title: K562 Essential DHS Tiling Cas9 Biological Replicate 1

city: Palo Alto

first: David

last: Yao

address: Michael Bassik/Room 4300, 240 Pasteur Dr.,

institute: Stanford University Bassik Lab

description: sgRNA library sequencing

data_processing:
Reads are trimmed to 20 bases covering the sgRNA spacer sequence
Bowtie1 alignment, v1.2.2, 0 mismatches allowed
Supplementary files format and content: tab-delimited text files include Bowtie alignment counts for each sample

extract_protocol:
Genomic DNA was harvested using QIAgen DNA Blood & Tissue Maxi Kit; Plasmid DNA was extracted from bacterial cultures using the QIAgen Maxi Prep Kit
The sgRNA sequence present on the plasmid or integrated into genomic DNA was amplified and barcoded using PCR, from either 320 ug of genomic DNA per sample, or 5 ng of plasmid DNA

value: Lymphoblast cells

value: Puromycin


title: K562 Essential DHS Tiling Cas9 Biological Replicate 2

status: Public on Jan 31 2023

type: SRA

state: CA California

country: USA

description: sgRNA library sequencing

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: patient 1_Vermilion 1

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

molecule: total RNA

source_name: human lip tissue

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: After centrifugation of the cells derived from vermilion and skin, the total RNA was extracted using a RNeasy mini kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s instructions.

tag: subject id

value: patient 1

tag: age

value: 3 months old

tag: gender

value: male

tag: tissue

value: lip


title: patient 4_Vermilion 4

extract_protocol: After centrifugation of the cells derived from vermilion and oral mucosa, the total RNA was extracted using a RNeasy mini kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s instructions.

value: patient 4

value: female


title: K562 Essential DHS Tiling dCas9 ZNF705 KRAB Biological Replicate 2

description: sgRNA library sequencing


title: K562 Essential DHS Tiling dCas9 ZNF705 KRAB Biological Replicate 1

description: sgRNA library sequencing


title: Young rep 2

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

library_source: transcriptomic

data_processing:
Quality check on raw sequence data, FastQC.
Read mapping. Reads were mapped to the Mus musculus genome assembly GRCm38 (mm10) with HISAT2 on default parameters.
Read counting. Reads were counted into Ensembl annotation intervals using HTSeq-count.
Data normalization and differential analysis. Differential expressed genes were estimated using DESeq2 with default parameters.
Assembly: mm10
Supplementary files format and content: DESeq2 normalized count

organism: Mus musculus

source_name: spleen

growth_protocol: Female C57BL/6J mice were used for all the experiments and were maintained in pathogen-free conditions at the Experimental Medicine Centre (Bialystok, Poland).

extract_protocol:
For RNA sequencing, RPMs (live, single, CD45+, B220-, GR1-, F4/80-high, CD11b-dim, TREML4+) were sorted into Trizol-LS (Invitrogen, 10296010). RNA was isolated using Direct-zol RNA Microprep Kit (Zymo Research, R2062) according to the manufacturer's instructions.
To prepare libraries from FACS-sorted RPMs (at least 100 000 cells/sample) we used the previously described Smart-seq2 protocol {Picelli, 2013 #1236}, suitable for low-input total mRNA sequencing. The quality of RNA and material during the preparation of libraries was checked by Bioanalyzer. .
The samples were sequenced on NextSeq500 (Illumina) with 75 bp single-end reads, with ~50 million reads/sample. RNAseq was performed at GeneCore at EMBL (Heidelberg, Germany)

treatment_protocol: Starting with the age of 4 weeks mice were fed a diet with a standard iron content (200 mg/kg, SAFE #U8958v0177; for Young and Aged), as described before,{Kautz, 2008 #10;Pagani, 2011 #238} or reduced iron content [25 mg/kg; SAFE #U8958v0294; for Aged iron reduced (IR)]. Diets were from SAFE (Augy, France). Mice were analyzed at 8-10 weeks (Young) and 10-11 months (Aged and Aged IR) of age. For supplementation with N-Acetyl-L-cysteine (NAC), aging mice (Aged NAC) were supplied with NAC dissolved in drinking water from 8 weeks of age until 10-11 months of age. Mice were delivered to the local facility at the IIMCB and sacrificed after short acclimatization, or subjected to additional procedures, if applicable.

tag: strain

tag: organ

value: spleen

tag: Sex

value: FACS-sorted red pulp macrophages

value: 8 weeks

tag: diet

value: standard 200 ppm Fe from the 5th week of life


title: K562 Essential DHS Tiling dCas9 Biological Replicate 1

description: sgRNA library sequencing


title: AV_MPRA_DNA5

status: Public on Jan 30 2023

city: Jamaica Plain

first: Xiaoran

last: Zhang

state: MA

address: 14 Perkins Square, Apt 11

department: Cardiology

institute: Boston Children's Hospital

data_processing:
Cutadapt 2.5 was used to remove primer sequences within each read.
MPRA pair-end reads were aligned to mm10 using Bowtie2 2.3.4.3 (--end-to-end) with default parameters.
A custom script was used to determine DNA and RNA read counts for each enhancer.
PCR duplicates were removed by UMI. Read counts were then normalized to sequencing depth (FPM).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include reads count values for each sample.
Library strategy: MPRA

organism: synthetic construct

source_name: AAV9 library

extract_protocol:
RNA was extracted using Trizol and purified with RNA Clean and Concentrator kit from Zymo; AAV genome was released by incubating with Proteinase K solution and then used as template for MPRA library construction.
DNA/RNA were reversed transcripted with UMI-primer which recognized the cloning sites of the specific enhancers. The P5 and P7 adapters were added through two cycles of touch-down PCR.

value: AAV9 library


title: AV_MPRA_DNA4


title: AV_MPRA_DNA3


title: AV_MPRA_DNA1


title: AV_MPRA_DNA2


title: Mutagenesis_MPRA_DNA2

data_processing:
Cutadapt 2.5 was used to remove primer sequences within each read.
Sequence reads were mapped to the library based on the barcode by a custom script.
PCR duplicates were removed by UMI. Read counts were then normalized to sequencing depth (FPM).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include reads count values for each sample.
Library strategy: MPRA


title: Mutagenesis_MPRA_DNA3


title: Mutagenesis_MPRA_DNA1


title: Mutagenesis_MPRA_DNA4


title: ATAC_V2

data_processing:
Fastq files were aligned to mouse genome assembly mm10 using Bowtie2 v2.3.4.3.
PCR duplicates were removed and peak calling for each sample was performed with MACS2 v2.2.6.
Wig files were generated as described for bioChIP-seq data, and then normalized using Danpos2.
Assembly: mm10
Supplementary files format and content: bigWig files

source_name: ventricle

extract_protocol:
The optimized-ATACSeq (omni-ATACSeq) libraries were generated from the isolated cardiomyocytes (two biological replicates) using the author’s recommended lysis steps and transposition protocol. Corces MR, et al. Nat Methods. 2017.
The DNA fragments were amplified with NEBNext High-fidelity 2x PCR master mix. Purify amplified library using Qiagen MinElute PCR Purification kit.

value: ventricle

value: cardiomyocytes

tag: genotype

value: WT


title: ATAC_V1


title: Mutagenesis_MPRA_DNA5


title: ATAC_A1

source_name: atrium

value: atrium


title: ventricular cardiomyocytes, rep1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30).
Trimmed sequence reads were mapped to GRCm38/mm10 using hisat2. The mapped reads were counted and assigned to chromatin features using FeatureCounts.
Transcripts Per Kilobase Million were calculated using the protocol from Li B et al., BMC Bioinformatics. 2011.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include reads count values for each Sample.

extract_protocol:
RNA was extracted using Trizol and purified with RNA Clean and Concentrator kit from Zymo.
RNA libraries were prepared for sequencing using ScriptSeq v2 library kit following the manufacturer's protocols.


title: ventricular cardiomyocytes, rep5


title: ATAC_A2


title: atrial cardiomyocytes, rep5


title: ventricular cardiomyocytes, rep3


title: atrial cardiomyocytes, rep3


title: ventricular cardiomyocytes, rep2


title: atrial cardiomyocytes, rep2


title: atrial cardiomyocytes, rep1


title: Tead1_V2

data_processing:
Raw reads were aligned by Bowtie v2.3.4.3 against mm10 reference genome. PCR duplicates were removed.
To generate the wig files, we extended the mapped reads to 200 bp and normalized read counts by computing RPKM (the numbers of reads per kilobase of bin per million of reads).
Genome wide quantile normalization among samples was performed using Danpos2 v3.0.0.
Assembly: mm10
Supplementary files format and content: bigWig files

extract_protocol:
Homogenized tissues were crosslinked in fresh 1% formaldehyde/PBS for 30 min, quenched with 500 mM glycine. Crosslinked nuclei were sonicated using a QSonica 700. Sonicated chromatin was centrifuged, and the supernatant used for chromatin immunoprecipitation (ChIP) with Invitrogen M280 Streptavidin DynaBeads (Life Technologies). DNA was RNase A and Proteinase K treated the following day and purified using Qiagen MinElute (cat. 28004) for subsequent NGS library synthesis.
Libraries for bioChIP DNA and corresponding input samples were synthesized using KAPA Hyper Prep library kit (#KK8502). Each library was generated according to manufacturer’s protocol.

tag: chip antibody

value: M280 Streptavidin Dynabeads


title: K562 Essential DHS Tiling dCas9 Biological Replicate 2

description: sgRNA library sequencing

value: Lymphoblast cells

value: Puromycin


title: Tead1_V1


title: Tbx5_V2


title: Tead1_A2


title: Tbx5_A2


title: Tbx5_V1


title: Tbx5_A1


title: ventricular cardiomyocytes, rep4


title: P300_A1


title: Srf_A1

value: SRFfb


title: P300_V1


title: P300_V2


title: P300_A2


title: Nkx2.5_V2


title: CD49f-NGFR-  Sir Tubulin + cells rep3

city: London

first: Andreas

last: Wack

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: ALI t10 sorted

data_processing:
fastq files were processed with nf-core/rnaseq pipeline v  3.8.1
pipeline was run using STAR and RSEM for alignment and quantification
Differential expressed genes were obtained from DESeq2 v1.34.0 within an R 4.1.1 environment
Genes are considered significant when padj < 0.05
Assembly: Mus_musculus, ensembl,GRCm38,release-95
Supplementary files format and content: rsem output, counts and TPMs per gene per sample as tab separate file

source_name: primary epithelia

growth_protocol: Primary cells isolated from tracheas by enzymatic treatment were seeded onto 0.4 μm pore size clear polyester membrane  coated with a collagen solution. At confluence, media was removed from the upper chamber to establish an air- liquid interface (ALI). Cells were collected at day 10 post air-exposure.

extract_protocol:
RNA was isolated from sorted cells  , using the Qiagen RNeasy mini kit
RNA (200 ng) was used to prepare cDNA libraries using the NEBNext_Low_Input_w_NEB_Ultra_II_FS Kit.

treatment_protocol: Cultures were trypsinized and sorted into  CD49f+NGFR+ (Basal Cells), CD49f-NGFR- SiRTubulin + (ciliated) and CD49f-NGFR- SiRTubulin - (secretory) subsets

value: airway epithelia

value: wt

value: ciliated


title: atrial cardiomyocytes, rep4


title: Srf_A2


title: Nkx2.5_A1


title: Mef2c_V2


title: Mef2c_V1


title: Nkx2.5_A2


title: Mef2c_A1


title: Mef2c_A2


title: Nkx2.5_V1


title: Mef2a_A2


title: Mef2a_A1


title: Gata4_A2


title: Tead1_A1


title: Gata4_A1


title: Srf_V2


title: Gata4_V1


title: Srf_V1


title: Epithelium organoid,SMAD2/3-LTF,SMAD4,rep1

city: Houston

first: Peixin

last: Jiang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Basecalls were performed using bcl2fastq v2.20 for NextSeq500 output.
Raw sequencing reads were aligned to the mm10 reference genome using bowtie2/2.2.7 in paired-end mode with parameters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
Raw sequencing reads for Spike-in were aligned to the  E. coli genome U00096.3 using bowtie2/2.2.7 in paired-end mode with parameters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
Duplicated reads were removed, and only uniquely mapped reads were kept.
Spike-in normalization was achieved through multiply primary genome coverage by scale factor (100000 / fragments mapped to E. coli genome).Then normalized alignments were converted into fragments using bedtools bamtobed(v2.29.2)
bigWig files were generated using the bedGraphToBigWig tool. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: Endometrium

extract_protocol:
Mouse endometrial organoids were digested with 0.25% Trypsin for 10 min at 37 ℃ to get single cell suspension, then washed and incubated with activated concanavalin A beads for 10 min at room temperature. Cells were then resuspended in antibody buffer containing 0.01% digitonin, 1ul of each antibody was added to individual cell aliquots, and tubes were rotated at 4°C overnight. The following day, targeted chromatin digestion and release were performed with 2.5 ul of Cutana pA/G-MNase and 1 ul of 100 mM CaCl2. Genomic DNA with 0.05ng of Spike-in DNA together was purified with phenol-chloroform and ethanol precipitated.
Sequencing libraries were prepared using  NEBNext Ultra II DNA Library Prep Kit (NEB E7645) following manufacture's protocol.

