep1.tsv.gz


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A2_ad002


title: B5079P3

city: East Lansing

middle: Rodrigo

last: Salcedo-Tacuma

state: Mi

address: 567 Wilson road

department: Physiology

institute: Michigan State University

description:
B5079P3
MatrixCountPostPartumD13.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, then mapped to bosTau7  whole genome using HISAT v2.1.0
After genome mapping, HTseq v.0.6.1 was used to count the number of reads to perform differential expression analysis
edgeR v3.4.2 was used to detect differentially expressed genes in pairwise comparisons
Genome_build: bosTau7
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: Adipose Tissue

extract_protocol:
Subcutaneous AT (SCAT) samples were obtained from the right flank at 11 days before expected calving date and 6 days and 13 days after parturition, using the surgical procedure. Five grams of SCAT were collected, snap-frozen in liquid nitrogen, and stored at -80° C for RNA extraction. Total RNA was extracted from frozen samples using Trizol and the Quick RNA MiniPrep kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adipose tissue

tag: time point

tag: state

value: PostPartum


title: HeLa cells, WT (sg-Control) 3 hours rep 2

description:
RNA lifetime profiling
lifetime_wildtype_sgControl_rep2.tsv.gz
lifetime_wildtype_sgControl_merged.tsv.gz

value: HeLa

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTO-GB1 and sg-Control for overall 48 hours. And actinomycin D was added to 5 ug/mL at 3 hours before cell scraping collection.


title: ALFB_rep2

source_name: Alcohol exposed Female Brain 2

value: Alcohol exposed

value: Female

value: Brain


title: HeLa cells, WT (sg-Control) 0 hour rep 2

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTO-GB1 and sg-Control for overall 48 hours. And actinomycin D was added to 5 ug/mL at 0 hour before cell scraping collection.


title: B5079P2

description:
B5079P2
MatrixCountPostPartumD6.txt


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A12_ad012


title: ALFB_rep1

source_name: Alcohol exposed Female Brain 1


title: B5090P3

description:
B5090P3
MatrixCountPostPartumD13.txt


title: HeLa cells, Mut (sg-SON) m6a rep1

description:
m6A-seq
m6a_peak_mutFTO_sgSON_rep1.tsv.gz

value: mutant FTO

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTOH201A D233A-GB1 and sg-SON for overall 48 hours.


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A12_ad010


title: tgs1hypo-testes-Rep1

value: Testes

value: Adult


title: ALMB_rep2

source_name: Alcohol exposed Male Brain 2

value: Male


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A12_ad002


title: B5090P2

description:
B5090P2
MatrixCountPostPartumD6.txt


title: HeLa cells, WT (sg-Control) 6 hours rep 2

value: WT

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTO-GB1 and sg-Control for overall 48 hours. And actinomycin D was added to 5 ug/mL at 6 hours before cell scraping collection.


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A2_ad006

value: CA

value: male


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A12_ad001


title: CTFB_rep3

source_name: Control Female Brain 3

value: short fin, 'AB' strain

value: Control


title: B5090P1

description:
B5090P1
MatrixCountPrepartum.txt

value: Adipose tissue

value: PrePartum


title: HeLa cells, WT (sg-Control) 0 hour rep1

description:
RNA lifetime profiling
lifetime_wildtype_sgControl_rep1.tsv.gz
lifetime_wildtype_sgControl_merged.tsv.gz

value: HeLa


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A12_ad008


title: ALMB_rep1

source_name: Alcohol exposed Male Brain 1

value: Alcohol exposed


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A12_ad007


title: B5165P3

description:
B5165P3
MatrixCountPostPartumD13.txt

value: PostPartum


title: CTFB_rep2

source_name: Control Female Brain 2

value: Female

value: Brain


title: HeLa cells, WT (sg-Control) 6 hours rep1

source_name: HeLa cells


title: HeLa cells, WT (sg-SON) 0 hour rep 2

description:
RNA lifetime profiling
lifetime_wildtype_sgSON_rep2.tsv.gz
lifetime_wildtype_sgSON_merged.tsv.gz

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTO-GB1 and sg-SON for overall 48 hours. And actinomycin D was added to 5 ug/mL at 0 hour before cell scraping collection.


title: B5165P2

description:
B5165P2
MatrixCountPostPartumD6.txt


title: B5176P1

description:
B5176P1
MatrixCountPrepartum.txt


title: CTFB_rep1

source_name: Control Female Brain 1


title: HeLa cells, WT (sg-SON) 6 hours rep 2

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTO-GB1 and sg-SON for overall 48 hours. And actinomycin D was added to 5 ug/mL at 6 hours before cell scraping collection.


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A12_ad006


title: HeLa cells, WT (sg-Control) 3 hours rep1

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTO-GB1 and sg-Control for overall 48 hours. And actinomycin D was added to 5 ug/mL at 3 hours before cell scraping collection.


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A12_ad004


title: CTMB_rep2

source_name: Control Male Brain 2

value: Male


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A11_ad012


title: B5169P3

description:
B5169P3
MatrixCountPostPartumD13.txt


title: Tapasin library sorted for rescue of surface HLA-A2 expression in tapasin-KO cells (Replicate 2)

