title: Muscle977

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

description:
smallRNA/noncodingRNA
390-MP-79

data_processing:
raw fastq files from ncRNA sequencing were 5’ trimmed using cutadapt (v3.2) as per manufacturers recommendation using the adapter sequence ‘AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC’
Using the built-in function for cutadapt, reads that were of low quality and <17bps were removed from the sequencing data
aligned to sheep reference genome (Oar_rambouillet_v1.0) using STAR (2.6.0c)
counting of reads for each class of ncRNA evaluated in this study was achieved by first subsetting the whole genome annotation files for the reference genome into files that contained only references for a particular ncRNA
aligned reads were then used in featureCounts (1.6.1) with genes as the identifier, with all multimapping reads included in the analysis, along with annotation files specific for each ncRNA to obtain counts
Genome_build: Oar_rambouillet_v1.0
Supplementary_files_format_and_content: normalized counts of long non-coding RNA
Supplementary_files_format_and_content: normalized counts of mircoRNA
Supplementary_files_format_and_content: normalized counts of small nucleolar RNA
Supplementary_files_format_and_content: normalized counts of small nuclear RNA

organism: Ovis aries

source_name: Muscle

extract_protocol:
Liver and skeletal muscle tissues were collected during the second breeding season at ~21 months of age following 48 hours fast. Tissues were collected during the follicular phase as the prenatal BPA-treated animals did not stop cycling. Estrous was synchronized with two injections of prostaglandin F2α (PGF2α, 10 mg, i.m.; Lutalyse, Pfizer Animal Health, Florham Park, NJ) administered 11 days apart. Tissues were harvested 24 hours after the second PGF2α injection during the late follicular phase. Animals were euthanized with barbiturate overdose (Fatal Plus; Vortech Pharmaceuticals, Dearborn, MI) and liver sampled from the tip of the left lobe and skeletal muscle from the vastus lateralis, snap frozen and stored at -80ºC freezer until processed. Liver and skeletal muscle tissues were homogenized in Trizol reagent (Life Technologies, Carlsbad, CA) and total RNA was isolated following the manufacturer’s recommendations. RNA was purified using RNeasy kit (Qiagen, Germantown, MD). Residual contaminating DNA was removed using RNeasy binding column, treating the column with RNAse free DNAse and eluting the RNA in nuclease free water. The quality of purified RNA including the purity and RNA integrity were evaluated using Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) at the University of Michigan Advanced Genomics Core.
Libraries for ncRNA were prepared from total RNA using NEBNext smallRNA kit (New England BioLabs, Ipswich, MA) at the University of Michigan Advanced Genomics Core as per manufacturers recommendations

treatment_protocol: Pregnant Suffolk sheep were randomly assigned to control and BPA treatment groups. Between days 30 and 90 of gestation, control animals received vehicle (corn oil) and the BPA-treated group received 0.5mg/kg/day BPA (purity ≥ 99%, catalog number 239658; Aldrich Chemical Co, Milwaukee, Wisconsin) solubilized in corn oil. Both injections of vehicle and BPA were administered daily, subcutaneously. The average BPA level achieved in the umbilical artery with this dose was ~2.6 ng/ml.

tag: treatment

value: BPA

tag: sheepid


title: Muscle984

status: Public on Jul 08 2022

type: SRA

country: USA

description:
smallRNA/noncodingRNA
390-MP-97

library_source: transcriptomic

molecule: total RNA


title: Muscle910

description:
smallRNA/noncodingRNA
390-MP-77


title: Muscle918

description:
smallRNA/noncodingRNA
390-MP-78


title: 129

city: Auburn

first: Marie

middle: E

last: Strader

state: AL

address: 101 Rouse Life Sciences, Biological Sciences Department

department: Biological Sciences

institute: Auburn University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Acropora millepora genome (v2.01) using bowtie2(v.2.2.9) --local --no-hd --no-sq --no-unal -k 5
gene counts were compiled using a custom perl script enabling samcounts. Script found at https://github.com/z0on/tag-based_RNAseq
Genome_build: Acropora millepora genome (v2.01)
Supplementary_files_format_and_content: txt files including gene counts values for each sample
Supplementary_files_format_and_content: VCF files for SNP calls

organism: Acropora tenuis

source_name: juvenile tissue

extract_protocol:
RNAqueous kit (Ambion)
tag-seq: https://github.com/z0on/tag-based_RNAseq

tag: cross

value: DRxSB

tag: temperature treatment

value: Ambient

tag: life-stage

value: juvenile

tag: symbiont


title: 126

value: CUxDR


title: Muscle908

description:
smallRNA/noncodingRNA
390-MP-74

value: C


title: Muscle928

description:
smallRNA/noncodingRNA
390-MP-76


title: vitamin D treated villi_rep 7

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Villi.txt, Results_VDR_VitDvsNoVitD_Villi.txt
sample name in processed data file:
2_D_Villi_Rep1

data_processing:
Alignment: RNA-seq: Kallisto v0.45.0.
RNA-seq Transcript Import: tximport 1.16.1
DESeq 1.28.1
Genome_build: RefSeq mm9
Supplementary_files_format_and_content: RNA-Seq: results table for reporting mean of normalized counts for all samples and through comparison of the treated condition vs untreated condition, log2 fold change, standard error, Wald statistic, Wald test p-value, and Benjamini-Hochberg adjusted p-value
Supplementary_files_format_and_content: RNA-Seq: fpkm table outputted by DESeq2 for fragment counts normalized per kilobase of feature length per million mapped fragments

organism: Mus musculus

source_name: vitamin D treated villi

extract_protocol:
Intestinal tissues were harvested from mice. About 10-15 cm of the proximal half of small intestine were used for the duodenum crypts and villi samples, and the entire colon tissues from the terminal cecum to rectum were used for colon samples. After flushing with cold PBS, the intestines were cut opened longitudinally, cut into 1 cm pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. The solution was discarded and the tissues were incubated with fresh 3mM EDTA/PBS in rotator for 10 min at 4 0C. After shaking the tubes gently for 10 times, the intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS, rotated for 30 min at 4 0C, then were shaken 30 times. The supernatant containing the whole epithelium tissues (crypts and villi) were collected and spun down at 200 rcf for 3 min at 4 0C. Resuspended the pellet with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes at 200 rcf for 3 mins at 4 0C and at 300 rcf for 30 seconds at 40C in order to remove any residual PBS. Proceeded to RNA extraction. For the colon samples, on an ice-cold plate, the colon was cut from the terminal end of the cecum to the rectum.   An 18-gauge needle attached to a 30 ml syringe was used to flush the feces out of the colon. The colon was cut open longitudinally and rinsed with cold PBS. Afterwards, the colon was scraped with a glass slide and a glass cover slip. The colon was scraped until the tissue turned transparent and only the muscle tissue was left. The scraped epithelial cell pellet was then collected in a 1.5 ml Eppendorf tube coated with 0.5% BSA and filled with 1ml of cold PBS. After pelleting the colon intestinal cell pellet in cold PBS at 300 rcf for 3 minutes in 4C twice, the supernatant was removed. Trizol was quickly added to the pellet by pipetting up and down until the pellet dissolved in the Trizol.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions. All nucleic acid extracts were gDNA Eliminator Solution for 15 s at 37 °C, in order to remove contaminating chromosomal DNA. Resulting RNA was analyzed for quantity and quality with a NanoDrop spectrophotometer ND-1000 (Isogen Life Science, Utrecht, The Netherlands).
RNA quality was examined via Agilent 2100, mRNA was enriched and reverse transcribed, and DNA nanoball synthesis was conducted by BGI. Sequencing was performed on BGISEQ-500 with paired-end, 100bp reads.

treatment_protocol: 12 – 14 week old vitamin D deficient mice were randomly separated and injected with either 0.1 ml vehicle (9:1 mix of propylene glycol and ethanol) or 1,25(OH)2D3 (from Cayman Chemical Company Ann Arbor, MI)  (ip 10ng/g body weight) and killed 4h after the injection

tag: genotype

value: wild type

tag: background strain

tag: tissue

value: Intestinal Epithelium

tag: Sex

value: pooled male and female

tag: age


title: Muscle902

description:
smallRNA/noncodingRNA
390-MP-73


title: 117

value: SBxSB

value: SED


title: 125

value: Hot

value: SS


title: 113


title: Liver984

description:
smallRNA/noncodingRNA
390-MP-72

source_name: Liver


title: 116

value: BKxBK


title: Liver977

description:
smallRNA/noncodingRNA
390-MP-71


title: Liver910

description:
smallRNA/noncodingRNA
390-MP-95


title: 134

value: DRxCU


title: Liver918

description:
smallRNA/noncodingRNA
390-MP-96


title: 112

value: DRxDR


title: Liver928

description:
smallRNA/noncodingRNA
390-MP-121


title: 110


title: Liver924

description:
smallRNA/noncodingRNA
390-MP-120


title: 111


title: Liver908

description:
smallRNA/noncodingRNA
390-MP-119


title: 109

value: LSxLS


title: Muscle924

description:
smallRNA/noncodingRNA
390-MP-75


title: 107


title: Muscle 984

data_processing:
Adapters from read1 of paired end reads were removed using trimmomatic using the parameters 2:30:10. Subsequently scanning with a 4bp window, reads with QC threshold below 3 and QC score below 15 were dropped.
Fastqc was performed on both the raw and trimmed files to determine mean read quality scores.
Reads were mapped to the sheep reference genome (Oar_rambouillet_v1.0) and the quality and number of reads mapped to the genome were determined by Quality of RNA-Seq Tool-set (QORTS, v1.3.6).
DESeq2 (v1.24.0) was used to evaluate the differential expression
Genome_build: Oar_rambouillet_v1.0
Supplementary_files_format_and_content: matrix of normalized counts

extract_protocol:
Liver and skeletal muscle tissues were collected during the second breeding season at ~21 months of age following 48 hours fast. Tissues were collected during the follicular phase as the prenatal BPA-treated animals did not stop cycling. Estrous was synchronized with two injections of prostaglandin F2α (PGF2α, 10 mg, i.m.; Lutalyse, Pfizer Animal Health, Florham Park, NJ) administered 11 days apart. Tissues were harvested 24 hours after the second PGF2α injection during the late follicular phase. Animals were euthanized with barbiturate overdose (Fatal Plus; Vortech Pharmaceuticals, Dearborn, MI) and liver sampled from the tip of the left lobe and skeletal muscle from the vastus lateralis, snap frozen and stored at -80ºC freezer until processed. Liver and skeletal muscle tissues were homogenized in Trizol reagent (Life Technologies, Carlsbad, CA) and total RNA was isolated following the manufacturer’s recommendations. RNA was purified using RNeasy kit (Qiagen, Germantown, MD). Residual contaminating DNA was removed using RNeasy binding column, treating the column with RNAse free DNAse and eluting the RNA in nuclease free water. The quality of purified RNA including the purity and RNA integrity were evaluated using Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) at the University of Michigan Advanced Genomics Core.
libraries were prepared with SMARTer universal low input RNA kit (Takara, Mountain View, CA) following ribosome depletion

value: BPA


title: Liver902

description:
smallRNA/noncodingRNA
390-MP-65


title: 108


title: 106


title: 114


title: 105


title: 115


title: Muscle 977


title: 163

value: DRxSB


title: 5/6Nx_PD [R2021-001611]

city: Milwaukee

first: Alison

middle: J.

last: Kriegel

state: WI

address: 8701 Watertown Plank Rd.