value: Endometrium

value: Epithelium

tag: antibody


title: Epithelium organoid,SMAD2/3-LTF,SMAD4,rep2


title: Mef2a_V2


title: Epithelium organoid,SMAD2/3-LTF,IgG,rep1

value: IgG


title: Epithelium organoid,SMAD2/3-LTF,IgG,rep2


title: Epithelium organoid,control,SMAD4,rep2

value: Smad2flox/flox; Smad3flox/flox


title: AV_MPRA_V4


title: Epithelium organoid,control,IgG,rep2


title: AV_MPRA_V3


title: AV_MPRA_V5


title: input

description: input

source_name: heart

value: heart


title: Mef2a_V1


title: AV_MPRA_V2

value: AAV9 library


title: AV_MPRA_A5


title: Epithelium organoid,control,IgG,rep1


title: AV_MPRA_A3


title: Mutagenesis_MPRA_V4

value: ventricle


title: AV_MPRA_A1

value: cardiomyocytes


title: AV_MPRA_V1

value: WT


title: Mutagenesis_MPRA_V1


title: Mutagenesis_MPRA_V3


title: AV_MPRA_A2

value: atrium


title: Gata4_V2

value: M280 Streptavidin Dynabeads


title: AV_MPRA_A4


title: Mutagenesis_MPRA_A5


title: Mutagenesis_MPRA_V2


title: Mutagenesis_MPRA_A4


title: HiChIP_V3

data_processing:
The paired-end H3K27ac HiChIP reads were aligned against the mm10 genome using the HiC-Pro pipeline v 3.0.0 with default settings. Valid interactions were identified using HiC-Pro default settings, and interaction matrices were generated.
Hichipper v 0.7.7 was used for loop calling with merged H3K27ac peaks as anchors.
Loops covered by 0 counts in at least two replicates were removed from downstream analysis. Kept loops were analyzed using the R package “diffloop”.
Assembly: mm10
Supplementary files format and content: All valid interaction read pairs (allValidPairs.txt). Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size
Library strategy: HiChIP

extract_protocol:
The extract protocol was using Arima-HiC+ kit following manufacturer's protocols.
Library was constructed with Swift ACCEL-NGS® 2S PLUS DNA LIBRARY KITS. Each library was generated according to manufacturer’s protocol.

value: Ab-H3K27ac (ACTIVE MOTIF:91193)


title: Mutagenesis_MPRA_A1


title: Mutagenesis_MPRA_A3


title: Mutagenesis_MPRA_A2


title: Epithelium organoid,control,SMAD4,rep1


title: HiChIP_V2


title: HiChIP_A3


title: HiChIP_V1


title: HiChIP_A1


title: HiChIP_A2


title: Whole blood, COVID positive, rep 202

city: Darlington

first: Tracy

last: Chew

state: NSW

address: Merewether Building (H04) City Rd & Butlin Ave

department: Sydney Informatics Hub

country: Australia

institute: University of Sydney

data_processing:
RNASeq-DE workflow (v1.0.0), available online at  https://github.com/Sydney-Informatics-Hub/RNASeq-DE
3’ adapter and polyA tails were trimmed from raw sequence reads with BBDuk (v37.89)
Quality checked, trimmed reads were aligned as pairs to the human reference genome, GRCh38 primary assembly and gene set release 106 (obtained from Ensembl) with STAR, setting –sjdbOverhand to 149
Sequencing batch level binary alignment (BAM) files were merged and indexed with SAMtools (v1.10) to obtain sample level BAMs.
HTSeq-count (v0.12.4) with -s reverse was used to obtain feature level raw counts.
Assembly: GRCh38
Supplementary files format and content: HTSeq-count output, containing raw counts per sample

source_name: Whole blood

extract_protocol:
Total RNA was isolated from whole blood samples stored and stabilized in PAXgene RNA tubes according to the manufacturer's guidelines (PreAnalytiX)
Libraries were prepared with 300ng of total RNA per sample using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (RZP) as per manufacturer instructions (Illumina, CA, USA).

