title: strawberry fruit, MYB46-OX, 2

city: Fuzhou

first: Bei

last: Zhang

address: 15 Shangxia Dian Road

institute: Fujian Agriculture and Forestry University

data_processing:
Raw reads were filtered by removing the adapter sequences and low-quality sequences with fastp v.0.20.1 (parameters:-l 50, others are default)
Trimmed reads were mapped to Fragaria vesca genome using hisat2 v.2.2.1 (parameters: default)
Tidy the alignment results and cut down the redundant sequences derived from PCR via Samtools v.1.9
Processing alignment results for gene quantification by FeatureCounts v.2.0.3
Reads count extraction and normalization to TPM through R 4.2.2
Assembly: Fragaria vesca Genome  v4.0
Supplementary files format and content: Excel files include TPM values for each Sample

organism: Fragaria vesca

source_name: fruit

extract_protocol:
Total RNA was extracted using the polysaccharide and polyphenolics-rich RNAprep Pure Kit (Tiangen, Beijing, China).
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: At least five fruits were taken from each treatment, frozen in liquid nitrogen and ground into power.

value: fruit

value: FvMYB46 overexpression

value: 7 Day


title: strawberry fruit, MYB46-OX Control, 2

status: Public on May 01 2023

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype

value: WT (MYB46-OX Control)

tag: treatment

value: Empty vector

tag: time


title: strawberry fruit, MYB46-OX, 1


title: strawberry fruit, VND4c-OX, 1

value: FvVND4c overexpression


title: strawberry fruit, VND4c-OX, 2


title: strawberry fruit, MYB46-OX Control, 1


title: Act5C-GS>Ras attP-GFP-LI-Clone3_rep1

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

data_processing:
FastQC was used for sequencing data quality control and MultiQC was used to aggregate the results.
Raw data processing was performed using STAR sequence aligner, the reads from 3 runs are added.
featureCounts were used to get gene counts from all samples into a single counts' matrix
Differential gene expression testing was performed by DESeq2
Assembly: Drosophila, FlyBase release r6.48
Supplementary files format and content: text file including read counts of each sample

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Cell cultures were grown and expanded in their respective media. All cell lines were cultured in Schneiders Drosophila Medium (Gibco Cat # 21720001), supplemented with 10% Fetal Bovine Serum (Cytiva Hyclone Cat SH30070.03). For Act5C-GS>Ras attP-GFP-LI-Clone 2, Act5C-GS>Ras attP-GFP-LI-Clone 3 and Act5C-GS>Ras attP-GFP-LB-Clone 6 cultures were grown in the same basal media supplemented with 10 nM of Mifepristone (Thermofisher Cat# H11001).

extract_protocol:
Total RNA was isolated from the pellets using the TRIzolTM reagent (Life technologies (Ambion), Cat#:15596018) as per manufacturer’s instructions. The isolated total RNA was subjected to a cleanup using the RNeasy Mini Kit (Qiagen, Cat#74104) and the RNA post-cleanup was eluted in RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Act5C-GS>Ras attP-GFP-LI-Clone3

tag: tissue specificity

value: hemocyte


title: Act5C-GS>Ras attP-GFP-LI-Clone3_rep2


title: Act5C-GS>Ras attP-GFP-LB-Clone6_rep2

value: Act5C-GS>Ras attP-GFP-LB-Clone6

value: neuronal-like


title: Serum_Ta_3mo_rep1

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

data_processing:
Single-end reads for miRNA were mapped to miRbase version 22 and the Rnor 6.0 Rattus norvegicus genome using sRNAbench and sRNAtoolbox.
Supplementary_files_format_and_content: Tab-delimited matrix table with raw read counts for every miRNA

organism: Rattus norvegicus

source_name: Serum

growth_protocol: Male Sprague–Dawley rats (Rattus norvegicus; age, approximately 30 d; weight, 75 to 100 g) were purchased from Envigo (Barrier 208A, Frederick, MD). Rats were allowed to acclimate in the AFRRI vivarium for at least 2 weeks prior to the start of experiments. The room was maintained at standard temperature (21 ± 2°C) and humidity (30% to 70%), with a 12:12-h light:dark cycle (lights on, 0600) and access to standard rat chow (Teklad Global Rodent Diet 8604, Envigo) and water ad libitum. Rats were pair-housed in plastic microisolation cages (23.8 × 45.4 cm) with filter tops and bedding (Teklad Sani-Chips, Envigo), changed 2 or 3 times weekly. All procedures involving animals were conducted to achieve maximal possible wellbeing of the rats, were IACUC-approved (protocol no. 2016-05-006) prior to the start of the study, and were performed in compliance with the guidelines set forth in the Guide for the Care and Use of Laboratory Animals in an AAALAC-accredited facility.

extract_protocol:
Total RNA was isolated from serum samples and assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Library preparation and sequencing was performed by Norgen Biotek. Briefly, library preparation was done using the Norgen Biotek Small RNA Library Prep Kit (Cat. 63600). Sequencing was performed using the NextSeq 500/550 High Output Kit v2 (51 Cycles using a 75-Cycle Kit) on the Illumina NextSeq 500 platform.

treatment_protocol: Pellets were surgically implanted into the gastrocnemius muscle, and each animal received 2 pellets per limb for a total of 4 pellets per rat. Prior to use, pellets were cleaned and chemically sterilized as previously described (https://doi.org/10.1177%2F1091581814565038)

tag: gender

value: Male

tag: strain

value: Sprague-Dawley

tag: metal

value: Ta


title: Act5C-GS>Ras attP-GFP-LB-Clone6_rep1


title: Act5C-GS>Ras attP-GFP-LI-Clone3_rep3


title: Mouse islets, 20% oxygen, biol_rep_1

city: Kumamoto

first: Tomonori

last: Tsuyama

state: Kumamoto

address: 1-1-1, Honjo Chuo-ku

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto university

data_processing:
Sequence reads were trimmed for universal illumina adaptors using TrimGalore.
Trimmed sequence reads were mapped to GENCODE36 genome sequence (for human) or M25 genome sequence (for mouse) using HISAT2 with default parameters setting. Mapped reads were sorted and converted to a binary alignment/map format using SAMtools.
Gene assembly and quantification were performed using Stringtie.
Assembly: GRCh38, GRCm38
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

organism: Mus musculus

source_name: Primary islets cells

extract_protocol:
RNA was extracted using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit (E7765L and E7770, New England Biolabs.) following manufacturer's protocols.

value: Primary islets cells

tag: cell type

value: Pancreatic endocrine cells

value: WT

value: 20percent_oxygen (24h)


title: strawberry fruit, VND4c-OX Control, 2

value: fruit

value: WT (VND4c-OX Control)


title: COA109met

city: Birmingham

first: Colin

middle: Quinn

last: Quinn

state: AL

address: 1670 University Blvd, Room 662

department: Surgery

institute: University of Alabama at Birmingham Heersink School of Medicine

data_processing:
Basecalls performed using Illumina bcl2fastq version 2.18.0.12
Raw FASTQ files were aligned using STAR version 2.7.6a with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from alignments using Cufflinks version 2.2.1 with parameters --library-type fr-firststrand -G -L
Cuffmerge/quant/diff from Cufflinks was then used to identify differentially expressed genes using default settings
Assembly: Gencode GRCh38 p13 Release 32
Supplementary files format and content: tab-delimited text file containing gene symbols and FPKM values for each sample

source_name: Tumor

growth_protocol: Propagated in athymic nude mice

extract_protocol:
Tumors were excised from mice, dissociated using a Miltenyi mouse tumor dissociation kit (Cat. #13009670), and RNA was extracted from tumor cell pellets using a Qiagen RNAeasy Kit (Cat. #74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: metastatic neuroendocrine tumor

tag: tumor type

value: gastroenteropancreatic neuroendocrine

tag: tumor location

value: peritoneal cavity


title: Act5C-GS>Ras attP-GFP-LI-Clone2_rep3

value: Act5C-GS>Ras attP-GFP-LI-Clone2


title: strawberry fruit, VND4c-OX Control, 1

value: Empty vector

value: 7 Day


title: COA109

value: primary neuroendocrine tumor

value: flank


title: Mouse islets, 20% oxygen, biol_rep_3


title: Act5C-GS>Ras attP-GFP-LI-Clone2_rep2

value: neuronal-like


title: A549,FS(Frame Shift) [A549-321-Hyg-12]

city: KunMing

first: Lu

state: YunNan

address: WuJiaYing Street

institute: YunNan University

data_processing:
derRNA using  Bowtie2(v2.3.5.1)
The sequenced reads (FATAQ format) are mapped to Homo Sapiens(hg38) genomes using STAR(v2.7.9a).
bamCoverage from deepTools (v3.5.1).
Read count extraction and normalization were performed using featureCounts(v2.0.1)
Supplementary files format and content: hg38
Supplementary files format and content: bigWig

organism: Homo sapiens

growth_protocol: HEK293T and A549 cell lines were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA extracted using TRIzol reagent, mRNA isolation using NEB Poly(A) mRNA Magnetic Isolation Module(E7490S/L)
VAHTS Universal V8 RNA-seq Library Prep Kit for MGI NRM605

treatment_protocol: HEK293T were transfected using calcium phosphate cell transfection kit

value: lung cancer cell line

value: HDAC-1-FS -OE


title: Act5C-GS>Ras attP-GFP-LI-Clone2_rep1


title: A549,FS(Frame Shift) [A549-321-Hyg-11]


title: 9605

city: Oklahoma City

first: Kurt

last: Zimmerman

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Internal Medicine

institute: University of Oklahoma Health Sciences Center

data_processing:
CellRanger version 5.0.1 mkfastq tool was used for basecalling, which created 4 fastq files per samples from the 4 lanes of the flowcell. So, R1 has 4 fastq files; R2 has 4 fastq files; and I (index) has 4 fastq files.
CellRanger version 5.0.1 count was used to create the matrix table for further processing.
The matrix was then loaded into Seurat version 3.1.5 for normalization, clustering and visualization.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing gene symbols with their respective expression for each cell/barcode.

