title: HEK293T_RNAseq_rep3

first: Irene

last: Zanin

address: Via Gabelli 63

institute: University of Padua

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (Galaxy Version 0.38.0)
Trimmed sequence reads were mapped to hg38 using HISAT2 (Galaxy Version 2.2.1+galaxy1)
Read count extraction and normalization were performed using featureCounts (Galaxy Version 2.2.1+galaxy1)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each sample

growth_protocol: HEK293T cell line was cultured in DMEM supplemented with 10% FBS and 1x Penicillin-Streptomycin. Cells were grown under standard conditions (5 % CO2, 95 % humidity, 37 °C).

extract_protocol:
RNA was harvested using GeneJET RNA Purification Kit (ThermoFisher Scientific). 2ug of total RNA were used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Quant Seq 3' mRNA-seq Library Prep kit (Lexogen) following manufacturer's protocols.

treatment_protocol: Cells were seeded in T-75, 1.5 million cells/flask and collected at 24h post-seeding, 3 million cells/sample were used for RNA extraction

value: Human embryonic kidney


title: replicate_1_AP1179_coT

status: Public on Aug 02 2023

type: SRA

city: Houston

first: Lanlan

last: Shen

state: Texas

address: 1100 Bates Ave

department: Pediatrics

country: USA

institute: Baylor College of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: matrix files

molecule: total RNA

organism: Mus musculus

source_name: Colon tumor

extract_protocol:
Adjacent mucosa were dissociated by 9mM EDTA for 1h, and then followed by TrypLE™ Express Enzyme (1X) (ThermoFisher Scientific) incubation (37°C, 5min) to dissociate into single cells. Colon tumor cells were dissociated using the Miltenyi Biotec MACS Tumor Dissociation Kit (Miltenyi Biotec) according to manufacturer instructions. Colon tumors and adjacent mucosa tissues were collected and processed on the same day for scRNA-seq.
Single cell Gene Expression Library was prepared according to Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics). In Brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR.  The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification.

tag: tissue

value: Colon tumor

tag: strain

tag: genotype

value: ApcMin/+; p16cis/cis

tag: Sex

value: Female

tag: age

value: 15 wks

tag: tumor size

value: Large tumor


title: SR UM Case17

city: Shanghai

first: Nestor

last: Zhang

address: Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

library_source: transcriptomic

data_processing:
Short reads were aligned to the reference human genome, GRCh38 using STAR (2.7.0d). All annotated and unannotated isoforms were merged to generate a combined isoform annotation file in “GTF” format.
With the cufflinks program and corresponding short reads data we estimated the expression level for each isoform based on the combined annotation file.
We used two different pipelines, including FLAIR and pinfish, to identify isoforms from long reads. For the FLAIR pipeline, “flair align” first aligns long reads to the reference human genome GRCh38 genome using minimap2, then “flair correct” corrects misaligned splice sites using GENCODE v24 annotations and corresponding short-read splice junctions, and finally “flair collapse” defines high-confidence isoforms from corrected long reads. For pinfish pipeline, we also use minimap2 to mapping the long reads to the reference genome, then “cluster_gff” clusters together the long reads having similar exon/intron. We used “polish_clusters” to creates error corrected long reads based on the cluster definitions generated by “cluster_gff”. Finally, we used “collapse_partials” to collapse identical isoforms to obtain final set of unique, full-length, high-quality isoforms.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Homo sapiens

source_name: eye

extract_protocol:
For short reads sequencing, total RNA was isolated using Trizol Reagent (Invitrogen Life Technologies), then the concentration, quality and integrity of RNA were determined by NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
For long reads sequencing, total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), and the concentration, quality and integrity were determined by NanoDrop spectrophotometer (Thermo Scientific).
For short reads sequencing, sequencing libraries were generated according to the following steps. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).
For long reads sequencing, A total of 1ug RNA was prepared for cDNA libraries using cDNA-PCR Sequencing Kit (SQK-PCS109) according to the instructions of Nanopore Technologies (ONT). Defined PCR adaptors were directly added to both ends of the first-strand cDNA by reverse transcriptase. After 14-cycle of PCR by LongAmp Tag (Martin,  #21), the PCR products were subjected to ONT adaptor ligation using T4 DNA ligase (Martin,  #21). Agencourt XP beads was used for DNA purification according to ONT protocol. The final cDNA libraries were added to FLO-MIN109 flow-cells and were sequenced on PromethION platform.

value: eye

tag: cell type

value: uveal melanoma cell


title: HEK293T_RNAseq_rep2

city: Padua

state: Italy

department: Molecular Medicine

country: Italy

library_source: genomic

molecule: genomic DNA

tag: cell line


title: SR UM Case16


title: replicate_4_AP1181_coT

description: 10x Genomics

value: Male

value: small tumor


title: TE_KO_2

city: Scottsdale

first: Henrique

last: Borges da Silva

state: Arizona

address: 13400 E Shea Blvd, 3-364 (Office)

department: Immunology

institute: Mayo Clinic Arizona

data_processing:
DNBSEQ-G50
Sequence reads were trimmed for adaptor sequence/low-quality sequence by the BGI Americas bioinformatics team.
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT. Clean reads were aligned to the reference genes using Bowtie2.
Read count extraction and normalization were performed by the BGI Americas bioinformatics team.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include TPM, FPKM, Read Counts values for each Sample; it also shows log2 fold differences, P-values and Q-Values (FDR) between: TE KO/TE WT, MP KO/MP WT, TE KO/MP KO and TE WT/MP WT.

source_name: Spleen CD8 T cells, Panx1-KO TE, 7d post LCMV-Arm

extract_protocol:
RNA was extracted using the QIAgen RNeasy kit following manufacturer instructions.
RNA samples were submitted to BGI Americas, where libraries were constructed and sequence was done using the DNBSEQ-G50 platform.

treatment_protocol: gp33-tetramer+ CD8+ T cells were sorted from pooled spleens (n=5 mice per group per replicate) of WT or T cell-specific Panx1-KO mice (CD4-Cre and CD4-Cre Panx1fl/fl, respectively) at day 7 post-LCMV-Armstrong infection. From each mouse cohort, TE cells (KLRG1+CD127-) or MP cells (CD127+KLRG1-) cells were sorted.

value: Spleen

value: CD8 T cell

tag: treatment

value: 7d post-LCMV Armstrong infection


title: replicate_7_AP1159_coT2

description: 10x Genomics

value: 22 wks


title: TE_KO_1


title: SR UM Case15


title: HEK293T_RNAseq_rep1


title: SR UM Case14


title: 93T449-H3K4me3-C&T

data_processing:
Sequencing data were uploaded to the Galaxy web platform and the public server at usegalaxy.org, together with R (version 3.4), were used to analyze all data.
Raw FASTQ reads were trimmed with TrimGalore! (v0.6.7) and aligned to GRCh38 using Bowtie2 (v2.4.2)
Normalized (RPGC, 1x Genome Coverage) coverage tracks were generated using deepTools (v3.5.1) bamCoverage with binSize 5 and the respective genome size.
Peaks were called with MACS2 (v2.1.1) and high confidence peaks sets between biological replicates were obtained with BEDTools merge function considering overlapping peaks within 250 bp as maximum peak distance.
Annotation of peaks was performed with the R packages “ChIPseeker” and "ChipPeakAnno".
For GVIZ visualization of genomic regions, bigwig files were merged using deeptools2 BigwigCompare function and scaled referring to the sample with the lowest sequencing depth.
BEDTools intersect function was used to identify iM/G4-unique and common peaks.
Assembly: hg38
Supplementary files format and content: bed file of narrow peaks called by MACS2
Library strategy: CUT&Tag

source_name: WDLPS

growth_protocol: WDLPS cell line was cultured in RPMI-1640 supplemented with 10% FBS and1x Penicillin-Streptomycin. HEK293T cell line was cultured in DMEM supplemented with 10% FBS and 1x Penicillin-Streptomycin. Cells were grown under standard conditions (5 % CO2, 95 % humidity, 37 °C).

extract_protocol:
Cells were harvested with trypsin and subjected to CUT&Tag protocol
pA-Tn5 adaptor complex was used for library preparation

value: WDLPS

value: Tumor fibroblast-like line derived from well-differentiated liposarcoma

tag: antibodies used

value: anti-H3K4me3 (C42D8)


title: TE_WT_2

source_name: Spleen CD8 T cells, WT TE, 7d post LCMV-Arm


title: replicate_2_AP1170_coT

description: 10x Genomics

value: 18 wks

value: Small tumor


title: HEK293T-H3K4me3-C&T

value: Human embryonic kidney


title: SR UM Case13


title: TE_WT_1


title: replicate_1_AP1152_coT1

description: 10x Genomics

value: Colon tumor

value: ApcMin/+; p16cis/cis

value: Female


title: SR UM Case12

value: eye


title: Erubilin treatment 72hr replicate 2 (cutnrun-human)

city: LEBANON

first: Diwakar

middle: Pattabiraman

last: Pattabiraman

state: NH

address: 1 Medical Center Drive

department: Molecular and Systems Biology

institute: Geisel School of Medicine at Dartmouth

description:
Tn5 fragmented genomic DNA
MDA-72hr.merged.bw
MDA-72.narrowPeak
MDA-72hr-2

data_processing:
FASTQ files were generated using bcl2fastq v2.20.0.422 from Illumina Inc.
Raw reads were trimmed with Cutadapt (v2.4) and aligned to hg38 using Bowtie (v2.2.6) in “--local” mode with parameters “--no-mixed --no-discordant”
Duplicate reads were identified and removed using MarkDuplicates (Picard Tools) to create filtered BAMs.
Peaks were called using MACS2 (v2.1.1) callpeak command with parameters ““-f BAMPE --keep-dup all -q 0.05 -g 2913022398 ”
Peaks were filtered against the ENCODE hg38 blacklist and those demonstrating 2-fold signal enrichment above background
Reproducible peak sets were identified for replicate pairs using BEDTools (v 2.30.0) command “intersect” with parameter “-a”.
A consensus peak set was generated by merging overlapping peaks called across all samples. Read counts in each consensus peak region were counted from BAM files using the featureCounts() function (Rsubread package) with options “isPairedEnd=TRUE, countMultiMappingReads=FALSE”
BAM files for sample replicates were merged using Picard MergeSamFiles before creation of BigWig files
Counts per million (CPM) normalized signal tracks were generated using deepTools8 (v3.3.0) bamCoverage command with parameters ““--binSize 20 --smoothLength 60 --normalizeUsing CPM --centerReads --extendReads” on the position-shifted BAM files
Assembly: GRCh38
Supplementary files format and content: matrix of raw read counts in txt format
Supplementary files format and content: Normalized signal tracks in BigWig format
Supplementary files format and content: peak files in BED format
Library strategy: CUT&RUN

source_name: Human Breast Cancer Cells

growth_protocol: Cells Grown in DMEM media supplemented with 10% FBS, 100 I.U./mL penicillin,100 (μg/mL) in a humidified incubator with 5% CO2 (According to ATCC protocol).

extract_protocol:
CUT&RUN was performed using  EpiCypher CUTANA™ CUT&RUN assays according to manufacturing protocol. ZEB1-DNA complexes were isolated using an anti-ZEB1 antibody.
NEB Ultra II with modifications from EpiCypher CUTANA Library Kit Manual v1.0

treatment_protocol: Cells were treated with 300nM eribulin for 24, 48, and 72h.

value: Erubilin

tag: time


title: SR UM Case11

value: uveal melanoma cell


title: replicate_3_AP1179_Adj

description: 10x Genomics

source_name: Adjacent mucosa

value: Adjacent mucosa

value: 15 wks


title: Spleen CD8 T cells, KO, IL15 polarized, rep1

data_processing:
BGISEQ-500, PE100 sequencing length
In this project, we sequence 10 samples used BGISEQ platform, averagely generating about 4.50G
Gb bases per sample. The average mapping ratio with reference genome is 97.37%, the average mapping ratio with gene is 88.12%; 15944 genes were identified.
We used HISAT to align the clean reads to the reference genome.
We used Bowtie2 to align the clean reads to the reference genes. Read count extraction and normalization were performed by BGI company.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include TPM, FPKM, Average Read counts, log2 FD, P-value and Q-value of: (WT IL15/KO IL15), (WT 72h/KO 72h), (WT IL15/WT 72h) and (KO IL15, KO 72h).

source_name: Spleen

growth_protocol: “72h” samples: Mouse CD8+ T cells (WT or Panx1-KO) were in vitro activated with anti-CD3 (10 ug/ml), anti-CD28 (20ug/ml) and IL-2 (10 ng/ml) for 72h.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). >1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the DNBseq Eukaryotic Strand-specific Transcriptome Resequencing; P_Stranded Library/Seq (PE100).

treatment_protocol: “IL15” samples: Mouse CD8+ T cells (WT or Panx1-KO) were in vitro activated as described above for 72h; after this period, cells were incubated for an additional 72h with recombinant IL-15 (10 ng/ml).