value: Whole blood

tag: disease state

value: COVID positive


title: Whole blood, COVID positive, rep 199


title: Whole blood, COVID positive, rep 197


title: Whole blood, COVID positive, rep 192


title: Whole blood, COVID positive, rep 194


title: Whole blood, COVID positive, rep 200


title: Whole blood, COVID positive, rep 198


title: Whole blood, COVID positive, rep 186


title: Whole blood, COVID positive, rep 189


title: Whole blood, COVID positive, rep 183


title: Whole blood, COVID positive, rep 187


title: Whole blood, COVID positive, rep 195


title: Whole blood, COVID positive, rep 181


title: Whole blood, COVID positive, rep 196


title: Whole blood, COVID positive, rep 188


title: Whole blood, COVID positive, rep 193


title: Whole blood, COVID positive, rep 201


title: Whole blood, COVID positive, rep 184


title: Whole blood, COVID positive, rep 190


title: Whole blood, COVID positive, rep 179


title: Whole blood, COVID positive, rep 180


title: Whole blood, COVID positive, rep 185


title: Whole blood, COVID positive, rep 203


title: Whole blood, COVID positive, rep 178


title: Whole blood, COVID positive, rep 176


title: Whole blood, COVID positive, rep 177


title: Whole blood, COVID positive, rep 174


title: Whole blood, COVID positive, rep 175


title: Whole blood, COVID positive, rep 191


title: Whole blood, COVID positive, rep 171


title: Whole blood, COVID positive, rep 160


title: Whole blood, COVID positive, rep 172


title: Whole blood, COVID positive, rep 159


title: Whole blood, COVID positive, rep 165


title: Whole blood, COVID positive, rep 168


title: Whole blood, COVID positive, rep 164


title: Whole blood, COVID positive, rep 170


title: Whole blood, COVID positive, rep 158


title: Whole blood, COVID positive, rep 161


title: Whole blood, COVID positive, rep 153


title: Whole blood, COVID positive, rep 152


title: Whole blood, COVID positive, rep 149


title: Whole blood, COVID positive, rep 156


title: Whole blood, COVID positive, rep 151


title: Whole blood, COVID positive, rep 167


title: Whole blood, COVID positive, rep 154


title: Whole blood, COVID positive, rep 157


title: Whole blood, COVID positive, rep 155


title: Whole blood, COVID positive, rep 166


title: Whole blood, COVID positive, rep 150


title: Whole blood, COVID positive, rep 146


title: Whole blood, COVID positive, rep 147


title: Whole blood, COVID positive, rep 169


title: Whole blood, COVID positive, rep 145


title: Whole blood, COVID positive, rep 173


title: Whole blood, COVID positive, rep 163


title: Whole blood, COVID positive, rep 162


title: Whole blood, COVID positive, rep 143


title: Whole blood, COVID positive, rep 142


title: Whole blood, COVID positive, rep 141


title: Whole blood, COVID positive, rep 140


title: Whole blood, COVID positive, rep 139


title: Whole blood, COVID positive, rep 148


title: Whole blood, COVID positive, rep 136


title: Whole blood, COVID positive, rep 135


title: Whole blood, COVID positive, rep 134


title: Whole blood, COVID positive, rep 133


title: Whole blood, COVID positive, rep 129


title: Whole blood, COVID positive, rep 132


title: Whole blood, COVID positive, rep 128


title: Whole blood, COVID positive, rep 124


title: Whole blood, COVID positive, rep 126


title: Whole blood, COVID positive, rep 125


title: Whole blood, COVID positive, rep 127


title: Whole blood, COVID positive, rep 131


title: Whole blood, COVID positive, rep 130


title: Whole blood, COVID positive, rep 123


title: Whole blood, COVID positive, rep 121


title: Whole blood, COVID positive, rep 122


title: Whole blood, COVID positive, rep 120


title: Whole blood, COVID positive, rep 118


title: Whole blood, COVID positive, rep 119


title: Whole blood, COVID positive, rep 144


title: Whole blood, COVID positive, rep 137


title: Whole blood, COVID positive, rep 116


title: Whole blood, COVID positive, rep 115


title: Whole blood, COVID positive, rep 113


title: Whole blood, COVID positive, rep 114


title: Whole blood, COVID positive, rep 111


title: Whole blood, COVID positive, rep 112


title: Whole blood, COVID positive, rep 110


title: Whole blood, COVID positive, rep 108


title: Whole blood, COVID positive, rep 109


title: Whole blood, COVID positive, rep 105


title: Whole blood, COVID positive, rep 107


title: Whole blood, COVID positive, rep 98


title: Whole blood, COVID positive, rep 101


title: Whole blood, COVID positive, rep 102


title: Whole blood, COVID positive, rep 103


title: Whole blood, COVID positive, rep 106


title: Whole blood, COVID positive, rep 104


title: Whole blood, COVID positive, rep 96


title: Whole blood, COVID positive, rep 97


title: Whole blood, COVID positive, rep 94


title: Whole blood, COVID positive, rep 95


title: Whole blood, COVID positive, rep 99


title: Whole blood, COVID positive, rep 93


title: Whole blood, COVID positive, rep 92


title: Whole blood, COVID positive, rep 90


title: Whole blood, COVID positive, rep 100


title: Whole blood, COVID positive, rep 89


title: Whole blood, COVID positive, rep 182


title: Whole blood, COVID positive, rep 86


title: Whole blood, COVID positive, rep 91


title: Whole blood, COVID positive, rep 83


title: Whole blood, COVID positive, rep 85


title: Whole blood, COVID positive, rep 82


title: Whole blood, COVID positive, rep 81


title: Whole blood, COVID positive, rep 78


title: Whole blood, COVID positive, rep 80


title: Whole blood, COVID positive, rep 75


title: Whole blood, COVID positive, rep 76


title: Whole blood, COVID positive, rep 77


title: Whole blood, COVID positive, rep 79


title: Whole blood, COVID positive, rep 73


title: Whole blood, COVID positive, rep 71


title: Whole blood, COVID positive, rep 72


title: Whole blood, COVID positive, rep 70


title: Whole blood, COVID positive, rep 69


title: Whole blood, COVID positive, rep 87


title: Whole blood, COVID positive, rep 66


title: Whole blood, COVID positive, rep 67


title: Whole blood, COVID positive, rep 68


title: Whole blood, COVID positive, rep 65


title: Whole blood, COVID positive, rep 88


title: Whole blood, COVID positive, rep 62


title: Whole blood, COVID positive, rep 61


title: Whole blood, COVID positive, rep 84


title: Whole blood, COVID positive, rep 59


title: Whole blood, COVID positive, rep 60


title: Whole blood, COVID positive, rep 58


title: Whole blood, COVID positive, rep 56


title: Whole blood, COVID positive, rep 57


title: Whole blood, COVID positive, rep 74


title: Whole blood, COVID positive, rep 55


title: Whole blood, COVID positive, rep 53


title: Whole blood, COVID positive, rep 51


title: Whole blood, COVID positive, rep 52


title: Whole blood, COVID positive, rep 50


title: Whole blood, COVID positive, rep 46


title: Whole blood, COVID positive, rep 48


title: Whole blood, COVID positive, rep 49


title: Whole blood, COVID positive, rep 47


title: Whole blood, COVID positive, rep 64


title: Whole blood, COVID positive, rep 63


title: Whole blood, COVID positive, rep 117


title: Whole blood, COVID positive, rep 44


title: Whole blood, COVID positive, rep 42


title: Whole blood, COVID positive, rep 41


title: Whole blood, COVID positive, rep 43


title: Whole blood, COVID positive, rep 40


title: Whole blood, COVID positive, rep 39


title: Whole blood, COVID positive, rep 38


title: Whole blood, COVID positive, rep 37


title: Whole blood, COVID positive, rep 36


title: Whole blood, COVID positive, rep 33


title: Whole blood, COVID positive, rep 34


title: Whole blood, COVID positive, rep 35


title: Whole blood, COVID positive, rep 30


title: Whole blood, COVID positive, rep 54


title: Whole blood, COVID positive, rep 31


title: Whole blood, COVID positive, rep 29


title: Whole blood, COVID positive, rep 28


title: Whole blood, COVID positive, rep 25


title: Whole blood, COVID positive, rep 26


title: Whole blood, COVID positive, rep 23


title: Whole blood, COVID positive, rep 24


title: Whole blood, COVID positive, rep 45


title: Whole blood, COVID positive, rep 22


title: Whole blood, COVID positive, rep 20


title: Whole blood, COVID positive, rep 19


title: Whole blood, COVID positive, rep 18


title: Whole blood, COVID positive, rep 17


title: Whole blood, COVID positive, rep 14


title: Whole blood, COVID positive, rep 16


title: Whole blood, COVID positive, rep 15


title: Whole blood, COVID positive, rep 32


title: Whole blood, COVID positive, rep 12


title: Whole blood, COVID positive, rep 11


title: Whole blood, COVID positive, rep 13


title: Whole blood, COVID positive, rep 9


title: Whole blood, COVID positive, rep 8


title: Whole blood, COVID positive, rep 138


title: Whole blood, COVID positive, rep 5


title: Whole blood, COVID positive, rep 10


title: Whole blood, COVID positive, rep 27


title: Whole blood, COVID positive, rep 7


title: Whole blood, COVID positive, rep 21


title: Whole blood, COVID positive, rep 3


title: Whole blood, COVID positive, rep 4


title: Whole blood, healthy control, rep 68

value: control


title: Whole blood, COVID positive, rep 2


title: Whole blood, healthy control, rep 69


title: Whole blood, healthy control, rep 70


title: Whole blood, healthy control, rep 66


title: Whole blood, healthy control, rep 62


title: Whole blood, healthy control, rep 60


title: Whole blood, healthy control, rep 61


title: Whole blood, healthy control, rep 63


title: Whole blood, healthy control, rep 65


title: Whole blood, healthy control, rep 64


title: Whole blood, healthy control, rep 67


title: Whole blood, COVID positive, rep 6


title: Whole blood, healthy control, rep 59


title: Whole blood, healthy control, rep 57


title: Whole blood, healthy control, rep 54


title: Whole blood, healthy control, rep 55


title: Whole blood, healthy control, rep 56


title: Whole blood, healthy control, rep 58


title: Whole blood, healthy control, rep 53


title: Whole blood, COVID positive, rep 1


title: Whole blood, healthy control, rep 52


title: Whole blood, healthy control, rep 71


title: Whole blood, healthy control, rep 50


title: Whole blood, healthy control, rep 48


title: Whole blood, healthy control, rep 49


title: Whole blood, healthy control, rep 51


title: Whole blood, healthy control, rep 47


title: Whole blood, healthy control, rep 46


title: Whole blood, healthy control, rep 43


title: Whole blood, healthy control, rep 44


title: Whole blood, healthy control, rep 45


title: Whole blood, healthy control, rep 39


title: Whole blood, healthy control, rep 38


title: Whole blood, healthy control, rep 40


title: Whole blood, healthy control, rep 36


title: Whole blood, healthy control, rep 37


title: Whole blood, healthy control, rep 33


title: Whole blood, healthy control, rep 35


title: Whole blood, healthy control, rep 34


title: Whole blood, healthy control, rep 31


title: Whole blood, healthy control, rep 28


title: Whole blood, healthy control, rep 26


title: Whole blood, healthy control, rep 27


title: Whole blood, healthy control, rep 30


title: Whole blood, healthy control, rep 29


title: Whole blood, healthy control, rep 32


title: Whole blood, healthy control, rep 24


title: Whole blood, healthy control, rep 23


title: Whole blood, healthy control, rep 25


title: Whole blood, healthy control, rep 21


title: Whole blood, healthy control, rep 22


title: Whole blood, healthy control, rep 20


title: Whole blood, healthy control, rep 41


title: Whole blood, healthy control, rep 42


title: Whole blood, healthy control, rep 18


title: Whole blood, healthy control, rep 17


title: Whole blood, healthy control, rep 19


title: Whole blood, healthy control, rep 15


title: Whole blood, healthy control, rep 8


title: Whole blood, healthy control, rep 13


title: Whole blood, healthy control, rep 10


title: Whole blood, healthy control, rep 7


title: Whole blood, healthy control, rep 9


title: Whole blood, healthy control, rep 12


title: Whole blood, healthy control, rep 11


title: Whole blood, healthy control, rep 6


title: Whole blood, healthy control, rep 2


title: Whole blood, healthy control, rep 1


title: Whole blood, healthy control, rep 3


title: 4T1/Tet-shUbr5-shCdc73(+Dox+Dov) bio rep1

status: Public on Jan 27 2023

city: New York

first: Ziqi

last: Yu

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

data_processing:
The libraries were sequenced with paired-end 50 bps on NovaSeq6000 sequencer
The raw sequencing reads in BCL format were processed through bcl2fastq 2.20 (Illumina) for FASTQ conversion and demultiplexing.
Trimming the adaptors with cutadapt (version1.18)
RNA reads were aligned and mapped to the GRCm38 mouse reference genome by STAR (Version2.5.2)
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples

growth_protocol: 4T1 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNAs was extracted using the RNeasy Mini Kit (QIAGEN. 74106) and RNAse-Free DNase Set (QIAGEN. 79254). cDNA was synthesized using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, 4368814).
RNA libraries were prepared for sequencing using Illumina Stranded mRNA Prep kits

treatment_protocol: All the cells were treated with Dox(100 ng/ml) for 3 days to induced Ubr5 and Cdc73 knockdown and treated with dovitinib(1µm) for 24 h

value: Mammary gland epithelial cells

value: Ubr5-Cdc73 knockdown

value: dovitinib-induced apoptosis


title: 4T1/Tet-shCdc73(+Dox+Dov) bio rep2

value: Cdc73 knockdown


title: 4T1/Tet-shUbr5-shCdc73(+Dox+Dov) bio rep2


title: Whole blood, healthy control, rep 5


title: 4T1/Tet-shUbr5(+Dox+Dov) bio rep2

value: Ubr5 knockdown


title: 4T1/Tet-shCdc73(+Dox+Dov) bio rep1


title: 4T1/Tet-Scr(+Dox+Dov) bio rep1


title: 4T1/Tet-shUbr5(+Dox+Dov) bio rep1


title: Whole blood, healthy control, rep 16


title: E. coli cell, soxR_point_mutant, rep3

status: Public on Jan 26 2023

city: Szeged

first: Gabor

last: Grezal

state: Csongrád

address: Temesvári krt. 62.

department: Institute of Biochemistry

country: Hungary

institute: Biological Research Centre

data_processing:
CLC Genomics Workbench v 7.5.1.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05).
Trimmed sequence reads were mapped to E. coli strain K-12 MG1655 / U00096.3  using CLC genomic benchwork (parameters- maximum number of mismatches: 2, minimum length: 0.8, similarity fractions: 0.8, unspecific match hit: 10)
Reads shorter than 50 bp were excluded.
Read count extraction were performed using CLC genomic benchwork.
Read count data were then imported into R version 3.0.249 excluding ribosomal DNA (rDNA) genes.
Assembly: U00096.3
Supplementary files format and content: Tab-delimited text files include raw gene counts for each Sample.

organism: Escherichia coli

growth_protocol: Strains were grown in Minimal salts (MS) medium supplemented with 0.1mM MgSO4, 0.54 μg/mL FeCl3, 1 μg/mL Tiamin, 0.2% Cas amino-acids and 0.2% glucose.

extract_protocol:
Cultures were started from single colonies and grown overnight in Erlenmeyer flasks (25 ml minimal medium). Approximately 109 cells (A600 nm ≈ 1) were taken as samples for RNA isolation. RNA was isolated in late exponential phase (OD around 0.8-1). QIAGEN RNA Protect bacteria reagent was used for freezing of samples (Cat. Num.: 76506). Macherey-Nagel NucleoSpin RNA Plant kit was used for RNA isolation (Cat. Num.: 740949.50). And additional DNase treatment was carried out with Ambion DNase I (Cat. Num.: AM2222). All steps were carried out according to the Manufacturer's instructions.
Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria, Cat.Num.: MRZGN126) was used for RNA depletion. SOLiD Total RNA-Seq kit was used for sequencing library generation (Cat. Num.: PN 4445374). All steps were carried out according to the Manufacturer's instructions.

treatment_protocol:
In the case of CC1_120, CC2_120 and CC3_120 lines, log phase cells of the ancestor were treated with a lethal concentration of ciprofloxacin (50 ng/ml) for 120 minutes.
In the case of CC1_0, CC2_0 and CC3_0 lines, log phase cells were treated with ciprofloxacin (50 ng/ml), and harvested immediately (0 minutes).

value: point mutant


title: E. coli cell, rpoC_point_mutant, rep3


title: Whole blood, healthy control, rep 14


title: E. coli cell, rpoC_point_mutant, rep1


title: E. coli cell, soxR_point_mutant, rep2


title: E. coli cell, soxR_point_mutant, rep1


title: E. coli cell, rpoC_point_mutant, rep2


title: E. coli cell, phoQ_point_mutant, rep1


title: E. coli cell, phoQ_point_mutant, rep2


title: Whole blood, healthy control, rep 4


title: E. coli cell, marR_point_mutant, rep2


title: E. coli cell, marR_point_mutant, rep1


title: E. coli cell, gyrA_point_mutant, rep1


title: E. coli cell, gyrA_point_mutant, rep3


title: E. coli cell, gyrA_point_mutant, rep2


title: E. coli cell, phoQ_point_mutant, rep3


title: E. coli cell, envZ_point_mutant, rep3


title: E. coli cell, envZ_point_mutant, rep2


title: E. coli cell, envZ_point_mutant, rep1


title: E. coli cell, antibiotic_treated,control, 0min, rep2

source_name: BW

value: BW

value: wild-type

value: ciprofloxacin

tag: concentration

value: 50 ng/ml

tag: time


title: E. coli cell, antibiotic_treated, 120min, rep3

tag: cell line


title: E. coli cell, antibiotic_treated,control, 0min, rep3

tag: cell type


title: 4T1/Tet-Scr(+Dox+Dov) bio rep2

value: WT

tag: treatment


title: E. coli cell, antibiotic_treated,control, 0min, rep1


title: E. coli cell, antibiotic_treated, 120min, rep2


title: E. coli cell, trkH_point_mutant, rep2


title: E. coli cell, trkH_point_mutant, rep3


title: E. coli cell, trkH_point_mutant, rep1


title: E. coli cell, marR_point_mutant, rep3


title: SmallRNA.Red.Jungle.Fowl.Davis.testis.wt.adult.ox.rep2

status: Public on Jan 24 2023

city: Yiwu

first: Jiafei

last: Shen

address: N1 Shangcheng Road

country: China

institute: International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine

description: small RNA-seq

data_processing:
Analyses were performed using piPipes v1.4. All data from the small RNA-seq, RNA sequencing, were analyzed using the latest mouse genome release galGal6 (GCA_000002315.5). Generally, one mismatch is allowed for genome mapping.
For RNA-seq reads, the expression per transcript was normalized to the top quartile of expressed transcripts per library calculated by Cuffdiff, and the tpm (transcripts per million) value was quantified using the Salmon software.
For small RNA-seq analysis, uniquely mapping reads excluding rRNA and miRNA  between 26 nt and 32 nt were selected for further analysis.
Genome_build: Gallus gallus: galGal6 (GCA_000002315.5)
Supplementary_files_format_and_content: For small RNA-seq, processed data files are unique genome alignment results in BED2 format (https://github.com/bowhan/piPipes/wiki/nomenclature). RNAseq quantification results are .sf files output by Salmon software.