source_name: kidney

extract_protocol:
After p erfusion of the mouse with PBS, kidneys were minced and digested in 1 ml of RPMI 1640 containing 1 mg/ml collagenase type I (Sigma-Aldrich) and 100 U/ml DNase I (Sigma-Aldrich) for 30 min at 37ºC with agitation. Kidney fragments were passed through a 70-µm mesh (Falcon; BD Biosciences) yielding single-cell suspensions. Cells were centrifuged at 1300rpm (330 X g) for 5 minutes and red blood cells lysed using ACK red blood cell lysis buffer (Quality Biological; 10128-802) at 37ºC for 5 minutes. Cells were spun at 1300 rpm (330 X g), resuspended in 1ml of 1% BSA containing Fc blocking solution (dilution 1:200) and incubated for 30 minutes on ice. After blocking, cells were spun and incubated with the following antibodies in 1% BSA for 30 minutes: BV786 rat anti-mouse CD45 (Catalog #: 557659, 30-F11, BD Pharmigen), eFluor®450 rat anti-mouse F4/80 (Catalog #:48-4801, BM8, eBioscience), APC rat anti-mouse CD11b (Catalog #:17-0112, M1/70, eBioscience), APC/Cy7 rat anti-mouse Gr-1 (Catalog #:557661, RB6-8C5, BD Pharmingen), and Fixable Aqua Dead Cell Stain (catalog no. L34957; Invitrogen). After staining for 30 minutes, cells were spun, washed with 1% BSA, and sorted using a Becton–Dickenson FACSAriaII. We sorted ~25,000 live CD11b+ and F4/80+ cells from individual animals (n=2 per group) into individual BSA coated tubes. Cells were counted and approximately 5,000 cells from each animal were subjected to 10X genomics. This was done for n=2 animals from each experimental group; all animals were female.
10xChromium single cell libraries were prepared according to the standard protocol outlined in the manual. Briefly, sorted single cell suspension, 10x barcoded gel beads, and oil were loaded into Chromium™ Single Cell A Chip to capture single cells in nanoliter-scale oil droplets by Chromium™ Controller and to generate Gel Bead-In-EMulsions (GEMs). Full length cDNA libraries were prepared by incubation of GEMs in a thermocycler machine. GEMs containing cDNAs were broken and all single cell cDNA libraries were pooled together, cleaned using DynaBeads MyOne™ Silane beads (Fisher PN 37002D), and pre-amplified by PCR to generate sufficient mass for sequencing library construction. Sequencing libraries were constructed by following the steps: cDNA fragmentation, end repair & A-tailing, size selection by SPRIselect beads (Beckman Coulter, PN B23318), adaptor ligation, sample index PCR amplification, and a repeat of SPRIselect beads size selection. The final constructed single cell libraries were sequenced by Illumina Nextseq machine with total reads per cell targeted for a minimum of 50,000.

treatment_protocol: No treatments; mice were harvested at ~6 weeks of age.

value: CX3CR1gfp/gfp knockout

tag: age and sex

value: ~6 weeks old female


title: 6906


title: 24B>Ras attP-L5-CloneB8_rep3

value: 24B>Ras attP-L5-CloneB8

value: muscle


title: 6789

value: CX3CR1gfp/wt control


title: A549,FS(Frame Shift) [A549-321-1]


title: A549,EV [A549-311-1]

value: FLAG -OE


title: S12_Zcchc6 Knockout_Litter3

first: Areum

last: Han

address: Karp Family Building, 7th Floor. 300 Longwood Ave.

institute: Boston Children's Hospital

data_processing:
Adaptor-trimmed RNA-seq reads were aligned to the mm10 genome and transcriptome using Tophat.
Reads per gene were counted by the HTSeq tool and further normalized as CPM(counts per million) values using the edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: txt, CPM values

source_name: Reticulocytes/Mature red blood cells

growth_protocol: Blood was collected from E18.5 embryos and red blood cells (Propidium Iodide-/hoechst 33342-/TER119+) are directly sorted to trizol.

extract_protocol:
RNA was isolated and treated with DNAse using the column from the Direct-zol RNA Kit.  Ribosomal RNA depletion
Libraries were prepared according to NEBNext Kit.

value: Zcchc6 Knockout

tag: background strain,

value: red blood cells/reticulocytes


title: 24B>Ras attP-G1-CloneG1_rep2

value: 24B>Ras attP-G1-CloneG1

value: mesodermal lineage


title: 24B>Ras attP-L5-CloneB8_rep1


title: A549,EV [A549-311-Hyg-11]


title: HEK293T, FL(Full  Length) [293T-322-2]

value: human embryonic kidney

value: WT

value: overexpress HDAC-1  for 24h


title: S10_Zcchc6 WT_Litter2

value: Zcchc6 WT


title: S11_Zcchc6 WT_Litter3


title: 24B>Ras attP-G1-CloneG1_rep3


title: 24B>Ras attP-G1-CloneG1_rep1


title: zcl_patient 12

type: RNA

city: Nanjing

first: Pengfei

last: Li

state: Jiangsu

address: NO.155 Hanzhong Road, Baixia District

department: Clinical Laboratory

institute: Jiangsu Province Hospital of TCM

description: severe SFTS

hyb_protocol: RNA samples were hybridized on the miRCURY™ LNA Array (v.18.0) according to manufacturer’s instructions.

scan_protocol: Following the washing steps the slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.
Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: PBMC from SFTS

label_protocol: The RNAs were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit according to manufacturer’s instructions.

extract_protocol: Total RNA was harvested using TRIzol kit (Invitrogen)   according to manufacturer’s instructions. The integrity of RNA was assessed by electrophoresis on a denaturing agarose gel. The Nanodrop instrument is used for accurate for measurement of concentrations (abs 260), protein contamination (ratio abs260/abs280) or contamination with organic compounds (ratio abs260/abs230).

value: PBMC

tag: diagnosis

value: severe fever with thrombocytopenia syndrome (SFTS)


title: sky_patient 12

description: severe SFTS


title: ldk_patient 12

description: mild SFTS

value: mild fever with thrombocytopenia syndrome (SFTS)


title: ccg_patient 12

description: severe SFTS


title: wfl_patient 12

description: severe SFTS


title: HEK293T, FS(Frame Shift) [293T-321-2]

value: overexpress HDAC-1-FS  for 24h


title: S9_Zcchc6 Knockout_Litter2


title: 24B>Ras attP-G1-CloneF3_rep3

value: 24B>Ras attP-G1-CloneF3


title: 24B>Ras attP-L5-CloneB8_rep2

value: 24B>Ras attP-L5-CloneB8


title: A549,EV [A549-311-Hyg-10]

value: lung cancer cell line


title: 6788

value: CX3CR1gfp/wt control

value: ~6 weeks old female


title: S8_Zcchc6 WT_Litter1


title: whj_patient 12

description: mild SFTS


title: 24B>Ras attP-G1-CloneF3_rep2


title: zfq_patient 12

description: mild SFTS


title: S7_Zcchc6 Knockout_Litter1

value: Zcchc6 Knockout


title: 24B>Ras attP-G1-CloneF3_rep1


title: HEK293T, H3K9ac_FS

library_source: genomic

data_processing:
The sequenced reads (FATAQ format) are mapped to Homo Sapiens(hg38) genomes using Bowtie2(v2.3.5.1).
Mapped reads are normalized by RPGC provided by command bamCoverage from deepTools (v3.5.1).
Peaks were called uing MACS (v2.2.7.1) bdgdiff
Supplementary files format and content: hg38
Supplementary files format and content: bigWig,bed

molecule: genomic DNA

growth_protocol: HEK293T cell lines were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a ME220 focused-ultrasonicator (Covaris).
VAHTS Universal DNA Library Prep Kit for MGI (NDM607)


title: S6_Dis3l2 WT_Litter2

value: Dis3l2 WT

value: red blood cells/reticulocytes


title: scivMSC3

city: Hangzhou

first: Chunting

last: Hua

state: Zhejiang

address: 3 East Qingchun Road

institute: Sir Run Run Shaw Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus

source_name: Blood

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BALB/c

value: blood

value: scivMSC


title: S5_Dis3l2 WT_Litter2


title: S4_Dis3l2 Knockout_Litter2

value: Dis3l2 Knockout


title: HEK293T, H3K9ac_EV

value: human embryonic kidney

value: WT

value: overexpress FLAG empty vector for 24h


title: 309_normal

description: healthy control

source_name: PBMC from healthy control

value: PBMC

value: healthy control


title: lcm_patient 12

description: mild SFTS

value: mild fever with thrombocytopenia syndrome (SFTS)


title: 385_normal

description: healthy control


title: Ventral Respiratory Column, 7 days 6%-7 days 8%, Moderate CH, Replicate 6

city: Milwaukee

first: Kirstyn

middle: J

last: Grams

state: Wisconsin

address: 8701 W Watertown Plank Road

department: Physiology

institute: Medical College of Wisconsin

description: matrix column name: VRC-7d-6p-8p_rep6

data_processing:
MAP-RSeq3 workflow
Initial quality control and preprocessing of raw reads was completed with FASTQC and Trimmomatic
Alignment of preprocssed raw sequence reads were mapped to goat reference genome (GCA_001704415.1) using STAR package
Read counts were generated with featureCounts function of MAP-RSeq3 workflow and normalization values provided by MAP-RSeq3 workflow
Assembly: GCA_001704415.1
Supplementary files format and content: tab-delimited text files include raw RPKM values for each sample for each nuclei
Supplementary files format and content: xlsx file containing results from EdgeR DEG pairwaise analysis with each separate file representing comparison between RA vs CO2 condition across different nuclei

organism: Capra hircus

source_name: Brain (Medulla)

extract_protocol:
Total RNA was isolated on-column using Direct-Zol RNA Miniprep plus (Zymo Research, Irvine, CA, USA) per manufacture instructions
RNA libraries were prepared using SMARTer® Universal Low Input RNA Kit for Sequencing (Takara Bio, San Jose, CA, USA), per manufacturing recommendations

value: Brain (Medulla)

tag: treatment (co2 condition)

value: Moderate CH

tag: tissue region

value: Ventral Respiratory Column

tag: Sex

value: Female


title: Ventral Respiratory Column, 7 days 6%-7 days 8%, Moderate CH, Replicate 5

description: matrix column name: VRC-7d-6p-8p_rep5

tag: tissue


title: scivMSC2

tag: treatment


title: HEK293T,EV [293T-311-2]

tag: genotype


title: 297_normal

description: healthy control


title: Ventral Respiratory Column, 7 days 6%-7 days 8%, Moderate CH, Replicate 3

description: matrix column name: VRC-7d-6p-8p_rep3


title: S3_Dis3l2 Knockout_Litter2


title: scivMSC1


title: 12057

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
VDJ-Seq: The bioinformatic analysis of the VDJ-seq data was performed as described in detail in Chovanec et al., Nat. Protoc. 13, 2018. using the BabrahamLinkON pipeline: (1) preclean.py (default parameters), Includes trimming and alignment steps (BabrahamLinkOn pipeline) deduplicate.py (default parameters), based on UMI  (BabrahamLinkOn pipeline) (2) assemble_clones.py (default parameters)  (BabrahamLinkOn pipeline) (3) The resulting counts were summarized using customized scripts based on the statistical language R version 3.3.3. The relative usage of each VH gene is shown as percentage of all VDJH recombination events determined.
ChIP-Seq:  Reads were aligned against the Mus musculus genome version of July 2007 (NCBI37/mm9) with the Bowtie program version 0.12.5. Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM)., using 'bedtools' and 'kent source utilities'.
RNA-Seq: The number of reads per gene was counted using the featureCounts version 1.5.0 with default settings. Transcripts per million (TPM) values were calculated as described previously.
total RNA-Seq: Reads were aligned with STAR version 2.4.2 to the Mus musculus genome version of July 2007 (NCBI37/mm9). Read coverages were calculated with the BEDTool program, were normalized to reads per millions (RPM) using the SAMTools as well as the KentTools.
Assembly: mm9 (total RNA-Seq, RNA-Seq,ChIP-Seq), mm10 (VDJ-Seq)
Supplementary files format and content: tab-delimited text files include RPM values for each VDJ-Seq sample and TPM values for RNA-Seq samples. bigWig files include read coverage for total RNA-Seq and ChIP-Seq samples.