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Adapter sequences were removed from the output RNA-Seq sequence reads using cutadapt (http://code.google.com/p/cutadapt/)
Reads with low base quality (<13) were further trimmed and, if less than 25 base pairs, removed by using the trim_glore tool, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/.
The trimmed sequence reads were then aligned to the rat reference genome and gene annotation database (rn6) using HISAT2 (v2.1.1) with mammalian default parameters (PMID:23618408)
Transcripts in all of the sequencing libraries were assembled by StringTie2 (v2.1.5)(PMID:25690850)
Transcripts present in less that 50% of samples (expression of zero) in each group were removed.
Differential gene expression was determined using the R package DESeq2.
The Benjamini-Hochberg method was used to control false discovery rate in differential expression analysis to provide an adjusted p-value.
Supplementary files format and content: "Nasci et al._Individual Sample_RNA Seq Results" Contains normalized transcript abundance values for each sample/library sequenced.
Supplementary files format and content: "Nasci et al. DEG Results_All Comparisons" Contains results for statistical analysis of group comparisons, including log2 fold-change, p-value and q-value  for each transcript.

organism: Rattus

source_name: Left Ventricle

extract_protocol:
RNA extraction was performed on cryogenically pulvarized tissue using the standard Trizol/chloroform extraction method.
Automated library construction was performed by the Genomic Sciences and Precision Medicine Center (GSPMC) at the Medical College of Wisconsin using Illumina TruSeq stranded mRNA library prep kit
Individual libraries were prepared for each tissue with unique dual 8 base pair indexes for samples on each sequencing run

value: Left Ventricle

tag: group

value: male

tag: strain

value: Sprague Dawley

value: Peritoneal Dialysis


title: 5/6Nx_PD [R2021-001604]


title: 5/6Nx_PD [R2021-001608]


title: 5/6Nx_PD [R2021-001603]


title: 5/6Nx_PD [R2021-001607]


title: 5/6Nx_PD [R2021-001614]


title: 5/6Nx_PD [R2021-001626]


title: 5/6Nx_PD [R2021-001600]

source_name: Kidney

value: Kidney


title: Muscle 918


title: 103

value: Ambient

value: juvenile


title: Muscle 910


title: 5/6Nx_PD [R2021-001585]


title: 5/6Nx_PD [R2021-001588]


title: 5/6Nx_PD [R2021-001582]


title: Muscle 928

value: C


title: 102


title: Muscle 924


title: 101


title: Muscle 908


title: 5/6Nx_Ctrl. [R2021-001620]

value: Control


title: 100


title: 5/6Nx_Ctrl. [R2021-001610]


title: Muscle 902


title: 5/6Nx_Ctrl. [R2021-001615]


title: 99

value: SBxSB


title: Liver 977


title: 162

value: CUxDR

value: Hot

value: SED


title: 5/6Nx_Ctrl. [R2021-001606]


title: 5/6Nx_Ctrl. [R2021-001594]


title: 5/6Nx_PD [R2021-001581]


title: Liver 910


title: 5/6Nx_Ctrl. [R2021-001590]


title: 5/6Nx_Ctrl. [R2021-001605]


title: 70


title: 86

value: BKxBK


title: 85


title: 5/6Nx_Ctrl. [R2021-001609]


title: Liver 918


title: Liver 928


title: Liver 984


title: 5/6Nx_Ctrl. [R2021-001580]


title: 5/6Nx_PD [R2021-001578]


title: 5/6Nx_PD [R2021-001577]


title: 5/6Nx_Ctrl. [R2021-001584]


title: 5/6Nx_Ctrl. [R2021-001616]


title: 5/6Nx_Ctrl. [R2021-001589]


title: 5/6Nx_Ctrl. [R2021-001579]


title: 84

value: DRxDR


title: Sham_PD [R2021-001627]

value: Sham


title: 5/6Nx_Ctrl. [R2021-001583]


title: Sham_PD [R2021-001625]


title: 83


title: Liver 908


title: Sham_PD [R2021-001621]


title: Sham_PD [R2021-001617]


title: 69


title: Liver 902


title: 81


title: Sham_PD [R2021-001591]


title: Sham_PD [R2021-001595]


title: 80


title: Sham_PD [R2021-001612]


title: Sham_PD [R2021-001586]


title: Sham_Ctrl [R2021-001624]


title: Liver 924


title: Sham_PD [R2021-001601]


title: 79

value: SS


title: Sham_Ctrl [R2021-001622]

value: Left Ventricle


title: 76


title: Sham_PD [R2021-001587]

value: male


title: Sham_PD [R2021-001599]

value: Sprague Dawley


title: Q108-CONTROL

city: Lexington

first: Barry

middle: A.

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

institute: University of Kentucky

data_processing:
The Fastq files were evaluated for read quality using FastQC 0.11.4
Trim Galore 0.4.1 was used for adapter and read quality trimming (Phred score threshold of 30).
Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using the software STAR 2.5.3a (Dobin, Davis et al. 2013)
Reads were annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1
Fragments per kilobase per million (FPKM) were used to determine the expression level of genes
Cuffdiff 2.2.1 was used to calculate differentially expressed genes (DEG) between samples from the control and urea groups
Significance level was set at FDR-adjusted p-value of the test statistic < 0.1 using a Benjamini-Hochberg correction
Genome_build: EquCab 3.0
Supplementary_files_format_and_content: Normalized abundance measurements- Cufflink Gene.FPKM.Tracking

organism: Equus caballus

source_name: Uterus

extract_protocol:
Total cellular RNA was extracted from endometrial samples using a RNeasy Mini Kit (Qiagen, Gaithersburg, MD). A total of 1 μg of RNA was treated with DNase I (Ambion Inc., Austin, TX) for 30 minutes at 37℃ to remove genomic DNA according to manufacturer’s instructions. Endometrial samples were processed for RNA extraction using a RNeasy Mini Kit (Qiagen, Gaithersburg, MD) following the manufacturer’s recommendations. After extraction, RNA concentration and quality were analyzed using a Nanodrop 2000 spectrophotometer Thermo Fisher Scientific) and a Bioanalyzer® (Agilent, Santa Clara, CA). Samples had a 260/280 ratio > 2.0, 28S:18S rRNA ratios >1.8 and RNA integrity number (RIN) was 9.78  0.06 (mean  SEM).
A TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA) was used to prepare libraries for mRNA sequencing. Libraries were loaded onto an Agilent DNA 1000 chip and validated on an Agilent 2100 Bioanalyzer (Agilent). Quantitation was performed with the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems. Libraries were run on a NextSeq 500 v2 (Illumina) 300cycles High Output kit in a 2x150 base pairs with paired-end reads.

treatment_protocol: At the day of ovulation (D0), oral treatment started and continued until D7. Mares received the treatment or control diet in a random order (n= 11 mares/group) in a crossover design, and the intervening estrous cycle served as a washout cycle between two experimental cycles. The treatment group was fed 0.4 g of feed-grade urea (Hallway Feeds, Lexington, KY) per kg of body weight daily, mixed with 2.4 kg of sweet feed (Poize 10% crude protein, Hallway Feeds), molasses and mixed grass hay (8.4% crude protein). The control group received identical sweet feed, molasses and hay. Daily meals were divided in two equal amounts given in the morning and afternoon using individual feeding pens. Mares had ad libitum access to water.

value: Endometrium


title: Q114-UREA

value: Urea


title: Q108-UREA


title: Q114-CONTROL


title: Q110-UREA


title: 78

value: Ambient


title: Sham_Ctrl [R2021-001618]


title: 77

value: LSxLS

value: juvenile


title: Q110-CONTROL

value: Control


title: Sham_Ctrl [R2021-001623]


title: Sham_PD [R2021-001613]

value: Peritoneal Dialysis


title: 75

value: SBxSB


title: Sham_Ctrl [R2021-001593]


title: Sham_Ctrl [R2021-001628]

value: Kidney


title: 74


title: Q112-UREA


title: Sham_Ctrl [R2021-001619]


title: 73


title: Sham_Ctrl [R2021-001597]


title: Q109-UREA


title: Sham_Ctrl [R2021-001598]


title: Sham_Ctrl [R2021-001592]


title: Sham_Ctrl [R2021-001596]


title: Q112-CONTROL


title: GC-2spd hypoxia rep2 that growth under hypoxic conditions

city: Shanghai

first: Yunfang

last: Zhang

address: 1239 Siping Road

department: Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology

country: China

institute: Tongji University

data_processing:
Data filtrated - Cutadapt
Mapping - Hisat2
Expression level quantified - StringTie
Assembly: mm10
Supplementary files format and content: gene expression level for each smaple

growth_protocol: GC-2spd cells cultured in DMEM medium supplemented with 10% fetal bovine serum  and 1% antibiotics (100 U/ml penicillin and 100 U/ml streptomycin)

extract_protocol:
Total RNA of cells was extracted with TRIZOL reagent according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols, mRNA with polyA was enriched by Oligo (DT) magnetic beads from total RNA. Then mRNA was randomly interrupted, linked with connectors and reverse transcribed to cDNA for library construction. Finally, double pair-end (PE) sequencing was conducted based on Illumina NovaSeq sequencing platform.