organism: Gallus gallus

source_name: testis

growth_protocol: Animals mice were maintained and used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester. Chickens were used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester.

extract_protocol:
Total RNAs were extracted using mirVana miRNA Isolation Kit (ThermoFisher, AM1560).
1, Strand-specific RNA-seq: libraries were constructed following the TruSeq RNA sample preparation protocol. rRNAs were depleted from total RNAs by Ribo-Zero Gold (Epicentre Biotechnologies, Madison, WI, USA).  2, Small RNA-seq: Testes samples were lysed and treated with sodium periodate for library constrution. The 3'-adapter is TGGAATTCTCGGGTGCCAAGG and has been trimmed in the raw data.

treatment_protocol: Rooster testes from a 15 months-old White Leghorn of the Cornell Special C strain were used for high-throughput sequencing.

value: whole testis

tag: breed

value: Red Jungle Fowl

value: adult

value: wildtype

tag: fraction

value: oxidized  small RNA


title: Enterocyte_Placebo

city: Cranbury

first: Paul

last: Kayne

state: New Jersey

address: 4-B Cedar Brook Drive

institute: Palatin Technologies

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
After sequencing, gene counts were generated by Cell Ranger v6.0.1 (10x Genomics) using the rat reference genome Rattus norvegicus 6.0.97. Introns were included in the analysis. CellBender was applied to eliminate empty droplets and technical artifacts. Only genes detected in a minimum of 3 cells, cells with at least 200 genes, and cells with <5% of mitochondrial reads were retained. Each sample was normalized using sctransform, part of the Seurat toolkit v4.0.3. To analyze complete data sets and perform downstream comparative analysis between treatment groups (PL8177 vs sham, PL8177 vs vehicle), we combined 3 PL8177 samples and 3 sham or vehicle samples and used the Seurat integration method to remove batch effects and enable identification of shared population across samples within each treatment group.
Assembly: Rattus norvegicus 6.0.97
Supplementary files format and content: CSV files and raw count matrix

organism: Rattus norvegicus

source_name: colon

extract_protocol:
Nuclei were isolated from 9 flash-frozen rat colon tissue samples using a proprietary extraction method (Singulomics, Bronx, NY). Nuclei were captured using 10X Genomics Chromium manufacturer's protocol (10X Genomics, Pleasanton, CA).
Captured nuclei were used to construct 3’ single cell gene expression libraries (Next GEM v3.1) using the 10x Genomics Chromium system (10x Genomics, Pleasanton, CA). Libraries were sequenced with ~150 million read pairs (PE150) per sample on an Illumina NovaSeq sequencing system (Illumina, San Diego, CA). Manufacturer's instruction were used for library construction

treatment_protocol: All animals, except those in the sham group, received 5% DSS in the drinking water for 3 days, from day 1 to day 3, which was then changed to normal drinking water for the following 5 days in the study. The rats in the sham group were given drinking water only. Vehicle control placebo capsules or PL8177 capsules at 50ug/animal were administered by oral gavage twice daily at an interval of 6 hours starting on day 4 through day 7, for a total of 4 consecutive days.

value: colon

value: Enterocyte

value: Wildtype

value: Placebo


title: Enterocyte_PL8177-50ug

description: 10x Genomics


title: Tcells_Placebo

description: 10x Genomics

value: T cells


title: SmallRNA.Red.Jungle.Fowl.Davis.testis.wt.adult.ox.rep1

description: small RNA-seq

tag: age


title: Tcells_PL8177-50ug

description: 10x Genomics

tag: tissue


title: Tcells_Sham

description: 10x Genomics

value: Sham


title: RNAseq.Red.Jungle.Fowl.Davis.testis.wt.adult.rep1

description: RNA-seq

value: rRNA depleted RNA


title: E. coli cell, antibiotic_treated, 120min, rep1

value: BW


title: RNAseq.Red.Jungle.Fowl.Davis.testis.wt.adult.rep2

description: RNA-seq


title: Enterocyte_Sham

description: 10x Genomics


title: ZT(Lowest)_12month_WT

status: Public on Jan 20 2023

city: Nanjing

first: Wang

last: Haiquan

address: Hankou Road

institute: Nanjing University

data_processing:
After sequencing and removal of low-quality reads that contained adaptor contamination, low-quality bases and undetermined bases using fastp software, the sequenced reads were aligned to the mouse genome(mm10) using HISAT2. FeatureCounts was used to determine the mRNA expression levels.
Assembly: mm10
Supplementary files format and content:  tab-delimited text files include estimated counts for each sample

molecule: polyA RNA

source_name: Liver

extract_protocol:
liver were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
mRNAs were enriched with poly-T oligo-attached magnetic beads using NEBNext First Strand Synthesis Reaction Buffer (5×) and then fragmented into small pieces. These cleaved RNA fragments were reverse-transcribed to create a cDNA library using Illumina's NEBNext® UltraTM RNA Library Prep Kit; the average insert size for the paired-end libraries was 300 bp (± 50 bp).

value: Liver

value: ZT(Lowest)

value: wild type


title: ZT(Lowest)_12month_KO

description: tab-delimited text files include estimated counts for each sample


title: ZT(Lowest)_6month_KO


title: ZT(Hightest)_6month_KO

value: ZT(Hightest)


title: ZT(Hightest)_12month_KO


title: ZT(Hightest)_12month_WT


title: ZT(Lowest)_6month_WT


title: Primary tumor, Patient #5

city: Hangzhou

first: Kelie

last: Chen

address: #886 Yuhangtang Road

institute: Zhejiang University

data_processing:
Raw reads were mapped to the reference genome (Homo sapiens, ensemble, GRCh38) using Bowtie2 with the default settings.
Numbers of reads assigned to genes were counted by featureCounts.
DEGs were retrieved by R package DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include estimated read values for each Sample

source_name: Ovary

extract_protocol:
The RNA was extracted according to the BGI's standard protocol. Briefly, main steps goes as follows: 1 Tissue Sample Fragmentation and Lysis; 2 Sample Purification with Chloroform/isoamyl alcohol and Isopropyl alcohol.
Library was constructed according to the BGI's standard protocol. Briefly, main steps go as follows: 1 Sample QC; 2 rRNA Removal; 3 RNA Fragmentation; 4 cDNA synthesis; 5 End repair and Adaptor ligation; 6 PCR; 7 Library QC; 8 Sequencing.

value: Ovary

tag: histological subtype

value: serous ovarian cancer

tag: Stage

value: IIIc

tag: grade


title: Omentum tumor, Patient #1

source_name: Omentum

value: Omentum


title: Omentum tumor, Patient #2


title: Omentum tumor, Patient #3


title: Omentum tumor, Patient #5


title: Primary tumor, Patient #1


title: Omentum tumor, Patient #4


title: ZT(Hightest)_6month_WT


title: Primary tumor, Patient #4


title: ZT(Lowest)_2month_KO


title: ZT(Lowest)_2month_WT


title: ZT(Hightest)_2month_KO


title: ZT(Hightest)_2month_WT


title: Primary tumor, Patient #3


title: ZT21_12month_C57BL/6J


title: Primary tumor, Patient #2


title: ZT5_12month_C57BL/6J


title: ZT17_12month_C57BL/6J


title: ZT9_12month_C57BL/6J


title: ZT13_12month_C57BL/6J


title: ZT17_6month_C57BL/6J


title: ZT1_12month_C57BL/6J


title: ZT13_6month_C57BL/6J


title: ZT21_2month_C57BL/6J


title: ZT17_2month_C57BL/6J


title: ZT9_2month_C57BL/6J


title: ZT5_6month_C57BL/6J


title: ZT1_2month_C57BL/6J


title: ZT5_2month_C57BL/6J


title: ZT13_2month_C57BL/6J


title: USZ-21_CIC1

status: Public on Jan 18 2023

city: Zurich

first: Alicia

last: Pliego Mendieta

address: Schmelzbergstrasse 12

country: Switzerland

institute: University Hospital Zurich

data_processing:
Dragen Illumina
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Dragen RNA pipeline
Trimmed sequence reads were mapped to GRCh38 using Dragen RNA pipeline
Quantification was performed using Salmon in Dragen Illumina RNA pipeline
Salmon quantification files were processed to generate raw counts using tximport in R
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include raw count values for each Sample

source_name: sarcoma tumor

extract_protocol:
RNA from patient-derived sarcoma cell models was extracted using the Maxwell RSC simplyRNA Tissue kit (Promega AS1340). The extracted RNA was quantified with a Nanodrop (ThermoFisher Scientific) and the High Sensitivity RNA ScreenTape Assay for TapeStation systems (Agilent 5067).
RNA-sequencing libraries were prepared using the Illumina Stranded mRNA sample preparation protocol following the manufacturer’s instructions

value: sarcoma tumor

value: no treatment


title: USZ-21_LG1


title: ZT9_6month_C57BL/6J


title: USZ-20_REA1


title: OH931


title: PM197


title: USZ-22_EMC2


title: USZ-21_MFS2


title: USZ-21_UPS1


title: NMFH-1


title: 91113

status: Public on Jan 06 2023

city: Shanghai

first: Yucui

last: Zhao

state: Please Select

address: No. 650 Xinsongjiang Road, Hongkou District, Shanghai

department: cancer center

institute: Shanghai general hospital

description: SMART-seq

data_processing:
raw reads from Illumina sequencing were initially trimmed and filtered by fastp.
The clean paired-end reads were mapped to the reference genome GRCh38 by HISAT2 (v 2.0), and tringTie was used to assemble transcripts and estimate gene expression level.
FPKM value (Fragments Per Kilobase of transcript per Million mapped reads) was determined using RSEM and Bowtie2.
After data estimation using DEBrowser and data filtering excluding batch effect, differentially expressed genes (DEGs) was computed with DESeq2 with a log2 Fold Change cutoff of 1 and an adjusted p-value cutoff of 0.01.
Assembly: mm10

extract_protocol:
Tumor cells were firstly minced with PBS consisting of 2U/μL RNAase inhibitor. Under a microscope, single cells were selected and aspirated with pipettes. The selected cells were immediately added lysis buffer for single-cell RNA extraction, reverse transcription and cDNA amplification using Single Cell Full Length mRNA-Amplification Kit (Vazyme, N712) per manufacturer’s protocol.
RNA-seq libraries were constructed from purified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to the manufacturer’s instruction. cDNA libraries were then sequenced on an Illumina NextSeq 500.

value: colorectal cancer cells

value: Day 30


title: Ishikawa-HK2-siRNA [IH]

status: Public on Jan 14 2023

city: Guangzhou

first: Qingyan

state: Guangdong

address: hongshan 2nd Road, Number 58

institute: the First Affiliated Hospital of Sun Yat-sen University

data_processing:
DESeq2 software (version 1.16.1) was applied to investigte differential expressions between two comparative combinations
Then the overlapping genes of Ishikawa and HEC1A were proceeded KEGG enrichment analysis (Kanehisa and Goto 2000)
Assembly: GRCH38
Supplementary files format and content: excel

source_name: Ishikawa

extract_protocol:
Total RNA extraction in four groups (Ishikawa-NC V.S Ishikawa-HK2-siRNA, HEC1A-NC V.S HEC1A-HK2-siRNA) was used by Trizol for library preparation.1. Place the cracked sample or homogenate at room temperature for 5-10min, so that the nucleoprotein and nucleic acid are completely separated.  2. Add 0.2ml chloroform, shake vigorously for 15sec, and leave at room temperature for 3min. Centrifuge at 12000rpm for 10min at 4°C.  3. Absorb the upper water phase and transfer it to a clean centrifuge tube. Add isopropyl alcohol in the same volume and mix well  min.  4. Centrifuge at 12000rpm for 10min at 4°C and discard the supernatant.  5. Add 1ml 75% ethanol to wash the precipitation. Centrifuge at 12000rpm for 3min at 4°C and discard the supernatant. Room temperature drying  5-10min.  6. Add 30-50μl RNase-free ddH2O to fully dissolve RNA. The resulting RNA solution was placed at -70°C  Store or use immediately for follow-up tests.  7. Qubit2.0 was used to detect RNA concentration, and agarose gel was used to detect RNA integrity and genome contamination.
1. Qubit RNA detection kit was used to accurately quantify total RNA to determine the total added RNA in library construction 2. mRNA purification and fragmentation 3. Double stranded cDNA synthesis. 4. Double stranded cDNA Purification.5. End repair /dA tail addition: 6. Joint connection: 7. Purification of connection products and fragment size sorting. 8. Library amplification.

