title: W-3 mRNA-seq

status: Public on Nov 20 2021

city: lanzhou

first: jinqiang

last: quan

address: No. 1 Yingmen Village, Anning District

department: College of Animal Science & Technology

institute: Gansu Agricultural University

description: Potato tuber tissue samples 12

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: ①removing reads containing adapters; ② removing reads containing more than 10% of unknown nucleotides (N); ③ removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the Solanum tuberosum genome (https://www.ncbi.nlm.nih.gov/genome/400) was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 with “-rna-strandness RF” and other parameters set as a default.
Genome_build: GCA_014189475.1

organism: Solanum tuberosum

source_name: Potato tuber tissue

growth_protocol: Four kinds of potatoes (Black kingkong, Red beauty, Longshu No.7 and LK99) were planted at Yuzhong Experimental Station of Lanzhou County, Gansu Academy of Agricultural Sciences. They were planted on 22 April 2019 and harvested on 28 September. All conditions during planting were kept consistent for all four varieties, such as irrigation, light, temperature, etc. At harvest, the materials of each variety were randomly sampled, with 3 replicates for each sample, for anthocyanin determination and transcriptome sequencing.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeq2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).

tag: cultivar

value: 150 days

value: tuber


title: W-1 mRNA-seq

type: SRA

country: China

description: Potato tuber tissue samples 10

library_source: transcriptomic

molecule: total RNA

tag: age

tag: tissue


title: Y-2 mRNA-seq

description: Potato tuber tissue samples 8

value: Longshu No.7


title: W-2 mRNA-seq

description: Potato tuber tissue samples 11


title: FS11

status: Public on Nov 22 2021

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

country: USA

institute: University of Wisconsin-Madison

data_processing:
The quality of the sequencing reads was evaluated using FastQC software (version 0.11.7). Read trimming was performed using Trim Galore software (version 0.4.4).
Reads were mapped to the mouse reference genome using Hisat2 sofware (version 2.1.0).
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Mouse genome assembly (GRCm39)
Supplementary_files_format_and_content: Tab-delimited text files including ensembl gene id and number of mapped reads

organism: Mus musculus

source_name: mammary gland

extract_protocol:
RNA extraction was performed using Qiagen RNeasy Micro Kit (Qiagen Germantown, MD).
All the RNA-sequencing procedures were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China). Sequencing libraries were prepared using a Poly-A tail capture method and sequenced with NovaSeq 6000.

value: mammary gland

tag: diet

value: folic acid supplemented diet

tag: drug

value: saline


title: R-2 mRNA-seq

description: Potato tuber tissue samples 5

value: Red beauty


title: FS2


title: Y-1 mRNA-seq

description: Potato tuber tissue samples 7


title: R-3 mRNA-seq

description: Potato tuber tissue samples 6


title: R-1 mRNA-seq

description: Potato tuber tissue samples 4


title: B-3 mRNA-seq

description: Potato tuber tissue samples 3

value: Black kingkong


title: W-3 miRNA-seq

description: Potato tuber tissue samples 12

data_processing:
Reads obtained from the sequencing machines included dirty reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get clean tags, raw reads were further filtered according to the following rules: 1) Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides(N); 2) Removing reads without 3’adapters; 3) Removing reads containing 5’adapters; 4) Removing reads containing 3’ and 5’ adapters but no small RNA fragment between them; 5) Removing reads containing ployA in small RNA fragment; 6) Removing reads shorter than 18nt (not include adapters).
All of the clean tags were aligned with small RNAs in GeneBank database (Release 209.0) to identify and remove rRNA, scRNA, snoRNA, snRNA and tRNA. Meanwhile all of the clean tags were aligned with small RNAs in Rfam database (11.0) to identify and remove rRNA, scRNA, sonRNA, snRNA and tRNA. All of the clean tags were also aligned with the Solanum tuberosum reference genome (https://www.ncbi.nlm.nih.gov/genome/400). Those mapped to exons or introns might be fragments from mRNA degradation, so these tags were removed. The tags mapped to repeat sequences were also removed.
All of the clean tags were then searched against miRBase database (Release 21) to identify known potato miRNAs (exist miRNAs). So far the miRNA sequences of some species were still not included in miRBase database. For those species the miRNAs alignment with other species was a dependable way to identify the known miRNAs. All of the unannotated tags were aligned with reference genome. According to their genome positions and hairpin structures predicted by software Mireap_v0.2, the novel miRNA candidates were identified. The default parameters of software Mireap_v0.2 were as follows: ① Minimal miRNA sequence length is 18nt. ② Maximal miRNA sequence length is 25nt. ③ Minimal miRNA reference sequence length is 20nt. ④ Maximal miRNA reference sequence length is 23nt. ⑤ Maximal copy number of miRNAs on reference is 20. ⑥ Maximal free energy allowed for a miRNA precursor is 18 kcal/mol. ⑦ Maximal space between miRNA and miRNA* is 300nt. ⑧ Minimal space between miRNA and miRNA* is 16nt. ⑨ Maximal bulge between miRNA and miRNA* is 4nt. ⑩ Maximal asymmetry of miRNA/miRNA* duplex is 4nt. ⑪ Flank sequence length of miRNA precursor is 20nt.
After tags were annotated as mentioned previously, the annotation results were determined in this priority order: rRNA etc > exist miRNA > exist miRNA edit > known miRNA > repeat > exon > novel miRNA > intron. The tags that cannot be annotated as any of the above molecules were recorded as unann.
Total miRNA consists of exist miRNA, known miRNA and novel miRNA, based on their expression in each sample, the miRNA expression level was calculated and normalized to transcripts per million (TPM). In addition, the expression of exist miRNA, known miRNA and novel miRNA was also analysed individually. Correlation analysis of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability. The correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1, the better the repeatability between two parallel experiments.
Genome_build: GCA_014189475.1

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted by TRIzol, the RNA molecules in a size range of 18–30nt were enriched by polyacrylamide gel electrophoresis (PAGE). Then the 3’ adapters were added and the 36-44nt RNAs were enriched. The 5’ adapters were then ligated to the RNAs as well. The ligation products were reverse transcripted by PCR amplification and the 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM 2500


title: W-2 miRNA-seq

description: Potato tuber tissue samples 11


title: B-2 mRNA-seq

description: Potato tuber tissue samples 2


title: Y-2 miRNA-seq

description: Potato tuber tissue samples 8


title: Y-1 miRNA-seq

description: Potato tuber tissue samples 7


title: W-1 miRNA-seq

description: Potato tuber tissue samples 10


title: R-3 miRNA-seq

description: Potato tuber tissue samples 6


title: Y-3 miRNA-seq

description: Potato tuber tissue samples 9


title: BS4

value: breeder diet


title: B-3 miRNA-seq

description: Potato tuber tissue samples 3


title: B-2 miRNA-seq

description: Potato tuber tissue samples 2


title: R-1 miRNA-seq

description: Potato tuber tissue samples 4


title: BF8

value: fluoxetine


title: B-1 miRNA-seq

description: Potato tuber tissue samples 1


title: M1 macrophages +PBM rep3 [C3]

city: Xi’an

first: Yangguang

last: Ma

address: Changle West Road No. 127

institute: Department of Orthopedics, The First Affiliated Hospital of Air Force Military Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: M1 macrophages +PBM

growth_protocol: The femur and tibia of 6- to 8-week-old C57BL/6 mice were extracted, and their bone marrow cavities were flushed with PBS. The cell-containing pellet was resuspended in pretreated Dulbecco’s modified Eagle’s medium (DMEM) containing 10% FBS, 1% penicillin/streptomycin solution, and 10 ng/mL macrophage colony-stimulating factor (M-CSF; R&D Systems).  Bone marrow cells were induced to M0 macrophages with M-CSF conditioned medium (10% FBS, 1% penicillin-streptomycin double-antibody, DMEM high-glucose medium, 10 ng/mL M-CSF). Cells were differentiated in fresh conditioned medium for 7 days until the cells matured in culture.

extract_protocol:
Total RNA was isolated from macrophage sample using the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA).  Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mature M0 macrophages were polarized to M1 macrophages after the addition of lipopolysaccharide (LPS; Sigma-Aldrich) and interferon-γ (IFN-γ; Sigma-Aldrich) to the medium.

tag: strain

tag: genotype

value: wild type

value: 6-8 weeks postpartum

value: femur and tibia

tag: cell type

value: Mouse bone marrow-derived macrophages

tag: treatment

value: photobiomodulation (PBM)


title: M1 macrophages +PBM rep2 [C2]


title: M1 macrophages rep3 [B3]

source_name: M1 macrophages


title: M1 macrophages rep2 [B2]


title: M1 macrophages +PBM rep1 [C1]


title: M1 macrophages rep1 [B1]


title: Y-3 mRNA-seq

description: Potato tuber tissue samples 9


title: ADAR1p110 replica 3

status: Public on Nov 17 2021

city: Vienna

first: Renata

last: Kleinova

address: Schwarzspanierstrasse 17

department: CACB

country: Austria

institute: Medical University of Vienna

data_processing:
For each sample raw reads were preprocessed by fastp (version 0.20) in order to trim low quality regions and remove potential adaptors. Fastp: fastp -i R1.fastq.gz -I R2.fastq.gz -o R1.trim.fastq.gz -O R1.trim.fastq.gz --detect_adapter_for_pe -x -q 25 -n 2 -l 35 -y -w 10
Cleaned reads were then aligned onto the mm10 mouse genome assembly by STAR (version 2.5) and providing Gencode annotations for known splice junctions. The mouse genome was obtained from Gencode. STAR: STAR --twopassMode Basic --limitBAMsortRAM 0 --runThreadN 10 --genomeDir mm10gencodevM22_75 --genomeLoad NoSharedMemory --outFileNamePrefix sample_ --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes All --readFilesCommand zcat --outFilterType BySJout --outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --readFilesIn R1.trim.fastq.gz R2.trim.fastq.gz
Multiple read alignments in the standard BAM format were sorted and indexed by SAMtools (version 1.9).
Editing sites in aligned BAMs were called using REDItools (REDItoolsKnown.py script) and a list of known RNA editing events downloaded from REDIportal.  REDItools: REDItoolKnown.py -i sample.bam -o sample-q20 -f GRCm38.p6.genome.fa -l editingsites_sorted.tab.gz -c0 -v0 -n0 -t 10
Genome_build: mm10
Supplementary_files_format_and_content: txt files containg information about A-to-I editing at known editing sites

source_name: Mouse Embryonic fibroblast

growth_protocol: MEFs were maintained in in high-glucose Dulbecco’s Modified Eagle Medium (DMEM) supplied with 10% fetal bovine serum, pyruvate and L-glutamine.