treatment_protocol: Cells were maintained in incubator containing 21% O2 and 5% CO2 or a hypoxia workstation containing 1% O2, 5% CO2 and 94% N2 at 37˚C.

tag: strain background

value: testis

tag: cell line

value: hypoxia exposure


title: Sham_Ctrl [R2021-001602]


title: 64

value: Hot

value: SED


title: Q109-CONTROL


title: 68


title: GC-2spd hypoxia rep3 that growth under hypoxic conditions


title: N127-UREA


title: GC-2spd control rep3 that growth under normal conditions

value: normal control


title: GC-2spd hypoxia rep1 that growth under hypoxic conditions


title: N127-CONTROL


title: GC-2spd control rep2 that growth under normal conditions


title: 67

value: DRxDR


title: 37


title: C3_G4

city: Harbin

first: lu

middle: yuan

last: sun

address: Heilongjiang

institute: Northeast Agricultural University

data_processing:
Raw reads were first filtered and trimmed using SOAPnuke with –lowQual = 20，–nRate = 0.005 and –qualRate = 0.5 to obtain clean reads. Q20, Q30, and GC contents of the clean reads were calculated by SOAPnuke
Paired-end clean reads were mapped to the reference genome and the coverage of RNA-seq reads was calculated by geneBody_coverage.py script of RSeQC software.
Then mapped reads were assembled using StringTie software in a reference-based approach.
Assembly: Sus scrofa 11.1,http://asia.ensembl.org/Sus_scrofa/Info/Index
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: semitendinosus

extract_protocol:
Six libraries, including three from longissimus thoracis and three from semitendinosus, RNA harvested using Trizol reagent,three µg total RNA per sample was used for library costruction.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

value: semitendinosus

value: WT


title: 161

value: DRxSB


title: 72

value: SS


title: Replicate 1 from 48 days post infection, VDJseq

city: Bern

first: Tural

last: Yarahmadov

address: Murtenstrasse 35

department: BioMedical Research

country: Switzerland

institute: University of Bern

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Feature barcode counting was performed using 10x Genomics cellranger v.3.0.2 count function with software-provided mouse reference genome mm10-3.0.0 and –expect-cells parameter value 5000.
We only analysed the GEX data in our project.
Assembly: mm10 v.3.0.0, provided by cellranger
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Mouse livers were cut into small pieces with a scalpel and crushed against a 50mm stainless steel mesh plate.  The mesh plate was rinsed with cold MACS buffer (PBS with 0.6% FBS and 0.5M EDTA) to release the cells into the collection plate.  Cells were washed with MACS buffer and centrifuged at 50G for 3 minutes at 4°C to get rid of most of the hepatocytes and the supernatant was collected (non-parenchymal cells).  The non-parenchymal cells were then centrifuged at 300G for 7 minutes at 4°C.  The pellet was resuspended in 10mL of 40% Percoll and overlaid with 70% Percoll.  The cells were centrifuged at 800G for 20 minutes at 4°C with no brake and the interphase with cells were collected and resuspended up to 15mL in MACS buffer.  The cells were centrifuged at 300G for 7 minutes at 4°C and the cell pellet was resuspended then counted with the BioRad cell counter (Bio-Rad, TC20). 0.25-0.5 million non-parenchymal cells were used with the EasySepTM Mouse T cell Isolation Kit (Stemcell Technologies, Cat. #19851) for negative selection of T cells, following kit protocol.  Briefly, cells are stained with a cocktail of antibodies bound to magnetic particles and specific for non-T cells. These cells are retained against the wall of the FACS tube when the EasySep magnet is applied, and the remaining cells (T cells) are poured out of the tube and counted for sequencing.
Library was performed according to the manufacter’s instructions (10x Genomics scSeq VDJ Reagents).
scRNA-seq (5’ Gene Expression library) with V(D)Jseq (TCR)

tag: cell type

value: CD3+ cells

value: Liver

value: 8 weeks old + 48 days

value: female


title: Replicate 2 from 48 days post infection, VDJseq

description: 10x Genomics


title: Replicate 3 from 21 days post infection, VDJseq

description: 10x Genomics

value: 8 weeks old + 21 days


title: Replicate 3 from 48 days post infection, VDJseq

description: 10x Genomics


title: Replicate 2 from 21 days post infection, VDJseq

description: 10x Genomics


title: C1_G4


title: GC-2spd control rep1 that growth under normal conditions


title: C3_BJ

source_name: longissimus thoracis

value: longissimus thoracis


title: Replicate 1 from 21 days post infection, VDJseq

description: 10x Genomics


title: 104

value: LSxLS

value: Ambient

value: juvenile


title: C2_BJ


title: 158

value: CUxDR

value: Hot


title: Replicate 1 from 10 days post infection, VDJseq

description: 10x Genomics

value: 8 weeks old + 10 days


title: Replicate 2 from 10 days post infection, VDJseq

description: 10x Genomics


title: Replicate 3 from 10 days post infection, VDJseq

description: 10x Genomics


title: Control from day 48, VDJseq

description: 10x Genomics


title: 61


title: Control from day 21, VDJseq

description: 10x Genomics


title: Control from day 10, VDJseq

description: 10x Genomics


title: 82


title: 50

value: DRxDR


title: Replicate 3 from 48 days post infection, scRNAseq

description: 10x Genomics


title: C1_BJ


title: C2_G4

value: semitendinosus


title: HiC-seq Hmga2 KO clone #1

city: Napoli

first: Pietro

last: Zoppoli

state: Napoli

address: via S.Pansini,5

department: DMMBM

country: Italy

institute: Università degli Studi di Napoli Federico II

library_source: genomic

data_processing:
Paired-end reads were aligned to the NCBI reference sequence (mm10) using the pipeline HiC-Pro (PMID: 26619908).
Files in .hic format were generated with HiC-Pro.
Assembly: mm10

molecule: genomic DNA

source_name: Hmga2 KO iPSC #1

growth_protocol: iPSCs were grown on mitotically inactivated fibroblast feeder layers and expanded in: GMEM supplemented with 2 mM glutamine, 100 U/mL penicillin/streptomycin, 1 mM sodium pyruvate, 1X non-essential amino acids, 0.1 mM β-mercaptoethanol, 15% FBS, 103 U/ml leukaemia inhibitory factor and 2i (3 μΜ PD0325901 and 1 μΜ CHIR-99021). E14Tg2a cells were expanded on gelatin-coated plates in GMEM supplemented with 2 mM glutamine, 100 U/mL penicillin/streptomycin, 1 mM sodium pyruvate, 1X non-essential amino acids, 0.1 mM β-mercaptoethanol, 10% FBS and 103 U/ml LIF.

extract_protocol:
cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature and incubated with 3M Tris pH 7.5 for 5 minutes at room temperature and then on ice for 15 minutes to quench the formaldehyde. The cells were centrifugated for 10 minutes at 800xg at 4° C, the pellet was resuspended in cold 1X PBS, and the cell density was determined.
Indexed libraries were prepared from 2x106 cells, with EpiTect® Hi-C (Qiagen) according to the manufacturer’s instructions. Libraries were quantified using the TapeStation 4200 (Agilent Technologies) and Invitrogen Qubit fluorometer (Thermo Fisher Scientific), then pooled such that each index-tagged sample was present in equimolar amounts, with final concentration of the pooled samples of 2nM.

treatment_protocol: To induce iPSCs and ESCs into EpiLCs, 2x10^4 cells/cm^2 were plated on plates coated with Geltrex™ LDEV-Free Reduced Growth Factor Basement Membrane Matrix in EpiLSC medium (DMEMF12/Neurobasal medium 1:1, 0,5% N2 supplement, 1% B27 supplement, BSA, 2 mM glutamine, 20 ng/mL Activin A, and 12 ng/mL bFGF).

value: iPSC

value: Hmga2 KO

value: induced into EpiLC


title: 49


title: Replicate 2 from 48 days post infection, scRNAseq

description: 10x Genomics

value: CD3+ cells


title: Replicate 1 from 48 days post infection, scRNAseq

description: 10x Genomics

value: Liver


title: HiC-seq Hmga2 wt clone #1

source_name: wt iPSC #1

value: WT


title: 48

value: SBxSB


title: 46

value: BKxBK


title: 45


title: 47


title: 44


title: HiC-seq Hmga2 KO clone #2

source_name: Hmga2 KO iPSC #2


title: 43


title: Geriatric Proximal Colon ATAC-seq replicate 3

description: OM PC 3

data_processing:
Adapter removal: Nextera transpose adapter reverse complement was removed from the 3’ end of the ATAC-seq reads using CutAdapt v1.9.1.
Genome alignment: The trimmed FASTQ files were aligned to the mouse (mm9) genome using Bowtie2. The SAM files were converted into BAM files using the SAMtoBAM utility included in SAMtools v0.1.19. These BAM files were then sorted using the SortBAM utility included in SAMtools v0.1.19.
BAM to BigWig operation: A BigWig file was generated for each sorted BAM file using the default parameters for the bamCoverage utility included in deeptools v2.4.2-4-99ec5c.
Replicate BigWig merging: The BigWig files for all replicates of a sample were merged using the BigWigMerge v2 utility included in the UCSC Genome Browser; a combined BedGraph file was generated from each sample. The combined BedGraph files were converted to BigWig files using the BedGraphToBigWig v4 utility also included in the UCSC Genome Browser.
Peak calling: A BED file was generated from each sorted BAM file using the BAMtoBED utility included in bedtools v2.17.0. The median insert size of each BED file was determined using the CollectInsertSizeMetrics utility included in the Picard v2.18.27 suite. Statistically significant enriched genomic regions (“peaks”) were identified from the BED files using MACS2 v2.1.0.20150731 with a 5’ shift of one-half the median insert length for each BED file.
DiffBind: The sorted BAM file generated by Bowtie2 and the peaks BED file generated by MACS2 for each sample were analyzed using DiffBind. Pairwise-comparisons were conducted between samples of the same tissue at different ages (tissue-constant comparisons) and between samples of different tissues at the same age (age-constant comparisons). For each pairwise comparison, DiffBind generated a set of differentially accessible peaks and their associated significance values. Any peak in the set of peaks generated by DiffBind that had a significance value < 2×10^-5 was counted as a significant differentially accessible peak. Any peak in the set of peaks generated by DiffBind that had a significance value ≥ 2×10^-5 was counted as a non-significant differentially accessible peak. The set of significant differentially accessible peaks was divided into a set of peaks that were more accessible in the first condition being compared and a set of peaks that were more accessible in the second condition being compared. The two sets of significant differentially accessible peaks were written to a BED file.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Excel spreadsheet files were generated by MACS2.
Supplementary_files_format_and_content: BED files were generated by DiffBind.