value: Ishikawa

value: human endometrial cancer cell

value: transfected


title: 91112

description: SMART-seq


title: Ishikawa-NC [INC]

value: NC


title: HEC1A-NC [HNC]


title: 91111

description: SMART-seq


title: HEC1A-HK2-siRNA [HH]


title: 91110

description: SMART-seq


title: ZT1_6month_C57BL/6J


title: USZ-20_SFT1


title: 91109

description: SMART-seq


title: 91107

description: SMART-seq


title: 61011

description: SMART-seq


title: 91108

description: SMART-seq


title: 61009

description: SMART-seq


title: 61007

description: SMART-seq


title: 91106

description: SMART-seq


title: 61006

description: SMART-seq


title: 61004

description: SMART-seq


title: 61010

description: SMART-seq


title: 61003

description: SMART-seq


title: 61001

description: SMART-seq


title: 61005

description: SMART-seq


title: 61002

description: SMART-seq


title: 8133

description: SMART-seq

value: Day 10


title: 80822

description: SMART-seq


title: 80823

description: SMART-seq


title: 80812

description: SMART-seq


title: 8028

description: SMART-seq


title: 80817

description: SMART-seq


title: 80813

description: SMART-seq


title: 8029

description: SMART-seq


title: 80818

description: SMART-seq


title: 80811

description: SMART-seq


title: 61008

description: SMART-seq


title: 80819

description: SMART-seq


title: 8027

description: SMART-seq


title: 8021

description: SMART-seq


title: 8025

description: SMART-seq


title: 8026

description: SMART-seq


title: 8022

description: SMART-seq


title: 7269

description: SMART-seq


title: 7265

description: SMART-seq


title: 7263-LBK1841

description: SMART-seq


title: 7262-LBK1840

description: SMART-seq


title: 80825

description: SMART-seq


title: 80210

description: SMART-seq


title: 7268

description: SMART-seq


title: 7261-LBK1839

description: SMART-seq


title: 72612

description: SMART-seq


title: 7267

description: SMART-seq


title: 7195

description: SMART-seq


title: 7192-LBK1848

description: SMART-seq


title: 7194

description: SMART-seq


title: 72613

description: SMART-seq


title: 72610

description: SMART-seq


title: 7191-LBK1847

description: SMART-seq


title: 708S3

description: SMART-seq


title: 61919-LBK1836

description: SMART-seq


title: 707G2

description: SMART-seq


title: 61913-LBK1835

description: SMART-seq


title: 617S4

description: SMART-seq


title: 617S1

description: SMART-seq


title: 707G3

description: SMART-seq


title: 708S1

description: SMART-seq


title: 617G4

description: SMART-seq


title: 1229S3

description: SMART-seq


title: 1229S4

description: SMART-seq


title: 1229S1

description: SMART-seq


title: 1229S2

description: SMART-seq


title: 1229G3

description: SMART-seq


title: 1219S3

description: SMART-seq


title: 1219G2

description: SMART-seq


title: 1206S5

description: SMART-seq


title: 1219G1

description: SMART-seq


title: 1219S1

description: SMART-seq


title: 1219G3

description: SMART-seq


title: 1206P3

description: SMART-seq

value: Day 7


title: 1206P4

description: SMART-seq


title: 1206P1

description: SMART-seq


title: 1118P5

description: SMART-seq


title: 1118P2

description: SMART-seq


title: 1118P4

description: SMART-seq


title: 1118P6

description: SMART-seq


title: 1118G8

description: SMART-seq


title: 1118G7

description: SMART-seq


title: 1229S5

description: SMART-seq


title: 1118G3

description: SMART-seq


title: 1115P7

description: SMART-seq


title: 1219S4

description: SMART-seq


title: 1115P8

description: SMART-seq


title: 1229G1

description: SMART-seq


title: 1115P9

description: SMART-seq


title: 1115P6

description: SMART-seq


title: 1115P5

description: SMART-seq


title: 1115P3

description: SMART-seq


title: 1115P2

description: SMART-seq


title: 1115P1

description: SMART-seq


title: 1115P4

description: SMART-seq


title: 1115N11

description: SMART-seq

value: Day 0


title: 1206P2

description: SMART-seq


title: 1085G

description: SMART-seq


title: 1084G

description: SMART-seq


title: 1083G

description: SMART-seq


title: 1081G

description: SMART-seq


title: 1082G

description: SMART-seq


title: 1206G6

description: SMART-seq


title: 10222G

description: SMART-seq


title: 0109N9

description: SMART-seq


title: 10221S

description: SMART-seq


title: 0109N8

description: SMART-seq


title: 0109N5

description: SMART-seq


title: 0109N7

description: SMART-seq


title: 0109N6

description: SMART-seq


title: 0109N10

description: SMART-seq


title: 1115N10

description: SMART-seq


title: 0109N1

description: SMART-seq


title: 0109N2

description: SMART-seq


title: OAC37NO

status: Public on Jan 05 2023

city: Southampton

first: Tim

last: Underwood

address: Somers Cancer Research Building, General Hospital

department: Cancer Sciences

institute: University of Southampton

description: DropSeq Barcoded Libraries

data_processing:
Raw reads were converted to fastqs using bcl2fastq v2.18 (Illumina)
Fastq's were ultimately processed through the DropSeq alignment cookbook v2.1 pipeline
https://github.com/broadinstitute/Drop-seq/releases/tag/v2.1.0
During the pipeline, captured transcripts were aligned to hg38 using STAR alignment (STAR 2.6.0a)
Dropseq was performed following a modified DropSeq protocol v3.1 (Macosko et al., 2015), where single cells from the suspension were co-encapsulated with a barcoded bead in nanolitre droplets. Droplets were broken and the bead yield underwent reverse transcription (Maxima H- RTase; ThermoFisher), followed by an exonuclease (Exonuclease I; NEB) and PCR step (KAPA HiFi HotStart ReadyMix; Roche). Each PCR reaction consisted of 2000 beads (estimated 100 cell transcriptomes) for 16 cycles. Products were purified (Ampure Beads XP at a 0.6 ratio), pooled (10 reactions estimated at 1000 cells), and re-purified (again at a 0.6 ratio). For each sample, 500pg of cDNA were used for a Nextera XT library prep kit (Illumina) before sequencing on a NextSeq 500, 75 cycle High output cartridge with a loading concentration 2.3pM.
Assembly: hg38
Supplementary_files_format_and_content: Digital Gene Expression Matrix

molecule: cytoplasmic RNA

source_name: Normal Esophagus

extract_protocol: Samples were relocated to the laboratory and placed in a tissue culture hood, moved to a petri dish and washed with PBS-A and then minced with a scalpel to approximately 1mm chunks. Minced tissue was transferred to a 50ml Falcon tube with 5ml of DMEM complete 100 ul of 150 U/ml Collagenase P and 100 ul of10 mg/ml DNase. The samples were placed in an incubator at 37o C with agitation for 60 minutes and disturbed at 15 minutes and 30 minutes with pipettes. Samples were then passed through a 70 um strainer and 10 ml of empty DMEM added.  Cells were then pelleted using centrifugation and media aspirated. Cells were resuspended in RBC lysis solution and incubated at 4oC for 10 minutes, 10 ml of empty DMEM was added and the suspension was passed through a 40 um strainer before being pelleted and resuspended in either 1 ml PBS or 1 ml of cell suspension buffer.   10 ul of cells in suspension and 10 ul of trypan blue was mixed together and cells were counted on a C-chip Fuchs-Rosenthal haemocytometer. A 150,000-cell aliquot was made up to 1.5 mls with cell suspension buffer and prepared for DropSeq.

value: Normal Esophagus


title: OAC42N

description: DropSeq Barcoded Libraries


title: OAC42T

description: DropSeq Barcoded Libraries

source_name: Esophageal Adenocarcinoma

value: Esophageal Adenocarcinoma


title: 0109N3

description: SMART-seq


title: OAC36T2

description: DropSeq Barcoded Libraries


title: OAC36NO

description: DropSeq Barcoded Libraries


title: OAC36T3

description: DropSeq Barcoded Libraries


title: OAC37T1

description: DropSeq Barcoded Libraries


title: OAC35TL

description: DropSeq Barcoded Libraries


title: 1115N12

description: SMART-seq


title: OAC35TJ

description: DropSeq Barcoded Libraries


title: OAC34N

description: DropSeq Barcoded Libraries


title: OAC33T3

description: DropSeq Barcoded Libraries


title: OAC35N

description: DropSeq Barcoded Libraries


title: 0109N4

description: SMART-seq


title: OAC33T1

description: DropSeq Barcoded Libraries


title: OAC33T2

description: DropSeq Barcoded Libraries


title: OAC32T1

description: DropSeq Barcoded Libraries


title: OAC32T2

description: DropSeq Barcoded Libraries


title: OAC32NOT

description: DropSeq Barcoded Libraries


title: OAC32NOC1

description: DropSeq Barcoded Libraries


title: OAC31T2

description: DropSeq Barcoded Libraries


title: OAC36T1

description: DropSeq Barcoded Libraries


title: OAC29T1

description: DropSeq Barcoded Libraries


title: OAC26rT3

description: DropSeq Barcoded Libraries


title: OAC31T3

description: DropSeq Barcoded Libraries


title: OAC26T3

description: DropSeq Barcoded Libraries


title: OAC34T

description: DropSeq Barcoded Libraries


title: OAC26rT1

description: DropSeq Barcoded Libraries


title: OAC29ON

description: DropSeq Barcoded Libraries


title: OAC25rT

description: DropSeq Barcoded Libraries


title: OAC26rT2

description: DropSeq Barcoded Libraries


title: OAC33NOC

description: DropSeq Barcoded Libraries


title: OAC26T2

description: DropSeq Barcoded Libraries


title: OAC23B

description: DropSeq Barcoded Libraries


title: OAC32T3

description: DropSeq Barcoded Libraries


title: OAC26T1

description: DropSeq Barcoded Libraries


title: OAC25B

description: DropSeq Barcoded Libraries


title: Jurkat, sg70_P260, stimulated and Ctrl-lentivector, rep2

status: Public on Dec 31 2022

city: Boston

first: Nauman

middle: Muhammad

last: Javed

address: 450 BROOKLINE AVE

department: Cancer Biology

institute: DANA-FARBER CANCER INSTITUTE INC

description: Stimulated Jurkats, sg70_P260 (targeting guide), ctrl_lentivector.

data_processing:
Basecalls were performed using bcl2fastq v2.20. Alignment, filtering, peak calling and QC were performed using ENCODE ATAC-seq pipeline v. 2.1.3(https://github.com/ENCODE-DCC/atac-seq-pipeline).
ATAC-seq reads were trimmed using cutadapt 2.5 with auto adapter detection and aligned using bowtie2 with the options -X2000 to GRCh38(https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/).
Low quality and duplicated reads were removed.
Peaks were called using MACS2 with a q_value cutoff <= 0.01 and a max peak number returned of 300000.
Differential accessibility analysis was conducted with the CSAW package v 1.2846. A consensus set of peaks was obtained from the union of peaks across all input samples/replicates. Peaks lying within blacklist regions and with low signal (less than -3 log10CPM) were removed. Reads were counted in 300 bp windows genomewide and merged to a maximum width of 5 kb. Finally, counts were TMM normalized and significant differentially accessible peaks were identified based on a genome-wide (for global analysis) or local window ( <= 1 Mb) FDR correction.
Coverage tracks were computed by merged replicates where applicable using samtools merge and creating signal tracks using DeepTools bamcoverage using the reads per genomic bin normalization (RPGC) options in DeepTools with the pre-computed effective genome size.
Assembly: hg38
Supplementary files format and content: Narrowpeak files contain MACS2 called top 300k peaks at q_value cutoff of 0.01 for each replicate. NarrowPeak format description can be found at: https://genome.ucsc.edu/FAQ/FAQformat.html#format12
Supplementary files format and content: Bigwigs are generated by merging replicates and conducting RPGC normalization using Deeptools.