value: Spleen

value: CD8 T cell

value: KO

value: IL15 polarized (after activation)


title: Spleen CD8 T cells, KO, IL15 polarized, rep2


title: Erubilin treatment 72hr replicate 1 (cutnrun-human)

description:
Tn5 fragmented genomic DNA
MDA-72hr.merged.bw
MDA-72.narrowPeak
MDA-72hr-1


title: replicate_4_AP1185_Adj

description: 10x Genomics

value: Male


title: replicate_3_AP1171_coT

description: 10x Genomics


title: SR UM Case10


title: Erubilin treatment 48hr replicate 2 (cutnrun-human)

description:
Tn5 fragmented genomic DNA
MDA-48hr.merged.bw
MDA-48.narrowPeak
MDA-48hr-2


title: Spleen CD8 T cells, WT, IL15 polarized, rep2

value: WT


title: SR UM Case9


title: replicate_1_AP1152_Adj

description: 10x Genomics

value: 22 wks


title: Erubilin treatment 48hr replicate 1 (cutnrun-human)

description:
Tn5 fragmented genomic DNA
MDA-48hr.merged.bw
MDA-48.narrowPeak
MDA-48hr-1


title: Erubilin treatment 24hr replicate 2 (cutnrun-human)

description:
Tn5 fragmented genomic DNA
MDA-24hr.merged.bw
MDA-24.narrowPeak
MDA-24hr-2


title: TE_WT_3

value: 7d post-LCMV Armstrong infection


title: Spleen CD8 T cells, WT, IL15 polarized, rep1


title: SR UM Case8


title: Spleen CD8 T cells, KO, 72h post-activation, rep3

value: 72h post-activation (anti-CD3 + anti-CD28 + IL-2)


title: Erubilin treatment 24hr replicate 1 (cutnrun-human)

description:
Tn5 fragmented genomic DNA
MDA-24hr.merged.bw
MDA-24.narrowPeak
MDA-24hr-1


title: SR UM Case7


title: Spleen CD8 T cells, KO, 72h post-activation, rep2


title: TBM-brain-2

first: Feng

last: Li

address: No.2901, Caolang Road

department: Department of Respiratory Disease and Critical Care Medicine

institute: Shanghai Public Health Clinical Center, Fudan University

data_processing:
cellranger 4.0.0 was used to generate feature-barcode matrices with default parameters
QC, dimensional reduction and clustering were performed using Seurat package (version: 3.2.3)
Assembly: mm10
Supplementary files format and content: Three files for each sample, UMI count in mtx format, genes and cells list in tsv format

source_name: The whole brain tissue from 6 mice were pooled together.

growth_protocol: All twenty-four 6-week C57BL6 mice were used in TBM model and control groups.

extract_protocol:
Single cells were obtained according to a previous protocol with brief modification, Briefly, the mouse was deeply anesthetized by isoflurane and decapitated. After the brain was removed, the hippocampus was rapidly dissected under microscope. The tissue was cut into pieces on ice and then transferred to a 1.5 mL tube containing 2 mg/mL pronase (Sigma, Cat# P6911-1G), 50 μg/mL DNaseІ (Sigma, cat. no. D5025) in 1 mL HABG who consist of Hibernate A (Invitrogen, cat. no. A1247501) and B27 (Invitrogen, cat. no. 17504). The tube was then shaked for 30 min at 30℃ in a shaker at the speed of 200 rpm. After digestion, the hippocampus was gently triturated by Pasteur pipette tips to obtain the single cells. The cells were purified by OptiPrep (Sigma, cat. no. D1556) density gradient centrifugation at 800 g for 15 min, the single cells were resuspended in calcium and magnesium-free 1x PBS containing 1% BSA, and centrifuged for further purifying at 200 g for 2 min. The precipitated single cells were resuspended in 50 - 100 μL 1x PBS containing 1% BSA. Total and viability cell numbers were counted, and only samples with cell survival rates above 80% were used for subsequent sequencing.
Total and viability single cell numbers were counted, and samples with cell survival rates above 80% were used for subsequent procedures. The qualified cells were washed and resuspended in PBS at a final concentration of 700~1200 cells/μL for 10x Genomics Chromium™ system operation. Then GEMs (Gel Beads-in-emulsion) were constructed for single cell isolation. Once the GEMs were successfully formed, they were collected and performed the reverse transcription to achieve labeling in a PCR machine. After that, the GEMs were damaged, then, magnetic beads were used to purify and enriched the first strand cDNA. Finally, they were subjected to cDNA amplification and quality control. A 10x Genomics Single Cell 3′ v2 Reagent Kit were applied for library construction by quality verified cDNAs, followed by fragmentation, adapters addition, and samples PCR indexing. Finally, the Illumina NovaSeq platform PE150 sequencing mode was performed for DNA sequencing and the sequencing volume criterion was set to > 50 k reads/cell.

treatment_protocol: To acquire a representative TBM expression of each group, 6 mice were pooled together for the following examinations. Each group was composed of two pooled samples: Control group (ctrl-brain-1 and ctrl-brain-2) and TBM group (TBM-brain-1 and TBM-brain-2)

value: Brain tissue

value: TBM group, M. bovis (BCG) injected.


title: Control replicate 2 (cutnrun-human)

description:
Tn5 fragmented genomic DNA
MDA-Cont.merged.bw
MDA.Cont.narrowPeak
MDA-Cont-2

value: Untreated


title: TBM-brain-1


title: SR UM Case6

value: eye


title: Spleen CD8 T cells, KO, 72h post-activation, rep1


title: ctrl-brain-2

value: Control, saline injected


title: SR UM Case5

value: uveal melanoma cell


title: replicate_2_AP1159_Adj

description: 10x Genomics

value: Adjacent mucosa

value: ApcMin/+; p16cis/cis


title: Control replicate 1 (cutnrun-human)

description:
Tn5 fragmented genomic DNA
MDA-Cont.merged.bw
MDA.Cont.narrowPeak
MDA-Cont-1


title: ctrl-brain-1


title: IgG control replicate 2 (cutnrun-human)

description:
Tn5 fragmented genomic DNA
MDA-IgG.merged.bw
MDA-IgG-2


title: SR UM Case4


title: Spleen CD8 T cells, WT, 72h post-activation, rep3

value: Spleen


title: SR UM Case3


title: IgG control replicate 1 (cutnrun-human)

description:
Tn5 fragmented genomic DNA
MDA-IgG.merged.bw
MDA-IgG-1


title: Myocytes-Treated-4

city: Toronto

first: Andrew

last: Advani

state: Ontario

address: 6-151 61 Queen Street East

department: Medicine

country: Canada

institute: St. Michael's Hospital

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software
Transcript abundances for each sample was estimated with StringTie , and the FPKM  value for gene and transcript level were calculated with R package Ballgown
Genome_build: GRCm38

source_name: Adult mouse ventricular cardiomyocytes

growth_protocol: Adult mouse cardiomyocytes were isolated from C57BL/6 mouse hearts and cultured in M199 medium supplemented with (–)-Blebbistatin, ITS and CD lipid for 24h

extract_protocol:
Total RNA from cardiomyocytes was isolated using Trizol and quantified using NanoDrop ND-1000
Total RNA was used to prepare sequencing libraries with a KAPA Stranded RNA-Seq Library Prep Kit (Illumina)
Sequencing was carried out using an Illumina NovaSeq 6000

treatment_protocol: CCR2+ cardiac macropahges were sorted from Ccr2gfp/+ mice four weeks after TAC surgery and cultured in M199 medium for 24 hrs and then this medium was supplemented with (–)-Blebbistatin, ITS and CD lipid before adding to adult cardiomyocytes isolated from C57BL/6 mice and cultured for 24h

tag: tissue source of cells

value: Heart

tag: culture condition

value: Conditioned media from CCR2+ cardiac macrophages


title: Myocytes-Treated-3


title: Spleen CD8 T cells, WT, 72h post-activation, rep2

value: CD8 T cell


title: Spleen CD8 T cells, WT, 72h post-activation, rep1


title: Myocytes-Treated-2


title: SR UM Case1


title: Myocytes-Treated-1


title: Single cells of human hepatoctye organoid cultures 5 days after infection, sample plate

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

country: Germany

institute: University Hospital Würzburg

description: Human hepatocytes infected with Plasmodium falciparum

data_processing:
Paired end reads were aligned to the reference transcriptomes GRCh37 and PF3D7 using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Assembly: GRCh37
Assembly: PF3D7
Supplementary files format and content: coutt files contain UMI barcode normalised abundance counts

source_name: Human hepatocyte organoids

extract_protocol:
Live single cells were sorted in 384- well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

value: Liver

tag: agent

value: Plasmodium falciparum


title: p10 rat DRG, cultured, rep 5

city: Cambridge

first: Caitlin

last: Lewarch

state: MA

address: 179 Sidney Street

institute: Quiver Bioscience

data_processing:
Reads were trimmed to remove Illumina adapter sequences and low-quality sequences using Trim Galore! (v.0.6.6, CutAdapt v2.8) with default settings.
Reads were pseudo-aligned to a rat reference transcriptome (with rat genomic decoys) with Salmon (v1.5.1) using default settings.
Count and TPM tables were imported into R (3.6.2) and summarized to gene-level values using tximport (1.14.2).
Assembly: Refseq: GCF_015227675.2_mRatBN7.2
Supplementary files format and content: Salmon quant.sf files for each sample.
Supplementary files format and content: The combinedTPMforGEO.txt file contains gene-level TPM values across all samples.  The first column contains gene symbols and following columns are TPM values for each sample according to the "library name" indicated in the sample information section.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: dorsal root ganglion (cultured)

growth_protocol: DRG neurons were prepared from Sprague Dawley rats, postnatal day 10. Animals were anesthetized by using CO2 inhalation and decapitated, and ganglia were removed. Dorsal root ganglia from one litter of 10 pups were treated at 37°C for 30 min in 2 mg/mL collagenase (Type IA; Sigma-Aldrich) and 5 mg/mL dispase II (Sigma-Aldrich) in dissection media and then washed with and placed in plating media. Individual cells were dispersed by trituration with a fire-polished Pasteur pipette and filtered through 100 µm cell strainer. Cells were then counted and plated at a density of 5,000 cells/well on Greiner full-area 96-well plates with a cyclic olefin copolymer (COC) bottom (Greiner Bio-one, Item No.: 655801) in plating media.

extract_protocol:
Cells were pooled in TRIzol (3 wells/sample) and RNA extraction was performed according to manufacturer instructions for TRIzol extractions (ThermoFisher Scientific, Waltham, MA, USA).
Library preparation (mRNA profiling using poly-A selection) was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Cells were cultured for 8 days prior to pooling and RNA extraction.  After 1 day of culture, cells were treated with 1XPBS.

value: dorsal root ganglion (cultured)

tag: developmental stage

value: cultured dorsal root ganglion

value: WT

value: cultured 8 days, PBS


title: p10 rat DRG, cultured, rep 4


title: Extracted RNA from human erythrocytes infected with Plasmdoium falciparum

description: Human red blood cells infected with Plasmodium falciparum

source_name: Human red blood cells

value: Blood


title: Single cells of human hepatoctye organoid cultures 5 days after the start of the experiment, control plate

description: Human hepatocytes

value: Uninfected


title: p10 rat DRG, cultured, rep 3


title: CH4_1000ppm_Rep1

city: Seattle

first: Erin

last: Wilson

state: WA

address: 185 E Stevens Way NE

department: The Paul G. Allen School of Computer Science & Engineering

institute: University of Washington

data_processing:
align reads to genome using BWA with the BWA-MEM algorithm (BWA version 0.7.17-r1198-dirty, default parameters)
convert read alignments into sorted BAM files (SAMTools version 1.9)
attribute reads to ORFs to estimate read counts with htseq-count (“HTSeq” framework version 2.0.2, modified: 10.5281/zenodo.7434230)
Assembly: NCBI accession NZ_CP035467.1
Supplementary files format and content: tab-delimited files with feature locus tag and raw read count

organism: Methylotuvimicrobium buryatense

source_name: bacterial cell

extract_protocol:
RNA was extracted as previously described (Chu and Lidstrom, 2016).
RNA sequencing and library construction was performed by Azenta/GENEWIZ (Indianapolis, IN)

treatment_protocol: cells grown in 1000ppm CH4

value: bacterial cell


title: Myocytes-Control-4

value: Normal growth media (M199)


title: Myocytes-Control-3


title: Single cells of human hepatoctye organoid cultures 4 days after infection, sample plate 2


title: CH4_500ppm_Rep2

treatment_protocol: cells grown in 500ppm CH4


title: CH4_500ppm_Rep1


title: p10 rat DRG, cultured, rep 1


title: p10 rat DRG, cultured, rep 2


title: Single cells of human hepatoctye organoid cultures 4 days after infection, sample plate 1


title: Myocytes-Control-1


title: Single cells of human hepatoctye organoid cultures 4 days after the start of the experiment, control plate

description: Human hepatocytes


title: SR UM Case2

value: eye

value: uveal melanoma cell


title: pAVSMCs cultured in Osteogenic Media (OM) for 5 days (d5)_replicate 3

status: Public on Aug 01 2023

city: Milwaukee

first: Joy

last: Lincoln

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

data_processing: Raw FASTQs were split into files containing ~40,000,000 total reads and checked for quality using the FASTX-Toolkit. The reads were filtered (removing sequences that did not pass Illumina’s quality filter) and trimmed based on the quality results (3 nucleotides at the left end of the R1 reads and 1nt at the left end of the R2 reads). Trimmed reads were mapped to reference genome (Sus Scrofa, GCF_000003025.6_Sscrofa11.1) with HISAT2. After the read mapping, Stringtie was used for transcript assembly. Expression profiles were calculated for each sample and transcript/gene as read count and FPKM (Fragment per Kilobase of transcript per Million mapped reads).

