title: PDX29_AA_SJBALL020579_Input_ChIP-seq

city: CHICAGO

first: Yu

last: Luan

state: Illinois

address: 303 E. Superior Simpson Querrey 7-518

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
ChIP-seq reads mad ATAC-seq were aliged to female_hg19 genome using Bowtie2, the peaks were called using MACS2.
RNA-seq reads were aligned to female_hg19_genome assembly using STAR
HiC reads were aligned to zv10 genome assembly using BWA
The TPM value of gene expression was caculated using RSEM
ChIP-seq and ATAC-seq peaks were called using MACS2 with the following  setting: ChIP-seq q-value <10e-2, p-value<10e-5, Change>1,FC>2. ATAC-seq: q-value<10e-2 and p-value<10e-5
HiC matrix was generated using  paritools
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The cool file were the matrix of Hi-C for each Sample.
Genome_build: female_hg19

source_name: Tissue

growth_protocol: ALL patient cells were intravenously injected into 8- to 10-week-old female NSG-SGM362 mice that were sublethally irradiated (250 RAD) 6–24 h before transplantation.  Human leukaemia engraftment was monitored in peripheral blood by performing serial retro-orbital bleeds monthly after injections. Peripheral blood samples were analysed by flow cytometry for human CD45+ cells and when CD45+ cells were >5%, mice were euthanized, and blood, bone marrow, and spleen samples were used to sort human leukemia cells, which were fixed with FA for following Hi-C or ChIP-seq experiments.

extract_protocol:
10 M cells are fixed with 1% FA for 15 mins in room temperature, then stoped with Glycine.  Chromatin was extracted with cell lysis buffer (1% SDS, 50 mM Tris-HCl pH 8, 20 mM EDTA). 100 ug chromatin was sonicated to 100-300 bp by Covaris E220, and 5 ug chromatin was used as input. Bead-antibody complex was prepared by incubating 11 ul of sheep anti-mouse IgG dynabeads (ThermoFisher, 11201D) with anti-GATA3 (Santa Cruz, sc268)  at 4°C for 4 hours with shaking. Then fragmented chromatin was incubated with bead-antibody complex overnight with shaking followed by stringent wash and elution.
To prepare the library, eluted chromatin was reverse crosslinked and purified by phenol-chloroform extraction. Then DNA was end-repaired by END-IT DNA end-repair kit (Epicentre, ER81050) according to kit’s protocol, added A using Klenow  fragment (3’->5’ exo-) (NEB, M0212S), ligated with Illumina TruSeq adaptor (Illumina, FC-121-3001) and subsequently amplified by PCR (Roche, kk2601). The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit (Agilent). The libraries were sequenced on Illumina HiSeq platform.

value: patient-derived xenografts

tag: chip-seq antibody

value: Input


title: PDX40_AC_SJBALL021102_Input_ChIP-seq

status: Public on Sep 13 2021

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue


title: PDX34_CC_SJBALL205_Input_ChIP-seq


title: PDX23_AA_SJBALL020589_Input_ChIP-seq


title: PDX19_A-C_SJBALL020625_Input_ChIP-seq


title: male liver 20week control rep1

type: RNA

city: Lausanne

first: Federica

last: Gilardi

address: chemin de la Vulliette 4

department: University Center of Legal Medicine

country: Switzerland

institute: University of Lausanne

description: gene expression data

hyb_protocol: Affymetrix Mouse Gene 1.0 ST arrays were hybridized with 2.5μg of biotinylated target, at  45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package

data_processing: Affymerix Expression Console 1.1.2637.26569, RMA normalization

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse LIVER

label_protocol: For each sample, 100ng of total RNA were amplified using the WT Expression kit (Invitrogen, Carlsbad, USA; catalogue no. 4411974); the resulting sense cDNA was fragmented using UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labelled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labelling kit (Affymetrix, Santa Clara, USA; catalogue no. 900671, Santa Clara, USA).

growth_protocol: mice were housed in standard 12h Light/12h dark light regimen

extract_protocol: Trizol extraction of total RNA, followed by purification with MagMax (Applied Biosystems) .

treatment_protocol: at the indicated developmental stage mice were decapitated and liver was collected for RNA extraction

tag: strain

value: Mixed C57BL6/SV129

tag: developmental stage

value: 20 WEEKS

value: liver

tag: genotype

value: control

tag: Sex

value: male


title: N6_nonoverexpressed_GATA3_Input_ChIP-seq_rep1

source_name: Cell

growth_protocol: Cells are cultured with RPMI-1640 medium (CORNING) with 15% Fetal Bovine Serum in 37 degree cell culture incubator

value: NALM-6 Adult B acute lymphoblastic leukemia


title: female liver 20week control rep3

description: gene expression data

value: female


title: male liver 20week PpargΔ/Δ rep2

description: gene expression data

value: Pparg delta/delta


title: N6_GATA3_overexpressed_Input_ChIP-seq_rep1


title: PDX31_CC_SJPHALL008_Input_ChIP-seq


title: PDX34_CC_SJBALL205_HiC

extract_protocol:
Hi-C in GM12878 cells and PDX samples were performed using the Arima-HiC kit as per the manufacturer’s instructions. Briefly, 1 million GM12878 WT,  A/A cells and PDX sample  were fixed with 1% formaldehyde, digested with restriction enzyme, end-labeled with Biotin-14-dATP, and then followed by ligation.  The ligated chromatin was reverse-crosslinked and sonicated by Covaris E220 to produce 300–500 bp fragments . Biotin labeled DNA fragments were isolated using dynabeads Streptavidin  C1 beads.
To prepare the library, eluted DNA was processed by end repair, adenylation, adaptor ligation, PCR amplification with KAPA DNA library prepare kit. The libraries were sequenced on Illumina HiSeq platform.


title: PDX17_A-C_SJBALL020980_Input_ChIP-seq


title: PDX29_AA_SJBALL020579_HiC


title: engineered_AA_Input_ChIP-seq_rep1

value: Cell line-engineered GM12878 cell


title: PDX17_A-C_SJBALL020980_HiC


title: PDX40_AC_SJBALL021102_HiC


title: PDX23_AA_SJBALL020589_HiC


title: PDX31_CC_SJPHALL008_HiC


title: PDX19_A-C_SJBALL020625_HiC


title: GM12878_CC_Input_ChIP-seq_rep1

value: Cell line-GM12878


title: PDX40_AC_SJBALL021102_GATA3_ChIP-seq

value: GATA3 antibody(Santa Cruz, sc268)


title: PDX34_CC_SJBALL205_GATA3_ChIP-seq


title: PDX31_CC_SJPHALL008_GATA3_ChIP-seq


title: male liver 20week control rep3

description: gene expression data


title: PDX17_A-C_SJBALL020980_GATA3_ChIP-seq


title: PDX23_AA_SJBALL020589_GATA3_ChIP-seq


title: PDX29_AA_SJBALL020579_GATA3_ChIP-seq


title: male liver 20week control rep2

description: gene expression data


title: PDX19_A-C_SJBALL020625_ATAC-seq

extract_protocol:
A total of 30,000-50,000 live cells were collected, washed once in PBS and resuspended in 50 ul ATAC-seq lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) followed by immediate centrifugation for 10 min at 4 °C. Cell pellets were then resuspended in 50 ul reaction solution which contained 1XTD buffer and 2.5 ul Tn5 transpose (Illumina, FC-121-1030) and incubated at 37 °C for 60 mins.
The fragmented DNA was purified by MinElute kit (Qiagen) and amplified by PCR. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent). Pair-end 2x50/2x100/2x150 bp high-throughput sequencing was performed using HiSeq platform (Illumina)


title: PDX19_A-C_SJBALL020625_GATA3_ChIP-seq


title: PDX23_AA_SJBALL020589_ATAC-seq


title: PDX17_A-C_SJBALL020980_ATAC-seq


title: PDX40_AC_SJBALL021102_ATAC-seq


title: PDX29_AA_SJBALL020579_ATAC-seq


title: PDX31_CC_SJPHALL008_ATAC-seq


title: GM12878_CC_HiC_rep1


title: UOCB1_ATAC-seq_rep2

value: UoC-B1 Childhood B acute lymphoblastic leukemia


title: GM12878_CC_HiC_rep2


title: PDX34_CC_SJBALL205_ATAC-seq


title: engineered_AA_HiC_rep1


title: UOCB1_ATAC-seq_rep1


title: brain_TS-seq_rep1

city: Ipswich

first: Madalee

last: Wulf

state: MA

address: 240 County Road

institute: New England Biolabs

library_source: transcriptomic

data_processing:
For 16 RNA analysis: reads were sorted and counted based on the identity of the two nucleotides preceding the sequence 'AGAACTTCGTCGAGTACGCTCAA', providing a list of 16 different possible sequences. Custom script used.
Basecalls performed using Illumina RTA software (v2.4.11 and v3.4.4) and fastq files were generated from the BCL files using Picard’s basecallstofastq
Cutadapt was used to remove (i) the preceding G’s of template switching libraries (4 Gs for capped libraries and 3 G’s for uncapped libraries) from their 5’ end, (ii) the adapter sequences, (iii) the low quality bases (q<20), and (iv) the poly(A) tails from the 3’ end of all the raw Illumina sequencing reads. This step also removed reads that became too short (<15 nt) after trimming.
miRXplore analysis: trimmed reads were mapped to the miRXplore reference sequences using bbmap (https://jgi.doe.gov/data-and-tools/bbtools/). Mapped reads were randomly downsampled using BBTools (https://sourceforge.net/projects/bbmap/) so that every sample included 1 million mapped reads. Transcript counts were obtained using idxstats from samtools. Considering the 962 miRNAs in miRXplore were present in equimolar amounts, an expected read count was generated by dividing the total number of mapped reads for each library by 962. Reads were then normalized by dividing the raw read counts by the expected read counts.
For human total RNA libraries, the trimmed reads were first mapped to the reference sequences of the Mix4v7 control and human ribosomal RNA and their associated spacer sequences using Bowtie2; only unmapped reads were kept for downstream analysis.
microRNA analysis: miRDeep2 was used to identify and quantify known miRNAs from the processed good quality non-control-non-rRNA reads based on the human reference genome (GRCh38) and the known human mature miRNAs and their precursor sequences downloaded from the miRBase database (miRBase release 22). Two filtering criteria were applied to call high-confident mature miRNAs from the mirDeep2 results: (i) randfold P-value <0.05 and (ii) miRDeep2 score >=0. For each identified miRNA species, the mean count of the reads that map to multiple genomic locations were calculated and used as the expression level for that miRNA
For transcriptome profiling, processed good quality non-control-non-rRNA reads were mapped to the human reference genome sequence (GRCh38) and the gene annotation on the primary assembly downloaded from GENCODE (release 36) using the STAR aligner. Gene count matrices were then generated from the STAR alignment results by the htseq-count function of the HTseq tool.
Genome_build: human: GRCh38
Supplementary_files_format_and_content: tab-delimited text files (output of transcriptome analysis): gene id, gene type, gene name and read counts.
Supplementary_files_format_and_content: miRDeep2 output csv file: miRDeep2 output which contains the number of identified novel and known miRDeep2 with different scores and the lists of novel and known miRNAs predicted by miRDeep2.
Supplementary_files_format_and_content: miRDeep2 output of expressed known miRNAs csv file: contains known miRNA names,  read counts and their associated precursors.

source_name: brain

extract_protocol: CapTS-seq samples were chemically capped, polyadenylated, reverse transcribed with template switching, and PCR amplified to introduce sequencing indeces. SMARTer samples followed the manufacturer's protocol.