extract_protocol:
RNA was extracted using TriFAST according to the manufacturer’s suggestions. Isolated RNA was treated with DNaseI and subsequently purified by phenol: chloroform, chloroform extraction and precipitated with ethanol.
100 ng of total RNA was subjected to rRNA depletion with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and subsequently to NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina.
rRNA depleted RNA-seq

value: Adar-/-; Adarb1-/-; Gria2R/R

tag: transfected with plasmid


title: ADAR1p110 replica 2


title: RFP - editase negative control

value: :RFP


title: ADAR1p110 replica 1


title: ADAR1p150 replica 3


title: ADAR1p150 replica 1


title: BG8 O2 B

city: Ithaca

first: Egidio

middle: F

last: Tentori

state: NY

address: 220 Hollister Hall

department: School of Civil and Environmental Engineering

institute: Cornell University

data_processing:
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with TrimGalore/cutadapt.
Processed reads were mapped to the reference genome/transcriptome with STAR using --quantMode GeneCounts to generate raw counts per gene.
Raw counts were analyzed in R with DEseq2.
Genome_build: GCF_000214275.2_ASM21427v3_genomic.gtf
Supplementary_files_format_and_content: raw counts
Supplementary_files_format_and_content: differential gene expression results

organism: Methylomicrobium album BG8

source_name: M. album BG8 bacteria

growth_protocol: Bacteria were grown suspended in continuous flow membrane bioreactors with NMS media. Steady state samples were provided both methane and oxygen while substate limited samples did not receive either methane or oxygen.

extract_protocol:
Pellet RNA was extracted using Trizol reagent. Extracted RNA was treated with Promega RQ1 RNase-Free DNase (Cat# M6101). Ribosomal RNA was subtracted using New England Biolabs NEBNext® rRNA Depletion Kit (Bacteria) (Cat# E6310), using 500-1000ng input total RNA.
TruSeq-barcoded RNAseq libraries were generated using New England Biolabs NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (Cat# E7765) following manufacturer instructions.

treatment_protocol: Reactor liquid samples were collected in 2-mL tubes and centrifuged at 10,000 rpm for 10 minutes at 4°C. Liquid supernatant was removed and extraction proceeded with bacterial pellet.

tag: reactor

value: 4 day retention time

value: substrate limited

tag: limitation

value: oxygen, 2 hr


title: BG8-PSS-B

value: steady state


title: B-1 mRNA-seq

description: Potato tuber tissue samples 1

value: 150 days

value: tuber


title: BS11

value: mammary gland

value: saline


title: BG8-CH4-A

value: 2 day retention time

value: methane, 2 hr


title: BG8-CH4-B


title: SS01A_auxin1hr_L2-L3_ArimaHiC_col838_rep1_JK09

status: Public on Nov 16 2021

city: New York

first: Ana

middle: Karina

last: Morao

state: New York

address: 29 Washington Place

department: Biology

institute: New York University

library_source: genomic

data_processing:
Basecalls were performed using CASAVA version 1.8.
Hi-C:  data was mapped to ce10 (WS220) reference genome using default parameters of the Juicer pipeline version 1.5.7 (Durand et al., 2016). For downstream analysis, inter_30.hic outputs from juicer pipeline were converted to h5 file to be used in HiCExplorer (version=3.5.1)(Ramirez et al., 2018; Wolff et al., 2018). Matrices of replicates were combined using hicSumMatrices. Each replicate or each summed matrix were normalized to match the depth of the smallest matrix in comparison using hicNormalize with the option --smallest. The replicate and summed matrices were ICE normalized using hicCorrectMatrix with the following parameters: --correction_method ICE, -t 1.7 5, --skipDiagonal, --chromosomes I II III IV V X.
Genome_build: WS220
Supplementary_files_format_and_content: Hi-C:  hic matrix files

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C.

extract_protocol:
Hi-C: Crosslinked worms were resuspended in 20 ul of PBS per 50ul of worm pellet then dripped into liquid nitrogen containing mortar. The worms were grounded with pestle until fine powder. Grounded worms were crosslinked again in 2% formaldehyde using the TC buffer as described by the Arima Hi-C kit, which uses two 4-base cutters, DpnII and HinfI. The Arima manufacturer’s protocol was followed.
Hi-C:  Library preparation was performed using the KAPA Hyper Prep Kit using the protocol provided by Arima.

treatment_protocol: Auxin treatment: synchronized L2/L3s were washed three times with M9 and split into two aliquots. Half of the worms were transferred to NGM plates containing 1mM of indole-3-acetic-acid (Fisher 87-51-4) prepared as in (Zhang et al., 2015). The other half were placed in normal NGM plates (no-auxin control) for the indicated time. Worms were then washed one time with M9 and processed accordingly to future application. For ChIP and Hi-C, L2/L3 worms were incubated in 2% formaldehyde for 30 minutes, followed by quenching with glycine, one wash with M9 and two washes with PBS, PMSF and protease inhibitors. For RNA-seq, worms were stored in Trizol.

value: SS01A (top-2::degron::GFP)

tag: developmental stage

value: auxin


title: SS01A_auxin1hr_L2-L3_ArimaHiC_col846_rep2_JK10


title: CA1200_auxin1hr_L2-L3_ArimaHiC_col845_rep2_JK08


title: CA1200_auxin1hr_L2-L3_ArimaHiC_col835_rep1_JK07


title: BG8-2d-PSS-B


title: SS01A_2hours-auxin_L2-L3_RNA_rep2_AKM117_RNA-seq

description:
SS01A-120-min-aux_over_SS01A-no-aux_DEseq2_fold-change.tab
SS01A_120-min-aux_over_CA1200-120-min-aux_DEseq2_fold-change.tab

data_processing:
Basecalls were performed using CASAVA version 1.8.
RNA-seq:We aligned reads to the WS220 genome version using HISAT2 version 2.2.1 (Kim et al., 2019) using the parameter --rna-strandness R. Count data was calculated using HTSeq version 0.13.5 (Anders et al., 2015). The raw counts were normalized FPKM using cufflinks version 2.2.1 (Roberts et al., 2011), and then FPKM was converted to TPM. The raw counts were used for the R package DESeq2 version 1.30.0 (Love et al., 2014).
Genome_build: WS220
Supplementary_files_format_and_content: RNA-seq: normalized counts (TPM and FPKM) for individual replicates. Log2fold change values generated using DEseq2

extract_protocol:
RNA-seq: Total RNA was purified following Trizol manufacturer’s instructions after freeze-cracking samples five times. RNA was cleaned up using Qiagen RNeasy MinElute Cleanup kit. mRNAs were purified using Sera-Mag Oligo (dT) beads (Thermo Scientific) from 10 µg of total RNA. cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212, cDNA synthesis was performed in the presence of dUTP in order to prepare stranded mRNA-seq libraries.
RNA-seq: cDNA was ligated to Illumina adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.


title: SS01A_30min-auxin_L2-L3_RNA_rep1_AM71_RNA-seq

description:
SS01A-30-min-aux_over_CA1200-30-min-aux_DEseq2_fold-change.tab
SS01A-30-min-aux_over_SS01A-no-aux_DEseq2_fold-change.tab


title: SS01A_1hour-auxin_L2-L3_RNA_rep1_AM72_RNA-seq

description:
SS01A-60-min-aux_over_SS01A-no-aux_DEseq2_fold-change.tab
SS01A-60-min-aux_over_CA1200-60-min-aux_DEseq2_fold-change.tab


title: SS01A_2hours-auxin_L2-L3_RNA_rep1_AM73_RNA-seq


title: SS01A_1hour-auxin_L2-L3_RNA_rep2_AKM116_RNA-seq


title: SS01A_0min-auxin_L2-L3_RNA_rep1_AM70_RNA-seq

description: SS01A-no-aux_over_CA1200-no-aux_DEseq2_fold-change.tab


title: CA1200_2hours-auxin_L2-L3_RNA_rep2_AKM132_RNA-seq


title: CA1200_30min-auxin_L2-L3_RNA_rep1_AKM119_RNA-seq


title: SS01A_0min-auxin_L2-L3_RNA_rep2_AKM114_RNA-seq


title: SS01A_30min-auxin_L2-L3_RNA_rep2_AKM115_RNA-seq


title: CA1200_2hours-auxin_L2-L3_RNA_rep1_AKM121_RNA-seq


title: BG8-2d-PSS-A


title: AM05_2hours-auxin_L2-L3_RNA_rep2_AKM136_RNA-seq

description:
AM05-120-min-aux_over_AM05-no-aux_DEseq2_fold-change.tab
AM05-120-min-aux_over_CA1200-120-min-aux_DEseq2_fold-change.tab

value: AM05 (top-1::degron::GFP)


title: AM05_30min-auxin_L2-L3_RNA_rep1_AKM126_RNA-seq

description:
AM05-30-min-aux_over_AM05-no-aux_DEseq2_fold-change.tab
AM05-30-min-aux_over_CA1200-30-min-aux_DEseq2_fold-change.tab


title: AM05_30min-auxin_L2-L3_RNA_rep2_AKM134_RNA-seq


title: AM05_1hour-auxin_L2-L3_RNA_rep2_AKM135_RNA-seq

description:
AM05-60-min-aux_over_AM05-no-aux_DEseq2_fold-change.tab
AM05-60-min-aux_over_CA1200-60-min-aux_DEseq2_fold-change.tab


title: CA1200_1hour-auxin_L2-L3_RNA_rep1_AKM120_RNA-seq


title: BG8-PSS-A


title: AM05_0min-auxin_L2-L3_RNA_rep2_AKM133_RNA-seq

description: AM05-no-aux_over_CA1200-no-aux_DEseq2_fold-change.tab


title: AM05_1hour-auxin_L2-L3_RNA_rep1_AKM127_RNA-seq


title: BG8 O2 A


title: AM05_0min-auxin_L2-L3_RNA_rep1_AKM125_RNA-seq


title: AM01_no-auxin_mixed-larvae_RNA_rep1_AM82_RNA-seq

description: AM01-no-aux_over_CA1200-no-aux_DEseq2_fold-change.tab

value: AM01 (dpy-27::degron::GFP)

value: mixed stage larvae

value: no-auxin


title: ADAR1p150 replica 2

value: Adar-/-; Adarb1-/-; Gria2R/R


title: AM01_no-auxin_L2-L3_RNA_rep1_AM66_RNA-seq


title: AM01_2hours-auxin_mixed-larvae_RNA_rep1_AM84_RNA-seq

description: AM01-120-min-aux_over_CA1200-120-min-aux_DEseq2_fold-change.tab


title: AM01_2hours-auxin_L2-L3_RNA_rep1_AM69_RNA-seq


title: Ge1018

city: Genève

first: Eliana

last: Marinari

address: Rue Michel-Servet 1

country: Switzerland

institute: UNIGE

data_processing:
Reads (100 bp) were mapped using TopHat.
Biological quality control and summarization were done with PicardTools v1.80.
Counts (total number of reads aligning to each genomic feature) were generated by HTSeq v.0.6.1
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: ex vivo sample