organism: Sus scrofa

source_name: porcine aortic smooth muscle cells (Cell Applications P354K-05)

growth_protocol: Porcine aortic valve interstitial cells (AVICs) were isolated as previously described, and cultured in conditioned media (DMEM media (containing L-glutamine), 10% fetal bovine serum, 1% penicillin/streptomycin). AVICs were utilized from passage number 2 to 6 for all the experiments reported. Porcine aortic vascular smooth muscle cells (AVSMC) were obtained from Cell Applications (P354-05) and cultured in recommended porcine smooth muscle cell media (P311-500) from Cell Applications.

extract_protocol:
RNeasy Mini Kit from Qiagen (#74104)
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep kit and sequenced on an Illumina platform.

value: wildtype

value: cultured in Osteogenic Media (CM) for 5 days (d5)


title: pAVSMCs cultured in 2.5mM Phosphate (Pi) for 5 days (d5)_replicate 2

value: porcine aortic smooth muscle cells (Cell Applications P354K-05)


title: pAVSMCs cultured in 2.5mM Phosphate (Pi) for 5 days (d5)_replicate 1


title: pAVSMCs cultured in Conditioned Media (CM) for 5 days (d5)_replicate 3


title: replicate_3_AP1152_coT2

description: 10x Genomics

value: Colon tumor

value: ApcMin/+; p16cis/cis

value: Female

value: 22 wks

value: Large tumor


title: pAVSMCs cultured in 2.5mM Phosphate (Pi) for 5 days (d5)_replicate 3


title: pAVSMCs cultured in Osteogenic Media (OM) for 5 days (d5)_replicate 1


title: pAVSMCs cultured in Conditioned Media (CM) for 5 days (d5)_replicate 2


title: CH4_1000ppm_Rep2


title: pAVSMCs cultured in 2.5mM Phosphate (Pi) for 3 days (d3)_replicate 2


title: pAVSMCs cultured in 2.5mM Phosphate (Pi) for 3 days (d3)_replicate 3


title: pAVSMCs cultured in 2.5mM Phosphate (Pi) for 3 days (d3)_replicate 1


title: pAVSMCs cultured in Conditioned Media (CM) for 5 days (d5)_replicate 1


title: pAVSMCs cultured in Osteogenic Media (OM) for 3 days (d3)_replicate 3

value: cultured in Osteogenic Media (CM) for 3 days (d3)


title: pAVSMCs cultured in Osteogenic Media (OM) for 3 days (d3)_replicate 1


title: pAVSMCs cultured in Conditioned Media (CM) for 3 days (d3)_replicate 3


title: pAVSMCs cultured in Conditioned Media (CM) for 3 days (d3)_replicate 1


title: pAVSMCs cultured in Osteogenic Media (OM) for 3 days (d3)_replicate 2


title: pAVSMCs cultured in Conditioned Media (CM) for 3 days (d3)_replicate 2


title: pAVICs cultured in 2.5mM Phosphate (Pi) for 5 days (d5)_replicate 3

source_name: primary porcine heart valve interstitial cells


title: pAVICs cultured in 2.5mM Phosphate (Pi) for 5 days (d5)_replicate 1

value: primary porcine heart valve interstitial cells


title: pAVICs cultured in Osteogenic Media (CM) for 3 days (d3)_replicate 3


title: pAVICs cultured in Osteogenic Media (CM) for 3 days (d3)_replicate 1


title: pAVICs cultured in 2.5mM Phosphate (Pi) for 3 days (d3)_replicate 3


title: pAVICs cultured in Conditioned Media (CM) for 5 days (d5)_replicate 1


title: pAVICs cultured in Conditioned Media (CM) for 5 days (d5)_replicate 2


title: pAVICs cultured in 2.5mM Phosphate (Pi) for 3 days (d3)_replicate 2


title: pAVICs cultured in 2.5mM Phosphate (Pi) for 3 days (d3)_replicate 1


title: pAVICs cultured in Osteogenic Media (OM) for 3 days (d3)_replicate 3


title: pAVSMCs cultured in Osteogenic Media (OM) for 5 days (d5)_replicate 2


title: pAVICs cultured in Osteogenic Media (OM) for 3 days (d3)_replicate 1


title: pAVICs cultured in Conditioned Media (CM) for 3 days (d3)_replicate 2


title: pAVICs cultured in Conditioned Media (CM) for 3 days (d3)_replicate 1


title: pAVICs cultured in Conditioned Media (CM) for 3 days (d3)_replicate 3


title: pAVICs cultured in Osteogenic Media (OM) for 3 days (d3)_replicate 2


title: Myocytes-Control-2

value: Heart


title: SWH1_mmlib_30min_2rep

city: Baltimore

first: Taekjip

last: Ha

state: Maryland

address: 3400 N. Charles Street

institute: Johns Hopkins University

library_source: other

data_processing:
Trim Illumina adaptor using Trim Galore software
Merge the pair-end reads with FLASh software
Reads alignment with Bowtie2 software
Calling the sequence identity and DNA cleavage location by using custom python script
Data imputation by linear regression with custom python script
Supplementary files format and content: .data file including estimated nucleosome positioning scores and cleavage counts for each sequence in the library
Library strategy: Slide-seq

molecule: other

organism: synthetic construct

source_name: mismatch library based on SWH1

growth_protocol: nucleosome libraries are reconstituted by salt-dialysis methods from synthetic DNA pools with Xenopus laevis histone octamers

extract_protocol:
phenol chloroform extraction of DNA
single-stranded 3’ end DNA fragments were converted into double-stranded DNA by Bst polymerase (NEB Bst 2.0 WarmStart). And NGS library was prepared with NEBUltraII kit (NEBNext Ultra II DNA Library Prep Kit) for Illumina sequecing.

treatment_protocol: nucleosomal DNA was photo-crosslinked site-specifically and cleavaged by alkaline treatment

value: 30 min Chd1 sliding


title: SWH1_IDlib_0min_2rep

source_name: insertion library based on SWH1

value: No Chd1 sliding


title: pAVICs cultured in Conditioned Media (CM) for 5 days (d5)_replicate 3


title: SWH1_30min

source_name: SWH1 gene +1 nucleosome sequence


title: SWH1_IDlib_30min_1rep


title: SWH1_mmlib_0min_2rep


title: SWH1_IDlib_30min_2rep


title: SWH1_IDlib_0min_1rep


title: SWH1_mmlib_30min_1rep


title: pAVICs cultured in Osteogenic Media (CM) for 3 days (d3)_replicate 2


title: RNA D3-delbelt-G1-G4-dimer products set2

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
The sequencing results of the two high-throughput assays were analyzed similarly. Each assay we obtained sequencing results for 4 samples, DNA dictionary, pri-mir-576shortLS substrate, and cleaved RNA of D3∆belt-G2 and D3∆belt-G1-G4-dimer. The adapter sequences at both ends of raw reads were trimmed using cutadapt (cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC) (Martin, 2011). The paired-end trimmed reads were joined using fastq-join (fastq-join -p 5) (Aronesty, 2013). The high-quality joined reads were collected using fastq_quality_filter (fastq_quality_filter -q 20 -p 90). The duplicated reads were removed using fastx_collapser. The fastq_quality_filter and fastx_collapser program were obtained from http://hannonlab.cshl.edu/fastx_toolkit/index.html. The 6-nt randomized barcodes in the 5p-end of the remaining reads were trimmed using cutadapt (cutadapt -u 6) (Martin, 2011). The trimmed reads now contained the 30-nt randomized barcodes (30N), the constant region (refDNA for the DNA dictionary, OS for the pri-mir-576shortLS substrate, and CP for cleaved RNAs), and the randomized sequences. Each trimmed read was spit into the 30-nt randomized barcode (30N), and the randomize sequence using cutadapt (cutadapt -g CCAACCGGAA -m 30 -M 30 --discard-untrimmed) (Martin, 2011). The 5'-CCAACCGGAA-3' sequence was the constant upstream region of 30N. As a result, each read was now presented as a pair of the 30N barcode and the randomized sequence, 30N-refDNA pair for DNA dictionary, 30N-OS pair for the pri-mir-576shortLS substrate, 30N-CP1, for the cleaved products of D3∆belt-G2, and 30N-CP21 for the cleaved products of D3∆belt-G1-G4-dimer. OS, original substrate, CP, cleaved products.   The refDNA in the DNA dictionary and OS in pri-mir-576shortLS substrate samples werewere mapped with the reference sequences containing 262,144 possible sequences (lablled from variant_000001 to variant_262144) of 64 randomized groups using BWA (Li and Durbin, 2010). The perfectly mapped sequences were collected. The 30N-refDNA and 30N-OS pairs in these samples were converted into 30N-variant pairs. We merged 30N-variant pairs in these two samples and removed any pairs sharing the same 30N by more than 2 variants and thus obtained a “30N-variant dictionary”, in which each variant had an unique associated 30N barcode.  We mapped the 30N of each 30N-CP1 or 30N-CP2 to the 30N barcodes in the “30N-variant dictionary” and identified the CP1-variant or CP2-variant pair, in which CP1 or CP2 and variant shared the same 30N barcode. As a result, each cleaved fragment (CP1 or CP2) were assigned to its original pri-mir-576shortLS substrate.
Assembly: Pri-miRNA construct sequences
Supplementary files format and content: reference_sequences.txt: Tab-delimited text file contains the reference sequences of all variants
Supplementary files format and content: control_count.txt: Tab-delimited text file contains the barcode and read counts of RNA substrate samples in 2 sets
Supplementary files format and content: product_count.txt: Tab-delimited text file contains the raw counts of cleaved products for each variants in 2 sets
Supplementary files format and content: variant_barcode_linkage_DNA_dictionary_set1.txt: Tab-delimited text file contains the variant-barcode linkage and the number of linkages in DNA dictionary set1 sample
Supplementary files format and content: variant_barcode_linkage_DNA_dictionary_set2.txt: Tab-delimited text file contains the variant-barcode linkage and the number of linkages in DNA dictionary set2 sample
Supplementary files format and content: variant_barcode_linkage_RNA_substrate_set1.txt: Tab-delimited text file contains the variant-barcode linkage and the number of linkages in RNA substrate set1 sample
Supplementary files format and content: variant_barcode_linkage_RNA_substrate_set2.txt: Tab-delimited text file contains the variant-barcode linkage and the number of linkages in RNA substrate set2 sample
Library strategy: pri-miRNA cleavage assay

source_name: RNA D3delbeltG1G4dimer products

extract_protocol:
Illumina adapter sequences were incorporated to the libraries using PCR.
The purified F3 fragments were ligated to 10 pmol 5ꞌ-adapter (RA5-6N, GUU CAG AGU UCU ACA GUC CGA CGA UCN NNN NNN) in a reaction mixture containing 1 μL T4 RNA ligase I (NEB, M0204L), 2 μL 10x T4 RNA ligase buffer, 6 μL of 50% PEG8000, and 0.5 μL of SUPERase•In RNase inhibitor (20 U/μL). The reaction was carried at 25°C for 16 h. The RA5-ligated RNAs were reverse-transcribed with R-RA3 primer (TTG GCA CCC GAG AAT TCC A) by Superscript IV reverse transcriptase (Invitrogen, 18090050). The resulting cDNA was PCR-amplified using a pair of sequencing primers RP1 and one of RPIx.   The original substrates were  reverse-transcribed with R-RA3 primer by Superscript IV reverse transcriptase (Invitrogen, 18090050). The cDNA was first PCR-amplified using a pair of primers F-RA5-18-comp (TTC AGA GTT CTA CAG TCC GAC GAT CCT GCC ATT TTA CAA TCC A) and one of RPIx. The resulting DNA was amplified using a pair of sequencing primers RP1 and one of RPIx.

tag: set

value: set 2


title: SWH1_0min


title: RNA D3-delbelt-G1-G4-dimer products set1

value: set 1


title: RNA D3-delbelt-G2 products set2

source_name: RNA D3delbeltG2 products


title: pAVICs cultured in 2.5mM Phosphate (Pi) for 5 days (d5)_replicate 2


title: RNA substrates set2

source_name: RNA substrates


title: RNA substrates set1


title: DNA dictionary set1

source_name: DNA dictionary


title: RNA D3-delbelt-G2 products set1


title: CHIP_25D_input

city: NYC

first: Kevin

last: Yang

state: New York

institute: New York University Medical Center

data_processing:
Bowtie2 (Langmead et al., 2012) was used for alignment.
Deeptools2 (Ramírez et al., 2016) was used for analysis.
Assembly: E. coli K12 MG1655
Supplementary files format and content: bedgraph.gz