source_name: H3K36me3 AB ChIP-Seq Pro-B cell Rag2(-/-)

extract_protocol:
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols
ChIP DNA Clean and Concentrator kit (Zymo Research)

value: bone marrow

tag: chip antibody

value: H3K36me3 Ab (D5A7) (Cell Signalling 4909S, Lot.:1)

value: Pro-B cell

value: Ex-vivo FACS sorted from bone marrow


title: Ventral Respiratory Column, 7 days 6%-7 days 8%, Moderate CH, Replicate 2

description: matrix column name: VRC-7d-6p-8p_rep2


title: 15835

source_name: H3K4me2 AB ChIP-Seq Pro-B cell Rag2(-/-) Ikzf1(_delta_/+)

value: H3K4me2 Ab (Millipore 07-030, Lot.:DAM1724042)


title: scMSC3

value: BALB/c

value: blood

value: scMSC


title: HEK293T, H3K9ac_FL

tag: cell line

value: human embryonic kidney

value: WT

value: overexpress HDAC-1  for 24h


title: S2_Dis3l2 Knockout_Litter1

value: Dis3l2 Knockout

value: red blood cells/reticulocytes


title: Ventral Respiratory Column, 7 days 6%-7 days 8%, Moderate CH, Replicate 1

description: matrix column name: VRC-7d-6p-8p_rep1

value: Brain (Medulla)


title: S1_Dis3l2 WT_Litter1

value: Dis3l2 WT


title: Ventral Respiratory Column, 7 days 6%-7 days 8%, Moderate CH, Replicate 4

description: matrix column name: VRC-7d-6p-8p_rep4

value: Moderate CH

value: Ventral Respiratory Column


title: scMSC2


title: 13017

source_name: H3K27ac AB ChIP-Seq Pro-B cell Rag2(-/-)

value: bone marrow

value: 4-days-in-vitro expansion


title: scMSC1


title: Ventral Respiratory Column, 14 days, Mild CH, Replicate 6

description: matrix column name: VRC-14d-6p_rep6

value: Mild CH

value: Female


title: 3_normal

description: healthy control

value: PBMC

value: healthy control


title: HCC827 8h

city: Wuhan City

first: jianjian

last: yang

address: No. 1095, Jiefang Avenue, Wuhan City, Hubei Province

department: Department of Thoracic Surgery

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China.

data_processing:
The main steps of applying Seqtk for filtering are as follows:1、Remove the sequence of joints contained in reads；2、Remove bases with 3 'end mass Q less than 20, that is, the base error rate is less than 0.01，among,Q=-10logerror_ratio；3、Remove reads with length less than 25；4、Remove ribosome RNA reads of the species。
Spliced mapping algorithm of Hisat2 (version:2.0.4) was applied to Genome mapping of preprocessed reads，Take default parameters. The alignment result generated by Mapping is BAM file
Application Stringtie (version: 1.3.0)in Hisat2 than after each gene Fragments could count to count, and then use TMM (trimmed mean of M values) normalization method, finally calculated using perl script FPKM value of each gene.
In order to make gene expression levels between different genes and samples comparable, reads were transformed into FPKM (Fragments Per Kilobase of exon model Per Million mapped reads) to standardize gene expression
EdgeR was used for gene analysis of differences between samples, and multiple hypothesis test and correction were carried out after p-value was obtained. The threshold value of p-value was determined by controlling FDR (False Discovery Rate), and the p-value after correction was q-value.Meanwhile, we calculate Fold-change according to FPKM.
Genome_build: GRCh38 (hg38)

source_name: lung adenocarcinoma

growth_protocol: A549 and HCC827 cells were grown in complete RPMI-1640 (GIBCO) supplemented with 10% fetal bovine serum (GIBCO), 1% penicillin/ streptomycin (Hyclone).

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#9109,TAKARA, Dalian, China) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 and HCC827 cells were  treated with 100UI/ml IFN-g for 1h, 8h, and 24h, respectively. total RNA of A549 and HCC827 cells was harvested.

value: lung adenocarcinoma

tag: ifn-g treatment time


title: HCC827 24h


title: HCC827 1h


title: Ventral Respiratory Column, 14 days, Mild CH, Replicate 5

description: matrix column name: VRC-14d-6p_rep5


title: Sirt2KO8

city: Chengdu

first: Xiaoqiang

last: Tang

address: Renminnan Road

institute: Sichuan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: Aorta

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Aorta


title: Sirt2KO7


title: Ventral Respiratory Column, 14 days, Mild CH, Replicate 4

description: matrix column name: VRC-14d-6p_rep4


title: DNCB2

value: BALB/c

value: blood

value: 0.5% DNCB solution


title: Sirt2KO4


title: DMSO vs GSK126 treatment of HT1197 cells

first: Sooryanarayana

last: Varambally

state: Alabama

address: 1824 6th Avenue S

department: Pathology

institute: University of Alabama

description: HT1197_DMSO Vs GSK126

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: Data from the two channel experiment arrays were lowess normalized usinf 'agilp' bioconductor package. Then, differential expression is measured by log2(reference/test).

source_name: DMSO treated  HT1197 cells

label_protocol: 1 µg of total RNA were primed with 2 µl of 100 µM T7-oligo-dT DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 400 U MMLV RTase (Agilent), and labeled with T7 polymerase with 100 µM each of dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-label or Cy3-label.

growth_protocol: Bladder cancer cell lines HT1197 (ATCC, Manassas, VA, USA), HT1376 (ATCC), T24 (ATCC), 5637 (ATCC) were grown in RPMI-1640 (Life Technologies, Carlsbad, CA, USA) with penicillin–streptomycin (100 U/ml) and 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA) in 5% CO2 cell culture incubator.

extract_protocol: Total RNA was isolated from bladder cancer cell lines using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Bladder cancer cell lines were seeded in 6-well plates. After 12 h overnight incubation, the cells were treated either with DMSO or  7.5 uM of GSK126.

value: Bladder cancer cell line

value: DMSO

tag: agent

source_name: GSK126 treated  HT1197 cells

value: bladder cancer cell line


title: DMSO vs GSK126 treatment of 5637 cells

description: 5637_DMSO Vs GSK126

source_name: DMSO treated  5637 cells

tag: cell type

source_name: GSK126 treated  5637 cells


title: HCC827 0h


title: Ventral Respiratory Column, 14 days, Mild CH, Replicate 3

description: matrix column name: VRC-14d-6p_rep3

value: Brain (Medulla)


title: DMSO vs GSK126 treatment of T24 cells

description: T24_DMSO Vs GSK126

source_name: DMSO treated  T24 cells

source_name: GSK126 treated  T24 cells


title: DMSO vs GSK126 treatment of HT1376 cells

description: HT1376_DMSO Vs GSK126

source_name: DMSO treated  HT1376 cells

source_name: GSK126 treated  HT1376 cells


title: DNCB1


title: A549 24h


title: Solvent3

value: vehicle only (acetone:olive oil = 3:1 v/v)


title: WT4

value: WT


title: A549 8h


title: Ventral Respiratory Column, 14 days, Mild CH, Replicate 1

description: matrix column name: VRC-14d-6p_rep1

value: Ventral Respiratory Column


title: WT2


title: DNCB3


title: A549 1h


title: Solvent2


title: Solvent1


title: mRNA_OVX_Xmo_4

city: Shaanxi

first: Yang

last: Liu

address: Yangling

institute: Northwest A&F University

description: mRNA

data_processing:
The quality of the original sequencing data is evaluated by FastQC(0.11.2 ).
Through Trimmomatic(0.36) for mass shearing, relatively accurate and effective data can be obtained.
Use Bowtie2(2.3.2) to compare the valid data of the sample to the reference genome and count the Mapping information.
Use StringTie(1.3.3b) and known gene models to evaluate gene expression.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hippocampi

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

value: ICR mice

value: hippocampi

value: OVX  treat with Xmo


title: Sample_32_RU486

city: Leiden

first: Jacobus

middle: Cornelis

last: Buurstede

state: Zuid-Holland

address: Albinusdreef 2

department: Endocrinology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Quality control was performed using FastQC and MultiQC
Reads were alligned to mm10 using Gsnap (version2017-09-11).
Gene-read quantification was perfromed using HTSeq-count (version 0.6.1) .
HTSeq-count output files were merged into the raw_gene_count_matrix.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every feature according to Ensembl88 for each sample.

source_name: Brain

extract_protocol:
From the snap-frozen, dissected hippocampi, total RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel).
mRNA was enriched and purified and a stranded library was constructed for 100bp paired-end sequencing on BGI's DNBseq platform.

value: Dorsal hippocampus

value: male

tag: auditory fear conditioning

value: yes


title: Ventral Respiratory Column, 14 days, Room Air, Replicate 5

description: matrix column name: VRC-14d-NCO2_rep5

value: Room Air

value: Female


title: mRNA_OVX_Xmo_3

description: mRNA


title: Ventral Respiratory Column, 14 days, Room Air, Replicate 3

description: matrix column name: VRC-14d-NCO2_rep3


title: A549 0h

value: lung adenocarcinoma


title: Sample_19_RU486


title: Sample_25_RU486


title: WT8

value: Aorta


title: (D) Emergency granulopoiesis neutrophils, after infection, rep 3

city: Auckland

first: Hannah

last: Darroch

address: Grafton

department: FMHS

country: New Zealand

institute: University of Auckland

data_processing:
The filtered clean reads were mapped to the Danio rerio reference genome (GRCz11) by HISAT2.
Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software.
DESeq was used to analyse the DEGs between sets of two groups as a control-treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05.
Assembly: GRCz11
Supplementary files format and content: Comma separated value files show FPKM, Log2FC, and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons
Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils after infection and used for GO:BP analysis

organism: Danio rerio

source_name: Neutrophil

growth_protocol: Tg(lyz:DsRED2) zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C

extract_protocol:
Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS-isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART-Seq v4 Ultra Low Input RNA kit for sequencing (Takara Bio)
Libraries were made using the Nextera XT DNA Library Preparation Kit (Illumina).