extract_protocol:
QIAGEN column extraction for mRNA
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: patient id

tag: age (at surgery)

tag: Sex

value: M

tag: tumor grade

value: IV

tag: overall survival

value: 18 months

value: radiation and TMZ

value: brain

tag: tumor type

value: glioma

tag: time

value: before standard treatment


title: Ge1007P8

value: 15 months

tag: tissue


title: Ge989

value: 27 months


title: Ge978

value: 35 months

value: after standard treatment


title: Ge989R2


title: Ge1007P6


title: Ge970

value: 13 months


title: CA1200_30min-auxin_L2-L3_RNA_rep2_AKM130_RNA-seq


title: Ge963

value: III

value: 30 months


title: Ge939R2

value: F

value: 32 months


title: CA1200_0min-auxin_L2-L3_RNA_rep2_AKM129_RNA-seq


title: Ge950

value: 11 months


title: CA1200_0min-auxin_L2-L3_RNA_rep1_AKM118_RNA-seq


title: Ge904

value: M


title: Ge893

value: IV

value: 41 months


title: Ge993

value: 18 months

value: radiation and TMZ


title: Ge893R2

value: brain

value: glioma


title: AM05_2hours-auxin_L2-L3_RNA_rep1_AKM128_RNA-seq

value: AM05 (top-1::degron::GFP)


title: Ge941

value: before standard treatment


title: Ge849R2


title: Ge849


title: Ge835P1

value: 10 months


title: Ge835R2

value: after standard treatment


title: Ge822P8

value: 5 months


title: Ge778P7

value: 35 months


title: Ge755P6


title: Ge699R2

value: 17 months


title: Ge699P7


title: Ge699P8


title: Ge977

value: F

value: 28 months


title: Tumor_OVA + CD8a ALN-3

status: Public on Nov 12 2021

city: Gent

first: Bram

last: Van Den Eeckhout

address: Albert Baertsoenkaai 3

country: Belgium

institute: VIB-UGent

data_processing:
Library strategy: CR-seq
RNA was reverse transcribed into cDNA with TCR-specific RT primers. Double-stranded cDNA was generated via second-strand synthesis, after which cDNA was end-repaired and A-tailed. Every original cDNA molecule was assigned a unique molecular identifier (UMI) by ligation of a 12-base random adaptor sequence. Target enrichment was performed via PCR with one primer against the constant region and another primer complementary to the adapter. The library was ultimately amplified via a second PCR, which also introduced platform-specific adaptor sequences and additional sample indices. Samples were then pooled and sequenced in two Illumina MiSeq v2 500 runs. The read data was merged and analyzed using the mouse “Immune Repertoire Analysis” workflow of the CLC Genomics Workbench (GWB) v21 (https://digitalinsights.qiagen.com/)4. The analysis was done using default parameters, except for “min UMI group size”, which was set to 1. The obtained clonotype results were used to produce count tables and figures.
Qiagen CLCGenomicsWorkbench used for:
Quality control
Remove and annotate with UMI
Create UMI reads from reads
Trim reads
Immune repertoire analysis
Genome_build: QIAseq Immune Repertoire Analysis Mouse IMGT Reference Sequences
Supplementary_files_format_and_content: Clonotype excel file that contains information on: Chain/V gene segment/J gene segment/CDR3 nucleotide sequence/CDR3 amino acid sequence/CDR3 length/Count/Productive

source_name: Tumor

extract_protocol:
CD8+ T cells were sorted (4 °C) from mixed cell populations and captured in RLT Plus lysis buffer + β-mercaptoethanol. RNA was isolated following the manufacturer’s instructions (RNeasy Plus Micro Kit, 74034, Qiagen). Concentration, quality and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent). Samples with RIN ≥ 8 and 280/260 and 260/230 values > 1.8 were used for library preparation.
The sequencing library was constructed using the Qiagen QIAseqTM Mouse TCR Panel Immune Repertoire RNA Library Kit (Qiagen) according to the manufacturer’s instructions.

value: Tumor

value: OVA + CD8a ALN


title: Tumor_OVA alone_2

value: OVA alone


title: Tumor_PBS_3

value: PBS


title: Tumor_OVA + CD8a ALN-1


title: TDLN_OVA + CD8a ALN-3

source_name: TDLN

value: TDLN


title: Ge970R2

value: M

value: IV

value: 13 months

value: radiation and TMZ


title: Tumor_OVA alone_3


title: Tumor_OVA + CD8a ALN-2


title: Tumor_OVA alone_1


title: TDLN_OVA + CD8a ALN-1


title: Ge755R2

value: 18 months

value: brain

value: glioma


title: TDLN_OVA + CD8a ALN-2


title: Tumor_PBS_1


title: Ge939

value: III

value: 32 months

value: before standard treatment


title: Ge856

value: 5 months

value: after standard treatment


title: Ge901

value: F

value: 37 months


title: Ge882

value: 24 months


title: TDLN_OVA alone_2

value: OVA alone


title: R-2 miRNA-seq

description: Potato tuber tissue samples 5

tag: cultivar

value: Red beauty

tag: age

value: 150 days

value: tuber


title: TDLN_OVA alone_3

tag: strain

value: TDLN


title: TDLN_PBS_3

value: PBS


title: TDLN_PBS_2


title: GFPpos_04

status: Public on Nov 11 2021

city: Philadelphia

first: Christopher

last: Hunter

state: PA

address: 301 S University Ave

department: Pathobiology

institute: University of Pennsylvania

description: Nur77-GFP+ OT-I

data_processing:
fastq files were aligned to version 79 of mouse reference genome GRCm38 using the Kallisto package.
Abundance files were summarized to genes using biomaRt
Expression data was normalized using the VOOM function in the Limma package in R
Genes with no transcripts in 3 or more samples were excluded from analysis
Differentially expressed genes (³0.3-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample

source_name: Brain

growth_protocol: C57BL/6 mice were obtained from Jackson Laboratories

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Qiagen) and processed according to manufacturer’s instructions.
libraries were prepared using the Clontech SMART Seq HT kit according to manufacturer's instructions. Adapters were ligated using the Nextera XT DNA Library Preparation Kit and Index Kit v2

treatment_protocol: Mice received an intravascular transfer of 5,000 CD45.1.2 Nur77-GFP OT-I 1 day prior to infection with T. gondii-OVA. At 14 days post infection, brain leukocytes were isolated and Nur77-GFP- and Nur77-GFP+ OT-I were double sorted by FACS.

tag: background strain

tag: genotype

value: wild-type

tag: gfp status


title: GFPpos_03

description: Nur77-GFP+ OT-I

value: brain


title: GFPpos_01

description: Nur77-GFP+ OT-I


title: GFPneg_04

description: Nur77-GFP- OT-I


title: GFPneg_02

description: Nur77-GFP- OT-I


title: GFPneg_03

description: Nur77-GFP- OT-I


title: GFPneg_01

description: Nur77-GFP- OT-I


title: CD8TcmRest_ctrl_TCF1_r1

status: Public on Nov 10 2021

city: Nutley

first: Haihui

last: Xue

state: NJ

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

institute: Hackensack University Medial Center

data_processing:
Paired end sequenced reads were trimmed for 30bp from both ends to remove the low quality base. RNA-seq reads were then mapped to mm10 genome with hisat2 and only reads with MAPQ>30 were considered in following analysis. Expression index (RPKM) is generated by Stringtie. Differential expression analysis were performed by DESeq2 with adjusted p.value < 0.1, fold change >=1.5 and RPKM in higher expression condition >=1. ATAC-seq reads were trimmed to 36bp from 3'end and then mapped to mm10 genome with bowtie2. Peaks were detected (with Q30 reads) using macs2 PE mode (with -q 0.01 and --keep-dup 1 parameters). ChIP-seq reads were trimmed to 51bp and then mapped to mm10 genome with bowtie2. Peaks were detected (with Q30 unique reads) using macs14 (with -p 1e-5, --nomodel and --shiftize 73 parameters).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files (generated by HT-seq) include raw reads count of genes in each RNA-seq Sample. Normalized signal track (in bigwig format) for each ATAC-seq and ChIP-seq sample. ChIP-seq peak file in bed format.

source_name: CD8+ central memory T cells

growth_protocol: CD45.2+ WT or Tcf1-deficient P14 TCR transgenic CD8 T cells were adoptively transferred into CD45.1+ B6.SJL recipients, followed by i.v. infection with LCMV-Armstrong. After ≥ 30 days, CD45.2+CD8+CD62L+ Tcm cells were sort purified  for downstream analysis.

extract_protocol:
WT Tcm cells were sort-purified from the spleen, crosslinked and immunoprecipitated with anti-Tcf1 antiserum
anti-Tcf1 is a house-made rabbit anti-Tcf1 polyclonal antibody, which is generated by immunization of rabbits with purified full length mouse Tcf1 protein.
The DNA segments from ChIP were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

treatment_protocol: Ex vivo sorted Tcm cells were used directly as resting cells. Another batch or portion of the sorted Tcm cells was cultured with GP33 peptide for 24 hrs and used as TCR-stimulated cells

value: splenocytes

value: resting WT Tcm cells

tag: cell phenotype

tag: chip antibody


title: Dflx3_Input (MAPR)

status: Public on Oct 28 2021

city: La Jolla

first: Anjana

last: Rao

state: California

address: 9420 Athena Cir

department: Signaling and Gene Expression

institute: La Jolla Institute for Allergy and Immunology

data_processing:
Library strategy: MapR
Paired-end (50bp) reads were mapped to the mouse genome mm10 GRCm38 (Dec. 2011, using Bowtie (V 1.1.2)
Reads that mapped to spike-ins were filtered out with samtools view; remaining reads in sam format were sorted and PCR duplicates were marked and kept with Picard (V 2.7.1).
Peaks were calculated with MACS2 (callpeak –keep-dup all -g mm --broad --broad-cutoff 0.1), asociated control as background.
Peaks from the replicates from same condition were merged with mergePeaks from HOMER and kept only those that intersected between the replicates.
Intersected peaks from the replicates were merged between the conditions to create the total number of peaks.
Tag directories were created and replicates were merged with makeTagDirectory from HOMER (-genome mm10);  makeMultiWigHub.pl was used to generate tracks.
Genome_build: mouse genome mm10 GRCm38
Supplementary_files_format_and_content: Comma separated file with the rpkm normalized R loops signal in G4 and Rloops union peaks

source_name: Spleen

growth_protocol: Primary B cells were isolated using EasySep Mouse Pan B cell isolation kit (#19844 Stem Cell Technology, Canada).

extract_protocol:
Cut and Run was performed with GST-RHΔ-Mnase.  DNA was extracted using phenol chloroform.
Library was prepared with NEB Ultra II library prep kit (NEB) following manufacturer’s instruction and was sequenced on an Illumina NovaSeq (50 bp paired-end reads).