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichiacoli, MG1655, rpoB 525D, CHIP input

extract_protocol:
Overnight cultures of rpoB wild-type rpoC-10X-His, and rpoB T525D rpoC-10X-His were diluted 1,000-fold and grown to an OD600 of 0.2 in 25 ml LB at 37℃ before the addition of 80 ug/ml rifampicin. After 1 hour treatment, cells were washed once in an equal volume LB. Cells were allowed to recover for 1h in LB at 37C before crosslinking with 1% formaldehyde at 37℃ for 20 minutes. A final concentration of 250 mM Glycine was added to quench the reaction. Cells were collected by centrifugation and washed twice with ice cold 1x PBS before being resuspended in 1 ml of lysis buffer (10 mM Tris pH8.0, 100mM NaCl, 1mM EDTA, 1mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-lauroylsarcosine) plus 2 mg/ml lysozyme with protease inhibitor (Roche) and incubated at 37℃ for 30 minutes. DNA was sheared using ultrasonicator Covaris M220 on a 10s on/10s off cycle for a total of 50 cycles. Supernatant was incubated with 6X-His-tag antibody (Proteintech) and incubated at 4℃ overnight. 50ul per sample of Protein A/G beads were pre-equilibrated with 1 ml ice cold 1xPBS +0.5% BSA and incubated with samples for 0.5h at 4℃. Samples were washed 5x in 1 ml RIPA buffer (50mM HEPES pH 7.5, 250mM LiCl, 1mM EDTA, 1% NP40, 0.7% Sodium Deoxycholate) and a final wash in 1x TE (100mM Tris-CL pH 8, 10mM EDTA pH 8). Complexes were uncrosslinked in 250 uL 1x TE + 4uL RNAseA for 1h at 37℃ and then overnight at 65℃ with 1% SDS and 1 mg/ml proteinase K. DNA was purified with ChIP Clean and Concentrate (Zymo). ChIP experiments were done in duplicate.
Libraries were prepared using the NEBNext ChIP-seq library kit (NEB) according to the manufacturer's instructions.

value: rpoB 525D rpoC-10X-His

tag: chip antibody

value: input


title: Wildtype cochlear nucleus 2

first: Hitomi

last: Sakano

address: 1902 Columbia Rd, CHDD, Rm CD176, Box357923

department: Otolaryngology

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bc2fastq version 2.19.1
Quality filtering and adapter removal were performed using FastP version 0.20.0 with parameters “-- length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j"
Cleaned reads were aligned to the Mus musculus reference genome (GRCm38.p6 + Gencode-M22 Annotation) using STAR_2.7.0f and parameters " --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} -- readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif -- outFilterIntronMotifs RemoveNoncanonical"
Gene-level read quantification was derived using the subread-1.6.4 package (featureCounts) with a GTF annotation file (Gencode M22) and parameters "-s 2 -t exon -g gene_name".
For comparative transcript expression analyses, transcript-level reads were quantified with Salmon-0.13.1.  Data normalization and differential expression analysis between genotypes was performed using DESeq2-1.22.1.
Assembly: mg38/M22
Supplementary files format and content: tab deliminated text files contain raw counts for each sample
Supplementary files format and content: tab deliminated text files contain RPKM values for each sample

source_name: cochlear nucleus

extract_protocol:
Tissues were homogenized in lysis buffer (10mM TrisHCl, 150mM NaCl, 10mM EDTA, 0.5% Triton™ X-100) and RNA purified with RNeasy Mini kits with DNase I digestion (QIAGEN)
RNA-seq libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina) with 200 ng of RNA

tag: tissue

value: cochlear nucleus

value: male

value: wildtype

value: two months


title: Wildtype cochlear nucleus 1

tag: strain


title: Fmr1 knock-out cochlear nucleus 3

tag: genotype

value: Fmr1 knock-out


title: CHIP_25D_pd

source_name: Escherichiacoli, MG1655, rpoB 525D, CHIP pulldown

value: 6X-His-tag antibody (Proteintech, 66005-1-Ig))


title: Wildtype cochlear nucleus 3

tag: Sex


title: SWH1_mmlib_0min_1rep


title: CHIP_WT_pd

source_name: Escherichiacoli, MG1655, WT, CHIP pulldown

value: WT rpoC-10X-His


title: Fmr1 knock-out cochlear nucleus 1

tag: age


title: Msn2_delMsn4_d450_642_1

city: Rehovot

first: Naama

last: Barkai

address: Herzl 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: ChEC-seq

data_processing:
library strategy: ChEC-seq
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)

organism: Saccharomyces cerevisiae

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD4 in SC medium with glucose

extract_protocol:
ChEC-seq: phenol chloroform
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al.


title: Rap1_1

description: ChEC-seq


title: Msn2_delMsn4_d450_642_2

description: ChEC-seq


title: Msn2_delMsn4_d150_350_2

description: ChEC-seq


title: Msn2_delMsn4_d250_450_1

description: ChEC-seq


title: Msn2_delMsn4_d150_350_1

description: ChEC-seq


title: DNA dictionary set2


title: Msn2_delMsn4_d350_550_1

description: ChEC-seq


title: Msn2_delMsn4_d250_450_2

description: ChEC-seq


title: Rap1_2

description: ChEC-seq


title: Gal11_MNase_d11_wMsn2_3

description: ChEC-seq

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)
Library strategy: ChEC-seq


title: Rsf2_VMA5prom_3

description: ChEC-seq


title: Gal11_MNase_d11_wMsn2_4

description: ChEC-seq


title: Msn4_VMA5prom_2

description: ChEC-seq


title: Crz1_VMA5prom_3

description: ChEC-seq


title: Rsf2_VMA5prom_4

description: ChEC-seq


title: Yap1_VMA5prom_2

description: ChEC-seq


title: CHIP_WT_input

source_name: Escherichiacoli, MG1655, WT, CHIP input


title: Fmr1 knock-out cochlear nucleus 2


title: Gal11_MNase_d11_wMsn2_1

description: ChEC-seq


title: Rsf2_VMA5prom_2

description: ChEC-seq


title: Rsf2_VMA5prom_1

description: ChEC-seq


title: Crz1_VMA5prom_1

description: ChEC-seq


title: Crz1_VMA5prom_4

description: ChEC-seq


title: Yap1_VMA5prom_1

description: ChEC-seq


title: Msn4_VMA5prom_1

description: ChEC-seq


title: Msn2_delMsn4_d350_550_2

description: ChEC-seq


title: Mig1_ddmig2mig3_2

description: ChEC-seq


title: Nrg2_dMot3_2

description: ChEC-seq


title: Msn2_dNfi1_2

description: ChEC-seq


title: Yap1_dCrz1_2

description: ChEC-seq


title: Msn2_dIxr1_2

description: ChEC-seq


title: Msn2_dAdr1_2

description: ChEC-seq


title: Mig1_dRgt1_1

description: ChEC-seq


title: Msn2_dNfi1_1

description: ChEC-seq


title: Msn2_dIxr1_1

description: ChEC-seq


title: Gal11_MNase_d11_wMsn2_2

description: ChEC-seq


title: Nrg2_dSko1_1

description: ChEC-seq


title: Yap1_dCrz1_1

description: ChEC-seq


title: Tda9_dCrz1_1

description: ChEC-seq


title: Mig1_ddmig2mig3_1

description: ChEC-seq


title: Nrg2_dMot3_1

description: ChEC-seq


title: Hsf1_2

description: ChEC-seq


title: Hsf1_1

description: ChEC-seq


title: Msn2_d4_spikeAro80_3

description: ChEC-seq


title: Msn2_VMA5prom_spikeAro80_3

description: ChEC-seq


title: Msn2_dAdr1_1

description: ChEC-seq


title: Msn2_spikeAro80_3

description: ChEC-seq


title: Msn2_d14_spikeAro80_2

description: ChEC-seq


title: Gal11_MNase_d12_2

description: ChEC-seq


title: Mig1_dRgt1_2

description: ChEC-seq


title: Nrg2_dSko1_2

description: ChEC-seq


title: Tda9_dCrz1_2

description: ChEC-seq


title: Msn2_d4_spikeAro80_2

description: ChEC-seq


title: Msn2_d14_spikeAro80_4

description: ChEC-seq


title: Msn2_d11_spikeAro80_2

description: ChEC-seq


title: Msn2_spikeAro80_2

description: ChEC-seq


title: Msn2_VMA5prom_spikeAro80_2

description: ChEC-seq


title: Gal11_MNase_d12_1

description: ChEC-seq


title: Msn2_d14_spikeAro80_1

description: ChEC-seq


title: Crz1_VMA5prom_2

description: ChEC-seq


title: Msn2_d4_spikeAro80_1

description: ChEC-seq


title: ZNF1_5a

description: ChEC-seq


title: Msn2_spikeAro80_1

description: ChEC-seq


title: Msn2_d11_spikeAro80_1

description: ChEC-seq


title: YJL206C_1b

description: ChEC-seq


title: YJL206C_2b

description: ChEC-seq


title: YLR278C_6b

description: ChEC-seq


title: WAR1_2b

description: ChEC-seq


title: YKL222C_3a

description: ChEC-seq


title: WAR1_1b

description: ChEC-seq


title: YLR278C_6a

description: ChEC-seq


title: YKL222C_1a

description: ChEC-seq


title: URC2_1a

description: ChEC-seq


title: UGA3C_2b

description: ChEC-seq


title: UGA3C_2a

description: ChEC-seq


title: URC2_3a

description: ChEC-seq


title: UGA3C_2c

description: ChEC-seq


title: UGA3C_1c

description: ChEC-seq


title: Msn2_VMA5prom_spikeAro80_1

description: ChEC-seq


title: UGA3C_1a

description: ChEC-seq


title: TOG1_1a

description: ChEC-seq


title: TEA1_1a

description: ChEC-seq


title: TEA1_1c

description: ChEC-seq


title: ZNF1_5b

description: ChEC-seq


title: STB5_2a

description: ChEC-seq


title: STB4_1b

description: ChEC-seq


title: TOG1_2a

description: ChEC-seq


title: YJL206C_1a

description: ChEC-seq


title: STB4_1a

description: ChEC-seq


title: SIP4_1b

description: ChEC-seq


title: WAR1_2a

description: ChEC-seq


title: RDS2_3d

description: ChEC-seq


title: RDS2_3a

description: ChEC-seq


title: RDS1_3b

description: ChEC-seq


title: RDS1_1b

description: ChEC-seq


title: RDS1_3a

description: ChEC-seq


title: RDS1_1a

description: ChEC-seq


title: RDR1_2a

description: ChEC-seq


title: RDR1_1a

description: ChEC-seq


title: PUL4_1f

description: ChEC-seq


title: TEA1_1b

description: ChEC-seq


title: PUL4_1e

description: ChEC-seq


title: PPR1_1f

description: ChEC-seq


title: PPR1_1g

description: ChEC-seq


title: HAP1_2d

description: ChEC-seq


title: OAF3_2a

description: ChEC-seq


title: LEU3_1a

description: ChEC-seq


title: OAF3_1a

description: ChEC-seq


title: HAP1_2a

description: ChEC-seq


title: STB5_1a

description: ChEC-seq


title: HAP1_2b

description: ChEC-seq


title: SIP4_1a

description: ChEC-seq


title: HAP1_2c

description: ChEC-seq


title: RDS2_3c

description: ChEC-seq


title: GSM1_2d

description: ChEC-seq


title: GSM1_2c

description: ChEC-seq


title: GAL4_1c

description: ChEC-seq


title: GAL4_1d

description: ChEC-seq


title: EDS1_2f

description: ChEC-seq


title: DAL81_1a

description: ChEC-seq


title: EDS1_2d

description: ChEC-seq


title: ERT1_2a

description: ChEC-seq


title: DAL81_2a

description: ChEC-seq


title: ARG81_1a

description: ChEC-seq


title: GAL4_1a

description: ChEC-seq


title: ARG81_1b

description: ChEC-seq


title: LEU3_1b

description: ChEC-seq


title: ERT1_1a

description: ChEC-seq


title: CAT8_1b

description: ChEC-seq


title: Skn7_delMsn4_d604_2

description: ChEC-seq

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
ChEC-seq: genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)
Library strategy: ChEC-seq