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

description: total RNA

data_processing:
Data was analyzed using python scripts in the Enrich package: http://depts.washington.edu/sfields/software/enrich/
Fuser command (Fragment A): python3 Paired_read_fuser.py --path naiveA/ --paired_mismatch_threshold 250 --read1 naiveA_R1.fastq --read2 naiveA_R2.fastq --wtseq GTTGAAGACGCTAGTGGTAAAGGGCTGGCTAAACGGCCAGGCGCACTTCTGTTGCGGCAAGGTCCGGGAGAACCACCTCCACGACCCGACTTGGACCCTGAATTGTACCTCTCTGTACACGACCCAGCTGGAGCACTCCAAGCTGCTTTCCGACGGTACCCAAGAGGTGCTCCAGCACCGCATTGC --read1_overlap_start 21 --read1_overlap_end 207 --read2_overlap_start 42 --read2_overlap_end 228 --mode B
Fuser command (Fragment B): python3 Paired_read_fuser.py --path naiveB/ --paired_mismatch_threshold 250 --read1 naiveB_R1.fastq --read2 naiveB_R2.fastq --wtseq GCACCGCATTGCGAGATGAGTCGGTTCGTTCCTTTGCCTGCGAGTGCAAAGTGGGCATCAGGTCTGACACCAGCACAAAACTGTCCACGAGCGCTTGATGGAGCGTGGCTGATGGTTTCCATAAGCTCTCCGGTGCTTTCACTGTCATCACTGCTCAGGCCACAACCTGAACCCCAACAAGAA --read1_overlap_start 19 --read1_overlap_end 202 --read2_overlap_start 46 --read2_overlap_end 229 --mode B
Fuser command (Fragment C): python3 Paired_read_fuser.py --path naiveC/ --paired_mismatch_threshold 250 --read1 naiveC_R1.fastq --read2 naiveC_R2.fastq --wtseq ACGGTAGTCCTTACGGTCCTTACGCATACACCAGCACCCAGGGTGCGATTGGGACAAGACGCACTCCTCGACCTTAGCTTTGCGTACATGCCACCAACCTCAGAGGCGGCTTCCTCTCTTGCACCAGGACCACCACCGTTCGGCCTTGAATGGAGACGACAGCACTTGGGGAAGGGC --read1_overlap_start 20 --read1_overlap_end 197 --read2_overlap_start 53 --read2_overlap_end 230 --mode B
Fuser command (Fragment D): python3 Paired_read_fuser.py --path naiveD/ --paired_mismatch_threshold 250 --read1 naiveD_R1.fastq --read2 naiveD_R2.fastq --wtseq GCTTTTGCTGCGTGGGATGATGACGAACCATGGGGACCATGGACTGGAAACGGGACTTTCTGGCTGCCAACAGTACAGCCCTTTCAAGAAGGAACGTATCTGGCCACCATCCATTTGCCTTATCTGCAAGGCCAGGTCACACTTGAACTCGCTGTCTATAAACCGCCTAAGGTGAGTCTCATGCCCGCAACTTTGGCTAGGGCAGCA --read1_overlap_start 19 --read1_overlap_end 226 --read2_overlap_start 23 --read2_overlap_end 230 --mode B
Fuser command (Fragment E): python3 Paired_read_fuser.py --path naiveE/ --paired_mismatch_threshold 250 --read1 naiveE_R1.fastq --read2 naiveE_R2.fastq --wtseq ttgctctgtttggtatcccatttctaccccagtggtggccttgaagtggaatgggaacttagaggaggaccaggtggtcgatctcagaaagctgaagggcagcgatggctctccgctctcaggcaccactcagacggatctgta --read1_overlap_start 18 --read1_overlap_end 162 --read2_overlap_start 87 --read2_overlap_end 231 --mode B
Fuser command (Fragment F): python3 Paired_read_fuser.py --path naiveF/ --paired_mismatch_threshold 250 --read1 naiveF_R1.fastq --read2 naiveF_R2.fastq --wtseq GGGCAGCGATGGCTCTCCGCTCTCAGGCACCACTCAGACGGATCTGTATCACTGTCAGGGCATTTGCAGCCACCGCCAGTTACCACCGAGCAGCATGGAGCTCGGTATGCGTGTCGCATTCACCACCCTAGCCTTCCGGCG --read1_overlap_start 21 --read1_overlap_end 162 --read2_overlap_start 88 --read2_overlap_end 229 --mode B
Aligner command (Fragment A): python3 Fused_read_aligner.py --path naiveA/ --infile naiveA_R1.fast_B_qc1 --referenceDNA GTTGAAGACGCTAGTGGTAAAGGGCTGGCTAAACGGCCAGGCGCACTTCTGTTGCGGCAAGGTCCGGGAGAACCACCTCCACGACCCGACTTGGACCCTGAATTGTACCTCTCTGTACACGACCCAGCTGGAGCACTCCAAGCTGCTTTCCGACGGTACCCAAGAGGTGCTCCAGCACCGCATTGC --referenceAA VEDASGKGLAKRPGALLLRQGPGEPPPRPDLDPELYLSVHDPAGALQAAFRRYPRGAPAPHC --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment A): python3 Fused_read_aligner.py --path naiveB/ --infile naiveB_R1.fast_B_qc1 --referenceDNA GCACCGCATTGCGAGATGAGTCGGTTCGTTCCTTTGCCTGCGAGTGCAAAGTGGGCATCAGGTCTGACACCAGCACAAAACTGTCCACGAGCGCTTGATGGAGCGTGGCTGATGGTTTCCATAAGCTCTCCGGTGCTTTCACTGTCATCACTGCTCAGGCCACAACCTGAACCCCAACAAGAA --referenceAA APHCEMSRFVPLPASAKWASGLTPAQNCPRALDGAWLMVSISSPVLSLSSLLRPQPEPQQE --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment A): python3 Fused_read_aligner.py --path naiveC/ --infile naiveC_R1.fast_B_qc1 --referenceDNA ACGGTAGTCCTTACGGTCCTTACGCATACACCAGCACCCAGGGTGCGATTGGGACAAGACGCACTCCTCGACCTTAGCTTTGCGTACATGCCACCAACCTCAGAGGCGGCTTCCTCTCTTGCACCAGGACCACCACCGTTCGGCCTTGAATGGAGACGACAGCACTTGGGGAAGGGC --referenceAA TVVLTVLTHTPAPRVRLGQDALLDLSFAYMPPTSEAASSLAPGPPPFGLEWRRQHLGKG --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment A): python3 Fused_read_aligner.py --path naiveD/ --infile naiveD_R1.fast_B_qc1 --referenceDNA GCTTTTGCTGCGTGGGATGATGACGAACCATGGGGACCATGGACTGGAAACGGGACTTTCTGGCTGCCAACAGTACAGCCCTTTCAAGAAGGAACGTATCTGGCCACCATCCATTTGCCTTATCTGCAAGGCCAGGTCACACTTGAACTCGCTGTCTATAAACCGCCTAAGGTGAGTCTCATGCCCGCAACTTTGGCTAGGGCAGCA --referenceAA AFAAWDDDEPWGPWTGNGTFWLPTVQPFQEGTYLATIHLPYLQGQVTLELAVYKPPKVSLMPATLARAA --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment A): python3 Fused_read_aligner.py --path naiveE/ --infile naiveE_R1.fast_B_qc1 --referenceDNA ttgctctgtttggtatcccatttctaccccagtggtggccttgaagtggaatgggaacttagaggaggaccaggtggtcgatctcagaaagctgaagggcagcgatggctctccgctctcaggcaccactcagacggatctgta --referenceAA LLCLVSHFYPSGGLEVEWELRGGPGGRSQKAEGQRWLSALRHHSDGSV --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment A): python3 Fused_read_aligner.py --path naiveF/ --infile naiveF_R1.fast_B_qc1 --referenceDNA GGGCAGCGATGGCTCTCCGCTCTCAGGCACCACTCAGACGGATCTGTATCACTGTCAGGGCATTTGCAGCCACCGCCAGTTACCACCGAGCAGCATGGAGCTCGGTATGCGTGTCGCATTCACCACCCTAGCCTTCCGGCG --referenceAA GQRWLSALRHHSDGSVSLSGHLQPPPVTTEQHGARYACRIHHPSLPA --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
MapCounts command: python mapCounts.py --path directory/ --infile sample_R1.fast_B_qc1_PRO_qc2
MapRatios command Example: python mapRatios.py --path directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts command: python mapParts.py --path directory/ --infile mapratios_sorted_library --mode mutations:1
Unlink script:  python mapUnlink.py --path directory/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size number_of_residues_in_fragment
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the frequency of each mutation in the naïve plasmid library.