value: brain

tag: vendor

tag: treatment

value: Uncapped CapTS-seq workflow

tag: rna type

value: total RNA


title: brain_SMARTer2_rep1

value: SMARter smRNA seq workflow


title: SEM_ATAC-seq_rep2

value: Childhood B acute lymphoblastic leukemia with t(v-11q23) KMT2A rearranged


title: engineered_AA_HiC_rep2


title: brain_TS-seq_rep2


title: brain_SMARTer2_rep2


title: SUPB15_ATAC-seq_rep2

value: SUP-B15 Childhood B acute lymphoblastic leukemia


title: MUTZ5_ATAC-seq_rep2

value: Menschliche Und Tierische Zellkulture-5 B acute lymphoblastic leukemia


title: SUPB15_ATAC-seq_rep1


title: brain_CapTS-seq2_rep1

value: CapTS-seq workflow


title: brain_CapTS-seq2_rep2


title: FFPE liver_NEBNext_A

source_name: liver

value: liver

value: Biochain #R2234149

value: NEBNext Ultra II RNA workflow


title: FFPE liver_NEBNext_B


title: MHHCAL4_ATAC-seq_rep2

value: MHH-CALL-4 Childhood B acute lymphoblastic leukemia


title: FFPE liver_SMARTer_B


title: MHHCAL4_ATAC-seq_rep1


title: MUTZ5_ATAC-seq_rep1


title: 697_ATAC-seq_rep1

value: B acute lymphoblastic leukemia cells with t(1-19)(q23-p13.3) E2A-PBX1 (TCF3-PBX1)


title: MHHCAL4_ATAC-seq_rep3


title: 697_ATAC-seq_rep2


title: FFPE liver_CapTS-seq_B


title: FFPE liver_CapTS-seq_A


title: SEM_ATAC-seq_rep1


title: FFPE liver_SMARTer_A


title: brain_SMARTer_B


title: brain_CapTS-seq_B


title: GM12878_CC_ATAC-seq_rep1

description: GM12878_AA_ATAC-seq.pooled.filter.narrowPeak


title: engineered_AA_ATAC-seq_rep2

description: engineered_AA_ATAC-seq.pooled.filter.narrowPeak

value: Cell line-engineered GM12878 cell


title: GM12878_CC_ATAC-seq_rep2

value: Cell line-GM12878


title: brain_SMARTer_A


title: N6_GATA3_nonoverexpressed_ATAC-seq_rep2

value: NALM-6 Adult B acute lymphoblastic leukemia


title: brain_CapTS-seq_A


title: PTEN_VAMP-seq_Exp5 (Multidimensional PTEN missense variant analysis)

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University

description:
PTEN_VAMP-seq_Exp5
Targeted barcode amplification from DNA

data_processing:
Libraries were sequenced on NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis software.
Ssequencing reads were converted to fastq format and de-multiplexed with bcl2fastq. FASTQ files from technical replicate amplification and sequencing runs were concatenated for analysis with Enrich2.
The count for each variant in a bin was divided by the sum of counts recorded in that bin to obtain the frequency of each variant within that bin. This calculation was repeated for every bin in each replicate experiment. The summed counts of each variant in all four bins of an experiment was divided by the summed counts of all variants in all four bins of an experiment to obtain the total frequency value for each variant for each experiment. This total frequency value was used for filtering low-frequency variants out of the subsequent calculations. Next, a weighted average (w_ave) was calculated for each variant, with all weighted average values ranged from a value of 0.25 to 1. Finally, for each experiment, an abundance score for each variant was obtained by subjecting the weighted average of each variant to min-max normalization, using the weighted average value of WT, which was given a score of 1, and the median weighted average value for non-terminal nonsense variants at positions 51 through 349 for PTEN, which was given an abundance score of 0. The final abundance score for each variant was calculated by taking the mean of the min-max normalized abundance scores across the eight replicate experiments in which it could have been observed. Only variants which were scored in two or more replicate experiments were retained in the analysis. A standard error for each abundance score was calculated by dividing the standard deviation of the min-max normalized values for each variant by the square root of the number of replicate experiments in which it was observed. Lastly, the lower bound of the 95% confidence interval was calculated by multiplying the standard error with the 97.5 percentile value of a normal distribution and subtracting this product from the abundance score. The upper bound of the 95% confidence interval was calculated by instead adding the product with the abundance score.
Supplementary_files_format_and_content: The PTEN_barcodeInsertAssignments.tsv.gz and TPMT_barcodeInsertAssignments.tsv.gz processed data files are in gzip-compressed tab-separated text file format, containing the variant-barcode maps determined by subassembly.

source_name: Human-derived cultured cell line

growth_protocol: HEK 293T TetBxb1BFP cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 2 μg/mL doxycycline.

extract_protocol:
Cells were transferred into a microfuge tube, pelleted and stored at -20˚C. Genomic DNA was prepared using the Dneasy kit (Qiagen).
Eight 50 μL first-round PCR reactions were each prepared with a final concentration of ~50 ng/μL input genomic DNA, 1x Kapa HiFi ReadyMix, and 0.25 μM of the KAM499/JJS_501a primers. The reaction conditions were 95 °C for 5 minutes, 98 °C for 20 seconds, 60 °C for 15 seconds, 72 °C for 90 seconds, repeat 7 times, 72 °C for 2 minutes, 4 °C hold. Eight 50 μL reactions were combined, bound to AMPure XP (Beckman Coulter), cleaned, and eluted with 40 μL water. 40% of the eluted volume was mixed with 2x Kapa Robust ReadyMix; JJS_seq_F and one of the indexed reverse primers, JJS_seq_R1a through JJS_seq_R12a were added at 0.25 μM each. Reaction conditions for the second round PCR were 95 °C for 3 minutes, 95 °C for 15 seconds, 60 °C for 15 seconds, 72 °C for 30 seconds, repeat 14 times, 72 °C for 1 minutes, 4 °C hold.  Amplicons were extracted after separation on a 1.5% TBE/agarose gel using a Quantum Prep Freeze ‘N Squeeze DNA Gel Extraction Kit (Bio-Rad).

treatment_protocol: Cells harboring variant libraries, prepared as described above, were sorted using a FACSAria III into bins according to the abundance of their expressed, EGFP tagged variant. First, live, single, recombinant cells were selected using forward and side scatter, mCherry and mTagBFP2 signals. Then, a FITC:PE-Texas Red ratiometric parameter in the BD FACSDIVA software was created. A histogram of the FITC:PE-Texas Red ratio was created and gates dividing the library into four equally populated bins based on the ratio were established.

tag: cell type

value: HEK 293T TetBxb1BFP


title: N6_GATA3_nonoverexpressed_ATAC-seq_rep1


title: PTEN_VAMP-seq_Exp7 (Multidimensional PTEN missense variant analysis)

description:
PTEN_VAMP-seq_Exp7
Targeted barcode amplification from DNA


title: N6_wild_type_ATAC-seq_rep1


title: PTEN_VAMP-seq_Exp4 (Multidimensional PTEN missense variant analysis)

description:
PTEN_VAMP-seq_Exp4
Targeted barcode amplification from DNA


title: PTEN_VAMP-seq_Exp1 (Multidimensional PTEN missense variant analysis)

description:
PTEN_VAMP-seq_Exp1
Targeted barcode amplification from DNA
PTEN_fillin_vampseq_combined.csv


title: PTEN_VAMP-seq_Exp6 (Multidimensional PTEN missense variant analysis)

description:
PTEN_VAMP-seq_Exp6
Targeted barcode amplification from DNA


title: Jurkat-iTAX + Doxycycline replicate 2

city: Liège

first: Jean-Claude

last: Twizere

state: Liège

address: CHU - B34 Quartier Hôpital Avenue de l'Hôpital,11

department: Molecular Biology of Diseases

country: Belgium

institute: GIGA Institute

description: Jurkat cell line after infection with lentivirus conditionally expressing TAX and puromicyn, Blasticidin selection for 12 days.

data_processing:
1. Illumina bcl2fastq v2.17 was used to generate fastq files with adapters trimmed
2. Trimming to 73bp per read with cutadapt
3.Removal of reads mapping to rRNA, tRNA, chrM with bowtie2
4. Mapping to hg19 reference genome using STAR quant mode
Additional Star option --alignEndsType EndToEnd used for rMATS compatibility
5. Genes filtered with Salmon v0.9.1.
6. Splicing analysis with rMATS v3.2.1.54.
Genome_build: hg19
Supplementary_files_format_and_content: *_ReadsPerGene.out.tab.txt = tab-delimited text files with gene raw counts from Star
Supplementary_files_format_and_content: *.MATS.JunctionCountsOnly.csv = csv files with splicing analysis results from rMATS

source_name: Jurkat T cell line

growth_protocol: RPMI with 10%FBS, 5%CO2, 37C°, split 1/10 every 3 days

extract_protocol:
Nucleospin RNA isolation kit- Macherey Nagel. Following manufacturer instructions.
Truseq stranded mRNA Sample Preparation Kits. Libraries were prepared following manufacturer instructions
Libraries were multipexed altogether and sequenced in two runs on Illumina NextSeq sequencers (2x 76bp)

treatment_protocol: 1ug/ml doxycycline for 48h in full growth media

tag: cell line

value: Jurkat T cell line

tag: viral protein expression

value: TAX

value: Doxycycline-treated


title: engineered_AA_ATAC-seq_rep1


title: N6_GATA3_overexpressed_ATAC-seq_rep3


title: Jurkat-iHBZ + Doxycycline replicate 2

description: Jurkat cell line after infection with lentivirus conditionally expressing HBZ and puromicyn, Blasticidin selection for 12 days.

value: HBZ


title: PTEN_VAMP-seq_Exp3 (Multidimensional PTEN missense variant analysis)

description:
PTEN_VAMP-seq_Exp3
Targeted barcode amplification from DNA


title: N6_GATA3_overexpressed_ATAC-seq_rep2


title: engineered_AA_H3K27ac_ChIP-seq

extract_protocol:
2 M cells are fixed with 1% FA for 15 mins in room temperature, then stoped with Glycine.  Chromatin was extracted with cell lysis buffer (1% SDS, 50 mM Tris-HCl pH 8, 20 mM EDTA). 100 ug chromatin was sonicated to 100-300 bp by Covaris E220, and 5 ug chromatin was used as input. 100 ug chromatin was sonicated to 100-300 bp by Covaris E220, and 5 ug chromatin was used as input. Bead-antibody complex was prepared by incubating 11 ul of sheep anti-mouse IgG dynabeads (ThermoFisher, 11201D) or sheep anti-rabbit IgG dynabeads (ThermoFisher, 11203D) with 3ug of anti-H3K4me1 (Abcam, ab8895), at 4°C for 4 hours with shaking. Then fragmented chromatin was incubated with bead-antibody complex overnight with shaking followed by stringent wash and elution.
To prepare the library, eluted chromatin was reverse crosslinked and purified by phenol-chloroform extraction. Then DNA was end-repaired by END-IT DNA end-repair kit (Epicentre, ER81050) according to kit’s protocol, added A using Klenow  fragment (3’->5’ exo-) (NEB, M0212S), ligated with Illumina TruSeq adaptor (Illumina, FC-121-3001) and subsequently amplified by PCR (Roche, kk2601). The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit (Agilent). The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp.

value: H3K27ac(Active motif, 39133)


title: PTEN_VAMP-seq_Exp2 (Multidimensional PTEN missense variant analysis)

description:
PTEN_VAMP-seq_Exp2
Targeted barcode amplification from DNA


title: Jurkat-iTAX untreated replicate 3

value: Untreated


title: GM12878_CC_GATA3_ChIP-seq_rep2

description: GM12878_CC_GATA3_ChIP-seq_pooled.narrowPeak

value: GATA3 antibody(Santa Cruz, sc268)


title: N6_GATA3_nonoverexpressed_GATA3_ChIP-seq_rep1

value: Cell line


title: Jurkat-iTAX untreated replicate 1


title: GM12878_AA_H3K27ac_ChIP-seq


title: Jurkat-iHBZ untreated replicate 3


title: engineered_AA_H3K4me1_ChIP-seq

value: H3K4me1(Abcam, ab8895)


title: N6_GATA3_overexpressed_GATA3_ChIP-seq_rep1

value: Cell line-Normal 6


title: GM12878_AA_H3K4me1_ChIP-seq


title: N6_GATA3_overexpressed_ATAC-seq_rep1


title: N6_wild_type_ATAC-seq_rep2


title: Jurkat-iHBZ untreated replicate 1


title: engineered_AA_RNA-seq_rep2

molecule: polyA RNA

extract_protocol:
Total RNAs were extracted from 5 million cells using Trizol (Invitrogen).
The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit (Agilent) according to the manufacturer’s protocol. Briefly, polyA RNA was purified from 1000 ng of total RNA using oligo (dT) beads (Invitrogen). Extracted RNA was first fragmented, then followed by reverse transcription, end repair, adenylation, adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems) and then followed by pair-end 2X 50 bp high-throughput sequencing using HiSeq platform (Illumina).