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. MNase-seq modified from Yaakov et al. 2021


title: Skn7_delMsn4_dTAD_1

description: ChEC-seq


title: Skn7_delMsn4_dTAD_2

description: ChEC-seq


title: Skn7_delMsn4_d604_1

description: ChEC-seq


title: Skn7_delMsn4_dMotA_1

description: ChEC-seq


title: Skn7_delMsn4_dMotA_2

description: ChEC-seq


title: Skn7_delMsn4_d570_2

description: ChEC-seq


title: Skn7_delMsn4_d570_1

description: ChEC-seq


title: Skn7_delMsn4_d450_642_2

description: ChEC-seq


title: Skn7_delMsn4_d470_2

description: ChEC-seq


title: Skn7_delMsn4_d520_2

description: ChEC-seq


title: Skn7_delMsn4_d470_1

description: ChEC-seq


title: Skn7_delMsn4_d420_2

description: ChEC-seq


title: Skn7_delMsn4_d450_642_1

description: ChEC-seq


title: Skn7_delMsn4_d420_1

description: ChEC-seq


title: Skn7_delMsn4_d520_1

description: ChEC-seq


title: Skn7_delMsn4_d370_1

description: ChEC-seq


title: Skn7_delMsn4_d370_2

description: ChEC-seq


title: CAT8_1a

description: ChEC-seq


title: Skn7_delMsn4_d350_550_2

description: ChEC-seq


title: Skn7_delMsn4_d320_1

description: ChEC-seq


title: Skn7_delMsn4_d350_550_1

description: ChEC-seq


title: Skn7_delMsn4_d200_2

description: ChEC-seq


title: Skn7_delMsn4_d250_450_1

description: ChEC-seq


title: Skn7_delMsn4_d250_450_2

description: ChEC-seq


title: Skn7_delMsn4_d150_350_2

description: ChEC-seq


title: Skn7_delMsn4_d135_2

description: ChEC-seq


title: Msn2_delMsn4_dTAD_1

description: ChEC-seq


title: Skn7_delMsn4_d135_1

description: ChEC-seq


title: Msn2_delMsn4_dMotA_1

description: ChEC-seq


title: Msn2_delMsn4_dTAD_2

description: ChEC-seq


title: Msn2_delMsn4_d570_2

description: ChEC-seq


title: Skn7_delMsn4_d200_1

description: ChEC-seq


title: Msn2_delMsn4_d520_2

description: ChEC-seq


title: Msn2_delMsn4_d570_1

description: ChEC-seq


title: Msn2_delMsn4_d470_1

description: ChEC-seq


title: Msn2_delMsn4_d520_1

description: ChEC-seq


title: Msn2_delMsn4_d470_2

description: ChEC-seq


title: Msn2_delMsn4_dMotA_2

description: ChEC-seq


title: Msn2_delMsn4_d420_2

description: ChEC-seq


title: Skn7_delMsn4_d150_350_1

description: ChEC-seq


title: Msn2_delMsn4_d420_1

description: ChEC-seq


title: Msn2_delMsn4_d370_1

description: ChEC-seq


title: Msn2_delMsn4_d370_2

description: ChEC-seq


title: Msn2_delMsn4_d604_1

description: ChEC-seq


title: Skn7_delMsn4_d320_2

description: ChEC-seq


title: Msn2_delMsn4_d320_2

description: ChEC-seq


title: Msn2_delMsn4_d320_1

description: ChEC-seq


title: Msn2_delMsn4_d200_2

description: ChEC-seq


title: Msn2_delMsn4_d200_1

description: ChEC-seq


title: Msn2_delMsn4_d135_1

description: ChEC-seq


title: Crz1_delMsn4_dTAD_2

description: ChEC-seq


title: Crz1_delMsn4_dMotA_1

description: ChEC-seq


title: Msn2_delMsn4_d135_2

description: ChEC-seq


title: Crz1_delMsn4_d604_2

description: ChEC-seq


title: Crz1_delMsn4_d604_1

description: ChEC-seq


title: Crz1_delMsn4_d570_1

description: ChEC-seq


title: Crz1_delMsn4_d370_2

description: ChEC-seq


title: Crz1_delMsn4_d320_1

description: ChEC-seq


title: Crz1_delMsn4_d520_2

description: ChEC-seq


title: Crz1_delMsn4_d520_1

description: ChEC-seq


title: Crz1_delMsn4_d570_2

description: ChEC-seq


title: Crz1_delMsn4_dMotA_2

description: ChEC-seq


title: Crz1_delMsn4_d470_1

description: ChEC-seq


title: Crz1_delMsn4_dTAD_1

description: ChEC-seq


title: Crz1_delMsn4_d450_642_1

description: ChEC-seq


title: Crz1_delMsn4_d350_550_2

description: ChEC-seq


title: Crz1_delMsn4_d250_450_2

description: ChEC-seq


title: Crz1_delMsn4_d350_550_1

description: ChEC-seq


title: Crz1_delMsn4_d250_450_1

description: ChEC-seq


title: Crz1_delMsn4_d370_1

description: ChEC-seq


title: Crz1_delMsn4_d450_642_2

description: ChEC-seq


title: Crz1_delMsn4_d420_1

description: ChEC-seq


title: Crz1_delMsn4_d200_2

description: ChEC-seq


title: Crz1_delMsn4_d135_1

description: ChEC-seq


title: Hsf1_delMsn4_dTAD_2

description: ChEC-seq


title: Crz1_delMsn4_d200_1

description: ChEC-seq


title: Crz1_delMsn4_d150_350_2

description: ChEC-seq


title: Hsf1_delMsn4_dMotA_2

description: ChEC-seq


title: Crz1_delMsn4_d135_2

description: ChEC-seq


title: Crz1_delMsn4_d150_350_1

description: ChEC-seq


title: Hsf1_delMsn4_dMotA_1

description: ChEC-seq


title: Hsf1_delMsn4_dTAD_1

description: ChEC-seq


title: Hsf1_delMsn4_d604_1

description: ChEC-seq


title: Crz1_delMsn4_d420_2

description: ChEC-seq


title: Hsf1_delMsn4_d570_2

description: ChEC-seq


title: Hsf1_delMsn4_d520_2

description: ChEC-seq


title: Hsf1_delMsn4_d520_1

description: ChEC-seq


title: Hsf1_delMsn4_d570_1

description: ChEC-seq


title: Hsf1_delMsn4_d470_2

description: ChEC-seq


title: Hsf1_delMsn4_d450_642_3

description: ChEC-seq


title: Hsf1_delMsn4_d450_642_2

description: ChEC-seq


title: Hsf1_delMsn4_d420_2

description: ChEC-seq


title: Hsf1_delMsn4_d450_642_1

description: ChEC-seq


title: Hsf1_delMsn4_d420_1

description: ChEC-seq


title: Hsf1_delMsn4_d470_1

description: ChEC-seq


title: Hsf1_delMsn4_d350_550_1

description: ChEC-seq


title: Hsf1_delMsn4_d370_2

description: ChEC-seq


title: Hsf1_delMsn4_d350_550_3

description: ChEC-seq


title: Hsf1_delMsn4_d604_2

description: ChEC-seq


title: Hsf1_delMsn4_d320_1

description: ChEC-seq


title: Hsf1_delMsn4_d350_550_2

description: ChEC-seq


title: Hsf1_delMsn4_d370_1

description: ChEC-seq


title: Hsf1_delMsn4_d320_2

description: ChEC-seq


title: Hsf1_delMsn4_d135_2

description: ChEC-seq


title: Hsf1_delMsn4_d200_2

description: ChEC-seq


title: Hsf1_delMsn4_d150_350_2

description: ChEC-seq


title: Hsf1_delMsn4_d200_1

description: ChEC-seq


title: Hsf1_delMsn4_d150_350_1

description: ChEC-seq


title: Hsf1_delMsn4_d135_1

description: ChEC-seq


title: Yap1_Msn2zfRpn4_2

description: ChEC-seq


title: Hsf1_delMsn4_d250_450_1

description: ChEC-seq


title: Yap1_d11_wMsn2_2

description: ChEC-seq


title: Yap1_d11_wMsn2_1

description: ChEC-seq


title: Skn7_Msn2zfRpn4_1

description: ChEC-seq


title: Tda9_Msn2zfRpn4_1

description: ChEC-seq


title: Tda9_d11_wMsn2_2

description: ChEC-seq


title: Yap1_Msn2zfRpn4_1

description: ChEC-seq


title: Tda9_d11_wMsn2_1

description: ChEC-seq


title: Skn7_Msn2zfRpn4_2

description: ChEC-seq


title: Skn7_d11_wMsn2_2

description: ChEC-seq


title: Rsf2_Msn2zfRpn4_2

description: ChEC-seq


title: Skn7_d11_wMsn2_1

description: ChEC-seq


title: Hsf1_delMsn4_d250_450_2

description: ChEC-seq


title: Hsf1_Msn2zfRpn4_2

description: ChEC-seq


title: Crz1_d11_wMsn2_2

description: ChEC-seq


title: Crz1_Msn2zfRpn4_2

description: ChEC-seq


title: Yap1_dGal11_1

description: ChEC-seq


title: Hsf1_Msn2zfRpn4_1

description: ChEC-seq


title: Crz1_d11_wMsn2_1

description: ChEC-seq


title: Yap1_dGal11_2

description: ChEC-seq


title: Tda9_dGal11_2

description: ChEC-seq


title: Skn7_dGal11_2

description: ChEC-seq


title: Skn7_dGal11_1

description: ChEC-seq


title: Rsf2_dGal11_2

description: ChEC-seq


title: Msn2_Msn2wRpn4DBD_A_2

description: ChEC-seq


title: Tda9_dGal11_1

description: ChEC-seq


title: Rsf2_dGal11_1

description: ChEC-seq


title: Msn2_Msn2wRpn4DBD_A_1

description: ChEC-seq


title: Hsf1_dGal11_2

description: ChEC-seq


title: Hsf1_dGal11_1

description: ChEC-seq


title: Crz1_dGal11_2

description: ChEC-seq


title: Sok2_d16_2

description: ChEC-seq


title: Sko1_d16_2

description: ChEC-seq


title: Sok2_d16_1

description: ChEC-seq


title: Skn7_d16_1

description: ChEC-seq


title: Sko1_d16_1

description: ChEC-seq


title: Rox1_d16_1

description: ChEC-seq


title: Skn7_d16_2

description: ChEC-seq


title: Rsf2_Msn2zfRpn4_1

description: ChEC-seq


title: Rox1_d16_2

description: ChEC-seq


title: Crz1_Msn2zfRpn4_1

description: ChEC-seq


title: Phd1_d16_2

description: ChEC-seq


title: Mot3_d16_1

description: ChEC-seq


title: Mig2_d16_1

description: ChEC-seq


title: Mig2_d16_2

description: ChEC-seq


title: Mot3_d16_2

description: ChEC-seq


title: Gal11_ddmsn_1

description: ChEC-seq


title: Ixr1_d16_2

description: ChEC-seq


title: Dot6_d16_1

description: ChEC-seq


title: Dot6_d16_2

description: ChEC-seq


title: Sok2_VMA5prom_2

description: ChEC-seq


title: Cyc8_d16_2

description: ChEC-seq


title: Tda9_VMA5prom_1

description: ChEC-seq


title: Skn7_VMA5prom_1

description: ChEC-seq


title: Phd1_VMA5prom_2

description: ChEC-seq


title: Cyc8_d16_1

description: ChEC-seq


title: Phd1_VMA5prom_1

description: ChEC-seq


title: Nrg1_d12_3

description: ChEC-seq


title: Crz1_dGal11_1

description: ChEC-seq


title: Nrg1_d12_2

description: ChEC-seq


title: Nrg1_d12_1

description: ChEC-seq


title: Msn2_d12cycmod_1

description: ChEC-seq


title: Msn2_d12cycmod_3

description: ChEC-seq


title: Ixr1_d16_1

description: ChEC-seq


title: Mig3_VMA5prom_2

description: ChEC-seq


title: Gis1_VMA5prom_2

description: ChEC-seq


title: Phd1_d16_1

description: ChEC-seq


title: Gis1_VMA5prom_1

description: ChEC-seq


title: Cyc8_VMA5prom_2

description: ChEC-seq


title: Cyc8_d7_2

description: ChEC-seq


title: Sok2_VMA5prom_1

description: ChEC-seq


title: Cin5_VMA5prom_2

description: ChEC-seq


title: Yap1_dmsn4_2

description: ChEC-seq


title: Cyc8_d7_1

description: ChEC-seq


title: Yap1_dmsn2_2

description: ChEC-seq


title: Yap1_dmsn4_1

description: ChEC-seq


title: Yap1_dmsn2_1

description: ChEC-seq


title: Cyc8_VMA5prom_1

description: ChEC-seq


title: Tda9_dmsn4_1

description: ChEC-seq


title: Mig3_VMA5prom_1

description: ChEC-seq


title: Tda9_dmsn2_1

description: ChEC-seq


title: Tda9_dmsn4_2

description: ChEC-seq


title: Cin5_VMA5prom_1

description: ChEC-seq


title: Sko1_dmsn4_2

description: ChEC-seq


title: Sko1_dmsn2_1

description: ChEC-seq


title: Sko1_dmsn2_2

description: ChEC-seq


title: Msn2_d12cycmod_2

description: ChEC-seq


title: Skn7_dmsn2_2

description: ChEC-seq


title: Skn7_dmsn2_1

description: ChEC-seq


title: Skn7_dmsn4_1

description: ChEC-seq


title: Mig3_d12_2

description: ChEC-seq


title: Mig3_d12_1

description: ChEC-seq


title: Rsf2_dmsn2_2

description: ChEC-seq


title: Hsf1_dmsn4_1

description: ChEC-seq


title: Hsf1_dmsn4_2

description: ChEC-seq


title: Hsf1_dmsn2_2

description: ChEC-seq


title: Hsf1_dmsn2_1

description: ChEC-seq


title: Gis1_dmsn4_2

description: ChEC-seq


title: Tda9_dmsn2_2

description: ChEC-seq


title: Gis1_dmsn2_2

description: ChEC-seq


title: Gis1_dmsn4_1

description: ChEC-seq


title: Cyc8_d12_2

description: ChEC-seq


title: Sko1_dmsn4_1

description: ChEC-seq


title: Crz1_dmsn4_1

description: ChEC-seq


title: Cyc8_d12_1

description: ChEC-seq


title: Crz1_dmsn2_2

description: ChEC-seq


title: Rsf2_dmsn4_1

description: ChEC-seq


title: Skn7_dmsn4_2

description: ChEC-seq


title: Asg1_VMA5prom_2

description: ChEC-seq


title: Asg1_VMA5prom_1

description: ChEC-seq


title: Crz1_dmsn2_1

description: ChEC-seq


title: Asg1_dmsn2_2

description: ChEC-seq


title: Asg1_dmsn2_1

description: ChEC-seq


title: Asg1_dmsn4_2

description: ChEC-seq


title: Rsf2_dmsn2_1

description: ChEC-seq


title: Sko1_d6_2

description: ChEC-seq