source_name: Jurkat

growth_protocol: Jurkat cells were grown in 37C, 5% CO2 in complete RPM consisting of RPMI (GIBCO), 10% fetal bovine serum (FBS, heat inactivated, Peak Serum), 20 mM HEPES (GIBCO), 1% sodium pyruvate (GIBCO), 1% penicillin-streptomycin (GIBCO), 1% NEAA (GIBCO), at a maximum density of 2 x 10^6 cells. Cells were routinely tested for mycoplasma.

extract_protocol:
Nuclei from 50000 cells per sample were isolated using ATAC-seq lysis buffer (10 mM Tris-HCL, 10 mM NaCl, 3mM MgCl2, 0.1% Tween-20, 0.1% NP40, 0.1% Digitonin, 1% BSA and ddH2O), wash buffer (10 mM-Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 1% BSA, and ddH2O), and resuspension buffer (PBS with 1% BSA).
Tagmentation of genomic DNA was conducted using Illumina tagmentation kit. Fragmented products were isolated using MiniElute Reaction Purification kit(QIAGEN) and library was constructed using Illumina Nextera XT SetA indices.

treatment_protocol: Jurkat cells were stimulated for 2 hours with 50 ng/ml PMA (Sigma-Aldrich) and 500 ng/ml ionomycin (Sigma, Aldrich). Lentivirus transduction was conducted using either sgCtrl_P258 (control guide RNA) or sg70_P260 (RE4 base editing guide RNA) constructs. Cells were plated at a density of 2-5 x 10^5 cells and treated with lentiviral supernatant supplemented with 8 ug/ml polybrene, centrifuged at 2000g 32 C for 60 minutes, and incubated overnight at 37C 5% CO2. Cells were changed into complete RMPI the following day and puromycin selection was conducted using 5 ug/ml for 3 days.

value: Jurkat

value: T-ALL

value: stimulated (PMA/ionomycin 5 hours)


title: Jurkat, sg70_P260, stimulated and Ctrl-lentivector, rep1


title: Jurkat, sg70_P260, stimulated and BHLHE40-OE, rep1

description: Stimulated Jurkats, sg70_P260 (targeting guide), BHLHE40-OE.

value: sg70_P260, BHLHE40-OE


title: Jurkat, sg70_P260, stimulated, rep1

description: Stimulated Jurkats, sg70_P260 (targeting guide).


title: Jurkat, sg70_P260, stimulated, rep2


title: Jurkat, sg70_P260, stimulated, rep2, BHLHE40

description:
BHLHE40-P260-2
Stimulated Jurkats BHLHE40 sg70_P260 (targeting guide).

data_processing:
Basecalls were performed using bcl2fastq v2.20. Alignment, filtering, peak calling and QC were performed using ENCODE ChIP-seq pipeline v. 2.1.6 (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters.
ChIP-seq reads were trimmed using cutadapt 2.5 with auto adapter detection and aligned using bowtie2 with the options -X2000 to GRCh38 (https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/).
Duplicates and low quality reads were removed.
Peaks were called using MACS v2.1.0 with -g hs -p q_value --nomodel --shift 0 --extsize extsize --keep-dup all -B SPMR where q_value <= 0.01 for H3K27ac and BHLHE40 ChIP and 0.05 for GATA3, and extsize = 145 for H3K27ac and 150 for GATA3/BHLHE40.
p-value bigWig files showing signal enrichment relative to input control were generated for merged filtered bams for each replicate using MACS2 bdgcmp -m FE.
Assembly: hg38
Supplementary files format and content: Bigwigs contain enrichment p-value for merged replicates for each condition/treatment relative to merged input controls (WCE-P258 or WCE-P260) generated using MACS2.

extract_protocol:
25 million cells per sample were pelleted and fixed using 1% formaldehyde and quenched with glycine. Pellets were washed with cold PBS+proteinase, resuspended in lysis buffer, and incubated on ice for 10 minutes. Sample was then diluted up to 1 ml in ChIP dilution buffer, sonicated using Covaris E220, and incubated overnight with H3K27ac antibody (Active Motif, 39133), GATA3 (CST-D13C9), or BHLHE40 (Novus Biological NB100-1800) and incubated overnight. Immunoprecipitation was performed using protein G beads, and DNA fragments were purified using AMPure XP beads.
Eluted fragments were then processed with DNA end-repair (Epicenter Biotech), Klenow a base adding (Klenow from NEB), adaptor ligation, PCR amplification, and purification using AMPure XP beads with final size of ~300 bp.

value: BHLHE40 (Novus Biological, NB100-1800)


title: Jurkat, sg70_P260, stimulated and BHLHE40-OE, rep2


title: Jurkat, sg70_P260, stimulated, rep3


title: Jurkat, sgCtrl_P258, stimulated, rep3

description: Stimulated Jurkats, sgCtrl_P258 (non-targeting guide).


title: Jurkat, sgCtrl_P258, stimulated, rep2


title: Jurkat, sgCtrl_P258, stimulated, rep1


title: Jurkat, sg70_P260, stimulated, rep2, GATA3

description:
GATA3-CST-P260-2
Stimulated Jurkats GATA3 sg70_P260 (targeting guide).


title: Jurkat, sg70_P260, stimulated, rep1, GATA3

description:
GATA3-CST-P260-1
Stimulated Jurkats GATA3 sg70_P260 (targeting guide).


title: US45103023_252665247204_S01_GE1-v5_95_Feb07_1_2

status: Public on Jan 02 2023

city: Firenze

first: Annarosa

last: Arcangeli

state: FI

address: Viale Morgagni 50

country: Italy

institute: University of Firenze

hyb_protocol: Hybridization was performed on human whole genome 44,000 (Agilent-014850) oligonucleotide microarrays using reagents and protocols provided by the manufacturer (Agilent Technologies, Manual Part Number G4140-90042) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07) to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: cDNA synthesis and Cy3 labeling were performed with 500 ng of total RNA by Agilent’s Quick Amp Labeling Kit.

extract_protocol: Total RNA was isolated by Trizol reagent according to the manufacturer’s protocol (Invitrogen S.R.L, Italy). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). High quality quantified RNA was purified on silica gel columns using the RNeasy MinElute Cleanup kit (QIAGEN S.p.A., Italy).

value: colorectal adenocarcinoma cell line

tag: growth

value: RPMI 10%FBS


title: US45103023_252665247204_S01_GE1-v5_95_Feb07_1_1


title: US45103023_252665247203_S01_GE1-v5_95_Feb07_1_3

source_name: Bevacizumab-adapted HCT116

value: RPMI 10%FBS + 250 μg/ml Bevacizumab


title: Jurkat, sgCtrl_P258, stimulated, rep1, BHLHE40

description:
BHLHE40-P258-1
Stimulated Jurkats BHLHE40 sgCtrl_P258 (non-targeting guide).

tag: genotype


title: US45103023_252665247203_S01_GE1-v5_95_Feb07_1_1


title: Jurkat, sg70_P260, stimulated, rep1, BHLHE40

description:
BHLHE40-P260-1
Stimulated Jurkats BHLHE40 sg70_P260 (targeting guide).

tag: chip antibody


title: Jurkat, sgCtrl_P258, stimulated, rep2, BHLHE40

description:
BHLHE40-P258-2
Stimulated Jurkats BHLHE40 sgCtrl_P258 (non-targeting guide).


title: US45103023_252665247204_S01_GE1-v5_95_Feb07_1_3


title: US45103023_252665247187_S01_GE1-v5_95_Feb07_1_2


title: US45103023_252665247187_S01_GE1-v5_95_Feb07_1_4


title: US45103023_252665247187_S01_GE1-v5_95_Feb07_1_1


title: Jurkat, sgCtrl_P258, stimulated, rep2, GATA3

description:
GATA3-CST-P258-2
Stimulated Jurkats GATA3 sgCtrl_P258 (non-targeting guide).


title: US45103023_252665247187_S01_GE1-v5_95_Feb07_1_3


title: US45103023_252665247203_S01_GE1-v5_95_Feb07_1_2


title: Jurkat, sg70_P260, stimulated, rep2, H3K27ac

description:
H3K27ac-P260-2
Stimulated Jurkats H3K27ac sg70_P260 (targeting guide).

value: H3K27ac (Active Motif 39133)


title: Jurkat, sgCtrl_P258, stimulated, rep1, GATA3

description:
GATA3-CST-P258-1
Stimulated Jurkats GATA3 sgCtrl_P258 (non-targeting guide).


title: Jurkat, sgCtrl_P258, stimulated, rep2, H3K27ac

description:
H3K27ac-P258-2
Stimulated Jurkats H2K7ac sgCtrl_P258 (non-targeting guide).


title: Jurkat, sg70_P260, stimulated, rep2, WCE

description:
WCE-P260-2
Stimulated Jurkats input control, sg70_P260 (targeting guide).


title: Jurkat, sgCtrl_P258, stimulated, rep1, H3K27ac

description:
H3K27ac-P258-1
Stimulated Jurkats H2K7ac sgCtrl_P258 (non-targeting guide).


title: Jurkat, sgCtrl_P258, stimulated, rep2, WCE

description:
WCE-P258-2
Stimulated Jurkats input control, sgCtrl_P258 (non-targeting guide).


title: Jurkat, sg70_P260, stimulated, rep1, WCE

description:
WCE-P260-1
Stimulated Jurkats input control, sg70_P260 (targeting guide).


title: cynoDRG_sample16

status: Public on Dec 21 2022

city: South San Francisco

first: Josh

last: Kaminker

state: CA

address: 1 DNA Way

department: OMNI Bx, gRED

institute: Genentech Inc

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: macFas5
Supplementary files format and content: h5 files
Supplementary files format and content: cynoallcelltypes.rds: Cynomolgus monkey Seurat object with cell type annotations for all cell types.

organism: Macaca fascicularis

source_name: Dorsal Root Ganglion

extract_protocol:
DRG samples from cynomolgus monkey were first cut into ~1-2 mm pieces with a scalpel while placed on a dissection tray over dry ice and then placed in the lysis buffer (20 mM NaCl, 5 mM MgCL2, 0.1% TX-100, 10 mM Tris-HCl pH7.2) containing EDTA-Free protease inhibitor, RNAse inhibitor, and RNase-free DNase. Dounce homogenization was used to dissociate all DRG tissues. Before douncing, 1 mL HBSS containing 3% BSA Fraction VI and RNAse inhibitor in nuclei suspension buffer (NSB) was added to the  2 mL Dounce Tissue Grinder. The DRGs were homogenized with an A (“loose”) pestle using 5 to 10 strokes. The homogenate was then filtered through a 70 micron filter and spun down. The pellet was resuspended in the NSB. The frozen DRGs were not allowed to thaw before placing in the lysis buffer and douncing. From this homegenate, nuclei were isolated using two different methods: density-gradient centrifugation and FACS. For density-gradient centrifugation method, the homogenate was layered over an Optiprep density (40%, 20% and 10% for primates) gradient and centrifuged at 2500 g for 20 min. Nuclei at the 20/40 interface were aspirated and mixed with an equal volume of NSB. Nuclei were re-pelleted, washed, and counted using a hemocytometer prior to loading into a 10X Genomics Chromium controller. For FACS, nuclei from the density gradient were pelleted by centrifugation, labeled with propidium iodide and DAPI, and sorted using the Aria Fusion Flow Cytometer. Nuclei were selected based on double labeling with DAPI and PI and sorted into eppendorf tubes containing 0.5 mL nuclei suspension buffer (NSB).  Nuclei were then counted, pelleted and resuspended prior to loading into a 10X Genomics Chromium controller.
Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics) were used for library preparation according to the manufacturer’s user guides. The Cell-RT mix was prepared to aim for 10,000 nuclei per sample and applied to the ChromiumTM Controller for GEM generation and barcoding. Then samples were subjected to post GEM-RT cleanup, cDNA amplification (11 cycles with v3.1), and library construction according to the user manual. Sample index PCR was done with 12 cycles. Libraries were then quantified by Qubit dsDNA HS Assay Kit and profiled by Bioanalyzer High Sensitivity DNA kit.