source_name: Synthetic coding sequences

extract_protocol:
Total RNA was extracted from FACS sorted cells using a GeneJet kit (Thermo Scientific), and cDNA was synthesized using high fidelity Accuscript (Agilent) primed from a gene-specific primer.  The tapasin cDNA was PCR amplified as four overlapping fragments for full coverage by Illumina sequencing.  In a first round of PCR, primer overhangs added sequences for annealing to the Illumina sequencing primers. In a second round of PCR, primer overhangs added unique barcodes and Illumina adaptors.  To determine the frequencies of mutations in the naive library, the library plasmid DNA was used as the template for PCR amplification and Illumina sequencing.
Primer pair for 1st round of PCR (Fragment A): Illumina_tapasin_5F (TCTTTCCCTACACGACGCTCTTCCGATCTGCCGTAATCGAGTGTTGGT) and Illumina_tapasin_235R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGGAACGAACCGACTCATC)
Primer pair for 1st round of PCR (Fragment B): Illumina_tapasin_183F (TCTTTCCCTACACGACGCTCTTCCGATCTGTACCCAAGAGGTGCTCCA) and Illumina_tapasin_405R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCGCCATTGTTATCAGTACGG)
Primer pair for 1st round of PCR (Fragment C): Illumina_tapasin_386F (TCTTTCCCTACACGACGCTCTTCCGATCTCCGTACTGATAACAATGGCG) and Illumina_tapasin_602R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTAGCAGCCAACAGCAAATG)
Primer pair for 1st round of PCR (Fragment D): Illumina_tapasin_630F (TCTTTCCCTACACGACGCTCTTCCGATCTAGCACAAGAGGGAGCCGTA) and Illumina_tapasin_876R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTCAGGTGGAGCTTCGCCA)
Primer pair for 1st round of PCR (Fragment E): Illumina_tapasin_858F (TCTTTCCCTACACGACGCTCTTCCGATCTGGCGAAGCTCCACCTGAA) and Illumina_tapasin_1040R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCAAATGCCCTGACAGTGA)
Primer pair for 1st round of PCR (Fragment F): Illumina_tapasin_951F (TCTTTCCCTACACGACGCTCTTCCGATCTGGTCGATCTCAGAAAGCTG) and Illumina_tapasin_1135R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTACCTCCGCTGATCTTCCT)
Primer pair for 2nd round of PCR (added I5 and I7 Illumina adaptors): MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced on a NovaSeq 6000 using a 2x250 nt paired end protocol.

treatment_protocol: Tapasin-KO Expi293F cells were transfected with a plasmid library encoding variants of synthetic tapasin. Library DNA was diluted with a large excess of carrier DNA to ensure that cells typically acquired no more than one tapasin variant, maintaining a tight genotype-to-phenotype link.  24 h post-transfection, cells with the highest surface HLA-A2 (the top 0.5% of fluorescent cells after staining with PE-conjugated anti-HLA-A2) were collected by FACS.

tag: protein

value: Tapasin

tag: sort gate

value: Top 0.5% of cells for surface HLA-A2 expression


title: CTMB_rep1

source_name: Control Male Brain 1

tag: condition


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A11_ad010

value: CA


title: HeLa cells, WT (sg-SON) 3 hours rep1

description:
RNA lifetime profiling
lifetime_wildtype_sgSON_rep1.tsv.gz
lifetime_wildtype_sgSON_merged.tsv.gz

value: WT

value: transfected with GCN4-GGS6-dCas13b, scFv-GGS6-FTO-GB1 and sg-SON for overall 48 hours. And actinomycin D was added to 5 ug/mL at 3 hours before cell scraping collection.


title: B5165P1

description:
B5165P1
MatrixCountPrepartum.txt


title: Tapasin library sorted for rescue of surface HLA-A2 expression in tapasin-KO cells (Replicate 1)

description: total RNA


title: B5169P2

description:
B5169P2
MatrixCountPostPartumD6.txt


title: HeLa cells, WT (sg-SON) 0 hour rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A11_ad002

value: male


title: Library of tapasin variants

description: plasmid DNA


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A11_ad001


title: lomA mutant_RNA m2011-3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description: lomA mutant_RNA

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11
Bowtie version 1.2 with default parameters, was used for alignment on the reference genome (L. interrogans serovar Manilae strain UP-MMC-NIID LP, from MicroScope Platform).
Genes were counted using featureCounts version 1.4.6-p35from Subreads package (parameters: -t CDS -g locus_tag -s 1)
Count data were analyzed using R version 3.5.15and the Bioconductor packageDE Seq2 version 1.20.0f. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between WT, complemented strain, and lomA. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: interrogans serovar Manilae strain UP-MMC-NIID LP, from MicroScope Platform
Supplementary_files_format_and_content: tabulated files from DESeq2

organism: Leptospira interrogans serovar Manilae

source_name: lomA mutant

growth_protocol: Exponential-phase cultures at 30°C.

extract_protocol:
Cells were collected by centrifugation and pelleted cells were resuspended in TRIzol. RNA was then purified according to the manufacturer's instructions (Invitrogen, Saint Aubin, Ile de France, France). DNA was degraded by using a Turbo DNA-free kit according to the manufacturer's instructions (Invitrogen).
From 0.5 μg of total RNA, we depleted ribosomal RNAs using the Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina. On these rRNA-depleted RNAs, the sequencing libraries were constructed using the TruSeq Stranded mRNA Sample preparation kit following the manufacturer’s instructions (Illumina). The directional libraries were controlled on Bioanalyzer DNA1000 Chips (Agilent Technologies) and concentrations measured with the Qubit® dsDNA HS Assay Kit (ThermoFisher).  Sequences of 65 bases were generated on the Illumina Hiseq 2500 sequencer.