treatment_protocol: At 4 days post fertilisation, neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection, or at 3 hours post infection with Salmonella.

value: Neutrophil

value: After infection


title: (D) Emergency granulopoiesis neutrophils, after infection, rep 4


title: (D) Emergency granulopoiesis neutrophils, after infection, rep 2


title: Ventral Respiratory Column, 14 days, Room Air, Replicate 4

description: matrix column name: VRC-14d-NCO2_rep4

source_name: Brain (Medulla)


title: Ventral Respiratory Column, 14 days, Mild CH, Replicate 2

description: matrix column name: VRC-14d-6p_rep2

value: Mild CH


title: Sample_12_RU486


title: mRNA_OVX_4

description: mRNA

value: OVX treat with saline


title: (D) Emergency granulopoiesis neutrophils, after infection, rep 1


title: mRNA_OVX_Xmo_1

description: mRNA


title: Sample_6_RU486


title: Ventral Respiratory Column, 14 days, Room Air, Replicate 1

description: matrix column name: VRC-14d-NCO2_rep1

value: Brain (Medulla)


title: mRNA_OVX_3

description: mRNA


title: (C) Emergency granulopoiesis neutrophils, before infection, rep 4

value: Before infection


title: Ventral Respiratory Column, 14 days, Room Air, Replicate 6

description: matrix column name: VRC-14d-NCO2_rep6

value: Ventral Respiratory Column


title: Sample_38_C118


title: mRNA_OVX_2

description: mRNA

value: ICR mice


title: (C) Emergency granulopoiesis neutrophils, before infection, rep 3


title: Retrotrapezoid Nucleus, 7 days 6%-7 days 8%, Moderate CH, Replicate 6

description: matrix column name: RTN-7d-6p-8p_rep6

value: Moderate CH

value: Retrotrapezoid Nucleus


title: Retrotrapezoid Nucleus, 7 days 6%-7 days 8%, Moderate CH, Replicate 5

description: matrix column name: RTN-7d-6p-8p_rep5


title: Sample_33_C118

value: Dorsal hippocampus


title: mRNA_OVX_Xmo_2

description: mRNA

value: hippocampi

value: OVX  treat with Xmo


title: (C) Emergency granulopoiesis neutrophils, before infection, rep 2


title: mRNA_OVX_1

description: mRNA


title: Retrotrapezoid Nucleus, 7 days 6%-7 days 8%, Moderate CH, Replicate 4

description: matrix column name: RTN-7d-6p-8p_rep4


title: mRNA_Sham_Xmo_4

description: mRNA

value: Sham treat with Xmo


title: Sample_20_C118

value: male

value: yes


title: Ventral Respiratory Column, 14 days, Room Air, Replicate 2

description: matrix column name: VRC-14d-NCO2_rep2

value: Room Air

value: Female


title: (C) Emergency granulopoiesis neutrophils, before infection, rep 1

value: Neutrophil


title: Retrotrapezoid Nucleus, 7 days 6%-7 days 8%, Moderate CH, Replicate 2

description: matrix column name: RTN-7d-6p-8p_rep2


title: mRNA_Sham_Xmo_3

description: mRNA


title: (B) Steady state neutrophils, after infection, rep 4

value: After infecton


title: Retrotrapezoid Nucleus, 7 days 6%-7 days 8%, Moderate CH, Replicate 3

description: matrix column name: RTN-7d-6p-8p_rep3


title: (B) Steady state neutrophils, after infection, rep 3


title: Sample_13_C118


title: mRNA_Sham_Xmo_2

description: mRNA


title: mRNA_Sham_Xmo_1

description: mRNA


title: Sample_7_C118


title: Retrotrapezoid Nucleus, 14 days, Mild CH, Replicate 6

description: matrix column name: RTN-14d-6p_rep6

value: Mild CH


title: Retrotrapezoid Nucleus, 7 days 6%-7 days 8%, Moderate CH, Replicate 1

description: matrix column name: RTN-7d-6p-8p_rep1

value: Brain (Medulla)


title: Sample_34_C108


title: mRNA_Sham_saline_3

description: mRNA

value: Sham treat with saline


title: Retrotrapezoid Nucleus, 14 days, Mild CH, Replicate 5

description: matrix column name: RTN-14d-6p_rep5


title: (B) Steady state neutrophils, after infection, rep 1


title: Sample_26_C108


title: Retrotrapezoid Nucleus, 14 days, Mild CH, Replicate 4

description: matrix column name: RTN-14d-6p_rep4


title: Sample_21_C108


title: (A) Steady state neutrophils, before infection, rep 3

value: Before infection


title: mRNA_Sham_saline_2

description: mRNA

value: ICR mice


title: (A) Steady state neutrophils, before infection, rep 4


title: Retrotrapezoid Nucleus, 14 days, Mild CH, Replicate 3

description: matrix column name: RTN-14d-6p_rep3


title: Sample_8_C108


title: mRNA_Sham_saline_1

description: mRNA


title: Sample_39_C108


title: Retrotrapezoid Nucleus, 14 days, Mild CH, Replicate 2

description: matrix column name: RTN-14d-6p_rep2


title: Retrotrapezoid Nucleus, 14 days, Mild CH, Replicate 1

description: matrix column name: RTN-14d-6p_rep1


title: (B) Steady state neutrophils, after infection, rep 2


title: (A) Steady state neutrophils, before infection, rep 1


title: Sample_30_Cort

value: Cort


title: Sample_17_Cort


title: Retrotrapezoid Nucleus, 14 days, Room Air, Replicate 6

description: matrix column name: RTN-14d-NCO2_rep6

value: Retrotrapezoid Nucleus


title: Retrotrapezoid Nucleus, 14 days, Room Air, Replicate 5

description: matrix column name: RTN-14d-NCO2_rep5


title: Sample_11_Cort

value: Dorsal hippocampus


title: VIT_10_vitiligo

city: Rome

first: Marika

last: Guercio

state: RM

address: Viale di San Paolo, 15

department: Oncohematology

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

description: VIT-10_Combined Rearrangements.csv

data_processing: For TCR Vβ statistical analysis, after sequencing, raw data were uploaded and analyzed by Adaptive Biotechnologies to report the normalized and annotated TCR-β repertoire profile for each sample using the immuneSEQ Analyzer suite of tools (ImmunoSEQ Analyzer 3.0 https://clients.adaptivebiotech.com/). Libraries were sequenced and organized providing productive and non-productive sequences (CDR3 regions explicitly encoding a premature stop, and those predicted to put the receptor gene out-of-frame downstream of the CDR3 rearrangement, were considered non-productive). An algorithm was applied to raw sequencing data for collapsing PCR and sequencing errors, resulting in unique rearrangements of the CDR3 genes. Productive TCR-β CDR3 frequencies were used for generating scatterplots.

source_name: Vitiligo Biopsy

extract_protocol:
Five to 10 slices of 5 µm thickness from vitiligo or primary/metastatic melanoma biopsies of the same patient were obtained from FFPE sample blocks and used for DNA extraction.For tissue samples, QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA) was used in conjunction with an incubation at 55°C for 4 hours to complete tissue lysis. Next, samples were incubated at 90°C for 1 hour to reverse formaldehyde modification of nucleic acids.For blood samples, DNA extraction from PBMCs was performed following the DNeasy Blood & Tissue Kit (Qiagen).Proteinase K was used for digestion and extraction of DNA following a blood/cell protocol with RNase treatment and using spin-column method. After isolation by QIAamp MinElute column (Qiagen), variable amounts of buffer were added to each column to elute the DNA.
Extracted DNA was used for TCR Vβ analysis using the ImmunoSEQ hsTCRB Kit (Adaptive Biotechnologies, Seattle, WA), according to the manufacturer's instructions (18-20). For PBMCs and metastasis samples, 1µg of total DNA was used for duplicate, whilst for primary melanoma samples, we used 200-1000 ng of total DNA for duplicates. Each sample presented a unique identification through the addition of universal adapter sequences and DNA barcodes to each PCR replicate. CDR3 regions were amplified through two PCR amplification steps. Following purification with the Agencourt™ AMPure™ XP Reagent (Beckman Coulter, Inc.), 10 µl of each sample were pooled in equimolar concentration into three final libraries (46 libraries/pool).
Final libraries were quantified using KAPA Library Quantification Kits (Roche, Switzerland, CH), diluted to 4 nM, and denatured using 0.2N NaOH. After denaturation, libraries were loaded at 20 pM on an Illumina NextSeq 550 system with 156 paired-end sequencing (Illumina, San Diego, CA). Data obtained were submitted to Adaptive Biotechnologies for survey level TCR-β sequencing.Sufficient material was not available from all specimens to allow for duplicate analysis.For vitiligo samples, a minimum of 50 ng of total DNA was used for duplicate. In select vitiligo specimens in which the total DNA content was too low and additional tissue was available, the assay was repeated. The larger (greater absolute TCR-β sequence count) specimen was used for analysis.