value: Dorsal Root Ganglion

tag: donor #

value: 8-9 years

tag: Sex

value: F

tag: drg level

value: Lumbar -Left

tag: archival method

value: Frozen

tag: nuclei isolation_method

value: Density gradient


title: Jurkat, sgCtrl_P258, stimulated, rep1, WCE

description:
WCE-P258-1
Stimulated Jurkats input control, sgCtrl_P258 (non-targeting guide).

tag: cell line

tag: cell type


title: Jurkat, stimulated and BHLHE40-OE, rep2

data_processing:
Basecalls were performed using bcl2fastq v2.20.
RNA-seq reads were trimmed using fastp v0.23.2 with automatic adapter trimming and default settings for paired end datasets.vGene quantifications were obtained with Salmon v.1.6 with the seqBias, gcBias, posBias, validateMappings, and automatic library type detection flags enabled.
Assembly: hg38
Supplementary files format and content: Gene quant files (*.gene_quants.sf) contain gene level quantifications for each sample obtained using Salmon v1.6 and GENCODE V38 gene annotations.
Supplementary files format and content: Jurkat_stim_BHLHE40OE_v_Ctrl.tar.gz contains hd5 formatted DESeqDataSet / SummarizedExperiment containing gene counts from salmon imported into DEseq with tximport and gencode v38 annotations, normalized with DESeqV2.
Supplementary files format and content: BHLHE40OE_v_WT_STIM_sig_protein_coding_all.tsv contains differentially expressed protein coding genes between BHLHE40-OE vs. WT at an FDR cutoff of 0.01 using DESeqV2.

extract_protocol:
RNA was extracted from 100000 cells per sample using QIAGEN RNeasy Microkit and polyA enriched using Dynabeads mRNA direct kit. RNA was then fragmented using RNA Fragmentation reagents (ThermoFisher) and DNase treated (Turbo DNase, ThermoFisher) and FastAP enzyme treated (EF0651). Fragmented RNA was cleaned up using Dynabeads MyOne Silane.
RNA-adaptors were ligated using T4 RNA ligase and cleaned using Dynabeads MyOne Silane. Frist strand synthesis of cDNA was achieved using AffinityScript RT Enzyme. Adaptor ligated cDNA was then PCR amplified using Phusion master mix with IDT adaptor indices, and the final library was cleaned up with AMPure XP beads to a final size ~280 bp.

tag: treatment


title: cynoDRG_sample6

description: 10X genomics

value: Thoracic 4-Right

value: Fresh

value: FACS


title: cynoDRG_sample5

description: 10X genomics

value: Lumbar 3-Right


title: cynoDRG_sample14

description: 10X genomics

value: Lumbar 4-Left


title: cynoDRG_sample7

description: 10X genomics

value: Cervical 3-Right


title: cynoDRG_sample10

description: 10X genomics

value: Thoracic 4-Left


title: cynoDRG_sample1

description: 10X genomics

value: Lumbar 4-Right


title: cynoDRG_sample13

description: 10X genomics


title: cynoDRG_sample4

description: 10X genomics

value: Lumbar 3,4- Right pooled


title: cynoDRG_sample15

description: 10X genomics

value: Thoracic -Left


title: Jurkat, stimulated and BHLHE40-OE, rep1

data_processing:
Basecalls were performed using bcl2fastq v2.20.
RNA-seq reads were trimmed using fastp v0.23.2 with automatic adapter trimming and default settings for paired end datasets. Gene quantifications were obtained with Salmon v.1.6 with the seqBias, gcBias, posBias, validateMappings, and automatic library type detection flags enabled.
Assembly: hg38
Supplementary files format and content: Gene quant files (*.gene_quants.sf) contain gene level quantifications for each sample obtained using Salmon v1.6 and GENCODE V38 gene annotations.
Supplementary files format and content: Jurkat_stim_BHLHE40OE_v_Ctrl.tar.gz contains hd5 formatted DESeqDataSet / SummarizedExperiment containing gene counts from salmon imported into DEseq with tximport and gencode v38 annotations, normalized with DESeqV2.
Supplementary files format and content: BHLHE40OE_v_WT_STIM_sig_protein_coding_all.tsv contains differentially expressed protein coding genes between BHLHE40-OE vs. WT at an FDR cutoff of 0.01 using DESeqV2.

value: Jurkat

value: T-ALL

value: stimulated (PMA/ionomycin 5 hours)


title: cynoDRG_sample12

description: 10X genomics

value: Dorsal Root Ganglion

value: 8-9 years

value: F

value: Cervical 4-Left


title: Jurkat, sg70_P260, stimulated, rep1, H3K27ac

description:
H3K27ac-P260-1
Stimulated Jurkats H3K27ac sg70_P260 (targeting guide).

value: H3K27ac (Active Motif 39133)


title: cynoDRG_sample3

description: 10X genomics

value: Cervical 4-Right

value: Fresh

value: Density gradient


title: cynoDRG_sample8

description: 10X genomics

value: Cervical 3,4-Right pooled

value: FACS


title: Jurkat, stimulated and Ctrl-lentivector, rep1

data_processing:
Basecalls were performed using bcl2fastq v2.20.
RNA-seq reads were trimmed using fastp v0.23.2 with automatic adapter trimming and default settings for paired end datasets.Gene quantifications were obtained with Salmon v.1.6 with the seqBias, gcBias, posBias, validateMappings, and automatic library type detection flags enabled.
Assembly: hg38
Supplementary files format and content: Gene quant files (*.gene_quants.sf) contain gene level quantifications for each sample obtained using Salmon v1.6 and GENCODE V38 gene annotations.
Supplementary files format and content: Jurkat_stim_BHLHE40OE_v_Ctrl.tar.gz contains hd5 formatted DESeqDataSet / SummarizedExperiment containing gene counts from salmon imported into DEseq with tximport and gencode v38 annotations, normalized with DESeqV2.
Supplementary files format and content: BHLHE40OE_v_WT_STIM_sig_protein_coding_all.tsv contains differentially expressed protein coding genes between BHLHE40-OE vs. WT at an FDR cutoff of 0.01 using DESeqV2.

value: WT


title: Jurkat, stimulated and Ctrl-lentivector, rep2


title: mouseDRG_sample10

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38
Supplementary files format and content: h5 files
Supplementary files format and content: mouseallcelltypes.rds: Mouse seurat object with cell type annotations for all cell types.

extract_protocol:
DRGs from lumbar levels from both right and left sides were collected in the ice-cold lysis buffer (20 mM NaCl, 5 mM MgCL2, 0.1% TX-100, 10 mM Tris-HCl pH7.2) containing EDTA-Free protease inhibitor, RNAse inhibitor, and RNase-free DNase. Dounce homogenization was used to dissociate all DRG tissues. Before douncing, 1 mL HBSS containing 3% BSA Fraction VI and RNAse inhibitor in nuclei suspension buffer (NSB) was added to the  2 mL Dounce Tissue Grinder. The DRGs were homogenized with an A (“loose”) pestle using 5 to 10 strokes. The homogenate was then filtered through a 70 micron filter and spun down. The pellet was resuspended in the NSB. The frozen DRGs were not allowed to thaw before placing in the lysis buffer and douncing. From this homegenate, nuclei were isolated using two different methods: density-gradient centrifugation and FACS. For density-gradient centrifugation method, the homogenate was layered over an Optiprep density (35%, 16%, 8% for rodents) gradient and centrifuged at 2500 g for 20 min. Nuclei at the 16/35 interface were aspirated and mixed with an equal volume of NSB. Nuclei were re-pelleted, washed, and counted using a hemocytometer prior to loading into a 10X Genomics Chromium controller. For FACS, nuclei from the density gradient were pelleted by centrifugation, labeled with propidium iodide and DAPI, and sorted using the Aria Fusion Flow Cytometer. Nuclei were selected based on double labeling with DAPI and PI and sorted into eppendorf tubes containing 0.5 mL nuclei suspension buffer (NSB).  Nuclei were then counted, pelleted and resuspended prior to loading into a 10X Genomics Chromium controller.
Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics) were used for library preparation according to the manufacturer’s user guides. The Cell-RT mix was prepared to aim for 10,000 nuclei per sample and applied to the ChromiumTM Controller for GEM generation and barcoding. Then samples were subjected to post GEM-RT cleanup, cDNA amplification (11 cycles with v3.1), and library construction according to the user manual. Sample index PCR was done with 12 cycles. Libraries were then quantified by Qubit dsDNA HS Assay Kit and profiled by Bioanalyzer High Sensitivity DNA kit.

tag: strain

value: 8 weeks

value: M

value: Lumbar 3-5 Left&Right pooled

value: Frozen


title: cynoDRG_sample11

description: 10X genomics

tag: age

value: Lumbar 4-Left


title: mouseDRG_sample9

description: 10X genomics

tag: tissue


title: cynoDRG_sample2

description: 10X genomics

value: Thoracic 4-Right


title: mouseDRG_sample8

description: 10X genomics

value: Dorsal Root Ganglion


title: mouseDRG_sample7

description: 10X genomics


title: mouseDRG_sample6

description: 10X genomics


title: cynoDRG_sample9

description: 10X genomics

value: 8-9 years


title: mouseDRG_sample4

description: 10X genomics

value: F


title: mouseDRG_sample5

description: 10X genomics


title: mouseDRG_sample3

description: 10X genomics


title: humanDRG_sample18

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 and v2.4.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: h5 files
Supplementary files format and content: humanallcelltypes.rds: Human Seurat object with cell type annotations for all cell types.

extract_protocol:
DRG samples from humans were first cut into ~1-2 mm pieces with a scalpel while placed on a dissection tray over dry ice and then placed in the lysis buffer (20 mM NaCl, 5 mM MgCL2, 0.1% TX-100, 10 mM Tris-HCl pH7.2) containing EDTA-Free protease inhibitor, RNAse inhibitor, and RNase-free DNase. Dounce homogenization was used to dissociate all DRG tissues. Before douncing, 1 mL HBSS containing 3% BSA Fraction VI and RNAse inhibitor in nuclei suspension buffer (NSB) was added to the  2 mL Dounce Tissue Grinder. The DRGs were homogenized with an A (“loose”) pestle using 5 to 10 strokes. The homogenate was then filtered through a 70 micron filter and spun down. The pellet was resuspended in the NSB. The frozen DRGs were not allowed to thaw before placing in the lysis buffer and douncing. From this homegenate, nuclei were isolated using two different methods: density-gradient centrifugation and FACS. For density-gradient centrifugation method, the homogenate was layered over an Optiprep density (40%, 20% and 10% for primates) gradient and centrifuged at 2500 g for 20 min. Nuclei at the 20/40 interface were aspirated and mixed with an equal volume of NSB. Nuclei were re-pelleted, washed, and counted using a hemocytometer prior to loading into a 10X Genomics Chromium controller. For FACS, nuclei from the density gradient were pelleted by centrifugation, labeled with propidium iodide and DAPI, and sorted using the Aria Fusion Flow Cytometer. Nuclei were selected based on double labeling with DAPI and PI and sorted into eppendorf tubes containing 0.5 mL nuclei suspension buffer (NSB).  Nuclei were then counted, pelleted and resuspended prior to loading into a 10X Genomics Chromium controller.
Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics) were used for library preparation according to the manufacturer’s user guides. The Cell-RT mix was prepared to aim for 10,000 nuclei per sample and applied to the ChromiumTM Controller for GEM generation and barcoding. Then samples were subjected to post GEM-RT cleanup, cDNA amplification (11 cycles with v3.1), and library construction according to the user manual. Sample index PCR was done with 12 cycles. Libraries were then quantified by Qubit dsDNA HS Assay Kit and profiled by Bioanalyzer High Sensitivity DNA kit.