source_name: proximal colon epithelial cells

extract_protocol:
Freshly harvested duodenum was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in 3 mM EDTA in PBS for 5 mins, 10 mins and 40 mins at 4 °C (refresh EDTA/PBS every time). The tissue was then violently shaken to release the epithelium from underlying muscular tissue. The intestine pieces were discarded and the supernatant was collected as whole epithelium fraction. 70-μm cell strainer was used to separate the villi and crypt fractions. Villi were collected from the top of a 70-μm cell strainer, while crypts passed through. Cells were pelleted by centrifugation at 170g at 4 °C, and followed by cold PBS wash. Duodenum villi and crypts were treated with pre-warmed 0.25% Trypsin for 8 mins at 37°C on a vortex station, neutralized with 10% FBS, and passed through a 40-μm cell strainer to obtain single cells for ATAC-seq. Whole duodenal epithelium fraction was used for juvenile ATAC-seq samples, whereas isolated duodenal villi and crypts were used for adult and geriatric samples.
Freshly harvested geriatric proximal colon (combined from 2 mice) was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in 5 mM EDTA in PBS for 5 mins, 10 mins and 40 mins at 4 °C (refresh EDTA/PBS every time). The tissue was then violently shaken to release the epithelium from underlying muscular tissue. The muscular intestine pieces were discarded and the supernatant was collected as colon epithelium fraction. Cells were pelleted by centrifugation at 170g at 4 °C, and followed by cold PBS wash. Colon epithelial cells were treated with pre-warmed 0.25% Trypsin for 8 mins at 37°C on a vortex station (speed set between 6 and 7), neutralized with 10% FBS, and passed through a 40-μm cell strainer to obtain single cells for ATAC-seq.
Freshly harvested juvenile (combined from 6 pups)/adult colon (combined from 2 mice) was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in EDTA chelation buffer (43.4 mM sucrose, 54.9 mM D-sorbitol, 0.5 mM DL-dithiothreitol and 2 mM EDTA in PBS) for 1 hour at 4 °C. After PBS wash, the tissue pieces were then rotated in digestion buffer (2.5% FBS, 200 U/ml type IV collagenase and125 μg/ml type II dispase in DMEM) for 2 hours at 37 °C. The tissue was then violently shaken to release the epithelium from underlying muscular tissue. The intestine pieces were discarded and the supernatant was collected as colon epithelium fraction. Cells were pelleted by centrifugation at 300g at 4 °C, and followed by cold PBS wash. Cells were resuspended in MACS buffer (0.5% FBS, 2mM EDTA in PBS), and passed through a 70-μm cell strainer. Cells were stained with the anti-CD326 (EpCAM) magnetic microbeads antibody (Miltenyi Biotec, 130-105-958) for 40 min on ice. To obtain single magnetic antibody conjugated EpCAM positive epithelial cells, stained cells were passed through a 40-μm cell strainer and then collected over a MS column (Miltenyi Biotec, 130-042-201) in a magnetic field. After washing with MACS buffer, EpCAM positive epithelial cells were used for ATAC-seq.
In all cases, 50,000 cells were used for ATAC-seq. Briefly, cells were centrifuged at 500g for 5mins at 4°C, and resuspended in ice-cold lysis buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40), followed by centrifugation at 500 g for 10 minutes at 4°C. The isolated nuclear pellets were incubated with a 50 μl reaction of Nextera Tn5 Transposase (Illumina FC-121-1030) for 30 min at 37°C. The transposed chromatin was purified with QIAquick PCR Purification Kit (QIAGEN) and PCR amplified with high-fidelity 2X PCR Master Mix (New England Biolabs M0541). The optimum number of additional cycles was based on 1/3 of the maximum fluorescent intensity. One sample from the geriatric colon couldn’t be processed due to low amount of DNA recovered. For other samples, the PCR amplified libraries were purified, fragment size was selected using Pippin Prep, and sequenced on Illumina NextSeq 500 cycle mid output.

tag: age at harvesting

value: 21 months

value: Proximal colon epithelial cells


title: Geriatric Proximal Colon ATAC-seq replicate 1

description: OM PC 1


title: Geriatric Crypt ATAC-seq replicate 2

description: OM CRYPT 2

source_name: duodenum crypt cells

value: Duodenum crypt cells


title: Replicate 3 from 21 days post infection, scRNAseq

description: 10x Genomics

value: 8 weeks old + 21 days

value: female


title: Replicate 2 from 21 days post infection, scRNAseq

description: 10x Genomics


title: Geriatric Crypt ATAC-seq replicate 3

description: OM CRYPT 3


title: BaP30_3: BEAS-2B cells induced with BaP lncRNA 3

type: RNA

city: Zhengzhou

first: Zhongqiu

last: Li

state: Henan

address: 100 Kexue Avenue

department: Department of Toxicology

institute: Zhengzhou University

description: lncRNA and mRMA expression data from BEAS-2B cells induced with BaP

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information.

organism: Homo sapiens

source_name: BEAS-2B cells induced with BaP

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol:
Establishment of malignant transformation cell model: BEAS-2B cells were treated with 2.4 μg/mL of CTP extract (30% of the IC50 of 8.11 μg/mL) for 72 hours.4 then passaged, the cells under went the same procedure for another four times, which named passage 1. After removal of CTP extract, the cells were passaged until passage 30. B(a)P (5 mg/mL) was used as the positive control .
HCC and matched non-tumor hepar tissues

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissues from HCC surgury and promptly frozen in liquid nitrogen.

value: Human bronchial epithelial cells (BEAS-2B cells)


title: Replicate 3 from 10 days post infection, scRNAseq

description: 10x Genomics

value: 8 weeks old + 10 days


title: Geriatric Crypt ATAC-seq replicate 1

description: OM CRYPT 1


title: Replicate 2 from 10 days post infection, scRNAseq

description: 10x Genomics


title: CTPE30_2: BEAS-2B cells induced with CTPE lncRNA 2

description: lncRNA and mRMA expression data from BEAS-2B cells induced with CTPE

source_name: BEAS-2B cells induced with CTPE


title: 42

value: Ambient

value: juvenile


title: BaP30_2: BEAS-2B cells induced with BaP lncRNA 2


title: BaP30_1: BEAS-2B cells induced with BaP lncRNA 1


title: Replicate 1 from 10 days post infection, scRNAseq

description: 10x Genomics


title: CTPE30_3: BEAS-2B cells induced with CTPE lncRNA 3


title: HiC-seq Hmga2 wt clone #2

source_name: wt iPSC #2

value: iPSC

tag: treatment


title: Normal2: BEAS-2B cells normal lncRNA 2

description: lncRNA and mRMA expression data from BEAS-2B normal  cells

source_name: BEAS-2B normal  cells


title: B-ALL [P190RagCreErg]

city: Melbourne

first: Goknur

last: Giner

state: VIC

address: 1G Royal Parade

department: Blood Cells and Blood Cancer

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: P190RagCreErg__99_C8HKNANXX_GGCTAC_L005_R1.fastq.gz.subjunc.BAM

data_processing:
Graphpad Prism software version 8.2.0 and  The R Project for Statistical Computing version 4.1.3
Sequence reads were mapped to GrCM38/mm10 using Rsubread version 2.2.6
Read count extraction and CPM normalization were performed using edgeR Bioconductor package version 3.34.15
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM normalised values for each sample

source_name: preB Leukemia

growth_protocol: MEF cells were cultured in DMEM supplemented with 10% FBS and 1 mM L-glutamine at 37C with 10% CO2. Lymphoma cells were cultured in FMA media at 37C with 10% CO2. Leukemia cells were cultured in IMDM media supplemented with 10% FBS with IL7 at 37C with 10% CO2.

extract_protocol:
RNA was harvested using Direct-zol RNA Microprep kit (Zymo Research). 1 ug of total RNA was used for the construction of sequencing libraries. Leukemia sample RNA was harvested using Qiagen RNA kit (Qiagen) and 1 ug of total RNA was used for sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (Illumina) following manufacturer's protocols.

treatment_protocol: No treatment applied.