title: engineered_AA_GATA3_ChIP-seq_rep2

description: engineered_AA_GATA3_ChIP-seq_pooled.narrowPeak


title: M2_Control_GD6_Jan21

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
The raw data were subjected to QC analyses using the FastQC tool.  The reads were then mapped to mouse genome (mm10) using the spliced reader aligner TopHat version 2.0.13.  Transcriptome assembly was performed using cufflinks v.2.2.1 with default parameters.  The transcripts were merged into two distinct, non-overlapping sets using cuffmerge, followed by cuffdiff to call the differentially regulated transcripts.  The significantly (p <0.05) regulated genes from conditional knockout mice were compared to control wild-type at the indicated time points.
Genome_build: mm10
Supplementary_files_format_and_content: gene_exp.diff

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control and conditional knockout mice on a C57BL6 background were used in this study. Timed pregnant mice were collected on gestation days 4, 5, and 6, with day of plug considered gestational day 1. Each library was generated from an equal pool of RNA from 3 mice.

value: Control

tag: time point

value: gestational days 6

tag: replicate


title: M2_Control_GD6_Dec20


title: engineered_AA_GATA3_ChIP-seq_rep1


title: Drosophila HB10 cells_14°C_Rep2

city: Zurich

first: Christian

middle: F.

last: Lehner

address: Winterthurerstrasse 190

department: DMLS

institute: University of Zurich

description: Gene expression after 24 hours at 14°C

hyb_protocol: The hybridization mix (55 µl) contained 1.65 µg of fragmented cRNA, 2.2 µl of 25x hybridization buffer, 11 µl of 10x blocking agent and RNase-free water. For hybridization, we used single-color gene-expression microarrays purchased from Agilent.

scan_protocol: After microarray hybridization and washing, signal intensities were recorded with Agilent Feature Extraction Software

data_processing: Raw data was processed using R limma package. Signal intensities were background-corrected with normexp convolution method and quantile-normalized.

organism: Drosophila melanogaster

source_name: Drosophila HB10 cells_14°C_24 hours

label_protocol: For generation of Cyanine 3 (Cy3)-labelled complementary RNA (cRNA) probes, we used the Low-Input QuickAmp kit (Agilent, Santa Clara, CA, USA). The resulting cRNA was purified using the Absolute RNA Nanoprep kit (Agilent).

growth_protocol: HB10 cells were cultured in Schneider’s medium (Gibco, cat# 21720, Thermo Fisher Scientific, Waltham, MA), supplemented with 10% fetal bovine serum (Gibco, cat# 10500-064) and 1% Penicillin-Streptomycin (Gibco, cat# 15140).

extract_protocol: Total RNA was isolated using TRIzol reagent (ThermoFisher Scientific, cat number  15596026) as described (Chomczynski and Sachi, 1987. Anal Biochem. 162:156-9)

treatment_protocol: Aliquots of 2.6 x106 cells were seed into 35 mm culture dishes. After 36 hours of incubation at 24°C, half of the aliquots were shifted to 14°C, while the other half was maintained at 24°C. Total RNA was isolated 24 hours later. Three biological replicates were processed.

value: HB10 cells

value: 24 hours at 14°C


title: Drosophila HB10 cells_14°C_Rep3

description: Gene expression after 24 hours at 14°C


title: engineered_AA_RNA-seq_rep1

value: Cell line-engineered GM12878 cell


title: GM12878_CC_RNA-seq_rep1

value: Cell line-GM12878


title: GM12878_CC_RNA-seq_rep2


title: M2_Control_GD6_Sep20


title: Drosophila HB10 cells_24°C_Rep1

description: Gene expression after 24 hours at 24°C

source_name: Drosophila HB10 cells_24°C_24 hours

value: 24 hours at 24°C


title: GM12878_CC_GATA3_ChIP-seq_rep1


title: Drosophila HB10 cells_24°C_Rep2

description: Gene expression after 24 hours at 24°C


title: M2_Control_GD5_Sep20

value: gestational days 5


title: Drosophila S2R+ cells_72h_Rep2

description: Gene expression after 72 hours at 14°C

source_name: Drosophila S2R+ cells_72h at 14°C

growth_protocol: S2R+ cells were cultured in Schneider’s medium (Gibco, cat# 21720, Thermo Fisher Scientific, Waltham, MA), supplemented with 10% fetal bovine serum (Gibco, cat# 10500-064) and 1% Penicillin-Streptomycin (Gibco, cat# 15140).

treatment_protocol: Aliquots of 1.4x106 cells were plated in 2.5 ml of medium in 60 mm culture dishes. After 36 hours of incubation at 25°C, culture aliquots were shifted to 14°C. Total RNA was isolated at different times after the downshift (0, 4, 12, 24 and 72 hours). In addition, instead of shifting to 14°C, control aliquots were grown for an additional 12 hours at 25°C before isolation of total RNA.

value: S2R+ cells

value: 72 hours at 14°C


title: Drosophila HB10 cells_24°C_Rep3

description: Gene expression after 24 hours at 24°C


title: Drosophila S2R+ cells_72h_Rep1

description: Gene expression after 72 hours at 14°C


title: M2_Control_GD4_Sep20

value: gestational days 4


title: Drosophila S2R+ cells_24h_Rep3

description: Gene expression after 24 hours at 14°C

source_name: Drosophila S2R+ cells_24h at 14°C


title: Drosophila S2R+ cells_24h_Rep4

description: Gene expression after 24 hours at 14°C


title: Drosophila HB10 cells_14°C_Rep1

description: Gene expression after 24 hours at 14°C


title: M2_cKO_GD4_Sep20

value: cKO


title: M2_cKO_GD5_Sep20


title: Drosophila S2R+ cells_72h_Rep4

description: Gene expression after 72 hours at 14°C


title: M2_cKO_GD4_Dec20


title: M1_Control_GD6_Sep20


title: M2_cKO_GD5_Dec20


title: M1_Control_GD6_Dec20


title: M2_cKO_GD6_Sep20


title: M2_cKO_GD4_Jan21


title: Drosophila S2R+ cells_24h_Rep5

description: Gene expression after 24 hours at 14°C


title: Drosophila S2R+ cells_24h_Rep1

description: Gene expression after 24 hours at 14°C


title: M1_Control_GD4_Jan21


title: Drosophila S2R+ cells_12h_Rep1

description: Gene expression after 12 hours at 14°C

source_name: Drosophila S2R+ cells_12h at 14°C

value: 12 hours at 14°C


title: Drosophila S2R+ cells_12h_Rep3

description: Gene expression after 12 hours at 14°C


title: Drosophila S2R+ cells_72h_Rep3

description: Gene expression after 72 hours at 14°C


title: M1_cKO_GD5_Sep20


title: M1_Control_GD4_Sep20


title: M1_cKO_GD5_Dec20


title: Drosophila S2R+ cells_24h_Rep2

description: Gene expression after 24 hours at 14°C


title: SY-H4-THIO 5uM-72h-2

city: Durham

first: Gao

last: Zhang

state: NC

address: 203 Research Dr | MSRB1, Rm 179

department: The Preston Robert Tisch Brain Tumor Center

institute: Duke University School of Medicine

data_processing:
Quality control using fastqc version 0.11.5
Sequenced reads were trimmed for adaptor sequence using Trim Galore version 0.6.5
Mapped to GRCh38 human genome using STAR2.7.6a
Count how many reads map to each gene using htseq-count version 0.12.4
Genome_build: GRCh38
Supplementary_files_format_and_content: Count file for each sample

source_name: SY-H4-THIO 5uM-72h

growth_protocol: M059K or H4 cells are cultured with DMEM and 10% Fetal Bovine Serum

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: M059K or H4 cells are treated with 5uM 6-thio-dG or DMSO for 72h

value: Patient-derived glioma cell line

value: 5uM 6-thio-dG for 72h


title: M1_Control_GD4_Dec20


title: M1_cKO_GD6_Sep20


title: Drosophila S2R+ cells_4h_Rep4

description: Gene expression after 4 hours at 14°C

source_name: Drosophila S2R+ cells_4h at 14°C

value: 4 hours at 14°C


title: Drosophila S2R+ cells_12h_25C_Rep2

description: Gene expression after 12 hours at 25°C

source_name: Drosophila S2R+ cells_12h at 25°C

value: 12 hours at 25°C


title: M1_cKO_GD4_Sep20


title: M1_Control_GD5_Sep20

value: Control


title: Drosophila S2R+ cells_12h_Rep2

description: Gene expression after 12 hours at 14°C


title: Drosophila S2R+ cells_4h_Rep5

description: Gene expression after 4 hours at 14°C


title: Drosophila S2R+ cells_4h_Rep2

description: Gene expression after 4 hours at 14°C


title: SY-H4-THIO 5uM-72h-1


title: Drosophila S2R+ cells_12h_25C_Rep3

description: Gene expression after 12 hours at 25°C


title: Drosophila S2R+ cells_12h_25C_Rep1

description: Gene expression after 12 hours at 25°C


title: M1_cKO_GD5_Jan21


title: Drosophila S2R+ cells_0h_Rep3

description: Gene expression after 0 hours at 14°C

source_name: Drosophila S2R+ cells_0h at 14°C

value: 0 hours at 14°C


title: Drosophila S2R+ cells_4h_Rep1

description: Gene expression after 4 hours at 14°C


title: Drosophila S2R+ cells_4h_Rep3

description: Gene expression after 4 hours at 14°C


title: SY-H4-Ctrl-72h-1

value: DMSO for 72h


title: SY-H4-Ctrl-72h-2


title: SY-M059K-Ctrl-72h-2


title: SY-M059K-THIO 5uM-72h-2

source_name: SY-M059K-THIO 5uM-72h


title: SY-M059K-THIO 5uM-72h-1


title: MEF_2HG(+)_3

city: Minato-ku, Tokyo

first: XUN

last: LIU

address: Shirokanedai 4-6-1

country: Japan

institute: The University of Tokyo

description: Sample 12

data_processing:
The sequencing reads were aligned to AmpliSeq_Mouse_Transcriptome_V1_Reference using Torrent Mapping Alignment Program (TMAP).
QC metrics and normalized read counts per gene were obtained using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Genome_build: AmpliSeq_Mouse_Transcriptome_V1_Reference
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each Sample.

source_name: MEF cells

growth_protocol: MEF cells were isolated from embryos of C57BL/6 mice at embryonic day 13.5 (ED13.5) and immortalized spontaneously by serial passages. MEF cells were grown (routinely passaged once every 5 days) in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific), and antibiotic/antimycotic solution (Sigma). All animal experiments were approved by the Ethics Committee for Animal Experimentation and conducted in accordance with the Guidelines for the Care and Use of Laboratory Animals of the Institute of Medical Science and Department of Medicine, the University of Tokyo.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen).
RNA libraries were prepared using 100 ng of total RNA with an Ion AmpliSeq Transcriptome Mouse Gene Expression kit (Thermo Fisher Scientific).

treatment_protocol: MEF cells were treated with 300 μM of 2-HG (Cayman) or DMSO (Wako) for 24 h.