value: Vitiligo Biopsy

value: FFPE


title: VIT_10_Primary Melanoma (6)

description: VIT-10_Combined Rearrangements.csv

source_name: Primary Melanoma Biopsy

value: Primary Melanoma Biopsy


title: Retrotrapezoid Nucleus, 14 days, Room Air, Replicate 4

description: matrix column name: RTN-14d-NCO2_rep4


title: Sample_4_Cort

value: male


title: VIT_10_Primary Melanoma (5)

description: VIT-10_Combined Rearrangements.csv


title: VIT_10_Primary Melanoma (4)

description: VIT-10_Combined Rearrangements.csv


title: Sample_36_Cort

value: yes


title: (A) Steady state neutrophils, before infection, rep 2


title: Retrotrapezoid Nucleus, 14 days, Room Air, Replicate 3

description: matrix column name: RTN-14d-NCO2_rep3

value: Room Air


title: Sample_29_Vehicle

value: Vehicle


title: VIT_10_Primary Melanoma (3)

description: VIT-10_Combined Rearrangements.csv


title: Sample_23_Vehicle


title: Retrotrapezoid Nucleus, 14 days, Room Air, Replicate 2

description: matrix column name: RTN-14d-NCO2_rep2

value: Female


title: VIT_10_Primary Melanoma(2)

description: VIT-10_Combined Rearrangements.csv


title: Sample_16_Vehicle


title: Sample_3_Vehicle


title: VIT_10_Primary Melanoma(1)

description: VIT-10_Combined Rearrangements.csv


title: VIT_10_PBMCs

description: VIT-10_Combined Rearrangements.csv

source_name: PBMCs

value: PBMCs

value: fresh-frozen


title: Nucleus Tractus Solitarii, 7 days 6%-7 days 8%, Moderate CH, Replicate 6

description: matrix column name: NTS-7d-6p-8p_rep6

value: Brain (Medulla)

value: Moderate CH

value: Nucleus Tractus Solitarii


title: Sample_27_Basal

value: no


title: Nucleus Tractus Solitarii, 7 days 6%-7 days 8%, Moderate CH, Replicate 5

description: matrix column name: NTS-7d-6p-8p_rep5


title: Retrotrapezoid Nucleus, 14 days, Room Air, Replicate 1

description: matrix column name: RTN-14d-NCO2_rep1


title: Sample_9_Basal


title: VIT_09_PBMCs

description: VIT-9_Combined Rearrangements.csv


title: Sample_14_Basal


title: VIT_09_Primary Melanoma

description: VIT-9_Combined Rearrangements.csv


title: Nucleus Tractus Solitarii, 7 days 6%-7 days 8%, Moderate CH, Replicate 4

description: matrix column name: NTS-7d-6p-8p_rep4


title: Nucleus Tractus Solitarii, 7 days 6%-7 days 8%, Moderate CH, Replicate 2

description: matrix column name: NTS-7d-6p-8p_rep2


title: Sample_1_Basal


title: VIT_09_vitiligo

description: VIT-9_Combined Rearrangements.csv


title: VIT_08_vitiligo

description: VIT-8_Combined Rearrangements.csv


title: Nucleus Tractus Solitarii, 7 days 6%-7 days 8%, Moderate CH, Replicate 1

description: matrix column name: NTS-7d-6p-8p_rep1


title: miRNA_OVX_Xmo_2

description: miRNA

value: ICR mice

value: hippocampi

value: OVX  treat with Xmo


title: VIT_08_Primary Melanoma

description: VIT-8_Combined Rearrangements.csv


title: VIT_08_PBMCs

description: VIT-8_Combined Rearrangements.csv


title: FeS2-grown NH3-amended cells, biol rep 2

city: Bozeman

first: Rachel

middle: L.

last: Spietz

state: MT

institute: Montana State University

data_processing:
Paired-end reads were processed using default settings in TrimGalore!, a wrapper that implements CutAdapt and FastQC to remove adapter sequences and filter reads, respectively.
Reads were aligned to the reference M. maripaludis S2 genome (ASM1158v1) using Bowtie2.
Reads were counted for each locus using HTSeq.
Normalization and statistical analyses were conducted in DESeq2 implemented in R v3.6.0.
Assembly: ASM1158v1
Supplementary files format and content: The processed data files are tab delimited count data generated in HTSeq.

organism: Methanococcus maripaludis

extract_protocol:
To harvest biomass, M. mari S2 cells were harvested via cetnrifugation under an anoxic headspace. Supernatant was decanted and the cell pellets were flash frozen in liquid nitrogen. Frozen cells were then stored at -80 °C until processing. Total RNA from M. maripaludis was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s protocol with slight modification. One mL of TRIzol was added to cell pellets and the resuspended cells were transferred to Lysis E tubes (MP Biomedicals, Irvine, CA) on ice. The cell samples were mechanically lysed by three cycles of 40 sec of bead beating and five mins of rest at room temperature (~20 °C). After the lysis procedure, 200 µL of molecular grade chloroform was added, the tubes were mixed by inversion and allowed to incubate for three mins at room temperature. The tubes were then centrifuged for 15 mins at 12,000 x g at 4°C and the upper aqueous phase containing RNA was transferred by pipette into a clean two mL tube. RNA was precipitated by the addition of 0.5 mL of 100% molecular grade isopropanol that had been pre-chilled to 4°C followed by ten mins incubation on ice. RNA was then pelleted by centrifugation for ten mins at 12,000 x g at 4°C. The supernatant was removed by pipette, and the RNA was washed in one mL of 75 % molecular grade ethanol. RNA was pelleted by centrifugation for five mins at 7,500 x g at 4 °C, the supernatant was removed, and the RNA pellet was air dried for ten mins. Once dried, the RNA was resuspended in 50 µL of RNA-free H2O (Fisher Scientific, Waltham, MA) by incubating at 55°C in a heat block for ten mins. RNA was treated to remove residual DNA by the addition of Turbo DNase (Invitrogen, Waltham, MA) according to the manufacturer’s instructions. The RNA was then subjected to a second round of precipitation, washing, drying, and resuspension steps as described above.
Quality control was performed with a Bioanalyzer (Agilent, CA, USA), and rRNA reduction was performed with a RiboZero-Bacteria rRNA removal kit (Illumina, CA, USA) with the addition of custom M. maripaludis S2-specific oligos designed using the sequences for M. maripaludis S2’s large and small ribosomal subunits. Stranded cDNA libraries were prepared from rRNA-depleted mRNA using the TruSeq Stranded Total and mRNA kit (Illumina, CA, USA).

value: FeS2-grown NH3-amended


title: miRNA_OVX_Xmo_3

description: miRNA


title: miRNA_OVX_Xmo_1

description: miRNA


title: FeS2-grown NH3-amended cells, biol rep 1


title: FeS2-grown NH3-amended cells, biol rep 3


title: Nucleus Tractus Solitarii, 14 days, Mild CH, Replicate 6

description: matrix column name: NTS-14d-6p_rep6

value: Mild CH


title: Nucleus Tractus Solitarii, 7 days 6%-7 days 8%, Moderate CH, Replicate 3

description: matrix column name: NTS-7d-6p-8p_rep3


title: miRNA_OVX_3

description: miRNA

value: OVX treat with saline


title: VIT_08_metastasis (spleen)

description: VIT-8_Combined Rearrangements.csv

source_name: Metastasis Biopsy

value: Metastasis Biopsy

value: FFPE


title: FeS2-grown N2-fixing cells, biol rep 2

value: FeS2-grown N2-fixing


title: Nucleus Tractus Solitarii, 14 days, Mild CH, Replicate 4

description: matrix column name: NTS-14d-6p_rep4


title: miRNA_OVX_2

description: miRNA


title: FeS2-grown N2-fixing cells, biol rep 3


title: VIT_08_metastasis (Lymph node)

description: VIT-8_Combined Rearrangements.csv


title: VIT_07_vitiligo

description: VIT-7_Combined Rearrangements.csv

value: Vitiligo Biopsy


title: VIT_07_Primary Melanoma

description: VIT-7_Combined Rearrangements.csv

value: Primary Melanoma Biopsy


title: FeS2-grown N2-fixing cells, biol rep 1


title: miRNA_OVX_1

description: miRNA


title: Nucleus Tractus Solitarii, 14 days, Mild CH, Replicate 5

description: matrix column name: NTS-14d-6p_rep5

value: Female


title: Nucleus Tractus Solitarii, 14 days, Mild CH, Replicate 3

description: matrix column name: NTS-14d-6p_rep3


title: Nucleus Tractus Solitarii, 14 days, Mild CH, Replicate 1

description: matrix column name: NTS-14d-6p_rep1


title: miRNA_Sham_Xmo_3

description: miRNA

value: Sham treat with Xmo


title: VIT_07_PBMCs

description: VIT-7_Combined Rearrangements.csv

value: PBMCs

value: fresh-frozen


title: miRNA_Sham_Xmo_2

description: miRNA


title: Fe(II)/HS-grown NH3-amended cells, biol rep 2

value: Fe(II)/HS-grown NH3-amended


title: Fe(II)/HS-grown NH3-amended cells, biol rep 1


title: VIT_06_Primary Melanoma

description: VIT-6_Combined Rearrangements.csv


title: Fe(II)/HS-grown NH3-amended cells, biol rep 3


title: Nucleus Tractus Solitarii, 14 days, Room Air, Replicate 6

description: matrix column name: NTS-14d-NCO2_rep6

value: Brain (Medulla)

value: Room Air

value: Nucleus Tractus Solitarii


title: VIT_06_vitiligo

description: VIT-6_Combined Rearrangements.csv


title: Nucleus Tractus Solitarii, 14 days, Room Air, Replicate 5

description: matrix column name: NTS-14d-NCO2_rep5


title: Nucleus Tractus Solitarii, 14 days, Room Air, Replicate 2

description: matrix column name: NTS-14d-NCO2_rep2


title: miRNA_Sham_Xmo_1

description: miRNA

value: ICR mice

value: hippocampi


title: Nucleus Tractus Solitarii, 14 days, Mild CH, Replicate 2

description: matrix column name: NTS-14d-6p_rep2

value: Mild CH


title: Fe(II)/HS-grown N2-fixing cells, biol rep 1

value: Fe(II)/HS-grown N2-fixing


title: Nucleus Tractus Solitarii, 14 days, Room Air, Replicate 4

description: matrix column name: NTS-14d-NCO2_rep4


title: Fe(II)/HS-grown N2-fixing cells, biol rep 3


title: miRNA_Sham_saline_3

description: miRNA

value: Sham treat with saline


title: Nucleus Tractus Solitarii, 14 days, Room Air, Replicate 3

description: matrix column name: NTS-14d-NCO2_rep3


title: VIT_06_PBMCs

description: VIT-6_Combined Rearrangements.csv


title: Fe(II)/HS-grown N2-fixing cells, biol rep 2


title: VIT_05_vitiligo

description: VIT-5_Combined Rearrangements.csv

value: FFPE


title: gMDSC-6

type: genomic

city: Boston

first: Ze

last: Zhang

address: 375 Longwood Ave

department: Medical Oncology & Population Sciences

institute: Harvard Medical School

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: R studio

label: Cy5 and Cy3

source_name: gMDSC

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Zymo Quick-DNA MiniPrep Plus kit according to standard instructions

tag: gmdsc

value: adult head and neck cancer peripheral blood gMDSC


title: g8-10

label: Cy5 and Cy5

value: cord blood gMDSC


title: g7-27


title: VIT_05_Primary Melanoma (2)

description: VIT-5_Combined Rearrangements.csv

value: Primary Melanoma Biopsy


title: gMDSC-4


title: miRNA_Sham_saline_2

description: miRNA


title: gMDSC-3


title: g8-4


title: VIT_05_metastasis (omentum)

description: VIT-5_Combined Rearrangements.csv

value: Metastasis Biopsy


title: VIT_05_Primary Melanoma (1)

description: VIT-5_Combined Rearrangements.csv


title: Nucleus Tractus Solitarii, 14 days, Room Air, Replicate 1

description: matrix column name: NTS-14d-NCO2_rep1

value: Female


title: miRNA_Sham_saline_1

description: miRNA


title: VIT_05_PBMCs

description: VIT-5_Combined Rearrangements.csv

value: PBMCs


title: Medial Prefrontal Cortex, 7 days 6%-7 days 8%, Moderate CH, Replicate 6

description: matrix column name: mPFC-7d-6p-8p_rep6

source_name: Brain (Cortex)