value: Spleen

tag: cell type

value: B cells

value: 10 weeks of age

value: Dfl

tag: treatment

value: Nuclei were incubated and digested with MNase (MNase only)


title: DKO3_Input (MAPR)

value: CD19 DKO


title: DKO1_Input (MAPR)


title: MiaPaCa-2 low glucose repl-1

status: Public on Nov 01 2021

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

data_processing:
Base calling and generation of FASTQ files were performed using standard CASAVA pipeline
RNA-seq quality was checked by running FastQC, and TrimGalore was used for adapter and quality trimming. RNA-seq reads were mapped against hg38 using STAR (v 2.7.0e) aligner with default parameters.
Differential gene expression analysis was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files of normalized abundance measurements.

source_name: Pancreatic cancer cell line

growth_protocol: Cells were maintained in medium recommended by the supplier.

extract_protocol:
Total RNA was extracted using PureLink RNA isolation (Life Technologies, 12183025) and treated with DNase (Life Technologies, AM2222).
Strandspecific RNA-seq library was prepared using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, Ipswich, MA) according to the manufacturer's protocols.

treatment_protocol: Low glucose for 48 hours (2.5 mM glucose)

tag: cell line

value: low glucose

tag: supplier

value: ATCC


title: DKO1 (MAPR)

value: Nuclei were incubated and digested with RHdelta-MNase (mutated RnaseH fused to MNase)


title: Dflx2_Input (MAPR)


title: Dflx1_Input (MAPR)


title: MiaPaCa-2 low glucose repl-2


title: DKO2_Input (MAPR)


title: Dflx3 (MAPR)


title: DKO2 (MAPR)


title: DKO3 (MAPR)


title: Dflx2 (MAPR)


title: CH_3d_3

status: Public on Oct 23 2021

city: Jinan

first: Qingyu

last: Zhang

state: Shandong Province

institute: Shandong Provincial Hospital affiliated to Shandong First Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing poly-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
Stringtie was used to assemble transcripts from clean reads that have been mapped to the genome and quantifies simultaneously.
Genome_build: Rn6
Supplementary_files_format_and_content: FPKM

organism: Rattus norvegicus

source_name: CH_3d, BMSCs

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
First, ribosomal RNA was removed by Epicentre Ribo-Zero™ Gold Kits. RNA fragmentation and short RNA strands were carried out by NEBNext First Strand Synthesis Reaction Buffer under elevated temperature. Subsequently, First cDNA strand was synthesized using random hexamer primers and RNA fragments as template. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair add poly(A) and adapter were implemented. In order to select cDNA fragments of preferentially 300bp in length, the library fragments were purified and the UNG enzyme was used to digest second strand of cDNA. PCR was performed, aimed products were to retrieve, and the library was completed.

value: Sprague Dawley

value: Bone marrow

value: Mesenchymal stem cells

value: CH


title: CH_3d_2


title: Dflx1 (MAPR)


title: CH_12h_3

source_name: CH_12h, BMSCs


title: CH_3d_1


title: TDLN_OVA alone_1

value: TDLN

value: OVA alone


title: CH_3h_3

source_name: CH_3h, BMSCs


title: CH_12h_1


title: TDLN_PBS_1

value: PBS


title: CH_3h_2


title: CH_3h_1


title: GFPpos_02

description: Nur77-GFP+ OT-I

value: brain

value: wild-type


title: OS_12h_3

source_name: OS_12h, BMSCs

value: OS


title: OS_3d_2

source_name: OS_3d, BMSCs


title: OS_3d_1


title: AD_3d_1

source_name: AD_3d, BMSCs

value: AD


title: OS_3h_1

source_name: OS_3h, BMSCs


title: AD_3d_3


title: OS_3d_3


title: OS_3h_3


title: OS_12h_2


title: OS_12h_1


title: AD_12h_2

source_name: AD_12h, BMSCs


title: AD_3d_2


title: AD_3h_2

source_name: AD_3h, BMSCs


title: CON_2

source_name: CON, BMSCs

value: CON


title: CON_3


title: AD_3h_3


title: AD_12h_1


title: AD_12h_3


title: CON_1


title: OS_3h_2


title: CH_12h_2


title: AD_3h_1


title: K012-3D-2

status: Public on Oct 15 2021

city: Tallahassee

first: li

last: sun

email: lsun2@fsu.edu, davidgmeckes@gmail.com

state: FL

address: 1115 west call st.

department: College of medicine

institute: Florida State University

description: Donor K012

data_processing:
RAW data were uploaded to BaseSpace (Illumina) for quality control and base calling.
Qulified reads were aligned to the hg38 human reference genome.
Data was uploaded to NetworkAnalyst 3.0 for further analysis and network visualization.
Total counts were filtered by following specifications: counts less than 10, variance less than 10% and unannotated, and then normalized by Log2-counts per million.
Genome_build: hg38
Supplementary_files_format_and_content: Process counts file (xlsx) was generated and normalized by NetworkAnalyst.

source_name: Bone marrow

growth_protocol: hMSCs were expanded and maintained in complete culture media (CCM) containing α-MEM with 10% fetal bovine serum and 1% Penicillin/Streptomycin in a standard incubator at 37°C with 5% CO2 and 20% O2. For 2D culture, hMSCs were seeded at a density of 1500 cells/cm2. For 3D culture, hMSCs at passage 4 to 7 were suspended in CCM and 1.0×105 hMSCs in 2.0 mL CCM were seeded in each well of ultra-low attachment (ULA) 6-well plates. The ULA plates were then placed on a rocking base of a WAVE Bioreactor in a standard humidified incubator (37°C, 5% CO2) under controlled rocking angles (i.e., 8°) and rocking speeds (i.e., 20 rockings/min, or rpm) for 48 hours.

extract_protocol:
Cell total RNA was isolated with Trizol under manufacturer's protocol.
Isolated RNA was incubated with DNase I to remove trace genomic DNA contamination. Then, mRNA library was prepared by combination of NEBNext Ultra RNA Library Prep Kit (NEB, E7530) and NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). The library ran on Bioanalyzer with HS DNA chip (Agilent; 5067-4626) for quality control and quantified by KAPA library qPCR kit (KAPA; KR0405).

treatment_protocol: Each triplicate of cell group was cultured under 2D or 3D culture conditions.

value: Mesenchymal Stem Cell

tag: source

value: Bone marrow derived


title: K001-3D-2

description: Donor K001


title: K012-3D-1

description: Donor K012


title: K012-2D-2

description: Donor K012


title: K012-2D-1

description: Donor K012


title: K001-3D-1

description: Donor K001


title: I005-3D-2

description: Donor I005


title: I005-2D-2

description: Donor I005


title: K001-2D-1

description: Donor K001


title: K001-2D-2

description: Donor K001


title: I005-3D-1

description: Donor I005


title: I005-2D-1

description: Donor I005


title: BMMSC-2D-1


title: BMMSC-2D-3


title: BMMSC-3D-3


title: ihfA::Kan infB::Chlor RDM logarithmic rep 1 - RNA-seq

status: Public on Oct 01 2021

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

data_processing:
Adapter removal using the common Illumina Truseq adapter sequences with cutadapt 1.8.1
Read ends were trimmed using Trimmomatic 0.33 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.1.0 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed
After alignment to the U00096.3 genome, we performed gene-level quantitation with htseq-count, using union mode for scoring and all mode for non-unique assignments (appropriate for polycistronic mRNAs where a single read is often expected to span multiple genes). Differential expression calling was then performed using deseq2 with default settings.
Genome_build: E. coli U00096.3
Supplementary_files_format_and_content: For all summary/processed files, note that we provide one file per experimental condition, which represents a consolidation of all replicates for that condition, as described in the accompanying manuscript. Ipod_vs_inp.gr files – Raw IPOD occupancy traces prior to ChIP subtraction, given as a log_2 ratio of extracted to input. The .gr file extension refers to a simple graph type, where the first column indicates a genomic position and the second a corresponding signal chip_vs_inp.gr files – RNA polymerase occupancy given as a log_2 ratio of extracted to input V6rzlog10p.gr files – ChIP-subtracted IPODHR occupancy, z-scored and then used to calculate enrichment p values as described in the text. Tsv files – differential expression calling from sleuth

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

source_name: Culture lysate

extract_protocol: RNA samples: NEBNext Ultra 2 Directional RNA kit

value: ihfA::Kan infB::Chlor

tag: media

value: M9 Rich Defined Media (RDM) + glucose

tag: time of harvest

value: logarithmic phase


title: ΔstpaΔhns RDM logarithmic rep 1 - RNA-seq

value: {delta}stpa{delta}hns


title: ΔstpaΔhns RDM logarithmic rep 2 -RNA-seq


title: BMMSC-3D-1


title: Orbital adipose/connective tissue from the tissue remains of healthy people after plastic surgery_excised-rep1

type: RNA

city: Shanghai

first: Zifan

last: Yue

address: No. 415 Fengyang Road, Hangpu District

department: Ophthalmology

institute: Shanghai Changzheng Hospital

description:
Control 1
810751

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent Technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent Technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat.# 5188-5327, Agilent Technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent Technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US).

data_processing:
Raw data were normalized by Quantile algorithm, limma packages in R.
After the original data were normalized with the limma package in the software R, the differential genes were screened using Fold-change (fold of expression difference) and T-test (Student's t-test) statistical methods, and the selection conditions were as follows: 1) Fold Change (linear) =< 0.5 or Fold Change (linear) >= 2. 2) T-test p-value <0.05 or <0.01.

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent Technologies, Santa Clara, CA, US), following the manufacturer’s instructions.

growth_protocol: Liquid nitrogen quick freezing, -80 degrees refrigerator storage.