value: Mouse embryonic fibroblast

value: treated with 300 μM of 2-HG for 24 h


title: MEF_2HG(+)_2

description: Sample 11


title: Drosophila S2R+ cells_0h_Rep2

description: Gene expression after 0 hours at 14°C


title: SY-M059K-Ctrl-72h-1


title: Drosophila S2R+ cells_0h_Rep1

description: Gene expression after 0 hours at 14°C


title: MEF_2MUT_3

description:
Sample 6
MEF cells expressing mutant IDH2

value: untreated


title: MEF_2HG(-)_3

description: Sample 9

value: treated with DMSO for 24h


title: MEF_2HG(-)_2

description: Sample 8


title: Jurkat-iTAX + Doxycycline replicate 3

value: Jurkat T cell line

value: TAX

value: Doxycycline-treated


title: MEF_2HG(+)_1

description: Sample 10


title: Jurkat-iTAX untreated replicate 2

value: Untreated


title: Jurkat-iTAX + Doxycycline replicate 1


title: Jurkat-iHBZ untreated replicate 2

value: HBZ


title: MEF_2HG(-)_1

description: Sample 7


title: Jurkat-iHBZ + Doxycycline replicate 1


title: MEF_control_2

description:
Sample 2
MEF cells expressing mock vector


title: shDRP1_RNAseq4

city: Baton Rouge

first: John

middle: P

last: Kirwan

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, 3.5.2(2018-12-2), Rstudio V1.2.1511 and biomaRt V2.38.0
DESeq2  V1.22.2 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: GRCm38.84 mm10
Supplementary_files_format_and_content: tab-delimited text containing raw counts and DESeq2 normalized counts

source_name: C2C12 cell lysate

extract_protocol:
Qiagen Rneasy kit
Quant-Seq  3' mRNA-Seq Library Prep Kit
indexed and pooled samples, 50bp forward read

value: early stage myotubes

tag: passages


title: shDRP1_RNAseq5


title: shDRP1_RNAseq3


title: MEF_control_3

description:
Sample 3
MEF cells expressing mock vector


title: MEF_2MUT_1

description:
Sample 4
MEF cells expressing mutant IDH2


title: MEF_control_1

description:
Sample 1
MEF cells expressing mock vector


title: shDRP1_RNAseq2


title: shDRP1_RNAseq1


title: 16RNA_rGrGrG_uncap_B

molecule: other

organism: synthetic construct

source_name: synthetic

value: synthetic construct

value: Template switching workflow

value: synthetic RNA


title: 16RNA_rGrGrG_uncap_A


title: 16RNA_rGrGrG_Gppp_C


title: shRandom5_RNAseq


title: 16RNA_rGrGrG_Gppp_D


title: Jurkat-iHBZ + Doxycycline replicate 3


title: shRandom4_RNAseq


title: MEF_2MUT_2

description:
Sample 5
MEF cells expressing mutant IDH2


title: 16RNA_rGrGrG_Gppp_A


title: shRandom3_RNAseq


title: shRandom2_RNAseq


title: AM6_8-5_S14

city: Manchester

first: Agrin

last: Moeini

address: Alderley Park

country: United Kingdom

institute: Cancer Research UK Manchester Institute

data_processing:
Basecalling was performed using Illumina bcl2fastq2 Conversion Software v2.16
Single-end sequencing reads were first trimmed using bbduk to remove the first 12 bases. Regions of length 20 or above with average quality of less than 10 were trimmed from the end of each read. Finally, trailing polyG and polyA were removed from the reads using cut adapt.
Trimmed reads were aligned to reference genome mm10 and assigned to features in the mm10 gene annotation using the STAR program.
The Feature Counts were preprocessed (minimum CPM of 0.5 in at least 3 samples) and normalized using the ‘voom’ model within the limma package of Bioconductor to produce log2 counts per million (CPM) reads
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: SZ14_log2CPM_matrix.txt
Supplementary_files_format_and_content: SZ14_raw_count_matrix.txt

source_name: Tumour

growth_protocol: Tumour cell in this study were grown in vitro under strandard conditions (RPMI 10%FBS, at 37C, 5%CO2)

extract_protocol:
RNA was preaperd from bulk tumors isolated on day 4 using Direct-ZOL kit (Zymo research) #R071 following manufacturer's instructions
Libraries were prepared with 500ng of total RNA using Lexogen QuantSeq 3′-mRNAseq Library Prep Kit (FWD, Cat. No. 015)

treatment_protocol: At day7 post-injection of tumour cells, mice were randomised to receive vehicle (60:40 ratio of DMSO-PEG400:dH2O, bidaily 200µl/dose),  prostaglandin E2 receptor EP2/4 antagonists at 3mg/mL (EPAT, bidaily 200µl/dose, 30mpk), anti-PD-1 (200µg/dose every 2-3 days) or anti-PD-1 plus EPAT for 2 and 5 days.

value: Braf-mutated melanoma tumor

tag: time-point

value: anti-PD-1 plus EPAT


title: 16RNA_SMARTer_B

value: SMARter smRNA seq workflow


title: shRandom1_RNAseq


title: 16RNA_CapTS-seq_B

value: CapTS-seq workflow


title: 16RNA_CapTS-seq_A


title: 16RNA_SMARTer_A


title: shRandom6_RNAseq


title: miRXplore_SMARTer_B

description: miRexplore_counts.csv (Uncap)

value: Miltenyi Biotec #130-093-521


title: AM6_8-4_S9


title: AM6_8-3_S38


title: 16RNA_rGrGrG_Gppp_B


title: AM6_8-2_S33


title: miRXplore_CapTS-seq_uncapped_B

data_processing:
Basecalls performed using Illumina RTA software (v2.4.11 and v3.4.4) and fastq files were generated from the BCL files using Picard’s basecallstofastq
Cutadapt was used to remove (i) the preceding G’s of template switching libraries (4 Gs for capped libraries and 3 G’s for uncapped libraries) from their 5’ end, (ii) the adapter sequences, (iii) the low quality bases (q<20), and (iv) the poly(A) tails from the 3’ end of all the raw Illumina sequencing reads. This step also removed reads that became too short (<15 nt) after trimming.
miRXplore analysis: trimmed reads were mapped to the miRXplore reference sequences using bbmap (https://jgi.doe.gov/data-and-tools/bbtools/). Mapped reads were randomly downsampled using BBTools (https://sourceforge.net/projects/bbmap/) so that every sample included 1 million mapped reads. Transcript counts were obtained using idxstats from samtools. Considering the 962 miRNAs in miRXplore were present in equimolar amounts, an expected read count was generated by dividing the total number of mapped reads for each library by 962. Reads were then normalized by dividing the raw read counts by the expected read counts.
Genome_build: human: GRCh38
Supplementary_files_format_and_content: miRexplore_counts2.csv

extract_protocol: CapTS-seq samples were chemically capped, polyadenylated, reverse transcribed with template switching, and PCR amplified to introduce sequencing indexes. SMARTer samples followed the manufacturer's protocol.

value: CapTS-seq workflow without capping


title: AM6_7-3_S34


title: miRXplore_CapTS-seq_uncapped_C


title: AM6_8-1_S7


title: AM6_7-2_S3


title: miRXplore_CapTS-seq_capped_C


title: miRXplore_CapTS-seq_capped_A


title: AM6_7-4_S20


title: 16RNA_rGrUrG_uncap_A


title: 16RNA_rGrUrG_uncap_C


title: Drosophila S2R+ cells - 29°C_ATAC-seq_Rep2

data_processing:
Sequencing adaptors were trimmed with Trimmomatic (version 0.38) (Bolger et al. 2014). All reads were mapped to Drosophila genome dm6 using Bowtie2 (Langmead et al. 2019) with the parameters -X 2000 --very-sensitive. Non-mapped, non-unique, and mitochondrial reads were filtered out with SAMtools (Li et al. 2009; Li 2011). PCR duplicates were marked and removed with Picard (https://broadinstitute.github.io/picard/).
All reads were adjusted for the binding footprint of Tn5 transposase, i.e., all reads aligning to the top strand were shifted by four bp and all reads aligning to bottom strand were shifted five bp in 5’ direction.
Peaks were called with MACS2 (Zhang et al. 2008) for each library with parameters -f BEDPE --keep-dup all -q 0.01 -g dm --nomodel. Differential peaks were analyzed with DiffBind (Stark, R., Brown, G. 2011). Read counts were obtained with the dba.count function. To keep the peaks at a consistent width, peaks were re-centered around the point of greatest enrichment with “summits = 250”
Genome_build: Drosophila melanogaster genome assembly Dmel_Release_6 (Hoskins et al. 2015. Genome Res 25(3):445-58)
Supplementary_files_format_and_content: raw and normalized counts for every peak in all samples

source_name: Drosophila S2R+ cells - 29°C

extract_protocol:
Cell harvest was performed quickly using 0.025% Trypsin-EDTA (ThermoFisher Scientific, 25200-056) within the incubators and at the temperatures used during the preceding 24 hour incubation, with solutions pre-equilibrated to the different incubation temperatures. The culture medium was removed and cells were rinsed once with PBS before addition of 1 mL Trypsin-EDTA solution for 5 minutes. The released cells were transferred into a 15 mL Falcon tube and combined with four rinses of the plates (each with 1 mL of complete medium). The resulting master cell suspension was diluted into ice-cold complete medium in order to obtain an Eppendorf tube with 75000 cells in 1 mL for each aliquot. Cells were sedimented (500×g for 5 min, 4°C) and washed once with 50 µL PBS. Cells were resuspended and lysed with 50 µL of cold lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). Lysed cells were sedimented (500×g for 10 min, 4°C). Tagmentation was performed during 30 minutes at 25°C in a 50 µL reaction in TD Buffer (Illumina, FC-121-1030) containing 2.5 µL Tn5 Transposes (Illumina, FC-121-1030) (Buenrostro et al. 2013).
Tagmented DNA was purified using a Qiagen MinElute Kit and amplified as described (Buenrostro et al. 2013) using a Nextera forward primer (Ad1_noMX) in combination with a replicate-specific bar-coded reverse Netera index primer (Ad2.1 to Ad2.9). Libraries were purified using Qiagen PCR Cleanup Kit.

treatment_protocol: Aliquots of S2R+ cells were plated (3.5 millions in 60 mm culture dishes) and incubated for 36 hours at 25°C. Thereafter, culture aliquots were shifted to either 14, 25 or 29°C. Cells were harvested 24 hours after the temperature shift.

value: S2R+ cells


title: miRXplore_CapTS-seq_uncapped_A


title: Drosophila S2R+ cells - 29°C_ATAC-seq_Rep3


title: 16RNA_rGrUrG_Gppp_C


title: AM6_7-1_S30


title: 16RNA_rGrUrG_Gppp_B


title: miRXplore_SMARTer_A

description: miRexplore_counts.csv (Uncap)


title: 16RNA_rGrUrG_uncap_D


title: 16RNA_rGrUrG_uncap_B


title: AM6_7-5_S35


title: AM6_6-3_S12

value: EPAT


title: Drosophila S2R+ cells - 25°C_ATAC-seq_Rep2

source_name: Drosophila S2R+ cells - 25°C


title: 16RNA_rGrGrG_uncap_C


title: Drosophila S2R+ cells - 29°C_ATAC-seq_Rep1


title: Drosophila S2R+ cells - 25°C_ATAC-seq_Rep3


title: AM6_6-4_S37


title: PTEN_PacBio (Multidimensional PTEN missense variant analysis)

description:
PTEN_PacBio
plasmid DNA
Library and barcode cassette sequencing from DNA
PTEN_subassembly_maps.csv

organism: Escherichia coli

source_name: Synthetic sequence


title: Drosophila S2R+ cells - 25°C_ATAC-seq_Rep1


title: AM6_6-1_S32


title: AM6_6-5_S8


title: miRXplore_CapTS-seq_capped_B


title: 16RNA_rGrGrG_uncap_D


title: AM6_6-2_S17


title: GFP_HUDEP2_clone3

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St. Jude Children's Research Hospital

data_processing:
transcript level quantification was calculated using default parameter of Kallisto quant (version 0.43.1)
transcript to gene level quantification was carried out using ensembl gene annotation version 75 for hg19
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include transcript per million (TPM) values for each Sample

growth_protocol: Cells were expanded in StemSpan serum-free expansion medium (SFEM; Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin

extract_protocol:
quick-RNA MiniPrep from Zymo Research (R1054) was used to extract RNA
TruSeq Stranded mRNA Library Prep Kit (Illumina) was used to create libraries for sequencing

treatment_protocol: CRISPR GFP integration was carried out using 3xNLS Cas9 protein and RL48-hGOLGA4-EGFP plasmid containing GFP expression cassettee

value: Human Umbilical cord blood-Derived Erythroid Progenitor-2 cells

tag: sample type

value: GFP inserted clone


title: AM6_5-4_S36


title: Drosophila S2R+ cells - 14°C_ATAC-seq_Rep3

source_name: Drosophila S2R+ cells - 14°C


title: GFP_HUDEP2_clone2

source_name: Human Umbilical cord blood-Derived Erythroid Progenitor-2


title: Drosophila S2R+ cells - 14°C_ATAC-seq_Rep1


title: GFP_HUDEP2_clone1


title: AM6_5-3_S6


title: 16RNA_rGrUrG_Gpppp_D


title: AM6_5-1_S19


title: 16RNA_rGrUrG_Gpppp_B


title: 16RNA_rGrUrG_Gppp_A


title: AM6_5-5_S29


title: AM6_5-2_S1


title: P107 early stage

city: Vienna

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (refdata-cellranger-GRCh38-3.0.0)  and counted using Cell Ranger (version 3.0.2; 10x Genomics).
Genome_build: GrCh38
Supplementary_files_format_and_content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

source_name: skin biopsy

extract_protocol:
For each described sample, one single 6mm punch biopsy was taken and processed immediately. Each sample was cut into small pieces and digested in the C Tube (Miltenyi Biotec, Bergisch Gladbach, Germany) using the enzyme mix as provided by the Whole Skin Dissociation Kit for human (Miltenyi Biotec) in a total volume of 0,5ml RPMI medium with enzymatic supplements as described in the manufacturer's instructions. The sample was then incubated for a total of one hour in a water bath at 37°C. The sample was then further dissociated using the gentleMACS Dissociator (Miltenyi Biotec) running the program h_skin_01. After termination of the program steps 10-14 were conducted as detailed in the manufacturer's instructions. Finally, the cell pellet was resuspended in PBS with 0,08% BSA reaching a total volume of not more than 100µl. A cell aliquot was stained with trypan blue and cell numbers and percentages of dead cells were assessed by manual counting. Samples with not more than 30% dead cells were then subjected to scRNA-seq processing as detailed below.
5' gene expression sequencing was performed using the Chromium Controller and Single Cell 5' Library  (10x Genomics) according to the manufacturer's protocol. Sequencing was performed using the Illumina NovaSeq 6000 platform and the 150bp paired-end configuration.