title: Sko1_d6_1

description: ChEC-seq


title: Sok2_d12_1

description: ChEC-seq


title: Gis1_dmsn2_1

description: ChEC-seq


title: Sok2_d12_2

description: ChEC-seq


title: Sko1_d12_1

description: ChEC-seq


title: Nrg2_d12_2

description: ChEC-seq


title: Crz1_dmsn4_2

description: ChEC-seq


title: Phd1_d12_2

description: ChEC-seq


title: Nrg2_d6_2

description: ChEC-seq


title: Mot3_d6_2

description: ChEC-seq


title: Mot3_d6_1

description: ChEC-seq


title: Phd1_d12_1

description: ChEC-seq


title: Mig3_d6_1

description: ChEC-seq


title: Mot3_d12_1

description: ChEC-seq


title: Asg1_dmsn4_1

description: ChEC-seq


title: Nrg2_d12_1

description: ChEC-seq


title: Ixr1_d12_2

description: ChEC-seq


title: Nrg1_d6_1

description: ChEC-seq


title: Mig2_d6_1

description: ChEC-seq


title: Mig2_d6_2

description: ChEC-seq


title: Mig1_d12_1

description: ChEC-seq


title: Mig2_d12_1

description: ChEC-seq


title: Sko1_d12_2

description: ChEC-seq


title: Ixr1_d12_1

description: ChEC-seq


title: Cin5_d12_1

description: ChEC-seq


title: Nrg2_d6_1

description: ChEC-seq


title: Yap1_ddmsn_1

description: ChEC-seq


title: Yap1_ddmsn_2

description: ChEC-seq


title: Tda9_ddmsn_2

description: ChEC-seq


title: Rsf2_ddmsn_2

description: ChEC-seq


title: Skn7_ddmsn_2

description: ChEC-seq


title: Tda9_ddmsn_1

description: ChEC-seq


title: Rsf2_ddmsn_1

description: ChEC-seq


title: Msn2_d14_3

description: ChEC-seq


title: Msn2_d14_2

description: ChEC-seq


title: Hsf1_ddmsn_1

description: ChEC-seq


title: Mig1_d12_2

description: ChEC-seq


title: Msn2_d14_1

description: ChEC-seq


title: Crz1_ddmsn_2

description: ChEC-seq


title: Gis1_ddmsn_2

description: ChEC-seq


title: Asg1_ddmsn_2

description: ChEC-seq


title: Hsf1_ddmsn_2

description: ChEC-seq


title: Msn2DBD_d11_2

description: ChEC-seq


title: Yap1_d11_2

description: ChEC-seq


title: Gis1_ddmsn_1

description: ChEC-seq


title: Crz1_ddmsn_1

description: ChEC-seq


title: Tda9_d7A_2

description: ChEC-seq


title: Tda9_d7A_1

description: ChEC-seq


title: Msn2DBD_d11_1

description: ChEC-seq


title: Cin5_d12_2

description: ChEC-seq


title: Tda9_d11_2

description: ChEC-seq


title: Skn7_ddmsn_1

description: ChEC-seq


title: Sko1_d7B_2

description: ChEC-seq


title: Tda9_d11_1

description: ChEC-seq


title: Sko1_d7B_1

description: ChEC-seq


title: Skn7_d11_2

description: ChEC-seq


title: Rsf2_d7A_1

description: ChEC-seq


title: Skn7_d11_1

description: ChEC-seq


title: Rsf2_d11_1

description: ChEC-seq


title: Msn4_d7B_1

description: ChEC-seq


title: Msn4_d11_2

description: ChEC-seq


title: Asg1_ddmsn_1

description: ChEC-seq


title: Msn2_d7B_4

description: ChEC-seq


title: Msn2_d7B_3

description: ChEC-seq


title: Msn2_d7B_2

description: ChEC-seq


title: Yap1_d11_1

description: ChEC-seq


title: Msn4_d11_1

description: ChEC-seq


title: Msn2_d7A_2

description: ChEC-seq


title: Msn2_d7A_1

description: ChEC-seq


title: Msn2_d7B_1

description: ChEC-seq


title: Gis1_d11_1

description: ChEC-seq


title: Crz1_d7B_2

description: ChEC-seq


title: Crz1_d7B_1

description: ChEC-seq


title: Msn2_d11_1

description: ChEC-seq


title: Crz1_d11_1

description: ChEC-seq


title: Crz1_d11_2

description: ChEC-seq


title: Yap1_d4_1

description: ChEC-seq


title: Skn7_d4_2

description: ChEC-seq


title: Yap1_d4_2

description: ChEC-seq


title: Yap1_d7A_1

description: ChEC-seq


title: Rsf2_d11_2

description: ChEC-seq


title: Skn7_d4_1

description: ChEC-seq


title: Msn2_d4_1

description: ChEC-seq


title: Crz1_d4_2

description: ChEC-seq


title: Rsf2_d7A_2

description: ChEC-seq


title: Msn2_VMA5prom_1

description: ChEC-seq


title: Crz1_d4_1

description: ChEC-seq


title: Msn2_d4_2

description: ChEC-seq


title: Msn2_VMA5prom_2

description: ChEC-seq


title: Mcm1_2

description: ChEC-seq


title: Mcm1_1

description: ChEC-seq


title: Msn2_d11_2

description: ChEC-seq


title: Gis1_d11_2

description: ChEC-seq


title: Sok2_cyc8_deg_30_1

description: ChEC-seq


title: Sok2_cyc8_deg_0_2

description: ChEC-seq


title: Asg1_1

description: ChEC-seq


title: Sko1_cyc8_deg_30_1

description: ChEC-seq


title: Sok2_cyc8_deg_30_2

description: ChEC-seq


title: Sko1_cyc8_deg_0_2

description: ChEC-seq


title: Asg1_2

description: ChEC-seq


title: Sko1_cyc8_deg_0_1

description: ChEC-seq


title: Sko1_cyc8_deg_30_2

description: ChEC-seq


title: Skn7_cyc8_deg_30_2

description: ChEC-seq


title: Skn7_cyc8_deg_30_1

description: ChEC-seq


title: Skn7_cyc8_deg_0_2

description: ChEC-seq


title: Mot3_cyc8_deg_30_2

description: ChEC-seq


title: Mot3_cyc8_deg_30_1

description: ChEC-seq


title: Skn7_cyc8_deg_0_1

description: ChEC-seq


title: Mot3_cyc8_deg_0_2

description: ChEC-seq


title: Mot3_cyc8_deg_0_1

description: ChEC-seq


title: Ixr1_cyc8_deg_30_2

description: ChEC-seq


title: Ixr1_cyc8_deg_0_2

description: ChEC-seq


title: Ixr1_cyc8_deg_30_1

description: ChEC-seq


title: MNase_seq_dmsn4_2

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
MNase-seq: genome coverage with bedtools: ‘-pc -fs 100’  size limit 100-200
ChEC-seq: genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)

extract_protocol:
Chromatin precipitation
One tube library construction based on Skeene et al. 2017 as described in Gera 2021


title: MNase_seq_dmsn4_1


title: MNase_seq_ddmsn_2


title: MNase_seq_Msn2_d11_SM_2


title: Ixr1_cyc8_deg_0_1

description: ChEC-seq


title: MNase_seq_d12_SM_2


title: MNase_seq_d12_SM_1


title: MNase_seq_Msn2_d11_SM_1


title: Liver Spring LKO Fasted 8

city: Amsterdam

first: Noam

last: Zelcer

address: Meibergdreef 9

department: Medical BIochemistry

country: Netherlands

institute: AMC

data_processing:
Quality control (fastQC, dupRadar, Picard Tools)  was performed on the reads.
Read were trimmed using Trimmomatic v0.32 29 and aligned to the mouse genome using HISAT2 (v2.1.0). Counts were obtained using corresponding GTF and HTSeq (v0.11.0).  Bioconductor v3.7
TMM (EdgeR)and limma/voomR packages were used to perform statistical analysis. Count data was transformed to log2-counts per million (logCPM) and normalized using the trimmed mean of M-values method.
Voom was used to precision weigh the data. Bayes moderated t-test was used to assess differential expression within limma’s linear model framework and the precision weights estimated by voom. The mouse ID was included as a random effect in the linear model to estimate the consensus correlation, using duplicateCorrelation from the limma package.
The p values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate and BiomaRt (release 94) was used to reannotate the genes.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file with raw counts for each sample
Supplementary files format and content: n/a

source_name: Liver

extract_protocol:
RNA tissue from liver was isolated with the Direct-Zol RNA column system (Zymo)
A KAPA mRNA hyperPrep kit (KAPA Biosystems) was used for mRNA library construction

treatment_protocol: We compared the hepatic gene expression profile of Ctrl mice to mice lacking hepatic expression of Spring (SPRING LKO). This was done in livers of fasted (20 h fasting; n Ctrl = 8; n LKO = 9) and refed (20h fasting followed by 4 h refeding; n Ctrl = 9; n LKO = 8) mice the as transition from the fasted to the fed state is accompanied by acute reprogramming of hepatic gene expression and induction of the SREBP-regulated pathway.

value: Liver

value: Spring liver knockout

value: 20 h fasting


title: Liver Spring LKO Fasted 9


title: Sok2_cyc8_deg_0_1

description: ChEC-seq


title: MNase_seq_ddmsn_1


title: MNase_seq_WT_2


title: Liver Ctrl Refed 8

value: WT

value: 20 h fasting - 4 h refeding


title: Liver Spring LKO Fasted 7


title: Liver Ctrl Fasted 8


title: Liver Spring LKO Refed 8


title: Liver Ctrl Fasted 7


title: Liver Spring LKO Refed 6


title: Liver Spring LKO Fasted 6


title: Liver Ctrl Refed 7


title: Liver Ctrl Fasted 6


title: HA + P19 vector AGL1 infiltration, 6 days, rep 1

city: Quebec

first: Louis-Philippe

last: Hamel

state: Quebec

address: 2552 boul. du Parc-Technologique

institute: Medicago

data_processing:
star:2.5.1b
cufflinks: 2.2.1
picard: 1.123
samtools: 1.2
trimmomatic: 0.32
bedtools: 2.17.0
Assembly: ucsc: v20140212
Supplementary files format and content: Count_matrix file contains counts for identified genes features for all samples
Supplementary files format and content: DGE file contains differential genes expression comparison via Deseq2 or EdgeR

organism: Nicotiana benthamiana

source_name: Leaf, LPI4-5

extract_protocol:
RNA extracted with Qiagen RNeasy plant kit
TrueSeq RNA sequencing adapters (Illumina)

value: Leaf, LPI4-5

value: N/Ap


title: HA + P19 vector AGL1 infiltration, 6 days, rep 3


title: Liver Spring LKO Refed 7


title: HA + P19 vector AGL1 infiltration, 6 days, rep 2


title: P19 vector AGL1 infiltration, 6 days, rep 3

value: P19 vector AGL1 infiltration, 6 days


title: P19 vector AGL1 infiltration, 6 days, rep 1


title: Empty vector AGL1 infiltration, 6 days, rep 3

value: Empty vector AGL1 infiltration, 6 days


title: P19 vector AGL1 infiltration, 6 days, rep 2


title: Liver Spring LKO Refed 5


title: Liver Ctrl Refed 5


title: Liver Ctrl Fasted 5


title: Liver Ctrl Refed 6


title: Liver Spring LKO Fasted 5


title: MNase_seq_WT_1


title: Empty vector AGL1 infiltration, 6 days, rep 2


title: Liver Ctrl Fasted 4


title: Liver Ctrl Fasted 3


title: Mock Infiltration, 6 days, Rep 3

value: Mock Infiltration, 6 days


title: Liver Spring LKO Fasted 4


title: Empty vector AGL1 infiltration, 6 days, rep 1


title: Mock Infiltration, 6 days, Rep 2


title: Mock Infiltration, 6 days, Rep 1


title: Liver Ctrl Refed 4


title: Liver Spring LKO Fasted 3


title: Non-Infiltrated, 6 Days, Rep 3

value: Non-Infiltrated, 6 Days


title: Liver Ctrl Fasted 2


title: Non-Infiltrated, 6 Days, Rep 2


title: Liver Ctrl Refed 9


title: Non-Infiltrated, 6 Days, Rep 1


title: Liver Ctrl Refed 3


title: HRDE-1, simr-1 mut-2 (adult) - IP, replicate 3

city: Los Angeles

first: Carolyn

middle: Marie

last: Phillips

state: CA

address: 1050 Childs Way, RRI 201

department: Biological Sciences

institute: University of Southern California

description: size-selected small RNA

data_processing:
Small RNA libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform.
Sequences were parsed from adapters using FASTQ/A Clipper (options: -Q33 -l 17 -c -n -a TGGAATTCTCGGGTGCCAAGG) and quality filtered using the FASTQ Quality Filter (options: -Q33 -q 27 -p 65) from the FASTX-Toolkit
Contamination from reads mapping to 18-mer and 28-mer size standards were filtered out using Cutadapt (version 3.4)
Filtered reads were mapped to the C. elegans genome WS258 using Bowtie2 v. 2.5.0 (default parameters)
Reads were assigned to genomic features using featureCounts (options: -t exon -g gene_id -O --fraction –largestOverlap) which is part of the Subread v. 2.0.1 package.
Assembly: WS258
Supplementary files format and content: Processed data files are tab-delimited text files including total reads mapping to each gene generated by FeatureCounts.