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100.

tag: diagnosis

value: Healthy

value: Orbital adipose/connective tissue

tag: gender

value: Female

tag: Stage

value: Stable period


title: Orbital adipose/connective tissue from the tissue remains of healthy people after plastic surgery_excised-rep2

description:
Control 2
811206

tag: tissue

value: Male


title: Orbital adipose/connective tissue_excised_rep2

description:
TAO 2
598426

source_name: Orbital adipose/connective tissue from orbital decompression surgery

value: Thyroid-associated ophthalmopathy (TAO)


title: Orbital adipose/connective tissue_excised_rep1

description:
TAO 1
597033


title: Δhfq RDM logarithmic rep 2 -RNA-seq

tag: strain

value: {delta}hfq


title: Δhfq RDM logarithmic rep 1 - RNA-seq


title: BMMSC-2D-2


title: ihfA::Kan infB::Chlor RDM logarithmic rep 2 - RNA-seq


title: BMMSC-3D-2


title: Orbital adipose/connective tissue_excised_rep3

description:
TAO 3
611331


title: Orbital adipose/connective tissue from the tissue remains of healthy people after plastic surgery_excised-rep3

description:
Control 3
2


title: Δfis RDM logarithmic rep 2 - RNA-seq

value: {delta}fis


title: Δfis RDM logarithmic rep 1 - RNA-seq


title: WT RDM logarithmic rep 1 - RNA-seq

value: wild type


title: HD3 Mono

status: Public on Sep 26 2021

city: Nijmegen

first: Glenn

middle: van

last: Wigcheren

address: Geert Grooteplein Zuid 28

department: Tumor Immunology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

description: Single cell suspension

data_processing:
Sequence reads were processed using the seq2science pipeline (https://github.com/vanheeringen-lab/seq2science).
Reads were trimmed and mapped to the human reference genome GRCh38.
Gene counts were obtained with HTSeq.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.counts.tsv: Tab-delimited text files include raw counts.

source_name: Donor 3 isolated Monocytes

extract_protocol:
Donor PBMCs using CD14 microbeads.
Dry pellets using liquid nitrogen and storage at -80°C. Total RNA was extracted from cell pellets using RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions.
30ng of RNA per sample was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems).

treatment_protocol: M-MDSC were generated in vitro according to generation protocol using recombinant human GM-CSF and IL-6 (see reference).

value: Monocytes

tag: donor

value: Donor 3


title: HNSCC29 Mono

description: Single cell suspension

source_name: HNSCC patient 29 isolated Monocyte

extract_protocol:
Monocytes were isolated from HNSCC patient PBMCs based on CD14+ and HLA-DR+ FACS sorting.
Dry pellets using liquid nitrogen and storage at -80°C. Total RNA was extracted from cell pellets using RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions.
30ng of RNA per sample was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems).

value: Monocyte

value: Patient 29

value: HNSCC


title: HNSCC29 MDSC

description: Single cell suspension

source_name: HNSCC patient 29 isolated MDSC

extract_protocol:
M-MDSCs were isolated from HNSCC patient PBMCs based on CD14+ and HLA-DR- FACS sorting.
Dry pellets using liquid nitrogen and storage at -80°C. Total RNA was extracted from cell pellets using RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions.
30ng of RNA per sample was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems).

value: MDSC


title: HD2 Mono

description: Single cell suspension

source_name: Donor 2 isolated Monocytes

value: Donor 2


title: HNSCC29 MDSCiv

description: Single cell suspension

source_name: HNSCC patient 29 in vitro generated MDSC

extract_protocol:
Days in X-Vivo-15 + 2% human AB male serum.
Dry pellets using liquid nitrogen and storage at -80°C. Total RNA was extracted from cell pellets using RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions.
30ng of RNA per sample was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems).

value: in vitro generated MDSC


title: HD1 Mono

description: Single cell suspension

source_name: Donor 1 isolated Monocytes

value: Donor 1

value: Healthy


title: SRSF2-P95L-3-rnaseq_R1

status: Public on Sep 17 2021

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: RNASeq

data_processing:
For eCLIP-seq, and RNA-seq, raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner. eCLIP peaks were called with CLIPPER and normalized to size-matched input sample
Genome_build: hg19, gencode v19
Supplementary_files_format_and_content: eCLIP input normalized and filtered peaks in BED format. Peaks files (bigwigs) for eCLIP. Featurecounts file for RNA-seq samples.

source_name: iPSC-HSPCs

growth_protocol: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID: 29681544)

extract_protocol:
Total RNA was extracted using Trizol and zymo's direct-zol RNA extration Kit.
500ng of total RNA was poly-A selected and processed using the TruSeq Stranded mRNA Preparation kit by Illumina according to manufacturer's instructions.

treatment_protocol: iPSC-HSPCs at day 11-14 were collected and dissociated with accutase into single cells and magnetic cell sorting of CD45+ cells was performed using the anti-CD45 MACS cell separation microbeads and reagents (Miltenyi Biotec).

tag: genotype

value: SRSF2 mutation

value: iPSC-HSPCs

tag: cell culture

value: Hematopoietic Differentiation as described in Chang et al. Cell Reports 2018 (PMID:29681544)

tag: selection

tag: day of differentiation


title: SRSF2-P95L-4-rnaseq_R1

description: RNASeq

tag: cell type


title: SRSF2-P95L-2-rnaseq_R1

description: RNASeq


title: U2AF1-S34F-2-rnaseq_R1

description: RNASeq

value: U2AF1 mutation


title: WT-2-rnaseq_R1

description: RNASeq

value: WT


title: WT-4-rnaseq_R1

description: RNASeq


title: U2AF1-S34F-3-rnaseq_R1

description: RNASeq


title: WT-1-rnaseq_R1

description: RNASeq


title: WT-5-rnaseq_R1

description: RNASeq


title: U2AF1-S34F-1-rnaseq_R1

description: RNASeq


title: WT-3-rnaseq_R1

description: RNASeq


title: SRSF2-P95L-1-rnaseq_R1

description: RNASeq


title: SRSF2_hpc.P95L-2_INPUT

description: eCLIP input

data_processing:
Library strategy: eCLIP-Seq
For eCLIP-seq, and RNA-seq, raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner. eCLIP peaks were called with CLIPPER and normalized to size-matched input sample
Genome_build: hg19, gencode v19
Supplementary_files_format_and_content: eCLIP input normalized and filtered peaks in BED format. Peaks files (bigwigs) for eCLIP. Featurecounts file for RNA-seq samples.

extract_protocol:
Total RNA was extracted using Trizol and zymo's direct-zol RNA extration Kit.
10M cells were UV-crosslinked, lysed and sonicated. RNA was fragmented and protein-RNA complexes were immunoprecipitated with a V5 antibody. Inputs (2% of lysate) were saved and run alongside IP samples. IP samples were stringently washed, and for all samples the RNA was dephosphorylated,, followed by on-bead ligation of barcoded RNA adapters to the 3’ end.. RNA-protein complexes were run on standard protein gels and transferred to nitrocellulose membranes where the RNA in the region 35 kDa – 110kDa was excised off the membrane and proteinase K treated. RNA was then reverse transcribed followed by treatedment with ExoSAP-IT to remove excess oligonucleotides. Samples were cleaned up with Dynabeads MyOne Silane and subject to qPCR to determine the appropriate number of PCR cycles.

tag: antibody

value: none (input)


title: SRSF2_hpc.P95L-1_INPUT

description: eCLIP input


title: SRSF2_hpc.P95L-1_IP

description: eCLIP IP

value: anti-FLAG (Sigma F1804)


title: U2AF1_hpc.WT-2_IP

description: eCLIP IP


title: U2AF1_hpc.WT-2_INPUT

description: eCLIP input


title: U2AF1_hpc.S34F-2_IP

description: eCLIP IP


title: U2AF1_hpc.S34F-2_INPUT

description: eCLIP input


title: SRSF2_hpc.WT-1_INPUT

description: eCLIP input


title: U2AF1_hpc.S34F-1_IP

description: eCLIP IP


title: SRSF2_hpc.P95L-2_IP

description: eCLIP IP


title: U2AF1_hpc.S34F-1_INPUT

description: eCLIP input


title: U2AF1_hpc.WT-1_INPUT

description: eCLIP input


title: U2AF1_hpc.WT-1_IP

description: eCLIP IP


title: MCZ21

status: Public on Aug 13 2021

city: Atlanta

first: Mark

middle: J

last: Czaja

state: GA

address: 615 Michael Street, Suite 201

department: Medicine

institute: Emory University School of Medicine

description: mRNA

data_processing:
FastQC was run for quality assessment. Trimmomatic was used to remove Illumina adapters from the sequencing.
Sequences were aligned to the mm10 reference genome using STAR aligner.
Gene quantification was done using HTSeq-count.
Differentially expressed genes among experimental groups were determined using DESeq2. Genes with low counts were filtered by mean normalized counts in DESeq2 and by expression of the counts per million (CPM) in edgeR.
Raw p-values were transformed using the Benjamini-Hochberg correction to account for multiple hypothesis testing.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Counts_Merged.txt: Tab-delimited text file includes raw counts.

source_name: liver

extract_protocol:
RNA extraction from flash frozen livers was performed using the miRNeasy mini kit (Qiagen) and quantified on the Infinite M200 Pro (Tecan). Quality of the RNA was evaluated on the 2100 bioanalyzer (Agilent).
Novogene (Sacramento, CA) performed the RNA sequencing library preparation with the NEBNext Ultra RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA). Agilent 2100 Bioanalyzer System (Agilent Technologies) was used to validate sequencing libraries that were subsequently quantified using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and by quantitative PCR (Applied Biosystems, Foster City, CA).
NovaSeq 6000 with a 2x150 Paired End (PE) configuration was used for the libraries sequencing. Sequences were quality-checked using FastQC for completeness, depth and read quality.

treatment_protocol: Erk1-/- Erk2Δhep mice without the Cre transgene (ERK1 single KO) were compared to Erk2Δhep (ERK2 KO) and Erk1-/- Erk2Δhep harboring the Cre transgene (ERK1/2 double KO). Mice were injected with a single subcutaneous dose of 3 mg of tamoxifen and liver harvested after 3 weeks for RNA extraction.

value: liver

tag: treatment

value: Tamoxifen

value: ERt-Alb-Cre-ERK2 Cre+


title: MCZ20

description: mRNA


title: WT-6-rnaseq_R1

description: RNASeq


title: WT RDM logarithmic rep 2 - RNA-seq

value: wild type

value: M9 Rich Defined Media (RDM) + glucose

value: logarithmic phase


title: MCZ18

description: mRNA


title: SRSF2_hpc.WT-2_IP

description: eCLIP IP


title: MCZ15

description: mRNA


title: MCZ14

description: mRNA

value: ERK1-/- -ERt-Alb-Cre-ERK2 Cre+


title: MCZ13

description: mRNA


title: SRSF2_hpc.WT-2_INPUT

description: eCLIP input


title: MCZ7

description: mRNA

value: ERK1-/- -ERt-Alb-Cre-ERK2 Cre-


title: MCZ10

description: mRNA


title: SRSF2_hpc.WT-1_IP

description: eCLIP IP


title: MCZ9

description: mRNA


title: MCZ16

description: mRNA


title: HEK293T, H4K16ac, CST

status: Public on Apr 20 2021

city: Chicago

first: Marta

last: Iwanaszko

state: IL

address: 303 E. Superior Street, Simpson Querrey 7th Floor,

department: Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig, narrowPeak (except for Input sample)

source_name: HEK293T cells

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: cell line

value: Human embryonic kidney cell

tag: chip antibody


title: MCZ12

description: mRNA


title: MCZ17

description: mRNA


title: HEK293T, Input


title: MCZ3

description: mRNA


title: MCZ6

description: mRNA


title: MCZ4

description: mRNA


title: MCZ5

description: mRNA


title: MCZ1

description: mRNA


title: HEK293T, H2AZ, CST


title: HEK293T, H3.3, EMDMillipore


title: MCZ11

description: mRNA


title: HEK293T, H2AZ, ABCAM

value: H2AZ (Abcam, #ab4174)


title: HEK293T, H3K79me2, CST


title: MCZ8

description: mRNA


title: DC, replicate 2, scRNAseq

status: Public on Apr 16 2021

city: Gothenburg

first: Malin

middle: E. V.