tag: lesion type

value: early stage

tag: diagnosis

value: Mycosis fungoides

tag: chemistry

value: Single Cell 5' PE


title: P138 early stage


title: AM6_4-5_S25

tag: strain

tag: tissue


title: P90 nonlesional

value: nonlesional


title: AM6_4-4_S13


title: Acomys cahirinus UUO day 5 rep2

city: Seattle

first: Daryl

last: Okamura

state: Washington

address: 1900 9th Ave

department: Center for Developmental Biology & Regenerative Medicine

institute: Seattle Children’s Research Institute

data_processing:
Salmon used for indexing and mapping to transcriptome (mm9 for Mus musculus, Tr2aacds from Mamrot et al 2017 for Acomys).
The transcript counts were imported into R (r-project.org) using the Bioconductor tximport package, and subsequently summarized at the gene level, generating counts per gene. The Bioconductor edgeR package was used to filter out genes with consistently low levels of expression, and to fit a linear model using the count data.
We made comparisons between UUO and sham treatment at each time point as well as between UUO treatment at the two time points using quasi-likelihood F-tests, incorporating a log fold change of 0.585, (1.5-fold on the linear scale, or a 50% difference), and a false discovery rate (FDR) of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file with log fold change and FDR for every gene, sham vs treated kidney samples as labeled.

organism: Acomys cahirinus

source_name: Kidney

extract_protocol:
Age-matched adult male C57BL/6J (B6) and A. cahirinus (2-4 months) were subjected to unilateral ureter obstruction (UUO) procedure at the left ureter. Kidneys from sham operated controls and UUO-treated animals after 2 and 5 days were collected after perfusion with ice-cold normal saline and flash frozen in liquid nitrogen. Total RNA was extracted from kidney using Trizol (Invitrogen) and Direct-zol RNA Kit (R2072, Zymo Research) according to manufacturers instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

tag: age

value: 10.4 weeks

tag: genotype

value: wild type

value: day 5 UUO


title: 16RNA_rGrUrG_Gpppp_C

value: synthetic construct

tag: treatment

value: Template switching workflow

value: synthetic RNA


title: 16RNA_rGrUrG_Gpppp_A

tag: rna type


title: P84 nonlesional


title: P90 lesional

value: lesional


title: 16RNA_rGrUrG_Gpp_D


title: Drosophila S2R+ cells - 14°C_ATAC-seq_Rep2

tag: cell type


title: AM6_4-3_S24

value: Braf-mutated melanoma tumor


title: Acomys cahirinus UUO day 5 rep1

tag: cell line


title: Acomys cahirinus UUO day 2 rep2

value: 10.3 weeks

value: day 2 UUO


title: 16RNA_rGrUrG_Gpp_C


title: P84 lesional


title: 16RNA_rGrUrG_Gpp_B


title: P73 nonlesional


title: 16RNA_rGrUrG_Uppp_D


title: AM6_3-5_S23


title: Acomys cahirinus UUO day 5 rep3

value: 9.9 weeks


title: Acomys cahirinus UUO day 2 rep1


title: P65 nonlesional


title: 16RNA_rGrUrG_Gpp_A


title: AM6_4-1_S18


title: AM6_3-4_S11


title: P65 lesional

value: lesional/early


title: 16RNA_rGrUrG_Uppp_C


title: MF311 nonlesional


title: Acomys cahirinus sham rep2

value: sham


title: AM6_4-2_S16


title: AM6_3-2_S26


title: AM6_3-1_S27


title: Acomys cahirinus sham rep1

value: 14.3 weeks


title: Acomys cahirinus UUO day 2 rep3


title: 16RNA_rGrUrG_Uppp_A


title: MF309 nonlesional

value: Mycosis fungoides

value: Single Cell 5' PE


title: AM6_2-5_S31

value: vehicle


title: P73 lesional


title: 16RNA_rGrUrG_Ippp_D


title: AM6_2-4_S2


title: STL_S2_Ecd_2

city: Orange

first: Matthew

last: Simon

state: CT

address: West Campus, 100 West Campus Drive, Ste MIC312A

department: MBB

institute: Yale University

description: Reads filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)

data_processing:
Reads were filtered for unique sequences using FastUniq (this step excluded for STL-seq)
Reads were trimmed using cutadapt (--minimum-length=20)
For TT-TL-seq, reads were aligned to the GRCh38 genome using HISAT2 aligned with default parameters and --mp 4,2 . For STL-seq reads were aligned with Bismark and Bowtie2 with default parameters and --local.
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available on Bitbucket). Only mutations at positions with a base quality score of greater than 40 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph), and tracks were normalized using DESeq2 (estimateSizeFactors).
Tracks were converted to binary format using IGVtools (toTDF).
Genome_build: GRCh38 or dm6
Supplementary_files_format_and_content: bedgraph

source_name: Drosophila Schneider 2 cells

growth_protocol: 293T were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco) and Pen/Strep (50 U/ml). S2 cells were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco) and Pen/Strep (50 U/ml). 293T cell cultures were maintained at 37℃. S2 cell cultures were maintained at 27℃.

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and isopropanol precipitation. For transient-transciptome-TimeLapse-seq (TT-TL-seq) genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA for transient-transciptome-TimeLapse-seq RNA was enriched with MTS-biotin and treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018. For Start-TimeLapse-seq, total RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018 using mCPBA as the oxidant and short capped RNA was enriched as described in Nechaev et al. Science 2010.
TT-TL-seq libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413). STL-seq libraries were generated with custom oligos following methods described in Nechaev et al. Science 2010.

treatment_protocol: S2 cells were treated with 42 µM 20-hydroxyecdysone or DMSO for 30 minutes, 500 nM flavopiridol or DMSO for 40 minutes, 10 µM triptolide or DMSO for 10 minutes, and/or 1mM s4U for 1.5, 3, 5, 7.5, 10, or 120 minutes. 293T cells were treated with 80 mM KCl for 1 hour and/or 1mM s4U for 5 minutes. In all cases the s4U labeling was the last 5 minutes of drug/stress treatment.

value: WT S2

tag: s4u feed status

value: Yes

tag: rna population

value: short, capped RNA


title: HC: Heathy control

first: Amanda

middle: S

last: MacLeod

state: North Carolina

address: 40 Duke Medicine

institute: Duke University

data_processing:
Basecalling and fastq files generated using 10X Cellranger v3.1.0 with default parameters
Alignment, counting, filtering, of single cell RNA-Seq of samples:- HS_1,HS_2,HS_3 and HC , using 10X Cellranger v3.1.0 with default parameters.
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: matrix.mtx:  Gene-barcode matrix in Market Exchange Format (MEX) for HS and HC samples. Columns correspond to individual cells(barcodes), while rows correspond to genes.
Supplementary_files_format_and_content: genes.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column.
Supplementary_files_format_and_content: barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.

source_name: Heathy control

extract_protocol:
HS and normal skin samples were obtained from surgical excisions. Tissue was manually disrupted using scissors, and processed using Dispase II (2.4U/ml, Thermo Fisher Scientific) and Collagenase type II (2 mg/mL, Thermo Fisher Scientific) at 1:1 ratio overnight at 4°C with intermittent vigorous shaking for single-cell isolation. The suspension was filtered through a 70 μm cell strainer. Dead cells and red blood cells were removed with Lympholyte Cell Separation Media, Human (Cedarlane).
10X Single Cell 3' v3

value: whole skin

tag: disease state

value: Heathy control


title: 16RNA_rGrUrG_Ippp_C

extract_protocol: CapTS-seq samples were chemically capped, polyadenylated, reverse transcribed with template switching, and PCR amplified to introduce sequencing indeces. SMARTer samples followed the manufacturer's protocol.

value: synthetic construct

value: Template switching workflow

value: synthetic RNA


title: HS_3: Hidradenitis suppurativa_rep3

source_name: Hidradenitis suppurativa

value: Hidradenitis suppurativa


title: Acomys cahirinus sham rep3

value: kidney

value: 10.1 weeks

value: wild type


title: STL_S2_Ecd_1


title: AM6_2-3_S39

value: Braf-mutated melanoma tumor


title: AM6_2-1_S5


title: STL_S2_UT_1


title: 16RNA_rGrUrG_Ippp_B


title: 16RNA_rGrUrG_Uppp_B


title: STL_S2_UT_2


title: 16RNA_rGrUrG_Ippp_A


title: HS_2: Hidradenitis suppurativa_rep2


title: AM6_2-2_S15


title: AM6_1-5_S10


title: 16RNA_rGrUrG_Cppp_D


title: HS_1: Hidradenitis suppurativa_rep1


title: AM6_1-4_S4


title: Drosophila adult male flies - 30°C_RNA-seq_Rep2 [t5.TF30_R2]

data_processing:
Read alignment was performed using STAR aligner.
For the analysis of transcript levels, raw counts were obtained with htseq-count.
For comparison of transcript levels in different conditions we used edgeR.
For the analysis of alternative polyadenylation, the position of the last nucleotide before the start of the poly(A) tail in a given read was determined for each read. This position represents the cleavage and polyadenylation site (PAS). The detected PAS positions were assigned to clusters using a window size from 25 nucleotides upstream to 25 nucleotides downstream of the actual PAS in a given read. PAS clusters corresponding to internal priming (IP) events were eliminated as follows. The genomic sequence in the region from -30 to 10 around each putative PAS was checked for each read and those containing seven or more consecutive A bases in this region were discarded before further analysis. In addition, PAS suggested by reads were also discarded, if the region from -30 to 0 did not contain any of the known polyadenylation signals (Gruber et al. 2016). The PAS remaining after the filtering step were assigned to genes. This was accomplished after extending the 3' UTR region annotated in FlyBase to include an additional 5000 nucleotides or up to the middle of the distance between the PAS and the start of the downstream gene. The database with all the filtered and assigned PAS was used for the generation of count tables.
For comparison of PAS usage in different conditions, we used DEXSeq.
Genome_build: dm6 (Ensembl version 98) with adjusted parameters (--genomeSAindexNbases 10)
Supplementary_files_format_and_content:
The files "RawCounts_matrix_RNA-Seq_flies.txt" and "RawCounts_matrix_RNA-Seq_cells.txt" display the read counts assigned to each gene for each sample isolated from flies and S2R+ cells, respectively. In addition, chromosomal coordinates for each gene and the number and positions of associated PASs are given.
The files "NormalizedCounts_matrix_RNA-Seq_flies.txt" and "NormalizedCounts_matrix_RNA-Seq_cells.txt" display normalized read counts assigned to each gene for each sample isolated from flies and S2R+ cells, respectively. In addition, chromosomal coordinates for each gene and the number and positions of associated PASs are given.
The files "RawCounts_matrix_RNA-Seq_APA_flies.txt" and "S2R+ cells (RawCounts_matrix_RNA-Seq_APA_cells.txt" display the read counts for each PAS for each sample isolated from flies and S2R+ cells, respectively. In addition, chromosomal coordinates for each PAS and its assigned gene are given.
The files "NormalizedCounts_matrix_RNA-Seq_APA_flies.txt" and "NormalizedCounts_matrix_RNA-Seq_APA_cells.txt" display the normalized read counts for each PAS for each sample isolated from flies and S2R+ cells, respectively. In addition, chromosomal coordinates for each PAS and its assigned gene are given.