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Sychronized animals were grown on enriched peptone plates seeded with OP50 E. coli at 20°C for 68 hours post-hatching (for 1-day-old adults ).

extract_protocol:
For immunoprecipitation, ~100,000 synchronized 1-day-old adult animals were collected in IP Buffer (50 mM Tris-Cl pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igapal CA-630, 0.5 mM PMSF, cOmplete Protease Inhibitor Cocktail, and RNaseOUT Ribonuclease Inhibitor), frozen in liquid nitrogen, and homogenized using a mortar and pestle. After further dilution into IP buffer (1:10 packed worms:buffer), insoluble particulate was removed by centrifugation and a sample was taken as “input.”  The remaining lysate was used for the immunoprecipitation. Immunoprecipitation was performed at 4°C for 1 hour, then washed at least 3 times in immunoprecipitation buffer. Trizol reagent was added to the remainder of each sample, followed by chloroform extraction, and isopropanol precipitation.
Small RNAs (18 to 30-nt) were size selected on denaturing 15% polyacrylamide gels from total RNA samples. Small RNAs were treated with 5’ RNA polyphosphatase and ligated to 3’ pre-adenylated adapter with Truncated T4 RNA ligase. Small RNAs were then hybridized to the TruSeq reverse transcription primer, ligated to the 5’ adapter with T4 RNA ligase), and reverse transcribed with Superscript III. Small RNA libraries were amplified using Q5 High-Fidelity DNA polymerase and size selected on a 10% polyacrylamide gel. Library concentration was determined using the Qubit 1X dsDNA HS Assay kit and quality was assessed using the Agilent BioAnalyzer.
small RNA-seq

value: Whole worm

tag: antibody

value: FLAG (Sigma Aldrich, A2220)

value: USC1475 - simr-1(cmp36) mut-2(cmp306) I; hrde-1(tor125[GFP::3xFLAG::hrde-1]) III

tag: Stage

value: 1-day-old adult

tag: temperature

tag: fraction

value: IP


title: HRDE-1, simr-1 mut-2 (adult) - IP, replicate 2

description: size-selected small RNA


title: Liver Spring LKO Refed 2

tag: treatment


title: Liver Spring LKO Refed 3


title: HRDE-1, simr-1 mut-2 (adult) - input, replicate 3

description: size-selected small RNA

value: Input


title: Liver Ctrl Refed 2

value: Liver


title: HRDE-1, simr-1 mut-2 (adult) - input, replicate 1

description: size-selected small RNA


title: HRDE-1, simr-1 mut-2 (adult) - input, replicate 2

description: size-selected small RNA


title: Liver Spring LKO Refed 1

value: Spring liver knockout


title: HRDE-1, mut-2; hrde-2 (adult) - IP, replicate 3

description: size-selected small RNA

value: USC1474 - mut-2(ne298) I; hrde-1(tor125[GFP::3xFLAG::hrde-1]) III; hrde-2/enri-3(qe20) V


title: HRDE-1, simr-1 mut-2 (adult) - IP, replicate 1

description: size-selected small RNA


title: Liver Ctrl Fasted 1

value: WT

value: 20 h fasting


title: Liver Spring LKO Fasted 2


title: Liver Spring LKO Fasted 1


title: Liver Spring LKO Refed 4

value: 20 h fasting - 4 h refeding


title: P21_64KO

city: Nanjing

first: Wukui

last: Zhao

address: Hankou Road 22nd

institute: Nanjing University

data_processing:
The raw paired-end RNA-Seq reads were aligned to the mouse genome (UCSC mm10) with TopHat 2.0.14.
Transcripts per million (TPM) were calculated using Cufflinks 2.2.1.
Gene expression analysis for differential expression was performed by Cuffdiff2 version 2.2.1.
Assembly: mm10
Supplementary files format and content: all_seq.txt: Tab-delimited text file includes TPM values for each Sample.

source_name: heart

extract_protocol:
Total RNA was isolated from the hearts of PDK1 cKO and wild-type mice using RNA iso Plus (Takara).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: heart

value: PDK1 CKO


title: HRDE-1, mut-2; hrde-2 (adult) - IP, replicate 1

description: size-selected small RNA


title: HRDE-1, mut-2; hrde-2 (adult) - input, replicate 3

description: size-selected small RNA


title: HRDE-1, mut-2; hrde-2 (adult) - IP, replicate 2

description: size-selected small RNA


title: Liver Ctrl Refed 1


title: P21_55KO


title: HRDE-1, mut-2; hrde-2 (adult) - input, replicate 2

description: size-selected small RNA


title: P7_75KO


title: P7_82KO


title: HRDE-1, mut-2; hrde-2 (adult) - input, replicate 1

description: size-selected small RNA


title: HRDE-1, mut-2 (adult) - IP, replicate 3

description: size-selected small RNA

value: USC1473 - mut-2(ne298) I; hrde-1(tor125[GFP::3xFLAG::hrde-1]) III


title: HRDE-1, mut-2 (adult) - IP, replicate 2

description: size-selected small RNA


title: HRDE-1, mut-2 (adult) - IP, replicate 1

description: size-selected small RNA


title: P21_63


title: HRDE-1, mut-2 (adult) - input, replicate 3

description: size-selected small RNA


title: P7_69KO


title: P21_60


title: P21_57


title: P7_76


title: HRDE-1, mut-2 (adult) - input, replicate 1

description: size-selected small RNA


title: HRDE-1, mut-2 (adult) - input, replicate 2

description: size-selected small RNA


title: P7_72


title: HRDE-1, simr-1 (adult) - IP, replicate 2

description: size-selected small RNA

value: USC1464 - simr-1 (cmp36) I;  hrde-1(tor125[GFP::3xFLAG::hrde-1]) III


title: HRDE-1, simr-1 (adult) - IP, replicate 3

description: size-selected small RNA


title: P7_77


title: P21_B6_2


title: HRDE-1, simr-1 (adult) - input, replicate 3

description: size-selected small RNA


title: HRDE-1, simr-1 (adult) - IP, replicate 1

description: size-selected small RNA


title: P7_heart1


title: HRDE-1, simr-1 (adult) - input, replicate 2

description: size-selected small RNA


title: P21_59KO


title: P7_heart3


title: HRDE-1, simr-1 (adult) - input, replicate 1

description: size-selected small RNA


title: HRDE-1, hrde-2 (adult) - IP, replicate 3

description: size-selected small RNA

value: USC1465 - hrde-1(tor125[GFP::3xFLAG::hrde-1]) III; hrde-2/enri-3(qe20) V


title: P1_H3


title: HRDE-1, hrde-2 (adult) - IP, replicate 2

description: size-selected small RNA

value: Whole worm


title: P1_H1


title: P1_H2


title: HRDE-1, hrde-2 (adult) - input, replicate 3

description: size-selected small RNA


title: HRDE-1, hrde-2 (adult) - input, replicate 2

description: size-selected small RNA


title: RNAseq_VU609_t_1_S8

first: Bart A.

last: Westerman

address: De Boelelaan 1117

department: Cancer Center Amsterdam - Neurosurgery

institute: Cancer Center Amsterdam CCA

data_processing:
Adaptor sequences are removed with cutadapt 1.14 with the following settings: -u 1 -m 15 -e 0.2 -O 7 --discard-untrimmed
Reads are separated based on library barcode by cutadapt 1.14 with option -e 0.2.
Unique Molecular Identifiers (UMIs) are extracted and clustered using umi_tools 0.5.5.
Reads are mapped to hg38 by bowtie 1.2.2 with the following setting: --chunkmbs 2000 -k 1 --best -S
UMIs are collapsed to remove sequencing errors and PCR errors. Umitools dedup was used for this purpose.
rRNA reads are removed based on coordinates of rRNA in GENCODE reference human genome (hg) 38 version 30.
https://github.com/Arthurhe/RiboReadCountByFrame
Supplementary files format and content: rds

source_name: VU609 RNA seq irradiated (t=30 min)

growth_protocol: GSCs were cultured in Neurobasal-A-Medium (NBM) supplemented with B27 without vitamin A, N2, Glutamax, human EGF, human FGF basic, heparin and penicillin/streptomycin.

extract_protocol:
total RNA was lysed and purified by Trizol extraction. RiboRNA was performed extracted using a buffer consisting of 20 mM Tris pH 7.5, 150 mM NaCl, 5 mM MgCl2, 100 µg ml-1 cycloheximide, 1% Triton X-100, 10 U ml-1 Turbo DNase I and nuclease free H2O
mRNA-seq libraries were generated from high quality RNA (average RNA Integrity Number (RIN) of 9.5)

treatment_protocol: Cells were irradiated once at room temperature with 2Gy using a Mark I Cesium-137 source

value: Glioblastoma

tag: cell line

tag: cell type

value: CNS derived tumor

value: IDH1 wild type

value: Irradiated


title: HRDE-1, hrde-2 (adult) - input, replicate 1

description: size-selected small RNA

value: 1-day-old adult

value: Input


title: HRDE-1, hrde-2 (adult) - IP, replicate 1

description: size-selected small RNA

value: FLAG (Sigma Aldrich, A2220)

value: IP


title: RNAseq_VU609_t_0_S7

source_name: VU609 RNA seq not irratiated (t=0 min)


title: RNAseq_VU609_t_2_S9

source_name: VU609 RNA seq irradiated (t=60 min)


title: RNAseq_VU598_t_2_S6

source_name: VU598 RNA seq irradiated (t=60 min)


title: P21_B6_3

value: WT


title: HRDE-1 (adult) - input, replicate 3

description: size-selected small RNA

value: JMC231 - hrde-1(tor125[GFP::3xFLAG::hrde-1]) III


title: HRDE-1 (adult) - IP, replicate 2

description: size-selected small RNA


title: HRDE-1 (adult) - IP, replicate 1

description: size-selected small RNA


title: RNAseq_VU598_t_1_S5

source_name: VU598 RNA seq irradiated (t=30 min)


title: RNAseq_VU598_t_0_S4

source_name: VU598 RNA seq not irratiated (t=0 min)


title: RNAseq_VU593_t_1_S2

source_name: VU593 RNA seq irradiated (t=30 min)


title: HRDE-1 (adult) - input, replicate 1

description: size-selected small RNA


title: HRDE-1 (adult) - IP, replicate 3

description: size-selected small RNA


title: RNAseq_VU593_t_0_S1

source_name: VU593 RNA seq not irratiated (t=0 min)


title: RNAseq_VU593_t_2_S3

source_name: VU593 RNA seq irradiated (t=60 min)


title: RNAseq_VU591_t_2_S69

source_name: VU591 RNA seq irradiated (t=60 min)

value: IDH1 mutant


title: RNAseq_VU591_t_1_S68

source_name: VU591 RNA seq irradiated (t=30 min)


title: RNAseq_VU591_t_0_S67

source_name: VU591 RNA seq not irratiated (t=0 min)


title: raw_Tg_20140607_P1 (Run 1)