last: Johansson

address: Medicinaregatan 9A

department: Department of Medical Biochemistry and Cell Biology

country: Sweden

institute: University of Gothenburg

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated values files and matrix files

source_name: Goblet cells

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Goblet cells

value: Distal colon

tag: age

value: 6-8 weeks old


title: Si8, replicate 2, scRNAseq

description: 10x Genomics

value: 8th section of the small intestine


title: DC, replicate 1, scRNAseq

description: 10x Genomics


title: MCZ19

description: mRNA


title: Si8, replicate 1, scRNAseq

description: 10x Genomics


title: control_male_4

status: Public on Apr 07 2021

city: Bryan

first: Rajesh

last: Miranda

address: 8447 Riverside Parkway

institute: Texas A&M University

data_processing:
The Cell Ranger analysis pipeline was used to demultiplex raw base call (BCL) files generated by the sequencer into FASTQ files and to perform genome alignment, filtering, and unique molecular index (UMI) quantification utilizing the Chromium cellular barcodes to generate gene‐barcode UMI matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered Feature-barcode matrices files from the Cell Ranger pipeline for each sample are included ,in addition to Loupe cell browser file.

molecule: polyA RNA

source_name: dorsal telencephalon single cell suspension

growth_protocol: Young adult C57/Bl/6J nulligravid females were time-mated in- house with C57/Bl/6J males. 1-2 females in proestrous/estrous phase were placed in the male cage for a period of 90 minutes during the start of their dark cycle (7 pm), and the next morning was designated as gestational day (GD) 0.5 ofor pregnancyt mice. Pregnancy was confirmed by Pregnancy was confirmed when a dam exhibits daily weight gain starting from GDon day 8.5 after mating.

extract_protocol:
On GD14.5, pregnant dams were anesthetized with ketamine (0.09 mg/gram)/xylazine (0.106 mg/gram) and fetal mice delivered by laparotomy as we previously published (Camarillo and Miranda, 2008; Santillano et al., 2005; Sathyan et al., 2007; Tingling et al., 2013). The dorsal telencephalon corresponding to the future isocortex of each mouse fetus in the litter was rapidly micro-dissected and immediately placed in chilled PBS in individual microcentrifuge tubes and centrifuged at 200xg for 3 minutes. The PBS was aspirated and tissue mechanically dissociated by trituration in 200 ul 0.25% EDTA free trypsin in PBS for 5 minutes at room temperature, followed by Trypsin inactivated with 1ml of 10% FBS in PBS. The cell suspension was washed twice in PBS and then filtered through a 40 micron filter, centrifuged and resuspended in 20 ul PBS. Pre-chilled methanol (80 ul) was added slowly, dropwise while mixing, to avoid cell clumping. The cell suspension was then placed on ice for 15 minutes before storage at -80oC. To determine the sex of each of the pups, we performed alkaline lysis (25mM NaOH and 0.2 mM EDTA) on tail snips from each pup, at 95oC for 15 minutes, followed by neutralization in 75 ul of Tris-HCl (40mM). Tissue debris were separated from the lysate by centrifugation and the supernatant, diluted 1:10, was assessed for sex-specific genes, using RT-PCR with primers specific for Xist (X-chromosome) and YMT (Y-chromosome).
We used the Chromium Single Cell 3′ Reagent Kit (10X Genomics, Pleasanton, CA; CG000183) to prepare for each sample a master mix using an input of 10,000 rehydrated cells. The single‐cell master mixes were subsequently loaded into Chromium Chip B (10X Genomics; PN‐1000074), and gel beads in emulsion were prepared according to the manufacturer's protocol followed by RT, cDNA amplification, and library preparation step.

treatment_protocol: On GD12.5, pregnant dams were placed in either control or alcohol vapor chambers (La Jolla Alcohol Research Inc, quad passive e-vape systemcompany and machine name), on absorbent pads, we placed napkins on the plexi glass chamber floor to avoid liquid accumulation in the chamber. Ethanol (95%) was injected into the system at a rate of 6 strokes/minute, with an the air-flow of between 4 and 5 L/minute. The exposure to control air or ethanol vapor occurred over a period ofthe animal was placed in the chamber for 50 minutes, and animals were thereafter placed under a heat lamp until locomotor activity resumedanimals recovered under heat lamp until they restored their locomotion ability. At After 30 minutes following the exposure period, 20ul of tail-vein blood was aspirated for analysis of of alcohol exposure, we wiped the tail with warm water (37 C) and nicked the tail and collected 20 ul of blood for blood alcohol levelcontent (BAC) quantification in a vial prepared forby gas chromatography  assessment. Pregnant mice were single- housed after ethanol or control air exposures until fetaluses collection on GD 14.5.

tag: Sex

value: Male

value: Control

tag: alcohol dose

value: 0 mg/dl

tag: dam id

tag: developmental stage

value: Gestational day 14.5


title: control_female_3

value: dorsal telencephalon single cell suspension

value: Female


title: control_female_4


title: MCZ2

description: mRNA

tag: tissue

value: liver

value: Tamoxifen


title: alcohol_female_3

tag: strain

value: Alcohol

value: 210 mg/dl


title: clonal hematopoiesis-negative, HTP0672A

status: Public on Mar 01 2021

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description:
globin-depleted, poly(A)+ RNA from whole blood
Counts_for_GEO.txt.gz
FPKMs_for_GEO.txt.gz

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the human reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files containing per gene strand-specific fragment counts or normalized fragments-per-kilobase-per-million-mapped (FPKM).

source_name: whole blood

extract_protocol:
Whole blood samples were collected into PAXgene Blood RNA Tubes (PreAnalytiX/Qiagen) and RNA purified using a PAXgene Blood RNA Kit (Qiagen). RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Globin RNA depletion, poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a GlobinClear kit, NEBNext® Poly(A) mRNA Magnetic Isolation Module, and NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by Novogene Co., Ltd.

value: whole blood

tag: clonal hematopoiesis

value: FALSE

tag: library type

value: strand-specific


title: clonal hematopoiesis-negative, HTP0613A


title: clonal hematopoiesis-negative, HTP0603A


title: clonal hematopoiesis-negative, HTP0531A


title: alcohol_female_2

value: 250 mg/dl


title: clonal hematopoiesis-negative, HTP0663A


title: alcohol_female_1

value: 260 mg/dl


title: alcohol_male_3


title: control_male_1


title: alcohol_male_2


title: clonal hematopoiesis-negative, HTP0658A


title: control_male_3


title: control_female_1


title: clonal hematopoiesis-negative, HTP0605A


title: clonal hematopoiesis-negative, HTP0625A


title: clonal hematopoiesis-negative, HTP0617A


title: alcohol_male_1


title: clonal hematopoiesis-negative, HTP0657A


title: clonal hematopoiesis-negative, HTP0666A


title: clonal hematopoiesis-negative, HTP0647A


title: clonal hematopoiesis-negative, HTP0626A


title: clonal hematopoiesis-negative, HTP0575A


title: clonal hematopoiesis-negative, HTP0563A


title: clonal hematopoiesis-negative, HTP0571A


title: clonal hematopoiesis-negative, HTP0552A


title: clonal hematopoiesis-negative, HTP0560A


title: clonal hematopoiesis-negative, HTP0553A


title: clonal hematopoiesis-negative, HTP0646A


title: clonal hematopoiesis-negative, HTP0550A


title: clonal hematopoiesis-negative, HTP0598A


title: clonal hematopoiesis-negative, HTP0612A


title: clonal hematopoiesis-negative, HTP0609A


title: clonal hematopoiesis-negative, HTP0545A


title: clonal hematopoiesis-negative, HTP0597A


title: clonal hematopoiesis-negative, HTP0549A


title: clonal hematopoiesis-negative, HTP0517A


title: clonal hematopoiesis-negative, HTP0587A


title: clonal hematopoiesis-negative, HTP0566A


title: clonal hematopoiesis-negative, HTP0479A


title: clonal hematopoiesis-negative, HTP0610A


title: clonal hematopoiesis-negative, HTP0564A


title: clonal hematopoiesis-negative, HTP0602A


title: clonal hematopoiesis-negative, HTP0066A2


title: clonal hematopoiesis-negative, HTP0540A


title: clonal hematopoiesis-negative, HTP0561A


title: clonal hematopoiesis-negative, HTP0443A2


title: clonal hematopoiesis-positive, HTP0461A

value: TRUE


title: clonal hematopoiesis-negative, HTP0430A


title: clonal hematopoiesis-positive, HTP0452A


title: clonal hematopoiesis-positive, HTP0469A


title: clonal hematopoiesis-positive, HTP0426A


title: clonal hematopoiesis-positive, HTP0418A


title: clonal hematopoiesis-positive, HTP0421A


title: clonal hematopoiesis-positive, HTP0420A


title: clonal hematopoiesis-positive, HTP0404A


title: clonal hematopoiesis-negative, HTP0629A


title: clonal hematopoiesis-negative, HTP0515A


title: clonal hematopoiesis-negative, HTP0459A


title: Neurosphere culture-Male

status: Public on Feb 10 2021

data_processing:
The Cell Ranger analysis pipeline was used to demultiplex raw base call (BCL) files generated by the sequencer into FASTQ files and to perform genome alignment, filtering, and unique molecular index (UMI) quantification utilizing the Chromium cellular barcodes to generate gene‐barcode UMI matrices.
Genome_build: mm10
Supplementary_files_format_and_content: A zipped file containing the output files from the Cell Ranger pipeline. The output includes a web summary HTML file, feature-barcode matrices,  HDF5 molecule info file , secondary analyses output files and Loupe Cell browser file

source_name: Neurosphere culture

growth_protocol: Neural stem and progenitor cells from the dorsal telencephalic vesicles of sex-segregated male and female gestational day (GD) 12.5 C57BL/6N mouse fetuses (Envigo; Catalog # 4440F) were propagated as nonadherent spheres in serum‐free, defined  mitogenic media, as previously published (Camarillo et al., 2007; Prock and Miranda, 2007; Santillano et al., 2005; Sathyan et al., 2007; Tsai et al., 2014).

extract_protocol:
Confluent neurospheres were trypsinized using 0.25% EDTA‐free trypsin (Thermo Fisher; Catalog # 15090046) for 5 minutes at room temperature with occasional pipetting. Trypsin was subsequently inactivated with 10% FBS, and cells were filtered through a 40‐micron filter to ensure single‐cell suspensions. The cells were then spun down followed by an ice‐cold PBS wash, and 10,000 cells were reserved for ice‐cold methanol fixation.
We used the Chromium Single Cell 3′ Reagent Kit (10X Genomics, Pleasanton, CA; CG000183) to prepare a single‐cell master mix using an input of 7,000 rehydrated cells. The single‐cell master mixes were subsequently loaded into Chromium Chip B (10X Genomics; PN‐1000074), and gel beads in emulsion were prepared according to the manufacturer's protocol followed by RT, cDNA amplification, and library preparation step.