source_name: Drosophila adult male flies - 30°C

growth_protocol: S2R+ cells were cultured in Schneider’s medium (Gibco, cat# 21720, Thermo Fisher Scientific, Waltham, MA), supplemented with 10% fetal bovine serum (Gibco, cat# 10500-064) and 1% Penicillin-Streptomycin (Gibco, cat# 15140). Flies were raised and cultured on standard Drosophiila food.

extract_protocol:
Total RNA was extracted from the S2R+ cells and the male flies using TRIzol (Invitrogen, cat# 15596026), followed by DNase digestion (DNA-free DNA Removal Kit, Ambion, cat# AM1906).
Libraries were generated with the QuantSeq 3’ mRNA-Seq Kit REV for Illumina (Lexogen)

treatment_protocol: Aliquots of S2R+ cells were plated into 60 mm dishes. The number of plated cells was adjusted according to the temperature to be analyzed eventually (30°C: 1.5x10^6 cells; 25°C: 1.7x10^6 cells; 14°C: 3.5x10^6 cells; 11°C: 4.5x10^6 cells) to arrive at comparable cell densities at the end of the treatment. After incubation at 25°C for 24 hours, aliquots were shifted to either 11, 14, 25 or 30°C. For the analyses with adult male flies, we started cultures with w1 flies at 25°C. Newly eclosed adult male flies (0-12 hours after eclosion) were collected and distributed in aliquots into fresh food vials. The aliquots were then shifted to either 11, 14, 25 or 30°C. Total RNA was isolated 24 hours after temperature treatment. Three biological replicates were performed.

tag: Sex

value: male

tag: developmental stage

value: adult (0-12 hours after eclosion)


title: 16RNA_rGrUrG_Cppp_C

data_processing:
For 16 RNA analysis: reads were sorted and counted based on the identity of the two nucleotides preceding the sequence 'AGAACTTCGTCGAGTACGCTCAA', providing a list of 16 different possible sequences. Custom script used.
Basecalls performed using Illumina RTA software (v2.4.11 and v3.4.4) and fastq files were generated from the BCL files using Picard’s basecallstofastq
Cutadapt was used to remove (i) the preceding G’s of template switching libraries (4 Gs for capped libraries and 3 G’s for uncapped libraries) from their 5’ end, (ii) the adapter sequences, (iii) the low quality bases (q<20), and (iv) the poly(A) tails from the 3’ end of all the raw Illumina sequencing reads. This step also removed reads that became too short (<15 nt) after trimming.
miRXplore analysis: trimmed reads were mapped to the miRXplore reference sequences using bbmap (https://jgi.doe.gov/data-and-tools/bbtools/). Mapped reads were randomly downsampled using BBTools (https://sourceforge.net/projects/bbmap/) so that every sample included 1 million mapped reads. Transcript counts were obtained using idxstats from samtools. Considering the 962 miRNAs in miRXplore were present in equimolar amounts, an expected read count was generated by dividing the total number of mapped reads for each library by 962. Reads were then normalized by dividing the raw read counts by the expected read counts.
For human total RNA libraries, the trimmed reads were first mapped to the reference sequences of the Mix4v7 control and human ribosomal RNA and their associated spacer sequences using Bowtie2; only unmapped reads were kept for downstream analysis.
microRNA analysis: miRDeep2 was used to identify and quantify known miRNAs from the processed good quality non-control-non-rRNA reads based on the human reference genome (GRCh38) and the known human mature miRNAs and their precursor sequences downloaded from the miRBase database (miRBase release 22). Two filtering criteria were applied to call high-confident mature miRNAs from the mirDeep2 results: (i) randfold P-value <0.05 and (ii) miRDeep2 score >=0. For each identified miRNA species, the mean count of the reads that map to multiple genomic locations were calculated and used as the expression level for that miRNA
For transcriptome profiling, processed good quality non-control-non-rRNA reads were mapped to the human reference genome sequence (GRCh38) and the gene annotation on the primary assembly downloaded from GENCODE (release 36) using the STAR aligner. Gene count matrices were then generated from the STAR alignment results by the htseq-count function of the HTseq tool.
Genome_build: human: GRCh38
Supplementary_files_format_and_content: tab-delimited text files (output of transcriptome analysis): gene id, gene type, gene name and read counts.
Supplementary_files_format_and_content: miRDeep2 output csv file: miRDeep2 output which contains the number of identified novel and known miRDeep2 with different scores and the lists of novel and known miRNAs predicted by miRDeep2.
Supplementary_files_format_and_content: miRDeep2 output of expressed known miRNAs csv file: contains known miRNA names,  read counts and their associated precursors.


title: MF318 patch

value: patch

value: Mycosis fungoides

value: Single Cell 5' PE


title: Drosophila adult male flies - 30°C_RNA-seq_Rep1 [t4.TF30_R1]


title: STL_S2_UT_unlab

value: WT S2

value: No


title: 16RNA_rGrUrG_Cppp_B


title: AM6_1-3_S22

tag: time-point

value: vehicle


title: MF312 plaque

tag: lesion type

value: plaque


title: AM6_1-1_S21


title: 16RNA_rGrUrG_Appp_D

value: synthetic construct


title: MF312 follow up

value: follow up

tag: diagnosis


title: MF318 plaque

tag: chemistry


title: Drosophila adult male flies - 25°C_RNA-seq_Rep3 [t3.TF25_R3]

source_name: Drosophila adult male flies - 25°C

tag: strain


title: AM6_1-2_S28

tag: tissue


title: MF311 follow up


title: Drosophila adult male flies - 25°C_RNA-seq_Rep2 [t2.TF25_R2]


title: SZ9_45_62

data_processing:
Basecalling was performed using Illumina bcl2fastq2 Conversion Software v2.16
Single-end sequencing reads were first trimmed using bbduk to remove the first 12 bases. Regions of length 20 or above with average quality of less than 10 were trimmed from the end of each read. Finally, trailing polyG and polyA were removed from the reads using cut adapt.
Trimmed reads were aligned to reference genome mm10 and assigned to features in the mm10 gene annotation using the STAR program.
The Feature Counts were preprocessed (minimum CPM of 0.5 in at least 3 samples) and normalized using the ‘voom’ model within the limma package of Bioconductor to produce log2 counts per million (CPM) reads
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: SZ9_log2CPM_matrix.txt SZ9_log2CPM_matrix.txt

treatment_protocol: At day7 post-injection of tumour cells, mice were randomised to receive vehicle (60:40 ratio of DMSO-PEG400:dH2O, daily 200µl/dose),  celecoxib at 3mg/mL (daily 200µl/dose, 30mpk), anti-PD-1 (200µg/dose every 2-3 days for a total of 2 doses) or anti-PD-1 plus celecoxib for 7 days.

value: Balb/c

value: CT26 tumor day7 post-treatment

value: anti-PD-1 plus celecoxib

tag: response

value: R


title: SZ9_66_63


title: MF312 patch


title: 16RNA_rGrUrG_Appp_B

value: Template switching workflow

value: synthetic RNA


title: 16RNA_rGrUrG_Appp_A


title: Drosophila adult male flies - 14°C_RNA-seq_Rep3 [c6.TF14_R3]

source_name: Drosophila adult male flies - 14°C

value: male


title: SZ9_14_61


title: Drosophila adult male flies - 14°C_RNA-seq_Rep2 [c5.TF14_R2]

value: adult (0-12 hours after eclosion)


title: SZ9_40_60


title: Drosophila adult male flies - 14°C_RNA-seq_Rep1 [c4.TF14_R1]


title: Drosophila adult male flies - 25°C_RNA-seq_Rep1 [t1.TF25_R1]


title: 16RNA_rGrGrG_Gpppp_C


title: MF311 patch

value: patch


title: 16RNA_rGrUrG_Cppp_A


title: 16RNA_rGrGrG_Gpppp_D


title: 16RNA_rGrGrG_Gpppp_B


title: Drosophila adult male flies - 11°C_RNA-seq_Rep3 [c3.TF11_R3]

source_name: Drosophila adult male flies - 11°C


title: MF309 patch

value: Mycosis fungoides


title: MF309 follow up

value: Single Cell 5' PE


title: SZ9_65_56


title: MF309 tumor

value: tumor


title: Drosophila adult male flies - 11°C_RNA-seq_Rep2 [c2.TF11_R2]


title: MF311 plaque


title: Drosophila adult male flies - 11°C_RNA-seq_Rep1 [c1.TF11_R1]


title: noci_18

city: Geneva

first: Ludwig

last: Stenz

address: Rue Michel-Servet 1

department: Department of Genetic Medecine and Development

institute: University of Geneva

data_processing:
RRBS librairies were sequenced in paired-end mode of 50 bases on a NovaSeq 6000 in equivalence with 1 full-lane for 5 multiplexed samples on a HiSeq 4000.
reads were trimmed using TrimGalore (version 0.6.0) with option: --non-directional, --paired, --rrbs, --phred33, as well as with cutadapt (version 2.3) using options: --quality 30, --length 35.
Trimmed reads were mapped against the human bisulfite genome (assembly GRCH38) using Bismark (version 0.22.1) running with Bowtie 2 (version 2.3.5.1) and with the specified options: --q, --phred33, --score-min L,0,-0.2, --ignore-quals, --no-mixed, --no-discordant, --devtail, --maxins 1000, option --non-directional
Methylation calls were performed using the Bismark methylation extractor with options --paired-end, --gzip, --bedGraph, --multicore 10, --cytosine_report, --ignore 3, --ignore_r2 3, --ignore_3prime_r2
Cmeth and Cunmeth located within known C to T polymorphisms were removed using a bash script.
fisherTests of the Bsseq package were used to test methylation differences between two groups for each of the three comparisons at the single CpG level.
CpG with a p-value <1.7e-9 and with a finite value for the logarithm in base 2 of the odd ratio were kept.
BSmooth was used to analyse differentially methylated regions (DMR) cf: Genome Biology volume 13, Article number: R83 (2012) https://doi.org/10.1186/gb-2012-13-10-r83.
Quantile-based cutoff of the t-statistic were setup at 0.025 and 0.975 and methylation changes should be present in at least 3 samples of the group with an absolute change in methylation of 0.25 or higher.
bsseq::dmrFinder function identify the DMR reported with the meanDiff and the areaStat parameters.
We kept DMR and significant CpG overlapping each other and presenting concordant changes.
Non-parametric Wilcoxon tests performed between groups in methylation percentages recorded at the single cytosine levels was the final selection step.
Genome_build: GRCH38
Supplementary_files_format_and_content: bismark.cov.gz files containing methylation data.