value: preB Leukemia

value: B cells


title: Geriatric Villi ATAC-seq replicate 3

description: OM VILLI 3

source_name: duodenum villus cells

value: Duodenum villus cells


title: Replicate 1 from 21 days post infection, scRNAseq

description: 10x Genomics

source_name: Liver

value: CD3+ cells

value: Liver


title: 41

source_name: juvenile tissue

value: DRxDR


title: Normal3: BEAS-2B cells normal lncRNA 3


title: 40

value: LSxLS


title: 34

value: Hot


title: B-ALL [P190CreERLSLErg]

description: P190CreERLSLErg__138_C8HKNANXX_TAGCTT_L005_R1.fastq.gz.subjunc.BAM


title: Geriatric Villi ATAC-seq replicate 2

description: OM VILLI 2

value: 21 months


title: Control from day 21, scRNAseq

description: 10x Genomics


title: IFNgR_wt3

city: Lund

first: Bengt

last: Johansson-Lindbom

address: BMC D1421b

department: Adaptive Immunity

country: Sweden

institute: Lund University

data_processing:
Paired-end RNA sequences were processed with AdapterRemoval (v. 2.1.3) setting the minimum quality to 20, minimum length to 25, collapsing reads when possible and removing Nextera adapters
The first seven base pairs were removed them using seqtk (v. 1.0).
For each sample, files with collapsed and singleton reads were aligned to the mouse genome using HISAT2 (v. 2.0.1)
Gene expression profiles were generated using HTSeq (v. 0.11.1)
For each group, genes that had >50 raw counts in >2 samples in either the wildtype- or the knockout condition were included in the analysis. Differential expression analyses were performed in R using the edgeR package.
Normalization factors were calculated using the trimmed mean of M-values (TMM) method. The edgeR general linear model was used for the differential expression analysis. Differentially expressed genes with a false discovery rate of <5% were considered statistically significant.
Assembly: Ensembl GRCm38.84
Supplementary files format and content: Raw counts
Supplementary files format and content: IFNAR processed data
Supplementary files format and content: IFNgR processed data

source_name: Spleen

growth_protocol: BM cells from age matched (8-12 weeks) congenic wt, Ifnar1-/-, or Ifngr1-/- donor mice were isolated and re-suspended in sterile PBS. A 1:1 mixture of wt and Ifnar1-/-, Il27r-/- or Ifngr1-/- BM cells (2-3x10e6 total cells) were transferred into lethally irradiated (900 cGy) recipients (CD45.1+CD45.2+ B6.SJL x C57Bl/6 or CD45.1+B6.SJL). Recipient mice were thereafter kept on Ciprofloxacin for 2 weeks, and left to recover for a total of 8 weeks after BM transfer

extract_protocol:
GC B cells (Live, singlet, B220+Fas+CD38- CD45.1+ or CD45.1-) were sorted from immunized recipients directly into RLT buffer supplemented with 1% -ME. mRNA was extracted with an RNeasy Micro Kit (Qiagen)
Libraries were constructed using standard Illumina protocols

treatment_protocol: Mice were transfered with 5000 OT-II T cells, iv. Mice were then immunized 16h later with 100 ug poly I:C together with 300ug OVA, by intraperitoneal injection. Cells were sorted 8 days after immunization.

value: Germinal Centre B Cells

value: WT

tag: chimeric mouse

value: WT/IFNgR KO


title: Geriatric Villi ATAC-seq replicate 1

description: OM VILLI 1


title: CTPE30_1: BEAS-2B cells induced with CTPE lncRNA 1

value: Human bronchial epithelial cells (BEAS-2B cells)


title: Normal1: BEAS-2B cells normal lncRNA 1


title: Adult Colon ATAC-seq replicate 3

description: D90 COLON 3

source_name: colon epithelial cells

value: 90 days

value: Colon epithelial cells


title: 51

tag: cross

value: Ambient

value: juvenile


title: IFNAR_wt1

value: WT/IFNAR KO


title: P7 cerebellum Eed-deleted rep3

city: Atanta

first: Tim

last: Gershon

state: GA

address: Emory University School of Medicine

department: Pediatrics

institute: Emory University

description: Drop-seq

data_processing:
Raw sequence data were processed in a Linux environment using Drop-seq Tools V1.13. (https://github.com/broadinstitute/Drop-seq/releases) to generate a digital expression (DGE) matrix
alignment: Star aligner was used version 2.5.4a
DGE creation: We first convert Fastq to BAM/SAM format and merge samples that were sequenced across multiple lanes.
full downstream pipeline code: https://github.com/malawsky/Gershon_single-cell
Assembly: Genome_build: mm10 genome
Supplementary files format and content: Supplementary_files_format_and_content: digital expression matrix

source_name: cerebellum

growth_protocol: see SAMPLES

extract_protocol:
Brains were cut in half sagittally and drop-fixed in 4% paraformaldehyde for IHC, and half cerebellum or tumor collected for Drop-Seq.Cells were dissociated using the Papain Dissociation System (Worthington Biochemical) according to the manufacturer’s protocol, as in our prior studies. https://www.nature.com/articles/s41467-019-13657-6#Sec18.
Drop-Seq 3' biased cell-indexed cDNA libraries were prepared according to the Drop-seq protocol V3.1 (ref. 32), with full details available online (http://mccarrolllab.com/dropseq/). Cell and bead concentrations were both set to between 95 and 110/μL.  to high-throughput sequencing facility that does their own QC before running samples.  cDNA libraries were prepared for sequencing using standard Illumina protocols (Multiplexed samples using nextera indexes so that libraries could be pooled)

treatment_protocol: see SAMPLES

value: cerebellum

value: Math1-Cre/Eed fl/fl


title: Adult Colon ATAC-seq replicate 2

description: D90 COLON 2


title: 60

value: SBxSB

tag: temperature treatment


title: Control from day 48, scRNAseq

description: 10x Genomics

value: CD3+ cells

value: Liver

value: 8 weeks old + 48 days

value: female


title: P7 cerebellum Eed-deleted rep2

description: Drop-seq


title: IFNgR_wt2


title: 33

value: Hot

tag: life-stage


title: Adult Colon ATAC-seq replicate 1

description: D90 COLON 1


title: Adult Crypt ATAC-seq replicate 3

description: D90 CRYPT 3

value: Duodenum crypt cells


title: IFNgR_wt1

value: Germinal Centre B Cells

value: WT


title: Adult Crypt ATAC-seq replicate 2

description: D90 CRYPT 2


title: 23

value: CUxCU

tag: symbiont

value: SED


title: IFNAR_ko3

tag: genotype

value: IFNAR KO


title: 24

value: Ambient


title: Control from day 10, scRNAseq

description: 10x Genomics

value: 8 weeks old + 10 days


title: IFNAR_ko4

value: WT/IFNAR KO


title: 22

value: juvenile


title: Adult Crypt ATAC-seq replicate 1

description: D90 CRYPT 1

value: 90 days


title: 21


title: IFNAR_ko2


title: 20


title: IFNgR_ko2

value: IFNgR KO

value: WT/IFNgR KO


title: Adult Villi ATAC-seq replicate 2

description: D90 VILLI 2

value: Duodenum villus cells


title: IFNgR_ko3


title: IFNAR_wt2


title: 19


title: IFNgR_ko1


title: Juvenile Colon ATAC-seq replicate 3

description: P15 COLON 3

value: 15 days

value: Colon epithelial cells


title: P7 cerebellum Eed-deleted rep1

description: Drop-seq

value: cerebellum

value: Math1-Cre/Eed fl/fl


title: Adult Villi ATAC-seq replicate 1

description: D90 VILLI 1


title: 18


title: IFNAR_wt4

value: Germinal Centre B Cells


title: 17


title: 16


title: 15

value: SS


title: Juvenile Colon ATAC-seq replicate 2

description: P15 COLON 2


title: enos_nn_db_np_t_9

first: Jennifer

last: Harder

state: Michigan

address: 1150 W. Medical Center Drive

department: Division of Nephrology

institute: The University of Michigan

data_processing:
FastQC
FastqScreen
fastx: clip front 14 bp: fastx_trimmer -Q33 -f 14
tophat:  -M -z0  --b2-very-sensitive
Cufflinks/merge/norm
Genome_build: GRCm37.2
Supplementary_files_format_and_content: gene expression abundance estimation generated by cuffnorm. GSE141680 samples are included.

source_name: eNOS-/-//db/+ treated

extract_protocol:
RNeasy Mini
TruSeq mRNA Sample Prep v2

value: kidney

value: yes


title: RNA-seq Hmga2 KO clone #2 24h biol rep 1

data_processing:
DESeq2
Supplementary files format and content: counts

extract_protocol: Total RNA was extracted using Tri-Sure, according to the manufacturer’s protocol. Full-length first cDNA strand was synthetized by RevertAid Reverse Transcriptase. RNA concentration and purity was determined using Nanodrop 2000c.

tag: time

value: iPSC

value: Hmga2 KO

value: induced into EpiLC


title: Adult Villi ATAC-seq replicate 3

description: D90 VILLI 3


title: Juvenile Colon ATAC-seq replicate 1

description: P15 COLON 1


title: RNA-seq Hmga2 KO clone #2 24h biol rep 2


title: RNA-seq Hmga2 KO clone #2 24h biol rep 3


title: enos_nn_db_np_t_8

tag: tissue


title: Juvenile Duodenum ATAC-seq replicate 2

description: P12 DUO 2

source_name: duodenum epithelial cells

value: 12 days

value: Duodenum epithelial cells


title: Juvenile Duodenum ATAC-seq replicate 1

description: P12 DUO 1


title: RNA-seq Hmga2 KO clone #1 24h biol rep 2

source_name: Hmga2 KO iPSC #1


title: enos_nn_db_np_t_7


title: 14

value: CUxCU

value: Ambient

value: juvenile


title: RNA-seq Hmga2 KO clone #1 24h biol rep 3


title: 13


title: Contralateral_eGFP_neg, Mouse_3

city: San Francisco

first: Ilia

middle: D.

last: Vainchtein

state: California

address: 1550 4th street

department: Psychiatry

institute: UCSF

data_processing:
QC with FastQC (all samples passed)
Pseudoaligned and counted reads using Kallisto (version 0.44.0) with kmer size 31 and bootstraps set to 100
DEGs calculated using DESeq2 (version 1.24.0).
TPM values per gene were calculated using DESeq2 (version 1.24.0) from the per isoform TPM values generated by Kallisto (version 0.44.0).
Assembly: GRCm38, mm10
Supplementary files format and content: excel, TPMs of all genes for each sample

source_name: VB Thalamus

extract_protocol:
Astrocytes were isolated from VB thalamus using papaine and 22% Percoll gradient, all on ice or 4C, and collected with FACS.
Nugen Ovation RNA-Seq System V2 kit

treatment_protocol: AAV2/5-Gfa104-eGFP was unilateral injected into VB thalamus and astrocytes were isolated three weeks later.