value: Brain (Cortex)

value: Moderate CH

value: Medial Prefrontal Cortex


title: gMDSC-9


title: Medial Prefrontal Cortex, 7 days 6%-7 days 8%, Moderate CH, Replicate 4

description: matrix column name: mPFC-7d-6p-8p_rep4


title: Medial Prefrontal Cortex, 7 days 6%-7 days 8%, Moderate CH, Replicate 5

description: matrix column name: mPFC-7d-6p-8p_rep5


title: Medial Prefrontal Cortex, 7 days 6%-7 days 8%, Moderate CH, Replicate 2

description: matrix column name: mPFC-7d-6p-8p_rep2


title: g6-14


title: g8-18


title: HNSCC1 gMDSC


title: glioma5 gMDSC

value: adult glioma peripheral blood gMDSC


title: VIT_04_PBMCs

description: VIT-4_Combined Rearrangements.csv

value: fresh-frozen


title: VIT_04_vitiligo

description: VIT-4_Combined Rearrangements.csv

value: Vitiligo Biopsy


title: Medial Prefrontal Cortex, 7 days 6%-7 days 8%, Moderate CH, Replicate 3

description: matrix column name: mPFC-7d-6p-8p_rep3


title: VIT_04_Primary Melanoma

description: VIT-4_Combined Rearrangements.csv


title: mom1 gMDSC

value: adult maternal peripheral blood gMDSC


title: Medial Prefrontal Cortex, 7 days 6%-7 days 8%, Moderate CH, Replicate 1

description: matrix column name: mPFC-7d-6p-8p_rep1


title: Rabbit_Aorta_Atherosclerosis_no18

city: CPH

first: Constance

middle: E

last: Grandjean

address: Blegdamsvej 3

department: Cluster for Molecular Imaging

country: Denmark

institute: University of Copenhagen

description: Atherosclerotic

data_processing: By using QIAGEN GeneGlobe analysis program

label: SYBR green

organism: Oryctolagus cuniculus

source_name: Aorta

label_protocol: Total RNA was extracted with TRIzol® Reagent and reverse-transcribed into cDNA using the RT2 First Strand Kit QIAGEN. And plated out on PCR array plates. Plates were read on the Mx3000P real-time PCR system (Stratagene, CA, USA) with paramters by 1 cycle 10 minutes of 95C and then 40 cycles  of 15s at 95C and 1 min at 60C

growth_protocol: The rabbits were housed with enrichment and had ad libitum of chow or High cholesterol diet, depending on their treatment

extract_protocol: We sacrificed the rabbits, and surgically removed the adbominal aortas. We flushed them with saline and put cut sectios into RNAlater for storage overnight in the fridge. Then the RNAlater was removed and the tissue was tored at -20C until extraction of RNA.

treatment_protocol: After surgical intervention the rabbits with Atherosclerosis were fed with 0.30% high cholesterol diet and after 8 weeks were switched to a maintance diet of 0.15% high cholesterol diet for a remainig of 12 weeks

tag: sample type

value: Male, NZW, abdonimal aorta, stable advanced atherosclerosis


title: Rabbit_Aorta_Atherosclerosis_no10

description: Atherosclerotic


title: Rabbit_Aorta_Atherosclerosis:_no20

description: Atherosclerotic


title: VIT_04_metastasis (Lymph node)

description: VIT-4_Combined Rearrangements.csv


title: Rabbit_Aorta_Atherosclerosis_no14

description: Atherosclerotic


title: VIT_03_vitiligo

description: VIT-3_Combined Rearrangements.csv


title: Rabbit_Aorta_Atherosclerosis_no8

description: Atherosclerotic


title: Medial Prefrontal Cortex, 14 days, Mild CH, Replicate 5

description: matrix column name: mPFC-14d-6p_rep5

value: Mild CH


title: VIT_03_Primary Melanoma

description: VIT-3_Combined Rearrangements.csv


title: Rabbit_Aorta_Atherosclerosis_no6

description: Atherosclerotic


title: Rabbit_Aorta_Atherosclerosis_no4

description: Atherosclerotic


title: Medial Prefrontal Cortex, 14 days, Mild CH, Replicate 4

description: matrix column name: mPFC-14d-6p_rep4


title: Rabbit_Aorta_Atherosclerosis_no2

description: Atherosclerotic


title: VIT_03_PBMCs

description: VIT-3_Combined Rearrangements.csv


title: Medial Prefrontal Cortex, 14 days, Mild CH, Replicate 3

description: matrix column name: mPFC-14d-6p_rep3


title: Medial Prefrontal Cortex, 14 days, Mild CH, Replicate 6

description: matrix column name: mPFC-14d-6p_rep6


title: HT_1.3 (HT1.3 vs HT0.3)

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

hyb_protocol: Hybridization at 65°C for 17 hours

scan_protocol: The arrays were scanned using  Agilent G2565CA Microarray Scanner

data_processing: All arrays were subject to background subtraction followed by loess normalization within each array and scale normalization across all arrays and log2 ratios (cy5/cy3) were computed using Partek GS.

label_protocol: RNA from each sample (HI/HT, 1/2) and the reference (basal - HI_0/HT_0) were hybridized to oligo (dT) primers at 65º C and then incubated at 42º C for 2 hours in the presence of reverse transcriptase, Cy5- or Cy3-dUTP and Cy5- or Cy3-dCTP, and a deoxynucleotide mix. In all cases, RNA samples were labeled with Cy5 and reference samples were labeled with Cy3.

extract_protocol: Lymphocytes isolation by gradient centrigugation, Total RNA extracted using Trizol

treatment_protocol: Heat tolerance - Recovery (HTT-R) test, performed to young males soldiers 2 months after an episode of exertional heat stroke, included: 2 hours of walking at a speed of 5km/h on a treadmill with 2% grade, at an environmental temperature of 40°C with 40% Relative humidity. Blood withdrawal at; 0' , 120' and 180'  (when the last 60' after termination of the test were at 24°C).

tag: individual

value: young male

tag: htt-r test outcomes

value: HT

tag: time point

value: 0 basal


title: HI_2.3 (HI2.3 vs HI0.3)

value: HI


title: HT_2.2 (HT2.2 vs HT0.2)


title: HT_1.2 (HT1.2 vs HT0.2)


title: VIT_02_vitiligo

description: VIT-2_Combined Rearrangements.csv

value: FFPE


title: Rabbit_Aorta_Control_no21

description: Control

value: Male, NZW, abdonimal aorta, healthy


title: Medial Prefrontal Cortex, 14 days, Mild CH, Replicate 2

description: matrix column name: mPFC-14d-6p_rep2

tag: treatment (co2 condition)

tag: tissue region

value: Female


title: g7-18

label: Cy5 and Cy4

tag: tissue

value: cord blood gMDSC


title: Medial Prefrontal Cortex, 14 days, Mild CH, Replicate 1

description: matrix column name: mPFC-14d-6p_rep1

value: Brain (Cortex)

tag: Sex


title: Medial Prefrontal Cortex, 14 days, Room Air, Replicate 6

description: matrix column name: mPFC-14d-NCO2_rep6

value: Room Air


title: HT_2.1 (HT2.1 vs HT0.1)


title: HT_1.1 (HT1.1 vs HT0.1)


title: Rabbit_Aorta_Control_no13

description: Control


title: Medial Prefrontal Cortex, 14 days, Room Air, Replicate 5

description: matrix column name: mPFC-14d-NCO2_rep5

value: Medial Prefrontal Cortex


title: Rabbit_Aorta_Control_no11

description: Control


title: Rabbit_Aorta_Control_no19

description: Control


title: HI_2.1 (HI2.1 vs HI0.1)


title: HI_2.2 (HI2.2 vs HI0.2)


title: Medial Prefrontal Cortex, 14 days, Room Air, Replicate 4

description: matrix column name: mPFC-14d-NCO2_rep4


title: VIT_02_metastasis (Lymph node)

description: VIT-2_Combined Rearrangements.csv

value: Metastasis Biopsy


title: Rabbit_Aorta_Control_no9

description: Control


title: HI_1.2 (HI1.2 vs HI0.2)


title: Medial Prefrontal Cortex, 14 days, Room Air, Replicate 3

description: matrix column name: mPFC-14d-NCO2_rep3


title: VIT_02_Primary Melanoma (2)

description: VIT-2_Combined Rearrangements.csv

value: Primary Melanoma Biopsy


title: HI_1.3 (HI1.3 vs HI0.3)


title: Rabbit_Aorta_Control_no7

description: Control


title: VIT_02_Primary Melanoma (1)

description: VIT-2_Combined Rearrangements.csv


title: Rabbit_Aorta_Control_no15

description: Control


title: VIT_01_vitiligo

description: VIT-1_Combined Rearrangements.csv

value: Vitiligo Biopsy


title: 80W mouse Acetaminophen 8h rep4

city: Sapporo

first: Naoki

last: Tanimizu

address: S1, W17, Chuou-ku

institute: Sapporo Medical University

description: Gene expression at 8h

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 80W mouse Acetaminophen 8h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy (Promega) following the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Liver tissue was frozen in liquid nitrogen and them homoginzed in Lysis buffer

value: Liver

tag: gender

value: Male

tag: age


title: VIT_01_Primary Melanoma

description: VIT-1_Combined Rearrangements.csv


title: VIT_02_PBMCs

description: VIT-2_Combined Rearrangements.csv

value: PBMCs

value: fresh-frozen


title: Medial Prefrontal Cortex, 14 days, Room Air, Replicate 2

description: matrix column name: mPFC-14d-NCO2_rep2


title: 80W mouse Acetaminophen 8h rep3

description: Gene expression at 8h


title: HI_1.1 (HI1.1 vs HI0.1)

value: young male


title: Rabbit_Aorta_Atherosclerosis_no12

description: Atherosclerotic

value: Male, NZW, abdonimal aorta, stable advanced atherosclerosis


title: VIT_01_PBMCs

description: VIT-1_Combined Rearrangements.csv


title: HNSCC2 gMDSC

value: adult head and neck cancer peripheral blood gMDSC


title: Medial Prefrontal Cortex, 14 days, Room Air, Replicate 1

description: matrix column name: mPFC-14d-NCO2_rep1


title: 80W mouse Acetaminophen 8h rep2

description: Gene expression at 8h


title: Rabbit_Aorta_Control_no1

description: Control


title: Rabbit_Aorta_Control_no3

description: Control


title: hnRNPA1_rep1

status: Public on Apr 30 2023

type: other

city: Frederick

first: Srinath

last: Seshadri

state: MD

address: 1050 Boyle St.