source_name: Whole blood extracted DNA

extract_protocol:
DNeasy Blood and Tissue kit (Qiagen)
MspI-derived RRBS libraries prepared with the Diagenode® Premium RRBS technology (Service Cat. G02020000) as referenced in Nat Methods 13, i–ii (2016). https://doi.org/10.1038/nmeth.f.391

tag: technique

value: RRBS

tag: condition

value: nocicepive chronic pain


title: SZ9_62_55

tag: treatment


title: Drosophila adult male flies - 30°C_RNA-seq_Rep3 [t6.TF30_R3]


title: SZ9_18_54


title: Drosophila S2R+ cells - 30°C_RNA-seq_Rep3 [t6.TC30C_R3]

source_name: Drosophila S2R+ cells - 30°C

value: S2R+ cells


title: 16RNA_rGrGrG_Gpp_C

source_name: synthetic

value: synthetic construct

tag: rna type


title: noci_17


title: 16RNA_rGrGrG_Gpp_B


title: noci_16


title: SZ9_80_52

source_name: Tumour


title: Drosophila S2R+ cells - 30°C_RNA-seq_Rep2 [t5.TC30C_R2]

tag: cell line


title: 16RNA_rGrGrG_Gpppp_A


title: SZ9_16_53


title: 16RNA_rGrGrG_Gpp_A


title: Drosophila S2R+ cells - 30°C_RNA-seq_Rep1 [t4.TC30C_R1]


title: noci_15


title: 16RNA_rGrGrG_Gpp_D


title: noci_14


title: Drosophila S2R+ cells - 25°C_RNA-seq_Rep3 [t3.TC25C_R3]

source_name: Drosophila S2R+ cells - 25°C


title: noci_13


title: 16RNA_rGrGrG_Uppp_D


title: SZ9_64_51

value: NR


title: 16RNA_rGrGrG_Uppp_C


title: Drosophila S2R+ cells - 25°C_RNA-seq_Rep2 [t2.TC25C_R2]


title: SZ9_82_50

value: Balb/c


title: noci_12


title: SZ9_61_49

value: CT26 tumor day7 post-treatment


title: 16RNA_rGrGrG_Uppp_B


title: Drosophila S2R+ cells - 25°C_RNA-seq_Rep1 [t1.TC25C_R1]


title: 16RNA_rGrGrG_Uppp_A


title: noci_11


title: noci_10


title: 16RNA_rGrGrG_Ippp_D


title: SZ9_67_46

value: anti-PD-1 plus celecoxib


title: Drosophila S2R+ cells - 14°C_RNA-seq_Rep3 [c6.TC14C_R3]


title: 16RNA_rGrGrG_Ippp_C


title: noci_9


title: 16RNA_rGrGrG_Ippp_B


title: SZ9_52_57


title: Drosophila S2R+ cells - 14°C_RNA-seq_Rep1 [c4.TC14C_R1]


title: SZ9_28_45

value: R


title: SZ9_75_44


title: Drosophila S2R+ cells - 11°C_RNA-seq_Rep3 [c3.TC11C_R3]

source_name: Drosophila S2R+ cells - 11°C


title: noci_7


title: 16RNA_rGrGrG_Ippp_A

value: Template switching workflow


title: SZ9_73_42


title: SZ9_07_41


title: noci_6


title: SZ9_68_40


title: SZ9_84_47


title: Drosophila S2R+ cells - 11°C_RNA-seq_Rep1 [c1.TC11C_R1]


title: 16RNA_rGrGrG_Cppp_B

value: synthetic RNA


title: Plasmablast_8

city: New Delhi

first: Anmol

last: Chandele

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: International Center for Genetic Engineering and Biotechnology

data_processing:
RTA v2.7.7 was used for base calling and bcl2fastq v2.20.0.422 was used for demultiplexing.
Quality of reads monitored by FastQC. Sequenced reads trimmed for adaptor sequences. Mapped to human GRCh38 whole genome using subread package.
Immunoglobulin (Ig) reads were removed prior to normalisation. Differential expression analysis done by DESeq2 package followed by removal of low count genes with FPKM < 10 in more than five samples of each cell type.
filter criteria: adjusted p value < 0.05; p value < 0.01; log2 fold change >= 1 (up); log2 fold change =< -1 (down)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: PBMC

extract_protocol:
PBMCs isolated from whole blood of dengue patients were sorted for naïve B cells (CD19+ CD20+ IgD+ CD71- CD27- CD38- ) and plasmablasts (CD19+/int CD20- IgD- CD71+ CD27+ CD38+). RNA isolated from sorted cell type of each patient using Qiagen Rneasy micro kit  with on-column DNase digestion. cDNA synthesized from 500 pg of total RNA using Clontech SMART-seq v4 ultra low input RNA kit as per the manufacturer's protocol.
Amplified cDNAs were appended with dual indexed barcodes using Nextera XT DNA library preperation kit (Illumina).

tag: cell type

value: Plasmablast

value: Secondary

tag: severity

value: Dengue warning


title: noci_4


title: Drosophila S2R+ cells - 14°C_RNA-seq_Rep2 [c5.TC14C_R2]

source_name: Drosophila S2R+ cells - 14°C


title: SZ9_22_39


title: noci_3


title: 16RNA_rGrGrG_Cppp_A


title: SZ9_70_38


title: Plasmablast_7

tag: disease state


title: 16RNA_rGrGrG_Appp_D


title: Drosophila S2R+ cells - 11°C_RNA-seq_Rep2 [c2.TC11C_R2]


title: noci_2


title: SZ9_34_37


title: noci_1


title: Plasmablast_4

value: Severe dengue


title: 16RNA_rGrGrG_Appp_C


title: 16RNA_rGrGrG_Appp_B


title: SZ9_19_36


title: neuro_19

value: neuropathic chronic pain


title: noci_5


title: Plasmablast_5

value: Primary


title: neuro_18

value: RRBS


title: SZ9_30_33


title: SZ9_47_34


title: Plasmablast_2


title: 16RNA_rGrGrG_Appp_A


title: SZ9_53_32


title: Plasmablast_6


title: noci_8

value: nocicepive chronic pain


title: Plasmablast_1


title: miRXplore_CapTS-seq_A

description: miRexplore_counts.csv (Cap)

tag: vendor

value: Miltenyi Biotec #130-093-521

value: CapTS-seq workflow


title: Naïve_8

value: Naive B cell


title: neuro_16


title: neuro_15


title: SZ9_23_26

value: Balb/c

value: NR


title: SZ9_71_31

value: CT26 tumor day7 post-treatment


title: Naïve_7


title: Naïve_6


title: neuro_13


title: SZ9_03_24


title: neuro_12


title: SZ9_83_25


title: Naïve_5


title: SZ9_56_23


title: SZ9_13_21


title: Naïve_4


title: neuro_11


title: neuro_14


title: Naïve_3


title: Naïve_2


title: neuro_9


title: neuro_17


title: neuro_10


title: Plasmablast_3


title: SZ9_08_19

value: celecoxib


title: neuro_8


title: Naïve_1


title: PTEN_Library_Plasmid (Multidimensional PTEN missense variant analysis)

description:
PTEN_Library_Plasmid
plasmid DNA
Library and barcode cassette sequencing from DNA

data_processing:
Libraries were sequenced on NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis software.
Ssequencing reads were converted to fastq format and de-multiplexed with bcl2fastq. FASTQ files from technical replicate amplification and sequencing runs were concatenated for analysis with Enrich2.
The count for each variant in a bin was divided by the sum of counts recorded in that bin to obtain the frequency of each variant within that bin. This calculation was repeated for every bin in each replicate experiment. The summed counts of each variant in all four bins of an experiment was divided by the summed counts of all variants in all four bins of an experiment to obtain the total frequency value for each variant for each experiment. This total frequency value was used for filtering low-frequency variants out of the subsequent calculations. Next, a weighted average (w_ave) was calculated for each variant, with all weighted average values ranged from a value of 0.25 to 1. Finally, for each experiment, an abundance score for each variant was obtained by subjecting the weighted average of each variant to min-max normalization, using the weighted average value of WT, which was given a score of 1, and the median weighted average value for non-terminal nonsense variants at positions 51 through 349 for PTEN, which was given an abundance score of 0. The final abundance score for each variant was calculated by taking the mean of the min-max normalized abundance scores across the eight replicate experiments in which it could have been observed. Only variants which were scored in two or more replicate experiments were retained in the analysis. A standard error for each abundance score was calculated by dividing the standard deviation of the min-max normalized values for each variant by the square root of the number of replicate experiments in which it was observed. Lastly, the lower bound of the 95% confidence interval was calculated by multiplying the standard error with the 97.5 percentile value of a normal distribution and subtracting this product from the abundance score. The upper bound of the 95% confidence interval was calculated by instead adding the product with the abundance score.
Supplementary_files_format_and_content: The PTEN_barcodeInsertAssignments.tsv.gz and TPMT_barcodeInsertAssignments.tsv.gz processed data files are in gzip-compressed tab-separated text file format, containing the variant-barcode maps determined by subassembly.

source_name: Synthetic sequence

extract_protocol:
Cells were transferred into a microfuge tube, pelleted and stored at -20˚C. Genomic DNA was prepared using the Dneasy kit (Qiagen).
Eight 50 μL first-round PCR reactions were each prepared with a final concentration of ~50 ng/μL input genomic DNA, 1x Kapa HiFi ReadyMix, and 0.25 μM of the KAM499/JJS_501a primers. The reaction conditions were 95 °C for 5 minutes, 98 °C for 20 seconds, 60 °C for 15 seconds, 72 °C for 90 seconds, repeat 7 times, 72 °C for 2 minutes, 4 °C hold. Eight 50 μL reactions were combined, bound to AMPure XP (Beckman Coulter), cleaned, and eluted with 40 μL water. 40% of the eluted volume was mixed with 2x Kapa Robust ReadyMix; JJS_seq_F and one of the indexed reverse primers, JJS_seq_R1a through JJS_seq_R12a were added at 0.25 μM each. Reaction conditions for the second round PCR were 95 °C for 3 minutes, 95 °C for 15 seconds, 60 °C for 15 seconds, 72 °C for 30 seconds, repeat 14 times, 72 °C for 1 minutes, 4 °C hold.  Amplicons were extracted after separation on a 1.5% TBE/agarose gel using a Quantum Prep Freeze ‘N Squeeze DNA Gel Extraction Kit (Bio-Rad).


title: SZ9_17_20


title: miRXplore_CapTS-seq_B

description: miRexplore_counts.csv (Cap)

value: synthetic construct


title: SZ9_10_18


title: neuro_7


title: SZ9_04_14


title: DBTRG-05MG THIO 5uM 72h-2

data_processing:
Quality control using fastqc version 0.11.5
Sequenced reads were trimmed for adaptor sequence using Trim Galore version 0.6.5 with command: trim_galore --illumina --paired --fastqc --clip_R1 15 --clip_R2 15 --three_prime_clip_R1 5 --three_prime_clip_R2 5 R1.fq.gz R2.fq.gz
Mapped to GRCh38 whole genome using STAR2.7.6a with default parameters
Count how many reads map to each gene using featureCount-2.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: 2224, DBTRG-05MG or A172 cells are cultured with DMEM and 10% Fetal Bovine Serum

treatment_protocol: 2224, DBTRG-05MG or A172 cells are treated with 5uM 6-thio-dG or DMSO for 72h

value: Patient-derived cell line

value: treatment


title: SZ9_60_13


title: neuro_6


title: DBTRG-05MG Ctrl 72h-2

value: untreatment


title: DBTRG-05MG THIO 5uM 72h-1


title: SZ9_86_12


title: Drosophila S2R+ cells_30°C_Rep 3

description: Gene expression after 24 hours at 30°C

data_processing: Raw data was processed with GeneSpringGX11.0 (Agilent). Inter array differences were corrected using the option “median scaling to a control sample” of this software and the three replicates obtained after incubation at 25°C as control samples.

source_name: Drosophila S2R+ cells_30°C_24 hrs

extract_protocol: Total RNA was isolated with the NucleoSpin RNAII kit (Macherey-Nagel, Oensingen, Switzerland)

treatment_protocol: S2R+ cells were plated in 60 mm culture dishes in 2.5 ml medium. The numbers of cells that were plated were adjusted to the temperature, to which they were shifted eventually (30°C: 1.5x106; 25°C: 1.7x106; 14°C: 3.5x106; 11°C: 4.5x106) so that comparable cell densities were present at the end of the temperature treatment. Twenty-four hours after plating, cells were shifted to different temperatures (11, 14, 25 or 30°C) for 24 hours before isolation of total RNA. Three biological replicates were performed.