value: contralateral

value: VB Thalamus

tag: gender

value: male

value: Astrocytes


title: enos_nn_db_np_t_6


title: Contralateral_eGFP_neg, Mouse_2


title: 98_3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Acropora millepora genome (v2.01) using bowtie2(v.2.2.9) --local --no-hd --no-sq --no-unal -k 5
gene counts were compiled using a custom perl script enabling samcounts. Script found at https://github.com/z0on/tag-based_RNAseq
Genome_build: Acropora millepora genome (v2.01)
Supplementary_files_format_and_content: txt files including gene counts values for each sample
Supplementary_files_format_and_content: VCF files for SNP calls

source_name: larval tissue

extract_protocol:
RNAqueous kit (Ambion)
tag-seq: https://github.com/z0on/tag-based_RNAseq

value: DRxSB

value: Pre

value: larval


title: RNA-seq Hmga2 KO clone #1 24h biol rep 1


title: enos_nn_db_np_t_5

value: kidney


title: IFNAR_wt3

value: Germinal Centre B Cells

value: WT

value: WT/IFNAR KO


title: 98_2


title: Juvenile Duodenum ATAC-seq replicate 3

description: P12 DUO 3


title: RNA-seq Hmga2 wt 24h biol rep 3

source_name: wt iPSC #1

value: iPSC

value: induced into EpiLC


title: Contralateral_eGFP_neg, Mouse_1


title: 98_1


title: enos_nn_db_np_t_4

value: yes


title: Ipsilateral_eGFP_pos, Mouse_3

value: ipsilateral


title: RNA-seq Hmga2 wt 24h biol rep 2


title: enos_nn_db_np_t_3


title: Ipsilateral_eGFP_neg, Mouse_3


title: 89_2

value: Hot


title: Ipsilateral_eGFP_neg, Mouse_2


title: RNA-seq Hmga2 KO clone #2 0h biol rep 3

source_name: Hmga2 KO iPSC #2

value: Hmga2 KO


title: enos_nn_db_np_t_1


title: RNA-seq Hmga2 KO clone #2 0h biol rep 1


title: Ipsilateral_eGFP_pos, Mouse_2


title: Ipsilateral_eGFP_neg, Mouse_1


title: enos_nn_db_np_t_0


title: 82_1

value: SBxSB


title: RNA-seq Hmga2 KO clone #2 0h biol rep 2


title: 82_2


title: RNA-seq Hmga2 KO clone #1 0h biol rep 3


title: RNA-seq Hmga2 KO clone #1 0h biol rep 2


title: enos_nn_db_np_nt_9

source_name: eNOS-/-//db/+ non-treated

value: no


title: Ipsilateral_eGFP_pos, Mouse_1

value: VB Thalamus

value: male


title: enos_nn_db_np_nt_8


title: enos_nn_db_np_t_2


title: RNA-seq Hmga2 wt 24h biol rep 1


title: 89_3

value: DRxSB


title: 79_3

value: SBxBK

value: Pre


title: RNA-seq Hmga2 KO clone #1 0h biol rep 1


title: 79_2

value: larval


title: RNA-seq Hmga2 wt 0h biol rep 3


title: enos_nn_db_np_nt_7

value: kidney


title: enos_nn_db_np_nt_6


title: null_cocaine_FosB_control_rep2

city: New York

first: Eric

last: Nestler

state: NY

address: 1425 Madison Ave L10-26

institute: Icahn School of Medicine at Mount Sinai

description:
CKOC2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

data_processing:
The NGS-Data-Charmer pipeline (Github commit date: June 18, 2020) was used for preprocessing, QC, and alignment of the dataset. Read alignment was performed with Bowtie2 (v2.4.1) (--dovetail --phred33) to the mm10 genome. Duplicated read pairs were subsequently removed using the samtools (v1.10) ‘rmdup’ module.
For generating combined bigwig files, bam files were merge using samtools  ‘merge’ module and corresponding index files were created using samtools ‘index’ module; bigwig files were then generated using Deeptools ‘bamCoverage’ module (bamCoverage --extendReads --ignoreDuplicates --centerReads --normalizeUsing CPM --binSize 10)
For each biological replicate and corresponding IgG control, peaks were called with MACS2 (v2.2.6) (macs2 callpeak -f BAMPE --pvalue 0.05 --keep-dup) and filtered through Irreproducible Discovery Rate (IDR) (v2.0.4.2) using 1% IDR threshold for bulk NAc datasets and 5% IDR threshold for NAc D1- and D2-MSN datasets. IDR output for each group were combined with Bedtools41 (v2.29.2) ‘merge’ module and the output containing high confidence peaks were utilized for further analysis.
Supplementary_files_format_and_content: combined bigwig files
Supplementary_files_format_and_content: peak text files

source_name: nucleus accumbens

extract_protocol:
Nuclei were prepared through discontinuous sucrose gradient centrifugation, isolated through INTACT approach, and subject to CUT&RUN procedures.
Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645, New England BioLabs) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (E7600S, New England BioLabs) based on manufacture instructions.

treatment_protocol: For IP-injection, animals received consecutive 7-day saline or cocaine injection. For self-administration, animals underwent 10-day 2hr per day introvenous self-administration.

value: Sox2-Cre; Fosb-flox/flox

value: bulk

tag: Sex

value: cocaine

tag: antibody

value: IgG (2729, Cell Signaling)

tag: administration

value: IP-injection


title: null_cocaine_FosB_control_rep3

description:
CKOC3C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 89_1


title: null_cocaine_FosB_control_rep1

description:
CKOC1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 82_3


title: 79_1


title: RNA-seq Hmga2 wt 0h biol rep 2

value: iPSC

value: WT

value: induced into EpiLC


title: enos_nn_db_np_nt_4


title: null_saline_FosB_control_rep2

description:
CKOS2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline


title: RNA-seq Hmga2 wt 0h biol rep 1


title: 69_3

value: LSxSB


title: null_cocaine_FosB_rep3

description:
CKOC3F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: FosB (2251, Cell Signaling)


title: 69_1


title: 69_2


title: enos_nn_db_np_nt_2

value: no


title: enos_nn_db_np_nt_5


title: 62_2

value: CUxBK


title: enos_nn_db_np_nt_0


title: 62_3


title: null_saline_FosB_control_rep1

description:
CKOS1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: female_cocaine_D2_H3K27me3_rep2

description:
FC2D2K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: female

value: H3K27me3 (9733, Cell Signaling)


title: female_cocaine_D2_H3K27ac_rep3

description:
FC3D2K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K27ac (ab4729, Abcam)


title: enos_nn_db_np_nt_1

value: kidney


title: null_cocaine_FosB_rep2

description:
CKOC2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: Sox2-Cre; Fosb-flox/flox

value: bulk

value: cocaine


title: female_cocaine_D2_H3K27ac_rep2

description:
FC2D2K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: enos_pp_db_pp_t_10

source_name: eNOS+/+//db/db treated

value: eNOS+/+//db/db

value: yes


title: 62_1

value: Pre

value: larval


title: female_cocaine_D2_H3K27me3_rep1

description:
FC1D2K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: flox_cocaine_FosB_control_rep3

description:
WTC3C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: Fosb-flox/+

value: IgG (2729, Cell Signaling)


title: null_saline_FosB_rep1

description:
CKOS1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline

value: FosB (2251, Cell Signaling)


title: null_cocaine_FosB_rep1

description:
CKOC1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: enos_pp_db_pp_t_9


title: female_cocaine_D2_H3K27ac_rep1

description:
FC1D2K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: female


title: 55_3

value: LSxCU


title: null_saline_FosB_rep2

description:
CKOS2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 55_2


title: flox_cocaine_FosB_control_rep2

description:
WTC2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: enos_pp_db_pp_t_8

value: kidney


title: female_cocaine_D2_H3K27me3_rep3

description:
FC3D2K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K27me3 (9733, Cell Signaling)


title: flox_cocaine_FosB_control_rep1

description:
WTC1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: bulk


title: female_cocaine_D2_H3K4me3_rep2

description:
FC2D2K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: cocaine

value: H3K4me3 (13-0041, EpiCypher)


title: enos_pp_db_pp_t_6

value: eNOS+/+//db/db


title: enos_pp_db_pp_t_7

value: yes


title: 55_1

value: Pre


title: flox_saline_FosB_control_rep2

description:
WTS2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: female_cocaine_D2_H3K4me3_rep3

description:
FC3D2K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 38_3

value: LSxLS

value: larval


title: female_cocaine_D2_H3K4me1_rep3

description:
FC3D2K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K4me1 (ab8895, Abcam)


title: enos_pp_db_pp_t_5


title: enos_pp_db_pp_t_4


title: flox_saline_FosB_control_rep1

description:
WTS1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: Fosb-flox/+

value: saline

value: IgG (2729, Cell Signaling)


title: 38_1


title: flox_cocaine_FosB_rep3

description:
WTC3F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male

value: FosB (2251, Cell Signaling)


title: female_cocaine_D2_H3K4me1_rep1

description:
FC1D2K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: female


title: female_cocaine_D2_H3K4me3_rep1

description:
FC1D2K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: female_cocaine_D2_H3K4me1_rep2

description:
FC2D2K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: enos_pp_db_pp_t_2

value: kidney


title: 33_2

value: CUxCU


title: flox_cocaine_FosB_rep1

description:
WTC1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: bulk

value: cocaine


title: flox_cocaine_FosB_rep2

description:
WTC2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: enos_pp_db_pp_t_3

value: eNOS+/+//db/db

value: yes


title: female_cocaine_D2_histone_control_rep3

description:
FC3D2HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: enos_pp_db_pp_t_1


title: female_cocaine_D2_histone_control_rep2

description:
FC2D2HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: flox_saline_FosB_rep2

description:
WTS2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 33_1

value: Pre


title: 38_2

value: LSxLS

value: larval


title: 33_3


title: male_cocaine_IP_FosB_control_rep3

description:
MC6C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: female_saline_D2_H3K27me3_rep3

description:
FS3D2K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K27me3 (9733, Cell Signaling)


title: female_cocaine_D2_histone_control_rep1

description:
FC1D2HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: enos_pp_db_pp_t_0


title: 187_2

value: Ambient


title: enos_pp_db_pp_nt_6

source_name: eNOS+/+//db/db non-treated

value: no


title: enos_nn_db_np_nt_3


title: enos_pp_db_pp_nt_4


title: 178_3

value: SBxBK


title: female_saline_D2_H3K27me3_rep1

description:
FS1D2K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline


title: flox_saline_FosB_rep1

description:
WTS1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: Fosb-flox/+

value: male

value: FosB (2251, Cell Signaling)


title: male_cocaine_IP_FosB_control_rep2

description:
MC5C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: IgG (2729, Cell Signaling)