treatment_protocol: The cultures were untreated.

value: untreated

value: Gestational day 12.5


title: Neurosphere culture-Female


title: Human fetal eye 2, 7.5 weeks

status: Public on Feb 04 2021

city: Lausanne

first: Gioele

last: La Manno

state: Vaud

address: Station 19

department: BMI

institute: EPFL

data_processing:
Cell Ranger 2.1.1 was used to convert Illumina base call files to FASTQ format.
Cell Ranger 3.1.0 was used to map FASTQ sequencing reads to the human GRCh38 reference transcriptome with the STAR aligner and to generate feature-barcode count matrices.
For cells isolated from rabbit retina were generated using a custom-built hybrid reference transcriptome combining both the human GRCh38 reference and the rabbit reference (Oryctolagus cuniculus 2.0.99, EMBL-EBI). FASTQ files were mapped to this hybrid reference with Cell Ranger 3.1.0 to generate count matrices. Reads were exclusively assigned either to a human or rabbit transcript.
The velocyto run10x command was used to produce loom files containing spliced and unspliced RNA count matrices
Downstream analyses, including dimensionality reduction and cell type annotation, were performed using both velocyto and scanpy in Python (version 3.7)
Genome_build: GRCh38 human reference, Oryctolagus cuniculus 2.0.99 EMBL-EBI rabbit reference
Supplementary_files_format_and_content: Processed data were stored in loom file format (http://loompy.org/) containing spliced and unspliced count matrices. For the human-rabbit cell mixture (rabbit1.tar.gz, rabbit2.tar.gz), processed data is provided as the 10X count matrices in mtx file format).

source_name: Human fetal retinal at 7.5 weeks

extract_protocol:
Two embryonic eyes from the same embryo were used from a 7.5 post-conception week embryo. The optic cups were dissected out and chopped in several small pieces to facilitate dissociation in 500 uL of digestion buffer.
Cells were transported at 4°C to the Eukaryotic Single Cell Genomics Facility (ESCG, SciLifeLab, Stockholm, Sweden) where a 3’ cDNA library was prepared for single cell RNA sequencing (scRNA-seq) using the 10X Genomics platform and NovaSeq 6000 software.

tag: tissue/cell type

value: retina


title: clonal hematopoiesis-positive, HTP0456A


title: Human adult eye 2

source_name: Human adult retina at 45 years

extract_protocol:
Human post-mortem research-consented donor eyes were obtained from the cornea bank at St. Erik Eye Hospital, Stockholm, Sweden. Donors did not present any clinical diagnosis of ocular disease, and samples were anonymized and processed under the general data protection regulation. Two human eyes from the same donor were used (45-year-old male, 32 hours post-mortem). The lens was dissected out and the rest of the retina, except the sclera, was chopped in several small pieces mixed together in 500 uL of digestion buffer (described below).
Cells were transported at 4°C to the Eukaryotic Single Cell Genomics Facility (ESCG, SciLifeLab, Stockholm, Sweden) where a 3’ cDNA library was prepared for single cell RNA sequencing (scRNA-seq) using the 10X Genomics platform and NovaSeq 6000 software.


title: Human adult eye 1


title: Undifferentiated hESC control

source_name: In vitro hESC-derived culture

extract_protocol:
A step-by-step protocol describing the differentiation procedure has been reported previously (Plaza Reyes et al., 2020a, 2020b). hESCs were plated at a cell density of 2.4x104 cells/cm2 on hrLN-521 (20 μg/mL) using NutriStem hPSC XF medium. A Rho-kinase inhibitor (Millipore, Y-27632) at a concentration of 10 μM was added during the first 24h, while cells were kept at 37°C, 5% CO2/5% O2. After 24h, hPSC medium was replaced with differentiation medium NutriStem hPSC XF without bFGF and TGFβ and cells were placed at 37°C, 5% CO2/21%O2. From day 6 after plating, 100 ng/mL of Activin A (R&D Systems, 338-AC-050) was added to the media. Cells were fed three times a week and kept for 30 days. Monolayers were then trypsinized using TrypLE Select (ThermoFisher Scientific, 12563011) for 10 min at 37°C, 5% CO2. The enzyme was carefully removed and the cells were collected in fresh pre-warmed NutriStem hPSC XF medium without bFGF and TGFβ by gentle pipetting to obtain a single cell suspension. Cells were centrifuged at 300 g for 4 min, the pellet was resuspended, passed through a cell strainer (ø 40 μm, VWR, 732-2757) and seeded on laminin coated dishes (hrLN-521 at 20μg/mL) at different cell densities ranging from 1.4x106 to 1.4x104 cells/cm2. Replated cells were fed three times a week during the subsequent 30 days with NutriStem hPSC XF medium without bFGF and TGFβ. For hPSC-RPE in vitro differentiation in 3D suspension embryoid bodies see our previous publication (Plaza Reyes et al., 2016).
Cells were transported at 4°C to the Eukaryotic Single Cell Genomics Facility (ESCG, SciLifeLab, Stockholm, Sweden) where a 3’ cDNA library was prepared for single cell RNA sequencing (scRNA-seq) using the 10X Genomics platform and NovaSeq 6000 software.

value: Undifferentiated hESC control


title: In vitro hESC-RPE differentiation day 60

value: Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE)


title: clonal hematopoiesis-negative, HTP0484A


title: In vitro hESC-RPE differentiation day 45


title: Human fetal eye 1, 7.5 weeks

extract_protocol:
Two embryonic eyes from the same embryo were used from a 7.5 post-conception week embryo. The optic cTwo embryonic eyes from the same embryo were used from a 7.5 post-conception week embryo. The optic cups were dissected out and chopped in several small pieces to facilitate dissociation in 500 uL of digestion buffer.
Cells were transported at 4°C to the Eukaryotic Single Cell Genomics Facility (ESCG, SciLifeLab, Stockholm, Sweden) where a 3’ cDNA library was prepared for single cell RNA sequencing (scRNA-seq) using the 10X Genomics platform and NovaSeq 6000 software.


title: In vitro hESC-RPE differentiation day 38


title: clonal hematopoiesis-positive, HTP0293A


title: clonal hematopoiesis-positive, HTP0236A2


title: clonal hematopoiesis-positive, HTP0262A2


title: clonal hematopoiesis-positive, HTP0403A


title: In vitro hESC-RPE differentiation day 30


title: clonal hematopoiesis-positive, HTP0424A


title: clonal hematopoiesis-positive, HTP0263A2


title: clonal hematopoiesis-positive, HTP0219A2


title: clonal hematopoiesis-positive, HTP0241A2


title: clonal hematopoiesis-positive, HTP0375A


title: clonal hematopoiesis-positive, HTP0406A


title: clonal hematopoiesis-positive, HTP0411A


title: clonal hematopoiesis-positive, HTP0396A


title: clonal hematopoiesis-positive, HTP0398A


title: clonal hematopoiesis-positive, HTP0243A3


title: clonal hematopoiesis-positive, HTP0386A


title: In vitro hESC-RPE neuronal differentiation day 70

extract_protocol:
Cell sorting was performed on hPSC-RPE cultures after 30 days of hESC-RPE differentiation. Samples were stained with BV421 Mouse Anti-Human CD140b (BD Biosciences 564124, clone [28D4], 10 μg/mL), BB515 Mouse Anti-Human CD56 (BD Biosciences 564489, clone [B159], 2.5 μg/mL), PE Mouse anti-human Ki-67 (Biolegend 350504, clone [Ki-67], 50 μg/mL) conjugated antibodies, diluted in 2% FBS and 1 mM EDTA (ThermoFisher Scientific, 10082147). Cells were incubated with the conjugated antibodies on ice for 30 min. Stained cells were then sorted using a BD FACS Aria Fusion Cell Sorter (BD Bioscience) using FACSDiva Software v8.0.1. Directly after sorting, 68,420 cells/cm2 were plated on matrigel coated plates. Cells were cultured until confluency in P1 media with DMEM/F12 (ThermoFisher Scientific, 11320033) as basal media containing B27 (ThermoFisher Scientific, 17504044), N2 (ThermoFisher Scientific, 17502048), 10ng/mL hDKK1 (R&D Systems, 5439-DK-010), 10ng/mL mouse Noggin (R&D Systems, 1967-NG-025), 10ng/mL hIGF-1 (R&D Systems, 291-G1-200), 5ng/mL bFGF (ThermoFisher Scientific, 13256029) and 50 U/mL of Penicillin-Streptomycin (ThermoFisher Scientific, 15140122). Thereafter and until day 40, cells were continued cultured in P1 with the addition of 40ng/mL 3,3′,5-Triiodo-L-thyronine T3 (Sigma, T-074-1ML) and 100uM Taurine (Sigma, T8691-25G). This protocol was based on previous work (Shao et al., 2017).
Cells were transported at 4°C to the Eukaryotic Single Cell Genomics Facility (ESCG, SciLifeLab, Stockholm, Sweden) where a 3’ cDNA library was prepared for single cell RNA sequencing (scRNA-seq) using the 10X Genomics platform and NovaSeq 6000 software.


title: clonal hematopoiesis-positive, HTP0390A


title: clonal hematopoiesis-positive, HTP0400A


title: P57_Blood

status: Public on Jan 29 2021

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

country: France

institute: Institut Curie

description: 5' RNA

data_processing:
sample de-multiplexing and alignment was performed using Cell Ranger Single Cell Software Suite (v2.0.1) and with for and (v3.0.2) for P57, P58, P60 and P61.
EmptyDrops R package (Lun et al. 2019) was used to call droplets for the samples processed without Cellranger v2.0.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files are raw count UMI matrices which are given by Cellranger pipeline and integrated Seurat objects with the original uncorrected matrix, in the "RNA" assay, and the batch-corrected matrix in the "integrated" assay

source_name: Blood sample

extract_protocol:
RNA from P34, P35, P42, P43 and P46 was extracted according to the Single Cell 3' Reagent Kits V2. RNA from P47, P55, P57, P58 and P61 was extracted according to the Single Cell VDJ 5' Reagent Kits
3' single cell RNA-seq; 5' for paired single cell RNA/TCR-seq

treatment_protocol: Tumor and adjacent normal lung tissue samples were gently cut in approximately 1mm3 pieces. Tissues were digested enzymatically, by an incubation of 20-40 minutes, based on the size of the tissue, at 37oC in agitation, in C02-independent medium (Invitrogen) with Collagenase I (2mg/ml, Sigma-Aldrich), Hyaluronidase (2mg/ml, Sigma-Aldrich) and DNase (25μg/ml, Sigma-Aldrich). The tissue pieces were gently triturated with a 20 ml syringe plunger on a 40 μ m cell strainer (BD) in 1X PBS (Invitrogen) with 1% fetal bovine serum (FBS) and 2mM EDTA (Gibco) until uniform cell suspensions were obtained. The suspended cells were subsequently centrifuged for 10 minutes at 400g and resuspended in PBS 1X buffer with 1% FBS and 2mM EDTA (Gibco). Isolation of tumor infiltrating lymphocytes and peripheral blood mononuclear cells was performed using Ficoll-paque PLUS solution (Sigma-Aldrich). CD3+ T cell isolationwas performed using CD3 microbeads and MACS separation (Miltenyi). Susequently dead cells and debris was removed following SOP (Dead cell removal kit; Debris removal kit; Miltenyi Biotec). Purified CD3+ T cells were resuspended in 1X PBS buffer with 0.04% BSA.