institute: NCI/CCR

description: hnRNP A1 binding assay at 1uM replicate 1

hyb_protocol: Hybridization solutions in the same buffer, containing appropriate concentrations of Cy5-labelled antibody, fluorescent small molecule, or GST-tagged protein were blotted onto an appropriate block of the array, and hybridized under a gasket for 1 hour at room temperature with gentle orbital shaking. The slides were washed twice with buffer and air dried; a secondary incubation with Cy5-labelled anti-GST antibody was performed for all 4 Protein Array samples, and then subsequently washed and dried.

scan_protocol: Slides were scanned immediately after washing using an Innopsys InnoScan 1100 ultra-high resolution three color microarray scanner. XDR high resolution scans (0.5 um pixel size) using a standard surface area were obtained and the 635nM excitation color image was exported for analysis.

data_processing: TIF images of microarray scans were uploaded to the MPix Software and aligned to the .gal file corresponding to the custom 8 X 60K i-Motif array (Design Name: Agilent_87164_221206_NIH_Sri). Spot fluorescence was extracted, expressed as a SNR635 value. The median SNR635 was calculated across probes containing an identical probe identifier (ProbeID).

molecule: other

source_name: hnRNP A1 protein 1uM, replicate 1

extract_protocol: We synthesized mitoxantrone.  We obtained anti-i-motif DNA [iMab] conjugated with FluoProbes®647H (Cy5-BG4) from Absolute Antibody (product number Ab01462-23.0).   N-terminal Glutathione S-transferase (GST) tagged human ASF/SF2, hnRNP K, hnRNP LL hnRNP A1 were synthesized by GenScript.

treatment_protocol: Agilent i-Motif 8 x 60K DNA arrays were pre-rinsed in 2X PBS, 100mM KCl, 0.05% Tween-20, as well as varying pH and BSA % indicated in the source name. The slides were then blocked in the same buffer containing 2% w/v milk protein for 1 hour, and then washed twice in 2X PBS, 100mM KCl, 0.05% Tween-20.

tag: condition

value: 2X PBS, 100 mM KCl, pH 6.5, 5% BSA

tag: dna type

value: ssDNA


title: ASF_rep1

description: ASF/SF2 binding assay at 1uM replicate 1

source_name: ASF/SF2 protein 1uM, replicate 1


title: hnRNPA1_rep2

description: hnRNP A1 binding assay at 1uM replicate 2

source_name: hnRNP A1 protein 1uM, replicate 2


title: hnRNPLL_rep2

description: hnRNP LL binding assay at 1uM replicate 2

source_name: hnRNPLL protein 1uM, replicate 2


title: 80W mouse Acetaminophen 8h rep1

description: Gene expression at 8h


title: 8W mouse Acetaminophe 8h rep4

description: Gene expression at 8h

source_name: 8W mouse Acetaminophe 8h


title: 8W mouse Acetaminophe 8h rep3

description: Gene expression at 8h


title: hnRNPLL_rep1

description: hnRNP LL binding assay at 1uM replicate 1

source_name: hnRNPLL protein 1uM, replicate 1


title: hnRNPK_rep2

description: hnRNP K binding assay at 1uM replicate 2

source_name: hnRNPK protein 1uM, replicate 2


title: 8W mouse Acetaminophe 8h rep2

description: Gene expression at 8h


title: 8W mouse Acetaminophe 8h rep1

description: Gene expression at 8h


title: hnRNPK_1.5uM

description: hnRNP K dose response assay

source_name: hnRNPK protein, 1.5 uM


title: hnRNPK_600nM

description: hnRNP K dose response assay

source_name: hnRNPK protein, 600nM


title: hnRNPK_200nM

description: hnRNP K dose response assay

source_name: hnRNPK protein, 200nM


title: Mx2uM_6.5_40

description: Mitoxantrone dose response assay at pH 6.5 40% BSA

organism: unidentified

source_name: Mitoxantrone, 2uM, pH 6.5, 40% BSA

value: 2X PBS, 100 mM KCl, pH 6.5, 40% BSA


title: hnRNPK_1uM

description: hnRNP K dose response assay

source_name: hnRNPK protein, 1uM


title: hnRNPK_400nM

description: hnRNP K dose response assay

source_name: hnRNPK protein, 400nM


title: hnRNPK_800nM

description: hnRNP K dose response assay

source_name: hnRNPK protein, 800nM


title: hnRNPK_rep1

description: hnRNP K binding assay at 1uM replicate 1

source_name: hnRNPK protein 1uM, replicate 1


title: ASF_rep2

description: ASF/SF2 binding assay at 1uM replicate 2

source_name: ASF/SF2 protein 1uM, replicate 2


title: iMab100nM_6.5_5

description: iMab binding assay at pH 6.5 5% BSA

source_name: iMab 100 nM monoclonal antibody, pH 6.5, 5% BSA


title: Mx6.1uM_6.5_40

source_name: Mitoxantrone, 6.1uM, pH 6.5, 40% BSA


title: iMab100nM_7.5_40

description: iMab binding assay at pH 7.5 40% BSA

source_name: iMab 100 nM monoclonal antibody, pH 7.5, 40% BSA

value: 2X PBS, 100 mM KCl, pH 7.5, 40% BSA


title: hnRNPK_100nM

description: hnRNP K dose response assay

source_name: hnRNPK protein, 100nM


title: Mx0.23uM_6.5_40

source_name: Mitoxantrone, 0.23 uM pH 6.5, 40% BSA


title: hnRNPK_2uM

description: hnRNP K dose response assay

source_name: hnRNPK protein, 2 uM


title: Mx55.5uM_6.5_40

source_name: Mitoxantrone, 55.5 uM, pH 6.5, 40% BSA


title: iMab100nM_6.5_40

description: iMab binding assay at pH 6.5 40% BSA

source_name: iMab 100 nM monoclonal antibody, pH 6.5, 40% BSA


title: Control ChIP-seq from left cerebral cortex (ENCLB128RHU)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR515UIB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR515UIB
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB128RHU
size range: 200-600

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Mus musculus strain B6CASTF1/J female adult (2 months) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

tag: biosample encode accession

tag: note

value: Bernstein pool J of 4 left cerebral cortex biosamples

value: female

tag: dev stage

value: adult

value: 2 month

tag: lab

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

tag: link

value: ENCBS590UIC at ENCODE; https://www.encodeproject.org/ENCBS590UIC/

value: derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: Control ChIP-seq from left cerebral cortex (ENCLB093UHX)

description:
https://www.encodeproject.org/experiments/ENCSR513BAE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR513BAE
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB093UHX
size range: 200-600

value: Bernstein pool I of 4 left cerebral cortex biosamples

value: ENCBS593FWT at ENCODE; https://www.encodeproject.org/ENCBS593FWT/


title: Control ChIP-seq from left cerebral cortex (ENCLB145QIX)

description:
https://www.encodeproject.org/experiments/ENCSR513BAE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR513BAE
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB145QIX
size range: 200-600


title: Histone ChIP-seq from layer of hippocampus (ENCLB172LNU)

description:
https://www.encodeproject.org/experiments/ENCSR527FRO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR527FRO
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR206ALY
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB172LNU
size range: 200-600

source_name: Mus musculus strain B6CASTF1/J male adult (2 months) layer of hippocampus tissue

tag: antibody

value: layer of hippocampus

value: Bernstein pool D of 7 layer of hippocampus biosamples

value: male

value: ENCBS169TOO at ENCODE; https://www.encodeproject.org/ENCBS169TOO/


title: Histone ChIP-seq from layer of hippocampus (ENCLB652TPP)

description:
https://www.encodeproject.org/experiments/ENCSR527FRO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR527FRO
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR206ALY
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB652TPP
size range: 200-600

value: Bernstein pool C of 7 layer of hippocampus biosamples

value: ENCBS512CTC at ENCODE; https://www.encodeproject.org/ENCBS512CTC/


title: Control ChIP-seq from left cerebral cortex (ENCLB601WVA)

description:
https://www.encodeproject.org/experiments/ENCSR515UIB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR515UIB
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB601WVA
size range: 200-600

value: left cerebral cortex

value: tissue


title: Control ChIP-seq from heart (ENCLB335FXC)

description:
https://www.encodeproject.org/experiments/ENCSR980YAL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR980YAL
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB335FXC
size range: 200-600

source_name: Mus musculus strain B6CASTF1/J female adult (2 months) heart tissue

value: heart

value: Bernstein pool G of 2 heart biosamples

value: female

value: ENCBS786IOZ at ENCODE; https://www.encodeproject.org/ENCBS786IOZ/


title: Histone ChIP-seq from layer of hippocampus (ENCLB150NJL)

description:
https://www.encodeproject.org/experiments/ENCSR527FRO/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR527FRO
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR206ALY
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB150NJL
size range: 200-600

value: adult

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory


title: Mx0.7uM_6.5_40

source_name: Mitoxantrone, 0.7uM pH 6.5, 40% BSA

value: 2X PBS, 100 mM KCl, pH 6.5, 40% BSA

value: ssDNA


title: Histone ChIP-seq from layer of hippocampus (ENCLB958EGD)

description:
https://www.encodeproject.org/experiments/ENCSR213YKJ/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR213YKJ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR148TRG
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB958EGD
size range: 200-600

value: layer of hippocampus

value: derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: iMab100nM_5.5_40

description: iMab binding assay at pH 5.5 40% BSA

source_name: iMab 100 nM monoclonal antibody, pH 5.5, 40% BSA

value: 2X PBS, 100 mM KCl, pH 5.5, 40% BSA


title: Histone ChIP-seq from layer of hippocampus (ENCLB663MZT)

description:
https://www.encodeproject.org/experiments/ENCSR213YKJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR213YKJ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR148TRG
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB663MZT
size range: 200-600

value: Bernstein pool D of 7 layer of hippocampus biosamples

value: male

value: ENCBS169TOO at ENCODE; https://www.encodeproject.org/ENCBS169TOO/


title: Histone ChIP-seq from left cerebral cortex (ENCLB288HYJ)

description:
https://www.encodeproject.org/experiments/ENCSR943LBN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR943LBN
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR515UIB
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB288HYJ
size range: 200-600

value: left cerebral cortex

value: tissue

value: Bernstein pool I of 4 left cerebral cortex biosamples

value: ENCBS593FWT at ENCODE; https://www.encodeproject.org/ENCBS593FWT/


title: Histone ChIP-seq from layer of hippocampus (ENCLB124DVV)

description:
https://www.encodeproject.org/experiments/ENCSR213YKJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR213YKJ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR148TRG
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB124DVV
size range: 200-600