treatment_protocol: no treatment

value: UP-MMC-NIID LP


title: HeLa cells, WT (sg-SON) 3 hours rep 2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A11_ad008

source_name: C57BL/6J Male P56 Mouse Brain


title: B5064P2

description:
B5064P2
MatrixCountPostPartumD6.txt

value: Adipose tissue


title: UC-35 FBs

city: Cleveland

first: Bo

last: Hu

state: Ohio

address: 9500 Euclid Ave

institute: Cleveland Clinic

data_processing:
demuplexing using cellranger
alignment using cellranger
filtering using cellranger
Genome_build: CRCh38
Supplementary_files_format_and_content: tsv and mtx: barcodes, features and counts

source_name: UC Colon

growth_protocol: Fibroblasts were isolated and cultured on tissue culture plates in DMEM with 10% FBS and 1% Pen/Strep. To generate induced organoids, iPSCs were differentiated to definitive endoderm (DE) by adding DE induction medium (RPMI 1640, 2 mM L-glutamine, penicillin-streptomycin and 100 ng/mL Activin A [Cell Guidance Systems]) supplemented with 0%, 0.2% and 2.0% defined FBS for 3 consecutive days. On day 4, DE was treated with hindgut induction medium (RPMI 1640, 2 mM L-glutamine, 2% dFBS, penicillin-streptomycin) supplemented with 500 ng/mL FGF4 (R&D Systems), and 2 μM CHIR99021 (StemGent). The medium was replaced daily for 4 days. To generate the organoids iHNO and iHUCO, spheroids were collected from 24-well plates pooled and plated in Matrigel (BD) with intestinal growth medium (Advanced DMEM/F-12, N2, B27, 15 mM HEPES, 2 mM L-glutamine, penicillin-streptomycin) supplemented with 100 ng/mL EGF (R&D Systems), 100 ng/mL Noggin (R&D Systems), and 500 ng/mL R-spondin 1 (R&D Systems).

extract_protocol:
For both fibroblasts and induced organoids  nuclei isolation, we used 2 ml of ice-cold EZ PREP buffer to homogenize the cell pellets with a glass dounce tissue grinder, x20 for each loose and tight pestle  and incubated on ice for 5 min, with an additional 2 ml of ice-cold EZ PREP. Next, nuclei were centrifuged at 500 × g for 5 min at 4 °C and washed with ice-cold EZ PREP and filtered through a 40μm cell strainer. After centrifugation, the nuclei were washed in 4 ml of nuclei Suspension Buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor) and filtered through a 20μm cell strainer and proceeded with the 10x genomic pipeline for sequencing.
Followed the 10X genomics pipeline

value: Colonic Fibroblasts

value: ulcerative colitis


title: B5064P1

description:
B5064P1
MatrixCountPrepartum.txt

value: PrePartum


title: UC-40 FBs


title: UC-5 FBs


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A11_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A11_ad006


title: lomA mutant_RNA m2011-1

description: lomA mutant_RNA


title: B5102P3

description:
B5102P3
MatrixCountPostPartumD13.txt

value: PostPartum


title: B5102P2

description:
B5102P2
MatrixCountPostPartumD6.txt


title: B5169P1

description:
B5169P1
MatrixCountPrepartum.txt


title: HeLa cells, WT (sg-SON) 6 hours rep1

value: HeLa


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A10_ad012


title: wild-type strain_RNA LP2

description: wild-type strain_RNA

source_name: wild-type strain


title: UC-35 iHUCO

value: iPSCs-derived Organoids


title: wild-type strain_RNA LP1

description: wild-type strain_RNA


title: wild-type strain_RNA LP3

description: wild-type strain_RNA


title: complemented strain_RNA C2-3

description: complemented strain_RNA

source_name: complemented strain


title: B5129P3

description:
B5129P3
MatrixCountPostPartumD13.txt

source_name: Adipose Tissue


title: B5102P1

description:
B5102P1
MatrixCountPrepartum.txt


title: UC-40 iHUCO


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A10_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A10_ad002


title: B5129P2

description:
B5129P2
MatrixCountPostPartumD6.txt


title: lomA mutant_RNA m2011-2

description: lomA mutant_RNA


title: UC-5 iHUCO


title: NL-34 FBs

source_name: Healthy Colon

value: healthy


title: complemented strain_RNA C2-1

description: complemented strain_RNA


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A10_ad008


title: complemented strain_RNA C2-2

description: complemented strain_RNA


title: B5129P1

description:
B5129P1
MatrixCountPrepartum.txt


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A10_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A11_ad004


title: NL-34 iHNO


title: CRL1541 FBs


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A10_ad006


title: B5054P2

description:
B5054P2
MatrixCountPostPartumD6.txt


title: orco_9

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

institute: Princeton University

data_processing:
fastq.gz files were aligned to the honey bee genome (vHAv3.1) with STAR v2.7.3a
count files were generated using the "featureCounts" function in Subread v2.0.0
Genome_build: HAv3.1
Supplementary_files_format_and_content: featureCounts output files

organism: Apis mellifera

source_name: antenna

growth_protocol: Honey bee embryos were injected with either a CRISPR RNP complex targeting the orco gene or injection buffer (control). Bees were reared in the lab and dissected within 24 hours after eclosion.

extract_protocol:
RNA  extracted via the Arcturus PicoPure™ RNA Isolation Kit (Applied Biosystems) and quality control was performed on a NanoDrop and Bioanalyzer.
Ribosomal RNA was removed with the Ribozero HMR Gold kit (Illumina). The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.
The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a NovaSeq 6000  using a NovaSeq SP reagent kit. Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).

treatment_protocol: Antennae were removed in ice-cold DPBS and stored on wet ice before long-term storage at -80C.

value: antenna

tag: development stage

value: adult

value: orco-KO


title: B4987P3

description:
B4987P3
MatrixCountPostPartumD13.txt


title: B5064P3

description:
B5064P3
MatrixCountPostPartumD13.txt


title: CRL1541 iHNO

tag: disease state


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A10_ad004


title: orco_5


title: B4987P1

description:
B4987P1
MatrixCountPrepartum.txt


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A1_ad012


title: B4987P2

description:
B4987P2
MatrixCountPostPartumD6.txt


title: Berberine_Roemerine

city: İstanbul

first: Fatma

middle: Gizem

last: Avci

address: Marmara Uni, Bioengineering  Dep., No:404  Kadıköy

department: Bioengineering

country: Turkey

institute: Marmara University

description: Processed data file: processed_data.txt

data_processing:
The raw reads were filtered. Data filtering includes removing adapter sequences, contamination and low-quality reads from raw reads.
Sequencing reads were aligned to B. subtilis 168 genome using the quantify and annotate short reads (QuasR) package in R.
Differential expression analyses were performed in R version 3.3.3 R using the package DESeq2.
Genome_build: RefSeq accession number NC_000964.3
Supplementary_files_format_and_content: processed_data.txt: Tab-delimited text file includes log2 values of differentially expressed genes.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis

growth_protocol: Cells were grown in nutrient broth at 37oC and 180 rpm.