value: S2R+ cells

value: 30°C, 24 hours


title: neuro_4

value: neuropathic chronic pain


title: neuro_5


title: SZ9_36_11


title: DBTRG-05MG Ctrl 72h-1

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols


title: SZ9_76_10

value: vehicle


title: 2224 THIO 5uM 72h-2


title: neuro_3

value: RRBS


title: 2224 THIO 5uM 72h-1


title: Drosophila S2R+ cells_30°C_Rep 2

description: Gene expression after 24 hours at 30°C


title: neuro_2


title: 16RNA_rGrGrG_Cppp_D

value: Template switching workflow

value: synthetic RNA


title: neuro_1


title: SZ9_87_8


title: SZ9_27_9


title: Drosophila S2R+ cells_30°C_Rep 1

description: Gene expression after 24 hours at 30°C


title: Drosophila S2R+ cells_25°C_Rep 2

description: Gene expression after 24 hours at 25°C

source_name: Drosophila S2R+ cells_25°C_24 hrs

value: 25°C, 24 hours


title: Drosophila S2R+ cells_25°C_Rep 3

description: Gene expression after 24 hours at 25°C


title: SZ9_46_7


title: 2224 Ctrl 72h-1


title: ctl_20

value: control


title: 16RNA_rGrGrG_Cppp_C


title: SZ9_01_5

value: Balb/c


title: SZ9_32_6

value: NR


title: 2224 Ctrl 72h-2


title: Skin_19ISP_rep2

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

country: China

institute: Zhejiang University

data_processing:
RNAseq data were trimmed and aligned to the guinea pig genome (Cavea porcellus, Cavpor 3.0 from Ensembl), with associated annotation file using STAR (v2.7.3a).
The aligned reads were quantified to Ensembl transcripts using the Partek E/M algorithm and the subsequent steps were performed on gene-level annotation followed by total count normalization.
The counts generated were processed by gene set analysis (GSA).
Genome_build: Cavpor3.0
Supplementary_files_format_and_content: tab-delimited text files include baseMean for each gene

organism: Cavia porcellus

extract_protocol:
Total RNA was extracted from whole blood obtained from guinea pigs 2 weeks after the final immunization.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin

value: 19ISP mRNA-LNPs


title: Drosophila S2R+ cells_14°C_Rep 3

description: Gene expression after 24 hours at 14°C

source_name: Drosophila S2R+ cells_14°C_24 hrs

value: 14°C, 24 hours


title: ctl_17


title: ctl_18


title: Drosophila S2R+ cells_14°C_Rep 2

description: Gene expression after 24 hours at 14°C


title: Skin_Control_rep2

value: IL-21/Firefly Luciferase (Luc) mRNA-LNP


title: Skin_Control_rep1


title: Drosophila S2R+ cells_25°C_Rep 1

description: Gene expression after 24 hours at 25°C


title: SZ9_29_1

value: CT26 tumor day7 post-treatment


title: SZ9_06_4


title: ctl_16


title: Drosophila S2R+ cells_14°C_Rep 1

description: Gene expression after 24 hours at 14°C


title: SZ9_54_2


title: Blood_19ISP_rep5

value: blood


title: PSD95-PDZ3_NM_abundance_output3

city: New York

first: Julia

last: Domingo

state: NY

address: 101 6th Av

institute: New York Genome Center

description:
from plasmid library
fitness_PSD95-PDZ3_Abundance_supp.txt

data_processing:
Library strategy: PCR amplicon
DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Supplementary_files_format_and_content: Tabular format. Heather: aa_seq=amino acid sequence, Nham_aa=Number of amino acid substitutions, WT=True if it is the wild type sequence, fitness=Average fitness of all replicates calculated by DiMSuM, sigma=standard error of the fitness measurement

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: For each of the two protein domains (GRB2-SH3 and PSD95-PDZ) and two assays (bindingPCA and abundancePCA), each of the growth competitions was performed right after yeast transformation. After the first cycle of post-transformation plasmid selection, a second plasmid selection cycle (input) was performed by inoculating SC -URA/MET/ADE at a starting OD600nm = 0.1 with the saturated culture. Cells were grown for 4 generations at 30ºC under constant agitation at 200 rpm. This allowed the pool of mutants to be amplified and enter the exponential growth phase. The competition cycle (output) was then started by inoculating cells from the input cycle into the competition media (SC -URA/MET/ADE + 200 ug/mL Methotrexate) so that the starting OD600nm was 0.05. For that, the adequate volume of cells were collected, centrifuged at 3,000 rpm for 5 minutes and resuspended in the pre-warmed output media. Meanwhile, each input replicate culture was splitted in two and harvested by centrifugation for 5 min at 5,000g at 4ºC. Yeast cells were washed with water, pelleted and stored at -20ºC for later DNA extraction. After ~5-5.2 generations of competition cycle, each output replicate culture was splitted into two and harvested by centrifugation for 5 min at 5,000g at 4ºC, washed twice with water and pelleted to be stored at -20ºC

extract_protocol:
Cell pellets (one for each experiment input/output replicate) were re-suspended in 4 mL of DNA extraction buffer, frozen by dry ice-ethanol bath and incubated at 62ºC water bath twice. Subsequently, 4 mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 4 g of acid-washed glass beads (Sigma Aldrich) and the samples were vortexed for 10 minutes. Samples were centrifuged at RT for 30 minutes at 4,000 rpm and the aqueous phase was transferred into new tubes. The same step was repeated twice. 0.4 mL of NaOAc 3M and 8.8 mL of pre-chilled absolute ethanol were added to the aqueous phase. The samples were gently mixed and incubated at -20ºC for 30 minutes. After that, they were centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet was allowed to dry overnight at RT. DNA pellets were resuspended in 2.4 mL TE 1X and treated with 20 uL of RNaseA (10mg/mL, Thermo Scientific) for 30 minutes at 37ºC. To desalt and concentrate the DNA solutions, QIAEX II Gel Extraction Kit was used (200 µL of QIAEX II beads). The samples were washed twice with PE buffer and eluted 500 µL of 10 mM Tris-HCI buffer, pH 8.5. Finally, plasmid concentrations in the total DNA extract (that also contained yeast genomic DNA) were quantified by qPCR.
The sequencing libraries were constructed in two consecutive PCR reactions. The first PCR (PCR1) was designed to amplify the mutated protein of interest and to increase the nucleotide complexity of the first sequenced bases by introducing frame-shift bases between the adapters and the sequencing region of interest. The second PCR (PCR2) was necessary to add the remainder of the Illumina adapter and demultiplexing indexes. To avoid PCR biases, PCR1 of each independent sample (input/output replicates of any of the yeast assays) was run with an excess of plasmid template 20-50 times higher than the number of expected sequencing reads per sample (Table S3). Each reaction started with a maximum of 1.25x107 template plasmid molecules per uL of PCR1, avoiding introducing more yeast genomic DNA that interfered with the efficiency of the PCR reaction. For this reason, PCR1s were scaled up in volume as specified in Table S3. The PCR1 reactions were run using Q5 Hot Start High-Fidelity DNA Polymerase (New England Biolabs) according to the manufacturer’s protocol, with 25 pmol of pooled frame-shift primers oGJJ52/54-58 and oGJJ84-89 (forward and reverse primers were independently pooled according to the nucleotide diversity of each oligo, Table S1). The PCR reactions were set to 60ºC annealing temperature, 10 seconds (for GRB2-SH3 libraries) or 15 seconds (for PSD95-PDZ3 libraries) of extension time and run for 15 cycles. Excess primers were removed by adding 0.04 uL of ExoSAP-IT (Affymetrix) per uL of PCR1 reaction and incubated for 20 min at 37 ̊C followed by an inactivation for 15 min at 80 ̊C. The PCRs of each sample were then pooled and purified using the MinElute PCR Purification Kit (QIAGEN) according to the manufacturer’s protocol. DNA was eluted in EB to a volume 6 times lower than the total volume of PCR1. PCR2 reactions were run for each sample independently using Hot Start High-Fidelity DNA Polymerase. The total reaction of PCR2 was reduced to half of PCR1, using 0.05 uL of the previous purified PCR1 per uL of PCR2. In this second PCR the remaining parts of the Illumina adapters were added to the library amplicon. The forward primer (5’ P5 Illumina adapter) was the same for all samples, while the reverse primer (3’ P7 Illumina adapter) differed by the barcode index (oligo sequences in Table S1), to be subsequently pooled together and demultiplex them after deep sequencing (indexes used in each replicate of each sequencing run found in Table S4). 10 cycles of PCR2s were run at 62ºC of annealing temperature and 15 seconds (for GRB2-SH3 libraries) or 20 seconds (for PSD95-PDZ3 libraries) of extension time. All reactions from the same sample were pooled together and an aliquot was run on a 2% agarose gel to be quantified. After quantification, samples with different Illumina indexes that were sequenced together in the same flow-cell were pooled in an equimolar ratio, run on a gel and purified using the QIAEX II Gel Extraction Kit.

value: Lab strain BY4742

tag: molecule subtype

value: PCR amplicon


title: ctl_19


title: ctl_15


title: Drosophila S2R+ cells_11°C_Rep 3

description: Gene expression after 24 hours at 11°C

source_name: Drosophila S2R+ cells_11°C_24 hrs

value: S2R+ cells

value: 11°C, 24 hours


title: Skin_19ISP_rep1


title: ctl_14

value: RRBS


title: ctl_13


title: Blood_19ISP_rep4


title: PSD95-PDZ3_NM_abundance_output2


title: Blood_19ISP_rep3


title: ctl_12


title: Treg_NT_3_S14

city: Bethesda

first: Amir

last: Foroushani

state: MD

address: 10 CENTER DR RM 11N306

department: NIAID

institute: NIH

data_processing:
bcl2fastq v2.17.1.14 was used for base calling
Reads were aligned to mm10 by STAR (version 2.5.2a)
alignments to transcriptome were then quantified using RSEM (version 1.2.31)
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited expression matrix text file. (Raw counts).

source_name: Treg

extract_protocol:
Mouse T cells were resuspended in TrizolTM Reagent (Thermo Fisher Scientific). Total RNA were isolated per manufacturer’s instruction and resuspended in RNase free water. RNA was quantified with Qubit® RNA HS Assay Kit (Thermo Fisher Scientific) and RNA intergrity was verified with Agilent RNA 6000 Nano kit on the 2100 Bioanalyzer (Agilent Technologies) according to the manufacturers’ protocol.
RNA-Seq libraries were prepared from 65 ng of total RNA with ERCC ExFold RNA Spike-In Mix 1 (Life Technologies) of 1 μL of 1:5000 (v/v) dilution with TruSeq® Stranded mRNA Library Prep for NeoPrepTM kit as per the NeoPrep Library Preparation System Guide on the instrument (Illumina). The libraries were diluted 1:5 (v/v), with 1 μL used to check the expected size (~300 bp) and the samples’ purity were verified with the Agilent High Sensitivity DNA Kit as manufacturer’s recommendation (Agilent Technologies). One μL of the diluted libraries were used to quantify as recommended in the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) with standard range from 0 to 14 ng/ well. Pooled libraries of 1 nM were denatured and diluted as per the Standard Normalization Method for the NextSeq® System (Illumina). Final loading concentration of 1.7 pM and 1% (v/v) PhiX was used with the NextSeq® 500/550 High Output Kit v2 (150 cycles) (Illumina Samples were sequenced paired-end with 75 cycles of each read  and single index of 6 cycles.

value: Treg

value: NT


title: ctl_11


title: PSD95-PDZ3_NM_abundance_output1


title: Drosophila S2R+ cells_11°C_Rep 2

description: Gene expression after 24 hours at 11°C


title: Blood_19ISP_rep2


title: ctl_10


title: PSD95-PDZ3_NM_abundance_input3


title: PSD95-PDZ3_NM_abundance_input2


title: Blood_19ISP_rep1


title: Treg_DMK_3_S15

value: DMK


title: Drosophila S2R+ cells_11°C_Rep 1

description: Gene expression after 24 hours at 11°C


title: Treg_DMK_2_S10


title: Blood_Control_rep5


title: Blood_Control_rep4


title: Treg_NT_2_S9


title: Treg_NT_1_S4


title: ctl_8

value: control


title: Blood_Control_rep3


title: Treg_DMK_1_S5


title: ctl_9


title: PSD95-PDZ3_NM_binding_output3

description:
from plasmid library
fitness_PSD95-PDZ3_Binding_supp.txt


title: PSD95-PDZ3_NM_binding_output2


title: ctl_7


title: Th1_NT_3_S12


title: Blood_Control_rep1


title: PSD95-PDZ3_NM_binding_output1


title: ctl_6


title: Th1_NT_1_S2


title: PSD95-PDZ3_NM_abundance_input1


title: Th1_DMK_3_S13


title: PSD95-PDZ3_NM_binding_input3


title: ctl_4


title: Th1_DMK_2_S8


title: ctl_5


title: PSD95-PDZ3_NM_binding_input1


title: ctl_3


title: Th1_DMK_1_S3


title: Blood_Control_rep2


title: GRB2-SH3_NM_abundance_output3

description:
from plasmid library
fitness_GRB2-SH3_Abundance_supp.txt


title: Th1_NT_2_S7


title: GRB2-SH3_NM_abundance_output2


title: ctl_2


title: ctl_1


title: Naive_day0_3_S11