city: Leiden

first: Jan

last: Wijnholds

address: Albinusdreef 2

department: Ophthalmology

institute: Leiden University Medical Center

data_processing:
•Performed sequencing using Life Technologies SOLiD5500, single end, 50 bp. Reads aligned against mm10, bamgen.mqv.threshold set to 20 (Lifescope v2.5)
•Genes with no counts in any of the samples were removed. Filtering: Genes with more than 1 count-per-million reads (CPM) in 5 or more of the samples were kept. Normalization: TMM (edgeR), weighted trimmed mean of M-values (to the reference) is used (Robinson & Oshlack, 2010).
•Original gene symbols mapped to other gene identifiers using biomaRt, using Ensembl (v90). The count data was transformed to log2-counts per million (logCPM) using voom, estimating the mean-variance relationship.
•Benjamini-Hochberg false discovery rate to correct for multiple testing of the resulting p-values. Analysis was performed using R v3.4.1 and Bioconductor v3.5.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and CPMs for each sample

source_name: neuro retina

growth_protocol: All mice used were maintained on a 99.9% C57BL/6JOlaHsd genetic background with a 12 h day-night cycle and supplied with food and water ad libitum. Crb1KO (Crb1-/-) mice (van de Pavert et al., 2004) were crossed with a retinal Crb2ΔRPC (Crb2F/FChx10CreTg/+ clone P1E9) mouse strain (Alves et al., 2013b; Rowan and Cepko, 2004) to ablate both Crb1 and Crb2 during retinal development from retinal progenitor cells. Cre starts to be expressed around E9.5 in the retina (Rowan and Cepko, 2004). The previously made Chx10Cre mice were generated by knocking in GFP-Cre-IRES-AP cDNA in exon-1 of the Chx10 gene on a Bacterial Artificial Chromosomes (BAC; -55 kb Chx10 of ATG to +22 kb off of the polyadenylation sequence) (Rowan and Cepko, 2004). Interestingly, the last exon of the Abcd4 gene is only ~7000 bp from the last exon of the Chx10 gene thus was on the BAC. Others have shown that large BACS containing several genes can lead to overexpression of flanking genes (Kolisnyk et al., 2013; Ting and Feng, 2014). We believe the integration of the cDNA in close proximity to the Abcd4 gene and being both on the BAC may have led to the overexpression of the Abcd4 gene in Crb1KOCrb2ΔRPC mice. Crb1KOCrb2ΔRPC mice were compared to littermate Crb1KOCrb2F/F mice not expressing Cre. C57BL/6JOlaHsd mice have a 365 kb deletion ablating the Mmrn1 and Snca and express low levels of Abcd4 (Gajović et al., 2006; Specht and Schoepfer, 2004). The C57BL/6J substrain (from the Jackson Laboratory) carries a 5-exon-spanning deletion in the Nnt gene but C57BL/6JOlaHsd have a wildtype Nnt gene (Huang et al., 2006).

extract_protocol: Ovation RNA-Seq System V2 (NuGEN) for cDNA amplificationV2.

treatment_protocol: Total of 50 Samples over two separate Runs (Run1/Run2). Two outliers were removed. Input RNA had RIN>8.

value: neuro retina

tag: genetic background

value: retinal cells

value: Crb1Crb2 double KO


title: raw_Tg_20140606_P1 (Run 1)


title: RNAseq_GCS34_t_2_S66

source_name: GSC34 RNA seq irradiated (t=60 min)


title: raw_Tg_20140604_P1 (Run 1)


title: RNAseq_GSC34_t_1_S65

source_name: GSC34 RNA seq irradiated (t=30 min)


title: RNAseq_GSC34_t_0_S64

source_name: GSC34 RNA seq not irratiated (t=0 min)


title: raw_Ctl_20140600_P1 (Run 1)

value: Crb1 knockout


title: raw_Ctl_20140602_P1 (Run 1)


title: raw_Ctl_20140601_P1 (Run 1)


title: RNAseq_GCS28t2_S91_L002

source_name: GSC28 RNA seq irradiated (t=60 min)


title: raw_Ctl_20140599_P1 (Run 1)


title: RNAseq_GSC28t1_S90_L002

source_name: GSC28 RNA seq irradiated (t=30 min)


title: HRDE-1 (adult) - input, replicate 2

description: size-selected small RNA

source_name: Whole worm


title: RNAseq_GSC28t0_S89_L002

source_name: GSC28 RNA seq not irratiated (t=0 min)


title: RNAseq_GSC20_t_2_S72

source_name: GSC20 RNA seq irradiated (t=60 min)


title: raw_C57_20141447_P1 (Run 2)

value: wild type


title: raw_C57_20141445_P1 (Run 2)


title: raw_Ctl_20140598_P1 (Run 1)


title: raw_C57_20141446_P1 (Run 2)


title: raw_Tg_20140605_P1 (Run 1)


title: RNAseq_GSC20_t_0_S70

source_name: GSC20 RNA seq not irratiated (t=0 min)


title: RNAseq_GSC2_t_1_S73

source_name: GSC2  RNA seq irradiated (t=30 min)

value: IDH1 wild type EGFR ampllified


title: raw_C57_20141444_P1 (Run 2)


title: RNAseq_GSC2_t_0_S72

source_name: GSC2  RNA seq not irratiated (t=0 min)

value: Glioblastoma


title: RNAseq_GSC2_t_2_S74

source_name: GSC2  RNA seq irradiated (t=60 min)

value: CNS derived tumor


title: raw_Tg_20140597_E17.5 (Run 1)


title: Riboseq_VU609

description: VU609 t0,t1,t2

data_processing:
Adaptor sequences are removed with cutadapt 1.14 with the following settings: -u 1 -m 15 -e 0.2 -O 7 --discard-untrimmed
Reads are separated based on library barcode by cutadapt 1.14 with option -e 0.2.
Unique Molecular Identifiers (UMIs) are extracted and clustered using umi_tools 0.5.5.
Reads are mapped to hg38 by bowtie 1.2.2 with the following setting: --chunkmbs 2000 -k 1 --best -S
UMIs are collapsed to remove sequencing errors and PCR errors. Umitools dedup was used for this purpose.
rRNA reads are removed based on coordinates of rRNA in GENCODE reference human genome (hg) 38 version 30.
https://github.com/Arthurhe/RiboReadCountByFrame
Supplementary files format and content: rds
Library strategy: Ribo-seq

source_name: VU609 t0,t1,t2 Riboseq RNA seq

value: IDH1 wild type

value: multiplexed sample:t0 none, t1 & t2 irradiated


title: raw_Tg_20140596_E17.5 (Run 1)


title: raw_Tg_20140603_P1 (Run 1)


title: raw_Tg_20140595_E17.5 (Run 1)


title: Riboseq_VU598

description: VU598 t0,t1,t2

source_name: VU598 t0,t1,t2 Riboseq RNA seq


title: raw_C57_20141443_P1 (Run 2)


title: raw_Tg_20140594_E17.5 (Run 1)


title: Riboseq_VU593

description: VU593 t0,t1,t2

source_name: VU593 t0,t1,t2 Riboseq RNA seq


title: raw_Ctl_20140592_E17.5 (Run 1)


title: RNAseq_GSC20_t_1_S71

source_name: GSC20 RNA seq irradiated (t=30 min)

value: Irradiated


title: Riboseq_GSC20_23

description: GSC20 t1, t2; GSC23 is irrelevant for this project

source_name: GSC20 t1, t2 Riboseq RNA seq


title: raw_Ctl_20140591_E17.5 (Run 1)

source_name: neuro retina


title: raw_Ctl_20140590_E17.5 (Run 1)


title: raw_Tg_20140593_E17.5 (Run 1)


title: raw_Ctl_20140588_E17.5 (Run 1)


title: raw_Ctl_20140589_E17.5 (Run 1)


title: Riboseq_GSC2_20

description: GSC2 t0 (0 min), t1 (30 min post RT) and t2 (60 min post RT); GSC20 t0

source_name: GSC2 t0,t1,t2; GSC20 t0 Riboseq RNA seq


title: TCR patient9_scACTP_1

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

data_processing:
The scTCR-Seq reads were aligned to the GRCh38 reference genome (refdata-cellranger-vdj-GRCh38-alts-ensembl-4.0.0) and quantified using cellranger vdj (10X Genomics, version 4.0.0).
Assembly: GRCh38
Supplementary files format and content: csv file ("all_contig_annotations.csv" output from Cellranger) containing the mapping of unique cells to TCR
Library strategy: scTCR-seq

source_name: melanoma

extract_protocol:
TILs were generated in the GMP manufacturing facilities of the Centre of Thérapies Expérimentales (CTE) of the Centre Hospitalier Universitaire Vaudois (CHUV) under specific conditions previously described (Gannon et al., Cytotherapy, 2020). Some TILs of the infusion product were cryopreserved in 90% human serum + 10% DMSO for translational studies. The day of the assay, the samples of the infused T cell product were thawed and TILs undergone overnight recovery in R8 medium supplemented with 3000 IU/mL IL-2 (Proleukin) or fresh TILs were directly used. TILs were resuspended in PBS + 0.04% BSA and DAPI (Invitrogen) staining was performed.
Live cells were sorted with a BD FACS Melody sorter and manually counted to assess viability with Trypan blue. Live TILs were resuspended at a density of 600-1200 cells µL-1 with a viability of >90% and subjected to a 10X Chromium instrument for single-cell analysis. The standard protocol of 10X Genomics was followed and the reagents for the Chromium Single Cell 5’ Library and V(D)J library (v1.0 or v1.1 Chemistry) were used. 15’000 cells were loaded per sample. Using a microfluidic technology, single-cell were captured and lysed, mRNA was reverse transcribed to barcoded cDNA using the provided reagents (10X Genomics). 14 PCR cycles were used to amplify cDNA and the final material was divided into two fractions: first fraction was target-enriched for TCRs and V(D)J library was obtained according to manufacturer protocol (10X Genomics). The second fraction was processed for 5’ gene expression library following the manufacturer’s instruction (10X Genomics). Barcoded V(D)J libraries and GEX libraries were pooled and sequenced by an Illumina HiSeq 4000 sequencer.

value: melanoma

tag: patient

tag: time

value: ACT product

value: expanded TILs


title: raw_C57_20141442_E17.5 (Run 2)

tag: developmental stage


title: TCR patient7_scACTP_1


title: TCR patient8_scACTP_1


title: TCR patient6_scACTP_1


title: raw_C57_20141439_E17.5 (Run 2)


title: raw_C57_20141440_E17.5 (Run 2)


title: raw_C57_20141438_E17.5 (Run 2)


title: raw_Tg_20141431_E15.5 (Run 2)


title: TCR patient4_scACTP_1


title: Riboseq_VU591

description: VU591 t0,t1,t2

source_name: VU591 t0,t1,t2 Riboseq RNA seq


title: Riboseq_GSC34

description: GSC34 t0, t1, t2

source_name: GSC34 t0,t1,t2 Riboseq RNA seq


title: TCR patient1_scACTP_1


title: raw_Tg_20141429_E15.5 (Run 2)


title: raw_Tg_20141430_E15.5 (Run 2)


title: TCR patient13_scACTP_1


title: TCR patient2_scACTP_1


title: TCR patient3_scACTP_1


title: Riboseq_GSC28

description: GSC28 t0,t1,t2

source_name: GSC28 t0,t1,t2 Riboseq RNA seq


title: raw_Tg_20140585_E15.5 (Run 1)


title: raw_Tg_20140587_E15.5 (Run 1)


title: raw_Tg_20141428_E15.5 (Run 2)


title: TCR patient12_scACTP_1


title: TCR patient11_scACTP_1


title: raw_Tg_20140584_E15.5 (Run 1)


title: raw_C57_20141441_E17.5 (Run 2)


title: GEX patient8_scACTP_1

data_processing:
The scRNA-Seq reads were aligned to the GRCh38 reference genome and quantified using cellranger count (10X Genomics, version 4.0.0). Filtered gene-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the threshold for cell detection were used and processed using the Seurat R package version 4.0.1.
For live-sorted cells from ACT product data (5`GEX), we defined and removed low-quality cells containing more than 10% of mitochondrial reads.
Assembly: GRCh38
Supplementary files format and content: Processed gene expression raw count with Gene Symbol mapping for filtered non-apoptotic cells in tab-separted format


title: raw_Tg_20140583_E15.5 (Run 1)


title: TCR patient5_scACTP_1


title: GEX patient7_scACTP_1


title: GEX patient9_scACTP_1


title: GEX patient6_scACTP_1


title: raw_Ctl_20140581_E15.5 (Run 1)


title: raw_Ctl_20140580_E15.5 (Run 1)


title: raw_Ctl_20140579_E15.5 (Run 1)


title: raw_Ctl_20140578_E15.5 (Run 1)


title: raw_C57_20141437_E15.5 (Run 2)


title: GEX patient4_scACTP_1


title: GEX patient3_scACTP_1


title: raw_C57_20141436_E15.5 (Run 2)


title: GEX patient1_scACTP_1


title: GEX patient13_scACTP_1


title: TCR patient10_scACTP_1


title: GEX patient12_scACTP_1


title: raw_Ctl_20140582_E15.5 (Run 1)


title: GEX patient10_scACTP_1