extract_protocol:
One-hour alkaloid and DMSO treated cells were placed in RNAprotect Bacteria Reagent (Qiagen, Germany) and incubated for 5 minutes at room temperature. Cell suspensions were centrifuged at 5,000xg for 10 minutes. Total RNA isolation was achieved using RNeasy Mini Kit (Qiagen, Germany) according to manufacturer’s protocol with mechanical disruption at 6 m/s for 40 seconds (FastPrep Instrument, MP Biomedicals, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 75 mg/ L of berberine chloride hydrate and 25 mg/ L (-)-roemerine as OD600 reached 0.55±0.05. Control cells were treated with DMSO.

tag: strain/background

value: Berberine + Roemerine


title: DMSO control

description: Processed data file: processed_data.txt

value: DMSO


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A1_ad008

value: CA


title: orco_12


title: orco_3


title: NL-33 iHNO


title: B4886P2

description:
B4886P2
MatrixCountPostPartumD6.txt


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A1_ad006


title: control_7

value: buffer-injected


title: B4886P1

description:
B4886P1
MatrixCountPrepartum.txt


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A1_ad007

value: male


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A1_ad004


title: control_6


title: Hybrid30_3_CNCCs

organism:
Pan troglodytes
Homo sapiens

source_name: iPSC-derived CNCCs


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A1_ad002


title: control_5


title: Hybrid30_2_CNCCs


title: aIPgSS3_RNAseq_rep1

city: Ashburn

first: Catherine

middle: Elizabeth

last: Schretter

state: VA

address: 19700 Helix Dr

institute: HHMI - Janelia

data_processing:
The libraries were pooled and sequenced on an Illumina NextSeq 550 with 75 base pair reads for bulk RNA-seq; 26 base read 1 + 50 base read 2 for low-cell samples (8 base barcode is in positions 2-9 in read 1, 10 base UMI is in positions 10-19 in read 1).
Sequencing adapters were trimmed from the reads with Cutadapt v2.1.0 (Martin, 2011) prior to alignment with STAR v2.7.5c (Dobin et al., 2013) to the Drosophila r6.34 genome assembly on Flybase (Thurmond et al., 2019).
The resulting transcript alignments were passed to RSEM v1.3.0 (B. Li & Dewey, 2011) to generate gene expression counts.
Genome_build: Drosophila melanogaster r6.34 genome assembly on Flybase (Thurmond et al., 2019).
Supplementary_files_format_and_content: single Microsoft Excel file that includes count values for each gene

source_name: aIPg

extract_protocol:
Drosophila adults were collected daily as they eclosed, and aged 3-5 days prior to dissection. For each sample, 60-100 brains were dissected in freshly prepared, ice cold Adult Hemolymph Solution (AHS, 108 mM NaCl, 5 mM KCl, 2 mM CaCl2, 8.2 mM MgCl2, 4 mM NaHCO3, 1 mM NaH2PO4, 5 mM HEPES, 6 mM Trehalose, 10 mM Sucrose), and the major tracheal branches removed. The brains were transferred to a 1.5 ml Eppendorf tube containing 500 μl 1 mg/ml Liberase DH (Roche, prepared according to the manufacturer’s recommendation) in AHS, and digested for 1 h at room temperature. The Liberase solution was removed and the brains washed twice with 800 μl ice cold AHS. The final wash was removed completely and 400 μl of AHS+2% Fetal Bovine Serum (FBS, Sigma) were added. The brain samples were gently triturated with a series of fire-polished, FBS-coated Pasteur pipettes of descending pore sizes until the tissue was homogenized, after which the tube was allowed to stand for 2-3 min so that the larger debris could settle. For hand sorting, the cell suspension was transferred to a Sylgard-lined Glass Bottom Dish (Willco Wells), leaving the debris at the bottom of the Eppendorf tube, and distributed evenly in a rectangular area in the center of the plate with the pipet tip. The cells were allowed to settle for 10-30 min prior to picking. Fluorescent cells were picked with a mouth aspirator consisting of a 0.8 mm Nalgene Syringe Filter (Thermo), a short stretch of tubing, a plastic needle holder, and a pulled Kwik-Fil Borosilicate Glass capillary (Fisher). Cells picked off the primary plate were transferred to a Sylgard-lined 35 mm Mat Tek Glass Bottom Microwell Dishes (Mat Tek) filled with 170 μl AHS+2%FBS, allowed to settle, and then re-picked. Three washes were performed in this way before the purified cells were picked and transferred into either 3 μl Lysis Buffer (0.2% Triton X-100, 0.1 U/μL RNAsin) for the low-cell method, or 50 μl extraction buffer from the PicoPure RNA Isolation Kit (Life Technologies), then lysed for 5 min at 42˚C for the bulk RNA-seq method, and stored at -80˚C. For FACS, the samples were triturated in AHS+2%FBS that was run through a 0.2 μm filter, and the cell suspension was passed through a Falcon 5 ml round-bottom tube fitted with a 35 μm cell strainer cap (Fisher). Samples were sorted on a SONY SH800 cell sorter gated for single cells with a fluorescence intensity exceeding that of a non-fluorescent control. For bulk samples, GFP+tdTom+ events were purity sorted directly into 50 μl PicoPure extraction buffer, the sample lysed for 5 min at 42˚C, and stored at -80˚C. For low-cell samples, replicates of approximately 40 cells were sorted to enrich for GFP+tdTom+ cells into 3 μL Lysis Buffer and flash frozen on dry ice.
For bulk samples, total RNA was extracted from 400-800 pooled cells using the PicoPure kit (Life Technologies) according to the manufacturer’s recommendation, including the on-column DNAse1 step. The extracted RNA was converted to cDNA and amplified with the Ovation RNA-Seq System V2 (NuGEN), and the yield quantified by NanoDrop (Thermo). The cDNA was fragmented and the sequencing adaptors ligated onto the fragments using the Ovation Rapid Library System (NuGEN). Library quality and concentration was determined with the Kapa Illumina Library Quantification Kit (KK4854, Kapa Biosystems), and the libraries were pooled and sequenced on an Illumina NextSeq 550. For low-cell samples, 1 μl harsh lysis buffer (50 mM Tris pH 8.0, 5 mM EDTA pH 8.0, 10 mM DTT, 1% Tween-20, 1% Triton X-100, 0.1 g/L Proteinase K (Roche), 2.5 mM dNTPs (Takara), and ERCC Mix 1 (Thermo-Fisher) diluted to 1e-7) and 1 μl 10 μM barcoded RT primer were added, and the samples were incubated for 5 min at 50˚C to lyse the cells, followed by 20 min at 80˚C to inactivate the Proteinase K. Reverse transcription master mix (2 μL 5X RT Buffer (Thermo-Fisher), 2 μL 5M Betaine (Sigma-Aldrich), 0.2 μL 50 μM E5V6NEXT template-switch oligo (Integrated DNA Technologies), 0.1 μL 200 U/μL Maxima H-RT (Thermo-Fisher), 0.1 μL 40U/μL RNAsin (Lucigen), and 0.6 μL nuclease-free water (Thermo-Fisher) was added to the lysis reaction and incubated at 42˚C for 1.5 h, followed by 10 min at 75˚C to inactivate the reverse transcriptase. PCR was performed by adding 10 μL 2X HiFi PCR Mix (Kapa Biosystems) and 0.5 μL 60 μM SINGV6 primer and incubating at 98˚C for 3 min, followed by 20 cycles of 98˚C for 20 s, 64˚C for 15 s, 72˚C for 4 min, and a final extension of 5 min at 72˚C. Groups of 8 reactions were pooled to yield ~250 μL and purified with Ampure XP Beads (0.6x ratio; Beckman Coulter), washed twice with 75% Ethanol, and eluted in 40 μL nuclease-free water. The DNA concentration of each sample was determined using Qubit High-Sensitivity DNA kit (Thermo-Fisher).