tag: tumor stage

value: pT3 N0

value: Blood sample

tag: smoking status

value: smoker

tag: tumor type

value: ADK

value: M


title: Injury Sciatic nerve H2AK119ub1 Input, rep2

status: Public on Dec 24 2020

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

description:
Injured input2
Input DNA
Combined-H2AK119Ub1_1dpi_090816.TagDir.ucsc.bedGraph.gz
ComK119Ub1_1dpi_080916peak.bed

data_processing:
Illumina Pipeline Casava 1.8.2.
There were two biological replicates for sham and injury, along with corresponding inputs. Reads were mapped to the Rattus norvegicus genome Rn5 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) to produce SAM files for further analysis.
Mapped reads were combined and Hypergeometric optimization of motif enrichment (HOMER) (Heinz et al., 2010) was used to determine enriched binding regions for H2AK119ub1-ChIP relative to sequencing of an input chromatin sample.
Genome_build: rn5 (Rnor_5.0)
Supplementary_files_format_and_content: bedGraph and peak bed files.

source_name: sciatic nerve

growth_protocol: Male Sprague Dawley rats (Harlan Laboratory) were housed with a normal light/dark cycles and ad libitum access to rat chow and water.

extract_protocol:
Sham and injured sciatic nerves of 2 adult male Sprague–Dawley rats were used in ChIP-seq analysis after micrococcal nuclease digestion of peripheral nerve chromatin as described (Ma et al, 2018) using an antibody for H2AK119ub1. Antibody used in the study: H2AK119ub1 Cell Signaling, catalog no. 8240.
Libraries were prepared from ChIP DNA, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.

treatment_protocol: Sciatic nerves of adult Sprague-Dawley rats were cut following the surgery protocol described previously (Hung et al., 2015). As a control, the contralateral limb also received a sham operation consisting of only a skin incision. The nerve tissue distal to the transection and contralateral (sham) nerves were isolated at 1 d post-transection.

value: Sprague Dawley

value: Male

value: Sciatic nerve

value: Injury


title: In vitro hESC-RPE differentiation day 7


title: Sham Sciatic nerve H2AK119ub1 Input, rep1

description:
Sham input1
Input DNA
Combined-H2AK119Ub1_Sham_090816.TagDir.ucsc.bedGraph.gz
Combined-H2AK119Ub1_Sham_080916.peak.bed

value: Sham


title: Injury Sciatic nerve H2AK119ub1 ChIP-seq, rep2

description:
Injured2 H2AK119
ChIP DNA
Combined-H2AK119Ub1_1dpi_090816.TagDir.ucsc.bedGraph.gz
ComK119Ub1_1dpi_080916peak.bed


title: Injury Sciatic nerve H2AK119ub1 Input, rep1

description:
Injured input1
Input DNA
Combined-H2AK119Ub1_1dpi_090816.TagDir.ucsc.bedGraph.gz
ComK119Ub1_1dpi_080916peak.bed


title: Sham Sciatic nerve H2AK119ub1 Input, rep2

description:
Sham input2
Input DNA
Combined-H2AK119Ub1_Sham_090816.TagDir.ucsc.bedGraph.gz
Combined-H2AK119Ub1_Sham_080916.peak.bed


title: Sham Sciatic nerve H2AK119ub1 ChIP-seq, rep2

description:
Sham2 H2AK119
ChIP DNA
Combined-H2AK119Ub1_Sham_090816.TagDir.ucsc.bedGraph.gz
Combined-H2AK119Ub1_Sham_080916.peak.bed


title: Sham Sciatic nerve H2AK119ub1 ChIP-seq, rep1

description:
Sham1 H2AK119
ChIP DNA
Combined-H2AK119Ub1_Sham_090816.TagDir.ucsc.bedGraph.gz
Combined-H2AK119Ub1_Sham_080916.peak.bed

extract_protocol:
Sham and injured sciatic nerves of 2 adult male Sprague–Dawley rats were used in ChIP-seq analysis after micrococcal nuclease digestion of peripheral nerve chromatin as described (Ma et al, 2018). Antibody used in the study: H2AK119ub1 Cell Signaling, catalog no. 8240.
Libraries were prepared from ChIP DNA, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.


title: Injury Sciatic nerve H2AK119ub1 ChIP-seq, rep1

description:
Injured1 H2AK119
ChIP DNA
Combined-H2AK119Ub1_1dpi_090816.TagDir.ucsc.bedGraph.gz
ComK119Ub1_1dpi_080916peak.bed


title: WT IgD neg rep1

status: Public on Dec 01 2020

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

description:
Kim-Jacobson-Dot1L-mouse-RNAseq.tsv
sample name in processed data file:
IgD-neg-2242_S2

data_processing:
Fastq files were aligned, and counted using RNASik-pipe v1.5.3. doi:10.5281/zenodo.1403976
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Spleen

extract_protocol:
B cell subsets were sort-purified and RNA isolated with a Qiagen micro kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

tag: cell type

value: CD19+ IgD- B cells

tag: time

value: 4 days post-immunization with NP-KLH in alum

tag: genotype

value: WT


title: Dot1L IgD neg rep1

description:
Kim-Jacobson-Dot1L-mouse-RNAseq.tsv
sample name in processed data file:
IgDneg-479_S6

value: Dot1L deletion


title: Dot1L naïve rep2

description:
Kim-Jacobson-Dot1L-mouse-RNAseq.tsv
sample name in processed data file:
IgDpos-480_S7

value: CD19+ IgD+ B cells


title: Dot1L naive rep1

description:
Kim-Jacobson-Dot1L-mouse-RNAseq.tsv
sample name in processed data file:
IgDpos-479_S5


title: Dot1L IgD neg rep2

description:
Kim-Jacobson-Dot1L-mouse-RNAseq.tsv
sample name in processed data file:
IgDneg-480_S8


title: WT naive rep1

description:
Kim-Jacobson-Dot1L-mouse-RNAseq.tsv
sample name in processed data file:
IgDpos-2242_S1


title: WT naïve rep2

description:
Kim-Jacobson-Dot1L-mouse-RNAseq.tsv
sample name in processed data file:
IgDpos-2243_S3


title: RU2Za_IGO_06937_17_S37_L007

status: Public on Nov 24 2020

city: New York

last: Poirier

address: 550 1st Ave

institute: NYU Langone Health

data_processing:
Trimming performed with cutadapt 2.10
Counts table generated by MaGECK 0.5.9.4
Genome_build: Human CRISPR Knockout Pooled Library (GeCKO v2)
Supplementary_files_format_and_content: raw counts table

source_name: HAP1 cells

extract_protocol:
Ammonium acetate salt precipitation
TruSeq
CRISPR

tag: cell line

value: HAP1 cells

tag: treatment

value: ZIKV

tag: replicate

value: A

tag: lane


title: RU2Za_IGO_06937_17_S37_L006


title: Human GeCKOv2 plasmid DNA library A_4567_4_CAGATC_L001

molecule: other

organism: synthetic construct

source_name: Human GeCKOv2 plasmid DNA library A

tag: sample type

value: Human GeCKOv2 plasmid DNA library A


title: Human GeCKOv2 plasmid DNA library_ B_4567_2-2_ACAGTG_L001

source_name: Human GeCKOv2 plasmid DNA library B

value: Human GeCKOv2 plasmid DNA library B


title: Human GeCKOv2 plasmid DNA library A_4567_1_TGACCA_L001


title: Human GeCKOv2 plasmid DNA library_ B_4567_2-1_TGACCA_L001


title: RU2Zb_IGO_06937_18_S30_L006

value: B


title: Human GeCKOv2 plasmid DNA library A_4567_3_GCCAAT_L001


title: RU2Yb_IGO_06937_15_S35_L007

value: YFV


title: RU2Ya_IGO_06937_14_S32_L007


title: RU2Yb_IGO_06937_15_S35_L006


title: Human GeCKOv2 plasmid DNA library A_4567_2_ACAGTG_L001


title: RU2Ya_IGO_06937_14_S32_L006


title: In vitro hESC-RPE differentiation day 14

value: Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE)


title: RU2Mb_IGO_06937_12_S31_L006

value: mock


title: RU2Mb_IGO_06937_12_S31_L007


title: RU2Ma_IGO_06937_11_S29_L007


title: RU2Ma_IGO_06937_11_S29_L006


title: RU2Mc_IGO_06937_13_S36_L007

value: C


title: WT IgD neg rep2

description:
Kim-Jacobson-Dot1L-mouse-RNAseq.tsv
sample name in processed data file:
IgD-neg-2243_S4


title: RU2Mc_IGO_06937_13_S36_L006


title: RU2Zc_IGO_06937_19_S28_L007


title: RU2Zc_IGO_06937_19_S28_L006


title: RU2Zb_IGO_06937_18_S30_L007


title: RU2Zc_IGO_06937_19_S1_L001


title: Human GeCKOv2 plasmid DNA library_ B_4567_2-4_CAGATC_L001


title: Human GeCKOv2 plasmid DNA library_ B_4567_2-3_GCCAAT_L001


title: RU2Yb_IGO_06937_15_S8_L001


title: RU2Ya_IGO_06937_14_S5_L001


title: RU2Zb_IGO_06937_18_S3_L001


title: RU2Ma_IGO_06937_11_S2_L002


title: RU2Mc_IGO_06937_13_S9_L001


title: clonal hematopoiesis-negative, HTP0450A

description:
globin-depleted, poly(A)+ RNA from whole blood
Counts_for_GEO.txt.gz
FPKMs_for_GEO.txt.gz

tag: tissue

value: whole blood

value: FALSE

value: strand-specific


title: RU2Mb_IGO_06937_12_S4_L002


title: RU2Ya_IGO_06937_14_S5_L002


title: RU2Yb_IGO_06937_15_S8_L002


title: RU2Mb_IGO_06937_12_S4_L001


title: RU2Za_IGO_06937_17_S10_L002


title: RU2Ma_IGO_06937_11_S2_L001