value: 48 years

value: Lumbar 5


title: mouseDRG_sample2

description: 10X genomics

value: 17 weeks

value: Lumbar 1-6; Left pooled


title: mouseDRG_sample1

description: 10X genomics

value: Fresh

value: Density gradient


title: humanDRG_sample14

description: 10X genomics

value: 21 years


title: humanDRG_sample15

description: 10X genomics

value: 38 years


title: humanDRG_sample13

description: 10X genomics

value: FACS


title: ZT21_6month_C57BL/6J

description: tab-delimited text files include estimated counts for each sample

value: Liver

tag: time

value: wild type


title: humanDRG_sample10

description: 10X genomics

value: M

value: Frozen


title: humanDRG_sample16

description: 10X genomics

value: 16 years


title: humanDRG_sample8

description: 10X genomics

value: Dorsal Root Ganglion

value: 31 years

value: Lumbar 4


title: humanDRG_sample9

description: 10X genomics

value: 48 years


title: humanDRG_sample7

description: 10X genomics

value: Thoracic 7


title: humanDRG_sample6

description: 10X genomics

value: 25 years

value: F

value: Lumbar 4-Right


title: humanDRG_sample5

description: 10X genomics

value: Lumbar 4-Left


title: humanDRG_sample11

description: 10X genomics

value: Lumbar 5


title: humanDRG_sample4

description: 10X genomics


title: humanDRG_sample12

description: 10X genomics

value: Density gradient


title: humanDRG_sample3

description: 10X genomics

value: FACS


title: humanDRG_sample1

description: 10X genomics

value: undisclosed


title: humanDRG_sample2

description: 10X genomics


title: gpDRG_sample 8

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: CavPor.3.0
Supplementary files format and content: h5 files
Supplementary files format and content: gpallcelltypes.rds: Guinea pig Seurat object with cell type annotations for all cell types.

organism: Cavia porcellus

extract_protocol:
DRGs from lumbar 3-5 levels from both right and left sides were collected in the ice-cold lysis buffer (20 mM NaCl, 5 mM MgCL2, 0.1% TX-100, 10 mM Tris-HCl pH7.2) containing EDTA-Free protease inhibitor, RNAse inhibitor, and RNase-free DNase. Dounce homogenization was used to dissociate all DRG tissues. Before douncing, 1 mL HBSS containing 3% BSA Fraction VI and RNAse inhibitor in nuclei suspension buffer (NSB) was added to the  2 mL Dounce Tissue Grinder. The DRGs were homogenized with an A (“loose”) pestle using 5 to 10 strokes. The homogenate was then filtered through a 70 micron filter and spun down. The pellet was resuspended in the NSB. The frozen DRGs were not allowed to thaw before placing in the lysis buffer and douncing. From this homegenate, nuclei were isolated using two different methods: density-gradient centrifugation and FACS. For density-gradient centrifugation method, the homogenate was layered over an Optiprep density (35%, 16%, 8% for rodents) gradient and centrifuged at 2500 g for 20 min. Nuclei at the 16/35 interface were aspirated and mixed with an equal volume of NSB. Nuclei were re-pelleted, washed, and counted using a hemocytometer prior to loading into a 10X Genomics Chromium controller. For FACS, nuclei from the density gradient were pelleted by centrifugation, labeled with propidium iodide and DAPI, and sorted using the Aria Fusion Flow Cytometer. Nuclei were selected based on double labeling with DAPI and PI and sorted into eppendorf tubes containing 0.5 mL nuclei suspension buffer (NSB).  Nuclei were then counted, pelleted and resuspended prior to loading into a 10X Genomics Chromium controller.
Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics) were used for library preparation according to the manufacturer’s user guides. The Cell-RT mix was prepared to aim for 10,000 nuclei per sample and applied to the ChromiumTM Controller for GEM generation and barcoding. Then samples were subjected to post GEM-RT cleanup, cDNA amplification (11 cycles with v3.1), and library construction according to the user manual. Sample index PCR was done with 12 cycles. Libraries were then quantified by Qubit dsDNA HS Assay Kit and profiled by Bioanalyzer High Sensitivity DNA kit.

value: Hartley

value: 5.5 months

value: Lumbar 3 -Right


title: gpDRG_sample 5

description: 10X genomics

value: 6 months

value: Lumbar 3 -Left

value: Frozen


title: gpDRG_sample 6

description: 10X genomics

value: Dorsal Root Ganglion


title: gpDRG_sample 4

description: 10X genomics

value: Lumbar 5 -Right

value: Fresh


title: gpDRG_sample 3

description: 10X genomics

value: Lumbar 5 -Left


title: humanDRG_sample17

description: 10X genomics

value: 21 years

value: M


title: gpDRG_sample 1

description: 10X genomics

value: F

value: Lumbar 4+5 -Left


title: sBLISS_RNAseq_10hr-Rep10

status: Public on Dec 16 2022

city: BOSTON

first: ELIZABETH

last: POLLINA

address: 220 LONGWOOD AVENUE, GOLDENSON 405

department: Neurobiology

institute: HARVARD MEDICAL SCHOOL

description: RNA-seq at indicated stimulation timepoint from mouse hippocampus, paired with sBLISS-seq data from the same sample

data_processing:
Quality read trimming was performed using trimmomatic/0.36 using the following command: java -jar $TRIMMOMATIC/trimmomatic-0.36.jar SE -threads 1 -phred33 [FASTQ_FILE] ILLUMINACLIP:/n/app/trimmomatic/0.36/bin/adapters/TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:45
For primary neuron culture RNA-seq, single-end reads were mapped to the mouse genome using subread with the following command: subread-align -i /[PATH TO GENOME REFERENCE]/ -t 0 -r |FASTQ_FILE}_trimmed.fq -o [FASTQ_FILE].sam --SAMoutput
For hippocampal tissue RNA-seq paired with sBLISS-seq, paired-end reads were mapped to the mouse genome using subread with the following command: subread-align -i /[PATH TO GENOME REFERENCE]/ -t 0 -r [FASTQ_FILE]_R1_paired_trimmed.fq -R [FASTQ_FILE]_R2_paired_trimmed.fq -o [FASTQ_FILE].bam
The featureCounts package was used to count mapped reads in RNA-seq data using a custom filtered annotation file: gencode.v17.annotation.gtf filtered for feature_type=”gene”, gene_type="protein_coding" and gene_status="KNOWN") to obtain read counts along genes for each sample.
Assembly: mm10
Supplementary files format and content: Counts matrices are provided from featureCounts. Rows are genes and columns represent each indicated sample and bioreplicate.

source_name: Mouse hippocampus

extract_protocol:
Hippocampal tissue was collected in Trizol reagent, and RNA was extracted using the RNeasy Kit (Qiagen) according to the manufacturer’s instructions.
Total RNA (1000 ng) was used to generate libraries following rRNA depletion (NEBNext, E6310X) according to the manufacturer’s instructions (NEBNext, E7420). 40 bp paired-end reads were generated on the Illumina NextSeq 500.
Bulk total RNA-seq

tag: cell/tissue type

value: Mouse hippocampus

tag: mouse strain

tag: timepoint

value: 10hr post KA injection


title: sBLISS_RNAseq_10hr-Rep8


title: sBLISS_RNAseq_10hr-Rep6


title: sBLISS_RNAseq_10hr-Rep7


title: sBLISS_RNAseq_10hr-Rep5


title: sBLISS_RNAseq_10hr-Rep3


title: sBLISS_RNAseq_10hr-Rep4


title: sBLISS_RNAseq_10hr-Rep2


title: sBLISS_RNAseq_2hr-Rep5

value: 2hr post KA injection


title: sBLISS_RNAseq_2hr-Rep6


title: sBLISS_RNAseq_2hr-Rep3


title: sBLISS_RNAseq_2hr-Rep7


title: sBLISS_RNAseq_10hr-Rep1


title: sBLISS_RNAseq_2hr-Rep1


title: sBLISS_RNAseq_0hr-Rep9

value: 0hr (PBS injected)


title: gpDRG_sample 7

description: 10X genomics

value: Hartley

value: 5.5 months

value: FACS


title: sBLISS_RNAseq_0hr-Rep7


title: sBLISS_RNAseq_2hr-Rep4


title: sBLISS_RNAseq_0hr-Rep6


title: sBLISS_RNAseq_0hr-Rep1


title: sBLISS_RNAseq_2hr-Rep2


title: sBLISS_RNAseq_0hr-Rep5


title: sBLISS_RNAseq_0hr-Rep8


title: gpDRG_sample 2

description: 10X genomics

value: 6 months

value: Lumbar 4+5 -Right


title: 45-ary memory T cells rep 1 (RNA-seq)

status: Public on Nov 17 2022

city: Minneapolis

first: David

last: Masopust

state: MN

address: 2101 6th St SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Adapters and low-quality segments were trimmed with Trimmomatic
Filtered reads were aligned to the mouse genome GRCm38 using Hisat2 and the count matrix was generated using featureCounts
All subsequent gene expression data analyses were done within the R software
Lowly expressed genes were filtered using the filterByExpr function and TMM normalized in edgeR.
Differentially expressed genes were determined using limma. The RNA-Seq samples were sequenced in two batches. Genes were considered significantly different if logFC >1 and FDR <0.05.
Assembly: mm10
Supplementary files format and content: csv files containing raw counts and TMM-normalized lcpm values (Samples Naïve 4, Naïve 5, and Naïve 6were the only samples used in the analysis.)

source_name: Spleen and Lymph Nodes

extract_protocol:
N-specific memory T cells were isolated and FACS-sorted from the spleen using an H-2Kb/N52-59 tetramer
Naïve samples 1-3, Primary, Tertiary, and 27° samples were prepared with the Takara/Clontech Stranded Total RNA-Seq Kit v1 - Pico Input Mammalian reagents following manufacturer's instructions. All other samples were prepared with the Takara/Clontech Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian reagents following manufacturer's instructions.

treatment_protocol: CD45.1+ C57Bl/6 female mice were immunized with three heterologous prime boost immunizations (VSV-NJ VV-N, VSV-Ind) at >= 60 day intervals. H-2Kb/N52-59+ CD45.1+ tertiary memory CD8 T cells were sorted from spleen and lymph nodes and 1x10^5 cells were transferred to congenic CD45.2 recipients, which subsequently received three immunizations (VSV-Ind, VV-N, VSV-NJ) at 60+d intervals. Transfer & boost scheme was repeated until 45 immunizations were reached.

value: Spleen and Lymph Nodes

value: T cells

value: B6 CD45.1 (B6.SJL-Ptprca Pepcb/BoyJ)

tag: genotype

value: wild type

value: 45 immunizations

tag: cohort


title: 39-ary memory T cells rep 3 (RNA-seq)

value: 39 immunizations


title: 45-ary memory T cells rep 3 (RNA-seq)


title: 45-ary memory T cells rep 2 (RNA-seq)


title: 39-ary memory T cells rep 2 (RNA-seq)


title: 39-ary memory T cells rep 1 (RNA-seq)


title: 30-ary memory T cells rep 1 (RNA-seq)

value: 30 immunizations


title: 27-ary memory T cells rep 3 (RNA-seq)

value: 27 immunizations


title: sBLISS_RNAseq_2hr-Rep8

value: Mouse hippocampus


title: 30-ary memory T cells rep 2 (RNA-seq)


title: sBLISS_RNAseq_0hr-Rep10


title: 18-ary memory T cells rep 3 (RNA-seq)

value: 18 immunizations


title: 27-ary memory T cells rep 2 (RNA-seq)


title: Nonary memory T cells rep 1 (RNA-seq)

value: 9 immunizations


title: 18-ary memory T cells rep 2 (RNA-seq)


title: 27-ary memory T cells rep 1 (RNA-seq)


title: 30-ary memory T cells rep 3 (RNA-seq)


title: Nonary memory T cells rep 3 (RNA-seq)


title: Senary memory T cells rep 1 (RNA-seq)

value: 7 immunizations


title: Senary memory T cells rep 2 (RNA-seq)


title: Nonary memory T cells rep 2 (RNA-seq)


title: Senary memory T cells rep 3 (RNA-seq)


title: Tertiary memory T cells rep 1 (RNA-seq)

value: 3 immunizations

value: Tertiary


title: Primary memory T cells rep 1 (RNA-seq)

value: 1 immunizations

value: Primary


title: Tertiary memory T cells rep 3 (RNA-seq)


title: Tertiary memory T cells rep 2 (RNA-seq)


title: Primary memory T cells rep 2 (RNA-seq)


title: Naive T cells rep 3 (RNA-seq)

value: 0 immunizations

value: Naive


title: Naive T cells rep 5 (RNA-seq)

description: Naïve 5

value: Spleen and Lymph Nodes

value: T cells


title: Naive T cells rep 2 (RNA-seq)

value: wild type


title: Naive T cells rep 4 (RNA-seq)

description: Navie 4


title: Naive T cells rep 1 (RNA-seq)