tag: genetic driver

tag: driver

value: bulk RNA-seq

tag: reporter

value: nlstdTomato

value: Female

tag: cell type

value: aIPgSS3 neurons


title: aIPgSS4_RNAseq_rep3

growth_protocol: Drosophila adults were collected daily as they eclosed, and aged 3-5 days prior to dissection.

tag: Sex

value: aIPgSS4 neurons


title: aIPgSS3_RNAseq_rep2


title: pC1d_pC1de_pC1e_RNAseq_reps

source_name: pC1d, pC1d+pC1e, pC1e

value: multiple

value: low-cell RNA-seq

value: pC1d_pC1de_pC1e neurons


title: control_4


title: B4886P3

description:
B4886P3
MatrixCountPostPartumD13.txt

value: Adipose tissue

value: PostPartum


title: Hybrid30_1_CNCCs


title: 2FL_rep1 [2A]

status: Public on Oct 08 2020

city: Amherst

first: Ezgi

last: Ozcan

state: MASSACHUSETTS

address: 424 Chenoweth Lab, 102 Holdsworth Way

institute: University of Massachusetts Amherst

data_processing:
Sequence reads were automatically trimmed for adaptor sequence by Illumina. Adaptor trimmed reads were obtained from Illumina BaseSpace.
Reads from each lane were concatenated as left and right sequences. Left and right reads were then checked for low-quality reads, bacteria 16S rRNA contamination. Then mapped to the Bifidobacterium longum subsp. infantis ATCC 15697  whole genome using bowtie2 v2.3.4.3 using parameters -p 8.
Aligned reads were name sorted using Samtools (v1.4.1) and total and specific gene counts were obtained by overlapping to a specific genomic locus(i.e. locus tag) with genomic feature and annotation file (GFF) using HTSeq (v0.10.0) with parameters --stranded=reverse --nonunique=all --mode=union --order=name .
Raw gene counts were subject to DEseq2 and log2 fold changes obtained for one condition relative to other
Genome_build: Bifidobacterium longum subsp. infantis ATCC 15697
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Normalized abundance measurements from DeSeq2

organism: Bifidobacterium longum subsp. infantis

source_name: human infant feces

growth_protocol: Bifidobacterium infantis  was routinely propagated in De Man Rogosa Sharp medium supplemented with 0.05 % (m/v) L-cysteine hydrochloride at 37°C under anaerobic conditions. Cells then transferred into modified MRS medium (no carbohydrate source, no acetate, no Tween80). Carbohydrate source is replaced with either 2% w/v lactose, 0.8% of 2FL and 2 % of 2FL. The cells were grown under same conditions.

extract_protocol:
Cell pellets stored in RNAlater were centrifuged at 14,000 × g for 3 min and cell pellets were washed with 1 mL cold 1X PBS buffer. Total RNA was extracted using Ambion RNAqeous kit with slight modifications. Accordingly, cells were suspended in 600 μL lysis buffer in beadbeating tubes using a FastPrep 24 bead beader (MP Biomedicals, USA). Total RNA, then,  were subjected to DNase treatment using the Ambion Turbo DNA-free kit. The RNA was evaluated for genomic DNA contamination using qRT-PCR. ribosomal RNA is depleted via RiboMinus kit with Magnetic Bead Clean up Module using the custom Pan-Prokaryote Probe Mix to target bacterial rRNA. Purified mRNA was used asseses for quality and used for RNA-seq library preparation.
mRNA enriched library preparation was performed with the NEBNext Ultra II Directional kit following the manufacturer's instructions

treatment_protocol: lactose and 2 different concentrations of 2fucosyllactose

tag: strain

value: 2% 2fucosyllactose


title: aIPgSS4_RNAseq_rep2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A1_ad001

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age


title: aIPgSS4_RNAseq_rep1


title: Lactose_rep2 [LacB]

tag: treatment

value: lactose


title: control_3

tag: tissue

value: antenna

value: adult


title: 2FL_rep2 [2B]


title: orco_11

value: orco-KO


title: 08FL_rep2 [0.8B]