value: Bernstein pool C of 7 layer of hippocampus biosamples

value: ENCBS512CTC at ENCODE; https://www.encodeproject.org/ENCBS512CTC/


title: Histone ChIP-seq from left cerebral cortex (ENCLB579JHT)

description:
https://www.encodeproject.org/experiments/ENCSR943LBN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR943LBN
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR515UIB
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB579JHT
size range: 200-600

value: Bernstein pool J of 4 left cerebral cortex biosamples

value: female

value: adult

value: 2 month

value: ENCBS590UIC at ENCODE; https://www.encodeproject.org/ENCBS590UIC/


title: Histone ChIP-seq from left cerebral cortex (ENCLB744UFQ)

description:
https://www.encodeproject.org/experiments/ENCSR943LBN/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR943LBN
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR515UIB
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB744UFQ
size range: 200-600

value: Barbara Wold, Caltech

value: The Jackson Laboratory


title: Histone ChIP-seq from layer of hippocampus (ENCLB883THT)

description:
https://www.encodeproject.org/experiments/ENCSR527FRO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR527FRO
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR206ALY
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB883THT
size range: 200-600

value: layer of hippocampus

value: derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: Control ChIP-seq from heart (ENCLB867JYD)

description:
https://www.encodeproject.org/experiments/ENCSR980YAL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR980YAL
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB867JYD
size range: 200-600

value: heart

value: Bernstein pool G of 2 heart biosamples

value: ENCBS786IOZ at ENCODE; https://www.encodeproject.org/ENCBS786IOZ/


title: Histone ChIP-seq from layer of hippocampus (ENCLB916TOH)

description:
https://www.encodeproject.org/experiments/ENCSR213YKJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR213YKJ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR148TRG
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB916TOH
size range: 200-600

value: tissue

value: Bernstein pool D of 7 layer of hippocampus biosamples

value: male

value: ENCBS169TOO at ENCODE; https://www.encodeproject.org/ENCBS169TOO/


title: Control ChIP-seq from layer of hippocampus (ENCLB596XOE)

description:
https://www.encodeproject.org/experiments/ENCSR206ALY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR206ALY
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB596XOE
size range: 200-600

value: Bernstein pool C of 7 layer of hippocampus biosamples

value: ENCBS512CTC at ENCODE; https://www.encodeproject.org/ENCBS512CTC/


title: Control ChIP-seq from layer of hippocampus (ENCLB611QVV)

description:
https://www.encodeproject.org/experiments/ENCSR206ALY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR206ALY
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB611QVV
size range: 200-600


title: Histone ChIP-seq from left cerebral cortex (ENCLB405ZBO)

description:
https://www.encodeproject.org/experiments/ENCSR491RBV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR491RBV
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR513BAE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB405ZBO
size range: 200-600

value: left cerebral cortex

value: Bernstein pool J of 4 left cerebral cortex biosamples

value: female


title: Histone ChIP-seq from left cerebral cortex (ENCLB798XRX)

description:
https://www.encodeproject.org/experiments/ENCSR491RBV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR491RBV
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR513BAE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB798XRX
size range: 200-600

value: Bernstein pool I of 4 left cerebral cortex biosamples

value: adult

value: 2 month

value: ENCBS593FWT at ENCODE; https://www.encodeproject.org/ENCBS593FWT/


title: Histone ChIP-seq from left cerebral cortex (ENCLB396QMS)

description:
https://www.encodeproject.org/experiments/ENCSR491RBV/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR491RBV
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR513BAE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB396QMS
size range: 200-600

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS590UIC at ENCODE; https://www.encodeproject.org/ENCBS590UIC/

value: derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: Histone ChIP-seq from left cerebral cortex (ENCLB369IMR)

description:
https://www.encodeproject.org/experiments/ENCSR491RBV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR491RBV
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR513BAE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB369IMR
size range: 200-600

value: tissue


title: Control ChIP-seq from heart (ENCLB689SLB)

description:
https://www.encodeproject.org/experiments/ENCSR477YXE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR477YXE
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB689SLB
size range: 200-600

value: heart

value: Bernstein pool H of 2 heart biosamples

value: ENCBS509WQM at ENCODE; https://www.encodeproject.org/ENCBS509WQM/


title: Histone ChIP-seq from gastrocnemius (ENCLB127YGY)

description:
https://www.encodeproject.org/experiments/ENCSR714ZJT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR714ZJT
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR121JUM
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB127YGY
size range: 200-600

source_name: Mus musculus strain B6CASTF1/J female adult (2 months) gastrocnemius tissue

value: gastrocnemius

value: Bernstein pool F of 2 gastrocnemius biosamples

value: ENCBS703UIG at ENCODE; https://www.encodeproject.org/ENCBS703UIG/


title: Control ChIP-seq from heart (ENCLB580RXX)

description:
https://www.encodeproject.org/experiments/ENCSR477YXE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR477YXE
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB580RXX
size range: 200-600


title: Histone ChIP-seq from gastrocnemius (ENCLB444XHG)

description:
https://www.encodeproject.org/experiments/ENCSR714ZJT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR714ZJT
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR121JUM
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB444XHG
size range: 200-600


title: Histone ChIP-seq from gastrocnemius (ENCLB468PMV)

description:
https://www.encodeproject.org/experiments/ENCSR714ZJT/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR714ZJT
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR121JUM
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB468PMV
size range: 200-600

value: Bernstein pool E of 2 gastrocnemius biosamples

value: ENCBS707VDM at ENCODE; https://www.encodeproject.org/ENCBS707VDM/


title: Histone ChIP-seq from gastrocnemius (ENCLB483NXC)

description:
https://www.encodeproject.org/experiments/ENCSR714ZJT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR714ZJT
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR121JUM
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB483NXC
size range: 200-600

value: female


title: Control ChIP-seq from layer of hippocampus (ENCLB630JHI)

description:
https://www.encodeproject.org/experiments/ENCSR148TRG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR148TRG
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB630JHI
size range: 200-600

value: layer of hippocampus

value: Bernstein pool D of 7 layer of hippocampus biosamples

value: male

value: adult

value: ENCBS169TOO at ENCODE; https://www.encodeproject.org/ENCBS169TOO/


title: TF ChIP-seq from layer of hippocampus (ENCLB143GUD)

description:
https://www.encodeproject.org/experiments/ENCSR877MSN/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR877MSN
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR148TRG
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB143GUD
size range: 200-600

value: CTCF

value: Bernstein pool C of 7 layer of hippocampus biosamples

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS512CTC at ENCODE; https://www.encodeproject.org/ENCBS512CTC/


title: TF ChIP-seq from layer of hippocampus (ENCLB148AZB)

description:
https://www.encodeproject.org/experiments/ENCSR877MSN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR877MSN
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR148TRG
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB148AZB
size range: 200-600

value: tissue

value: derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: Control ChIP-seq from gastrocnemius (ENCLB792OUL)

description:
https://www.encodeproject.org/experiments/ENCSR121JUM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR121JUM
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB792OUL
size range: 200-600

value: gastrocnemius

value: Bernstein pool F of 2 gastrocnemius biosamples

value: ENCBS703UIG at ENCODE; https://www.encodeproject.org/ENCBS703UIG/


title: Control ChIP-seq from gastrocnemius (ENCLB584LVM)

description:
https://www.encodeproject.org/experiments/ENCSR121JUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR121JUM
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB584LVM
size range: 200-600

value: female


title: TF ChIP-seq from layer of hippocampus (ENCLB330FTF)

description:
https://www.encodeproject.org/experiments/ENCSR877MSN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR877MSN
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR148TRG
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB330FTF
size range: 200-600

value: layer of hippocampus


title: Control ChIP-seq from layer of hippocampus (ENCLB593YIT)

description:
https://www.encodeproject.org/experiments/ENCSR148TRG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR148TRG
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB593YIT
size range: 200-600

value: Bernstein pool D of 7 layer of hippocampus biosamples


title: TF ChIP-seq from left cerebral cortex (ENCLB180ZFG)

description:
https://www.encodeproject.org/experiments/ENCSR644VYX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR644VYX
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR513BAE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB180ZFG
size range: 200-600

value: left cerebral cortex

value: Bernstein pool J of 4 left cerebral cortex biosamples

value: ENCBS590UIC at ENCODE; https://www.encodeproject.org/ENCBS590UIC/


title: TF ChIP-seq from layer of hippocampus (ENCLB600OJP)

description:
https://www.encodeproject.org/experiments/ENCSR877MSN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR877MSN
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR148TRG
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB600OJP
size range: 200-600

value: CTCF

value: male

value: adult


title: TF ChIP-seq from left cerebral cortex (ENCLB890UNK)

description:
https://www.encodeproject.org/experiments/ENCSR644VYX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR644VYX
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR513BAE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB890UNK
size range: 200-600

value: Bernstein pool I of 4 left cerebral cortex biosamples

value: 2 month

value: Barbara Wold, Caltech

value: ENCBS593FWT at ENCODE; https://www.encodeproject.org/ENCBS593FWT/


title: Histone ChIP-seq from left cerebral cortex (ENCLB106XWK)

description:
https://www.encodeproject.org/experiments/ENCSR943LBN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR943LBN
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR515UIB
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB106XWK
size range: 200-600

value: tissue

value: The Jackson Laboratory

value: derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: Histone ChIP-seq from heart (ENCLB445SWH)

description:
https://www.encodeproject.org/experiments/ENCSR846REF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR846REF
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR980YAL
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB445SWH
size range: 200-600

value: heart

value: Bernstein pool G of 2 heart biosamples

value: ENCBS786IOZ at ENCODE; https://www.encodeproject.org/ENCBS786IOZ/


title: Histone ChIP-seq from heart (ENCLB465UDI)

description:
https://www.encodeproject.org/experiments/ENCSR846REF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR846REF
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR980YAL
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB465UDI
size range: 200-600

value: female


title: Histone ChIP-seq from heart (ENCLB464JMO)

description:
https://www.encodeproject.org/experiments/ENCSR846REF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR846REF
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR980YAL
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB464JMO
size range: 200-600

value: Bernstein pool H of 2 heart biosamples

value: ENCBS509WQM at ENCODE; https://www.encodeproject.org/ENCBS509WQM/


title: Histone ChIP-seq from heart (ENCLB569DQA)

description:
https://www.encodeproject.org/experiments/ENCSR846REF/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR846REF
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR980YAL
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB569DQA
size range: 200-600


title: TF ChIP-seq from gastrocnemius (ENCLB779LVB)

description:
https://www.encodeproject.org/experiments/ENCSR798CCX/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR798CCX
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR820CZJ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB779LVB
size range: 200-600

value: gastrocnemius

value: Bernstein pool F of 2 gastrocnemius biosamples

value: ENCBS703UIG at ENCODE; https://www.encodeproject.org/ENCBS703UIG/