title: 178_1


title: 178_2


title: enos_pp_db_pp_nt_2

value: kidney


title: male_cocaine_IP_FosB_control_rep1

description:
MC4C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: bulk

value: cocaine


title: enos_pp_db_pp_nt_3

value: eNOS+/+//db/db


title: female_saline_D2_H3K27ac_rep3

description:
FS3D2K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: female

value: H3K27ac (ab4729, Abcam)

value: IP-injection


title: female_saline_D2_H3K27ac_rep2

description:
FS2D2K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: female_saline_D2_H3K27ac_rep1

description:
FS1D2K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: enos_pp_db_pp_nt_5


title: enos_pp_db_pp_nt_1


title: 175_3

value: DRxDR

value: larval


title: male_saline_IP_FosB_control_rep2

description:
MS5C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 187_3

value: CUxCU

value: Ambient


title: 187_1


title: male_saline_IP_FosB_control_rep1

description:
MS4C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline


title: enos_pp_db_pp_nt_0

value: no


title: 175_2


title: enos_pp_db_np_t_9

source_name: eNOS+/+//db/+ treated

value: yes


title: male_cocaine_IP_FosB_rep3

description:
MC6F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male

value: FosB (2251, Cell Signaling)


title: female_saline_D2_H3K4me3_rep3

description:
FS3D2K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: H3K4me3 (13-0041, EpiCypher)


title: enos_pp_db_np_t_8

value: kidney


title: female_saline_D2_H3K27me3_rep2

description:
FS2D2K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K27me3 (9733, Cell Signaling)


title: 175_1


title: female_saline_D2_H3K4me3_rep2

description:
FS2D2K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 168_3

value: LSxLS


title: male_cocaine_IP_FosB_rep2

description:
MC5F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: bulk

value: cocaine


title: male_saline_IP_FosB_control_rep3

description:
MS6C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IgG (2729, Cell Signaling)

value: IP-injection


title: female_saline_D2_H3K4me3_rep1

description:
FS1D2K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: female


title: enos_pp_db_np_t_7


title: female_saline_D2_H3K4me1_rep3

description:
FS3D2K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K4me1 (ab8895, Abcam)


title: 168_2

value: Ambient

value: larval


title: enos_pp_db_np_t_6


title: female_saline_D2_H3K4me1_rep2

description:
FS2D2K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline


title: 168_1


title: male_saline_IP_FosB_rep2

description:
MS5F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: enos_pp_db_np_t_5

value: yes


title: 167_3

value: SBxSB


title: male_saline_IP_FosB_rep1

description:
MS4F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male

value: FosB (2251, Cell Signaling)


title: enos_pp_db_np_t_4


title: female_saline_D2_H3K4me1_rep1

description:
FS1D2K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: female_saline_D2_histone_control_rep3

description:
FS3D2HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_cocaine_SA_FosB_control_rep3

description:
MC3C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: Self-administration


title: 167_2


title: 167_1


title: enos_pp_db_np_t_3

value: kidney


title: male_cocaine_IP_FosB_rep1

description:
MC4F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: female_saline_D2_histone_control_rep1

description:
FS1D2HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 166_3

value: CUxCU

value: Hot


title: male_cocaine_SA_FosB_control_rep2

description:
MC2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: bulk

value: cocaine


title: female_saline_D2_histone_control_rep2

description:
FS2D2HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IgG (2729, Cell Signaling)

value: IP-injection


title: male_cocaine_SA_FosB_control_rep1

description:
MC1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: enos_pp_db_np_t_0


title: male_saline_IP_FosB_rep3

description:
MS6F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 166_2


title: male_saline_SA_FosB_control_rep3

description:
MS3C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_cocaine_D2_H3K27me3_rep3

description:
MC3D2K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K27me3 (9733, Cell Signaling)


title: enos_pp_db_np_t_1


title: 166_1


title: male_cocaine_D2_H3K27me3_rep2

description:
MC2D2K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_saline_SA_FosB_control_rep2

description:
MS2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 163_3

value: CUxBK


title: male_cocaine_D2_H3K27me3_rep1

description:
MC1D2K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_saline_SA_FosB_control_rep1

description:
MS1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 163_2

value: larval


title: enos_pp_db_np_nt_8

source_name: eNOS+/+//db/+ non-treated

value: no


title: male_cocaine_D2_H3K27ac_rep3

description:
MC3D2K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K27ac (ab4729, Abcam)


title: enos_pp_db_np_nt_7


title: 163_1


title: male_cocaine_D2_H3K27ac_rep2

description:
MC2D2K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_cocaine_SA_FosB_rep1

description:
MC1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_cocaine_SA_FosB_rep3

description:
MC3F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_cocaine_SA_FosB_rep2

description:
MC2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: enos_pp_db_np_t_2

value: yes


title: male_cocaine_D2_H3K27ac_rep1

description:
MC1D2K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: enos_pp_db_np_nt_6


title: 161_3

value: DRxSB

value: Ambient


title: enos_pp_db_np_nt_5


title: male_cocaine_D2_H3K4me3_rep3

description:
MC3D2K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: H3K4me3 (13-0041, EpiCypher)


title: enos_pp_db_np_nt_3

value: kidney


title: male_saline_SA_FosB_rep3

description:
MS3F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline

value: FosB (2251, Cell Signaling)

value: Self-administration


title: enos_pp_db_np_nt_9


title: 161_2


title: enos_pp_db_np_nt_4


title: 161_1


title: male_cocaine_D2_H3K4me3_rep2

description:
MC2D2K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: cocaine


title: male_saline_SA_FosB_rep2

description:
MS2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: bulk


title: enos_pp_db_np_nt_2


title: male_cocaine_D2_H3K4me3_rep1

description:
MC1D2K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: male_saline_SA_FosB_rep1

description:
MS1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 16_2

value: CUxSB

value: Pre


title: male_cocaine_D2_H3K4me1_rep3

description:
MC3D2K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K4me1 (ab8895, Abcam)


title: male_cocaine_D2_H3K4me1_rep2

description:
MC2D2K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: enos_pp_db_np_nt_1

value: no


title: enos_pp_db_np_nt_0


title: M-liver-23

city: Nanjing

first: Jun

last: Liu

address: Longmiandadao

institute: CPU

description: after tail vein injection, obese mice were termed as treatment

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, the reads were  mapped to the mouse genome (mm10) using tophat2 by requiring 3 edit distance (mismatch+indel) at maximum
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using HTSeq
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include gene ID and expression level in reads count for each sample

source_name: Liver

growth_protocol: 8-week old of C57BL/6J male mice (bought from Beijing Vital River Laboratory Animal Technology Co., Ltd, China) were maintained at a 12 h light and 12 h dark cycle in a temperature/humanity-controlled and specific pathogen free environment. To establish the model, mice had free access to high-fat diet (Research Diet, D12492, USA) for 2 weeks at the same time of adenovirus injection.

extract_protocol:
Total RNA was extracted with RNAiso Plus (TaKaRa) from mice livers.
A cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq4000 by a 2X150 bp run.

treatment_protocol: Male, 8-week old, C57BL/6J mice were injected adenovirus via tail vein and fed with high-fat diet at the same time. Two weeks later, mice were sacrificed and sample were collected.

tag: strain

tag: diet

value: high fat

value: liver

tag: injected with

value: Chrna4-overexpressing adenovirus


title: M-liver-25

value: male


title: 158_3

value: Ambient

value: larval


title: enos_nn_db_pp_t_6

data_processing:
CASAVA_v1.8.2
Seqtk trimfq: trim first 13 bp
FastQC
read level QC
fastq_screen
detection of non-target sequences
Tophat 2.0.8
--b2-very-sensitive
cufflinks/cuffdiff v2.2.1
Genome_build: GRCm 37.2
Supplementary_files_format_and_content: Cufflinks normalized abundance measurements (FPKM)

source_name: kidney

extract_protocol:
At the time of euthanasia, kidney and dorsal root ganglia (DRG) were rapidly extracted and glomeruli were harvested from one kidney. At the time of euthanasia, glomeruli from diabetic and control mice were iron-perfused and magnetically solated. Total glomerular RNA was obtained using the RNeasy Mini Kit. Total RNA was isolated and RNA quality was assessed using TapeStation. Samples with RNA quality >=8 were further processed.
Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS-122-2001, RS-122-2002; Illumina, San Diego, CA)

treatment_protocol: Mice were fed a standard diet. Approximately, half of the mice in each genotype were treated with a combination of lisinopril 20 mg/day and losartan 30 mg/day, mixed in drinking water, from 10-12 wks to 26 wks of age.

value: eNOS-/-//db/db

tag: agent

value: RAAS blocking drug


title: 16_3


title: M-liver-21


title: male_cocaine_D2_histone_control_rep2

description:
MC2D2HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

tag: cell type

tag: treatment

value: IgG (2729, Cell Signaling)


title: 158_2

tag: cross


title: 158_1

tag: temperature treatment


title: male_cocaine_D2_histone_control_rep3

description:
MC3D2HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: cocaine


title: 154_3

value: LSxCU

tag: life-stage


title: enos_nn_db_pp_t_3


title: enos_nn_db_pp_t_5


title: male_cocaine_D2_histone_control_rep1

description:
MC1D2HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: enos_nn_db_pp_t_4


title: male_saline_D2_H3K27me3_rep3

description:
MS3D2K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline

value: H3K27me3 (9733, Cell Signaling)


title: M-liver-20

description: after tail vein injection, obese mice were termed as control

value: vehicle


title: 154_2

tag: symbiont


title: 154_1


title: M-liver-18


title: 16_1

value: CUxSB

value: Pre


title: enos_nn_db_pp_t_2

tag: genotype


title: male_saline_D2_H3K27me3_rep2

description:
MS2D2K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_cocaine_D2_H3K4me1_rep1

description:
MC1D2K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K4me1 (ab8895, Abcam)


title: enos_nn_db_pp_t_1


title: 152_3

value: Hot


title: male_saline_D2_H3K27me3_rep1

description:
MS1D2K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: AGS_sh_IGFBP7

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: File include Count and  FPKM values for each sample

source_name: AGS

growth_protocol: The gastric cancer cell line AGS was cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: IGFBP7-depleted AGS cells were seeded into 6-well plates. When the cell plating density reached 90%, cells were harvested for RNA sequencing.