value: 0.8% 2fucosyllactose


title: Cross A F4 susceptible S242

city: Fort Collins

first: Todd

last: Gaines

state: CO

address: 1177 Campus Delivery

department: Agricultural Biology

institute: Colorado State University

data_processing:
A de novo reference transcriptome was obtained by separately assembling Illumina reads from a Cross A 2,4-D-resistant RIL (R206) and a susceptible RIL (S242) with Trinity (Li and Godzik, 2006). The assembled contigs were filtered for minimum contig length of 500 bp. The two assemblies were compared using CDHit v4.6.6 (Li and Godzik, 2006) with a 95% confidence interval to eliminate redundant contigs and retain all contigs unique to either the R or S assembly. This resulted in a 72-Mb transcriptome with 37,223 contigs.
De novo reference transcriptome was annotated using Trinotate and TAIR10
Read alignments to the de novo reference transcriptome were conducted with Bowtie2 (Langmead and Salzberg, 2012) using the default "end-to-end" mode and the "sensitive" option. The minimum allowed fragment length was set to 100 and the maximum to 800 bp.
Raw read counts were extracted using SAMtools (Li et al., 2009). Counts-per-million (CPM) and gene expression differences were calculated with the package ‘edgeR’ (Robinson et al., 2010) using the statistical software R v3.3 (Team, 2013) and an expression threshold of ≥1 CPM in at least two samples. After normalization of the read depth the data was analyzed using the ‘classic approach’. Expression differences were compared between 2,4-D resistant and susceptible RILs within Cross A and B, respectively, as well as between all 2,4-D-resistant and -susceptible RILs. Differentially expressed transcripts were then filtered for a fold-change of ≥ |2| and a false discovery rate (FDR) adjusted p-value ≤ 0.05.
Single nucleotide polymorphism (SNP) calling was performed using SAMtools (v. 1.3.1) with the default options and the "mpileup" command. The command "bcftools" was used to retain only SNPs that had a quality score higher than 10 and read depth higher than 10. An additional filtering step was for SNPs that were heterozygous or homozygous in at least three individuals of all R and all S RILs.
Genome_build: Mustard_Trans_ConCat95.fasta.gz
Supplementary_files_format_and_content: Microsoft Excel worksheet file containing CPM expression values for each sample from edgeR
Supplementary_files_format_and_content: Microsoft Excel worksheet file containing statistical analysis results from edgeR for all samples with p<0.05
Supplementary_files_format_and_content: Microsoft Excel worksheet file containing predicted annotations for de novo reference transcriptome
Supplementary_files_format_and_content: text file containing SNP variant analysis (VCF file)
Supplementary_files_format_and_content: FASTA file containing transcriptome contigs

organism: Sisymbrium orientale

source_name: Leaf tissue

growth_protocol: The lines used for RNA-Sequencing were first germinated on agar plates, transplanted to 3×3cm pots filled with potting soil (Fafard, Sun Gro Horticulture), and grown in a growth chamber at 25/20 °C, 16/8 h light/dark photoperiod. At the four-leaf stage, the youngest expanded leaf was collected.

extract_protocol:
Samples were frozen immediately in liquid nitrogen and total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen). Sample quality was assessed by RIN score (Agilent TapeStation) as well as by gel electrophoresis.
DNase treatment, library preparation, and sequencing were conducted at the Roy J. Carver Biotechnology Center at the University of Illinois. Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

tag: line

value: 2,4-D susceptible


title: Cross B F3 susceptible SP9


title: Cross A F4 susceptible S207


title: Cross B F3 susceptible SP3


title: Cross B F3 susceptible SRP1


title: Lactose_rep1 [LacA]


title: Cross B F3 resistant RP6

value: 2,4-D resistant


title: Cross B F3 resistant RP8


title: Cross A F4 susceptible S205


title: Cross B F3 susceptible SP7


title: Cross A F4 resistant R221


title: Cross A F4 resistant R206


title: HEK293T 24h post infection Rep1

city: Cambridge

first: Shira

last: Weingarten-Gabbay

state: MA

address: 75 Ames St

institute: The Broad Institute

description:
293_24hr_COVID_1
Paired-end RNA-seq of transcripts after polyA enrichment

data_processing:
Sequencing reads were mapped to SARS-CoV-2 genome (RefSeq NC_045512.2) and human transcriptome (Gencode v32). Alignment was performed using Bowtie version 1.2.2 (Langmead et al., 2009) with a maximum of two mismatches per read.
The fraction of human and viral reads was determined based on the total number of reads aligned to either SARS-CoV-2 or human transcripts.
Genome_build: SARS-CoV-2 genome (RefSeq NC_045512.2) and human transcriptome (Gencode v32)
Supplementary_files_format_and_content: An xls file containing the number of reads aligned to the human transcriptome and SARS-CoV-2 genome and the percentages of total aligned reads in each cell line at each time point. Three biological replicates were done for HEK293T cells and the number of reads and percentages is indicated for each replicate

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: HEK293T 24h post infection

growth_protocol: A549 and HEK293T cells were seeded into 6-well plates at a density of 5 x 10^5 cells per well (one well per condition). After 11-24 hr, the cells were infected with SARS-CoV-2 at an  MOI of 3.

extract_protocol:
At 12, 18 and 24hr post-infection, the cells were lysed in Trizol (Thermo, 15596026) ,and the total RNA was isolated using standard phenol chloroform extraction.
Standard Illumina TruSeq Stranded mRNA (LT) was performed using 500 ng of total RNA (illumina, FC-122-2101). Oligo-dT beads were used to capture polyA-tailed RNA, followed by fragmentation and priming of the captured RNA (8 minutes at 94ºC). Immediately first strand cDNA synthesis was performed. Second strand cDNA synthesis was performed using second strand marking master and DNA polymerase 1 and RNase H. cDNA was adenylated at the 3’ ends followed immediately by RNA end ligation single-index adapters (AR001-AR012). Library amplification was performed for 12-15 cycles under standard illumina library PCR conditions. Library quantitation was performed using Agilent 2200 TapeStation D1000 ScreenTape (Agilent, 5067-5582). RNA sequencing was performed on the NextSeq 550 System using a NextSeq V2.5 High Output 75 cycle kit (illumina, 20024906) or 150 cycles kit (illumina, 20024907) for paired-end sequencing (70nt of each end).
PolyA enrichment followed by Illumina TrueSeq adaptor ligation

tag: cell line

value: human embryonic kidny cells

value: infected with SARS-CoV-2 at an MOI of 3

tag: timepoint

value: 24h post infection


title: Cross A F4 resistant R202


title: HEK293T 24h post infection Rep3

description:
293_24hr_COVID_3
Paired-end RNA-seq of transcripts after polyA enrichment


title: 08FL_rep1 [0.8A]


title: HEK293T 18h post infection Rep1

description:
293_18hr_COVID_1
Paired-end RNA-seq of transcripts after polyA enrichment

source_name: HEK293T 18h post infection

value: 18h post infection


title: HEK293T 12h post infection Rep3

description:
293_12hr_COVID_3
Paired-end RNA-seq of transcripts after polyA enrichment

source_name: HEK293T 12h post infection

value: 12h post infection


title: A549 24h post infection

description:
A549_24hr_COVID
Paired-end RNA-seq of transcripts after polyA enrichment

source_name: A549 24h post infection

value: lung carcinoma cells


title: HEK293T 18h post infection Rep2

description:
293_18hr_COVID_2
Paired-end RNA-seq of transcripts after polyA enrichment


title: HEK293T 12h post infection Rep2

description:
293_12hr_COVID_2
Paired-end RNA-seq of transcripts after polyA enrichment


title: A549 12h post infection

description:
A549_12hr_COVID
Paired-end RNA-seq of transcripts after polyA enrichment

source_name: A549 12h post infection


title: A549 18h post infection

description:
A549_18hr_COVID
Paired-end RNA-seq of transcripts after polyA enrichment

source_name: A549 18h post infection


title: tof1_60min_HU_rep1_input

city: Brighton

first: Andrea

last: Keszthelyi

address: University of Sussex, Sussex House, Falmer

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

data_processing:
ChIP-seq: Sequences were aligned to a reference genome (R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database) using Bowtie 2 generating a SAM output file for each sample (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Reads from MySeq were trimmed 25 bp from 3’ and 1 bp from the 5’ end, while reads from NextSeq were not trimmed.
ChIP-seq: SAM files were then converted into sorted BAM files by using SAMtools (http://samtools.sourceforge.net/):
ChIP-seq: Duplicates were then removed using picard (https://broadinstitute.github.io/picard)
ChIP-seq: BAM files were used for Model-based Analysis of ChIP-Seq (MACS2). We used the ‘call peak’ function which also generates genome wide score data. These were used to generate fold enrichment tracks.
ChIP-seq: The data then was sorted into 50 bp bins, normalized to have a mean value of 1, and used for meta data analysis using custom-made R programs
Sync-seq analysis was done by using LocalMapper shell script and Repliscope R package from https://github.com/DNAReplicationLab/ (Dzmitry G Batrakou1, Carolin A Müller1, Rosemary H C Wilson1 and Conrad A Nieduszynski, DNA copy number measurement of genome replication dynamics by high-throughput sequencing – the sort-seq, sync-seq and MFA-seq family – accepted to Nature protocols)
Genome_build: R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database
Supplementary_files_format_and_content: ChIP-seq .wig files were generated by custom R script. Scores represent RPA1 enrichment.
Supplementary_files_format_and_content: Sync-seq .wig files were generated by custom R script. Scores represent ratio between non-replicated and replicated samples.

source_name: Saccharomyces cerevisiae

extract_protocol:
Cells were lysed using of 0.5 mm zirconia/silica beads and the FastPrep-24 (MP Biomedicals). . Samples were sonicated using the Focused-Ultrasonicator (Covaris) (Average incident power – 7.5 Watts, Peak Incident Power – 75 Watts, Duty Factor – 10 %, Cycles/Burst – 200, Duration – 20 min for G1 samples and 13.5 for HU and released samples) before ChIP-seq.
Following ChIP with RPA1 antibody (1:10000, Agrisera, AS07214) samples were de-cross-linked by overnight incubation on 65°C with 5 M NaCl and proteinase K (Invitrogen), then RNAse treated. The resulting ssDNA was used to synthetize second strand with random primers (8N, 3 mg/ml stock) by T4  polymerase (NEB). The resulting dsDNA was used to create libraries using the Ultra II library kit (NEB) as per the manufacturer’s instructions with 13 cycles at the amplification step.

treatment_protocol: Cells were grown in YP +2% raffinose to mid-log phase at 25 °C, before being arrested with 10 µg/ml alpha factor peptide. After 1hr 45 min 2% galactose and an additional 5 µg/ml alpha factor was added. After 2hr, when cells were >90% unbudded, 25 µg/ml doxycycline was added. 15 minutes after doxycycline addition temperature was switched to 37°C  and incubated for 1hr. Cells were then released by washing 3 times with pre-heated YP 2% raffinose 2% galactose with 25 µg/ml doxycycline and resuspended in the same media supplemented with 200 mM HU. Time 0 was taken as the time from the first wash. Samples were then incubated for 1 hr at 37°C before being fixed by resuspending in YP + 1% formaldehyde (Sigma) for 45 min at 25 °C. 125 mM glycine was then added followed by a 5 min incubation at 25 °C. Cells were washed with PBS before being pelleted and snap-frozen in liquid nitrogen.

tag: genotype

value: JB1991 + TOF1::hphMX

tag: chip antibody

value: none (input)


title: wt_60min_HU_rep1_input

value: MATa, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3


title: tof1_762_60min_HU_rep1_RPA

value: JB1991 + TOF1::tof1-codon-optimised-762-1238_delta (NATNT2)

value: RPA1 antibody (1:10000, Agrisera, AS07214)


title: tof1_60min_HU_rep1_RPA


title: tof1_762_60min_HU_rep1_input


title: wt_60min_HU_rep1_RPA


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H8_ad012

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

source_name: C57BL/6J Male P56 Mouse Brain

value: DG

value: male


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H9_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H8_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H9_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H9_ad008


title: HEK293T 24h post infection Rep2

description:
293_24hr_COVID_2
Paired-end RNA-seq of transcripts after polyA enrichment


title: HEK293T 18h post infection Rep3

description:
293_18hr_COVID_3
Paired-end RNA-seq of transcripts after polyA enrichment


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H9_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H9_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H8_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H8_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H8_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H7_ad001


title: HEK293T 12h post infection Rep1

description:
293_12hr_COVID_1
Paired-end RNA-seq of transcripts after polyA enrichment


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H7_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H7_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H7_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H7_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H9_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H8_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H7_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H6_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H6_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H6_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H6_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H6_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H6_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H6_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H5_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H5_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H5_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H5_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H4_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H4_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H4_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H7_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H4_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H3_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H3_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H2_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H3_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H4_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H2_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H2_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H2_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H2_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H12_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H12_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H12_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H12_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H12_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H12_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H11_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H11_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H5_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H11_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H11_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H11_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H10_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H10_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H10_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H10_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H1_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H10_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H11_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H10_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H10_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H1_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G9_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H11_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G9_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G9_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H1_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G9_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H11_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G9_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G9_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G8_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G8_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G8_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H10_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G7_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G7_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G7_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G7_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G8_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H1_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_H1_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G6_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G7_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G6_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G6_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G9_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G6_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G7_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G6_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G5_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G6_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G5_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G5_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G4_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G5_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G5_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G5_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G4_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G8_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G5_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G4_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G4_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G4_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G4_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G4_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G3_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G2_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G3_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G2_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G2_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G2_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G2_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G12_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G12_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G2_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G2_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G12_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G12_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G11_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G11_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G11_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G11_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G11_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G11_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G12_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G11_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G10_ad012


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G10_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G10_ad004


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G10_ad002


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G1_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G1_ad010


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G1_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G10_ad007


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G10_ad008


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G3_ad001


title: CEMBA190219_9J_3_CEMBA190219_9J_4_G10_ad006


title: CEMBA190219_9J_3_CEMBA190219_9J_4_F9_ad006


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