tag: cell line

value: AGS

value: gastric cancer cell

value: Knockdown


title: M-liver-22

value: high fat

tag: tissue

value: liver


title: male_saline_D2_H3K27ac_rep3

description:
MS3D2K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: H3K27ac (ab4729, Abcam)


title: enos_nn_db_pp_t_0

city: Ann Arbor

value: eNOS-/-//db/db

value: RAAS blocking drug


title: 152_1

city: Auburn

first: Marie

last: Strader

address: 101 Rouse Life Sciences, Biological Sciences Department

institute: Auburn University

value: LSxCU

value: larval


title: 152_2


title: MDA436_sh29_r2

first: Yadi

last: Wu

state: KY

address: 741 S. Limestone

department: Department of Pharmaceutical Sciences

institute: the University of Kentucky

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 hg38 whole genome using Hisat2.
Reads were counted using featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MDA-MB-436_EFB1 shRNA

extract_protocol:
Total RNA was isolated using Purelink RNA Mini Kit (ThermoFisher).
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (cat# E7760S) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols on Hiseq 4000 platform.

value: human triple-negative breast cancer cells

value: EFB1 shRNA


title: enos_nn_db_pp_nt_8

value: non-treated


title: 150_3

value: LSxSB

value: Ambient


title: enos_nn_db_pp_nt_7


title: male_saline_D2_H3K27ac_rep2

description:
MS2D2K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male

value: saline

value: IP-injection


title: MDA436_ctrl_r3

value: control


title: 150_2


title: MDA436_sh29_r1


title: male_saline_D2_H3K27ac_rep1

description:
MS1D2K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_saline_D2_H3K4me3_rep3

description:
MS3D2K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K4me3 (13-0041, EpiCypher)


title: enos_nn_db_pp_nt_6


title: MDA436_ctrl_r2


title: male_saline_D2_H3K4me3_rep2

description:
MS2D2K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: MDA436_ctrl_r1


title: 150_1


title: AGS_NC

value: AGS

value: gastric cancer cell

value: Negative control


title: enos_nn_db_pp_nt_4

value: eNOS-/-//db/db


title: MDA157_sh29_r3

source_name: MDA-MB-157_EFB1 shRNA


title: MDA436_sh29_r3


title: male_saline_D2_H3K4me3_rep1

description:
MS1D2K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: 144_2

value: CUxBK


title: enos_nn_db_pp_nt_3


title: enos_nn_db_pp_nt_2


title: MDA157_sh29_r2


title: male_saline_D2_H3K4me1_rep3

description:
MS3D2K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K4me1 (ab8895, Abcam)


title: 144_1

value: larval


title: male_saline_D2_H3K4me1_rep1

description:
MS1D2K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: MDA157_ctrl_r3

value: human triple-negative breast cancer cells


title: MDA157_sh29_r1

value: EFB1 shRNA


title: enos_nn_db_pp_nt_1

value: non-treated


title: enos_nn_db_pp_nt_0


title: 14_2

value: DRxDR

value: Pre


title: MDA157_ctrl_r2


title: 144_3

value: Ambient


title: enos_nn_db_pp_nt_5


title: male_saline_D2_histone_control_rep2

description:
MS2D2HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male

value: saline

value: IgG (2729, Cell Signaling)

value: IP-injection


title: 132_3

value: CUxSB

value: Hot


title: male_saline_D2_histone_control_rep3

description:
MS3D2HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: MDA157_ctrl_r1

value: control


title: MDA157_nor_r2_Input

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 using hg38 genome reference.
PCR duplicates and low mapping score reads were removed before peak calling.
Peaks were called using MASC2 and peaks overlap with ENCODE Blacklist were removed.
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

extract_protocol:
Lysates were clarified from Mnase digested chromatin and transcriptioin factor-DNA complexes were isolated with antibody.
Libraries were prepared according to NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645). Briefly, DNA was end-repaired. After adapter ligation DNA was PCR amplified with Illumina primers for 8-10 cycles and library fragments of ~250 bp were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

tag: chip antibody

value: normoxia

value: human triple-negative breast cancer cell


title: day 9- cells treated by RA+BMP4 between day 3-5  [M9-Rep2]

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

data_processing:
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using mm10 RefSeq as reference
Removal of low expressed transcripts (minimum of 5 counts for at 10 samples)
Normalization by TMM, regressed for PC1, PC2 and PC3 from picard QC matrix
mm10
Supplementary_files_format_and_content: Significant_geneList_FDR0.1_EdgeR.csv

growth_protocol: mESCs were differentiated as adherant cultures in triplicates under bFGF/CHIR for the first two days to direct NMPs, and then treated with different combinations of RA+BMP4. Differentiations were terminated at day 9 when neuronal morphology was apparent in some samples.

extract_protocol:
At each timepoints, cells were washed with 1X PBS and then cell lysate was collected with RLT buffer (Qiagen). Total RNA was extracted using Rneasy mini kit (Qiagen)
Libraries were constructed with Universal plus mRNA sequencing kit (NuGEN) and sequenced onto 2 lanes of NovaseqS1 to generate 30 million reads/sample.

treatment_protocol: mESC-derived NMPs were treated with three conditions- (1) 100nM RA for 48 hrs between day 3-day 4 (R-conditions) (2) 100nM RA for 24hrs (day 3-day4) followed by 24hr pulse of 100nM RA+ 10ng/ml BMP4 (day 4-day5, B-conditions), (3) combined treatment of 100nM RA+10ng/ml BMP4 for 48 hrs (day3-day 5, C-conditions)

tag: time point

value: day 9

value: mESCs


title: 14_1

value: larval


title: day 9- cells treated by RA+BMP4 between day 3-5  [M9-Rep1]


title: day 9- cells treated by RA+BMP4 between day 3-5  [M9-Rep3]


title: female_cocaine_D1_H3K27me3_rep3

description:
FC3D1K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

tag: Sex

value: female

value: cocaine

tag: antibody

value: H3K27me3 (9733, Cell Signaling)


title: 132_2


title: day 9- cells treated by RA-> BMP4 sequence between day 3-5  [B9-Rep3]


title: MDA157_nor_r1_Input


title: day 9- cells treated by RA-> BMP4 sequence between day 3-5  [B9-Rep2]


title: male_saline_D2_H3K4me1_rep2

description:
MS2D2K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K4me1 (ab8895, Abcam)

tag: administration


title: MDA157_nor_r2_EBF1


title: 132_1


title: female_cocaine_D1_H3K27me3_rep2

description:
FC2D1K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 131_3

value: BKxBK

value: Ambient


title: 14_3

value: DRxDR

value: Pre


title: female_cocaine_D1_H3K27me3_rep1

description:
FC1D1K27M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: 131_2


title: day 9- cells treated by RA-> BMP4 sequence between day 3-5  [B9-Rep1]


title: female_cocaine_D1_H3K27ac_rep3

description:
FC3D1K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K27ac (ab4729, Abcam)


title: MDA157_nor_r1_EBF1


title: MDA157_hyp_r2_HIF1A

value: hypoxia


title: MDA157_hyp_r2_Input


title: 131_1


title: male_saline_D2_histone_control_rep1

description:
MS1D2HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male

value: saline

value: IgG (2729, Cell Signaling)


title: female_cocaine_D1_H3K27ac_rep2

description:
FC2D1K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 13_2

value: Hot


title: MDA157_hyp_r1_Input

value: human triple-negative breast cancer cell


title: MDA157_hyp_r2_EBF1


title: 13_3

value: larval


title: day 9- only RA treated cells between day 3-5  [R9-Rep1]

value: day 9

value: mESCs


title: day 9- only RA treated cells between day 3-5  [R9-Rep2]


title: female_cocaine_D1_H3K27ac_rep1

description:
FC1D1K27A
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: female

value: cocaine


title: female_cocaine_D1_H3K4me3_rep1

description:
FC1D1K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K4me3 (13-0041, EpiCypher)


title: day 7- cells treated by RA+BMP4 between day 3-5  [M7-Rep1]

value: day 7


title: female_cocaine_D1_H3K4me3_rep3

description:
FC3D1K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: day 7- cells treated by RA+BMP4 between day 3-5  [M7-Rep3]


title: female_cocaine_D1_H3K4me3_rep2

description:
FC2D1K4M3
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: day 7- cells treated by RA+BMP4 between day 3-5  [M7-Rep2]


title: MDA157_hyp_r1_HIF1A


title: 13_1

value: BKxBK


title: 124_3

value: LSxLS


title: MDA157_hyp_r1_EBF1


title: 124_2


title: day 9- only RA treated cells between day 3-5  [R9-Rep3]


title: female_cocaine_D1_H3K4me1_rep3

description:
FC3D1K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: H3K4me1 (ab8895, Abcam)

value: IP-injection


title: 107_3

value: Pre


title: female_cocaine_D1_H3K4me1_rep1

description:
FC1D1K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: day 7- cells treated by RA-> BMP4 sequence between day 3-5  [B7-Rep3]


title: female_cocaine_D1_H3K4me1_rep2

description:
FC2D1K4M1
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 124_1


title: day 7- cells treated by RA-> BMP4 sequence between day 3-5  [B7-Rep2]


title: female_cocaine_D1_histone_control_rep3

description:
FC3D1HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: day 7- cells treated by RA-> BMP4 sequence between day 3-5  [B7-Rep1]


title: female_cocaine_D1_histone_control_rep2

description:
FC2D1HC
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 107_2


title: NR_6

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

description: Non-reverant

data_processing:
Illumina for basecalling
The sequences were trimmed using trim_galore 0.4.1 and cutadapt 1.15  with cutoff 20
The sequences were aligned using Bismark (version 0.19.0) with default options.The deduplicate_bismark function in Bismark with default parameters was used to remove duplicated reads, and reads with  coverage greater than 500 were removed to control PCR bias.
tab-delimited file generated with bismark2bedGraph with options -CX --ample_memory
Genome_build: Arabidopsis TAIR 10
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>fields

organism: Arabidopsis thaliana

growth_protocol: Seeds were sown on peat mix in square pots in reach-in chambers at 12hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light)

extract_protocol:
genomic DNA extraction using DNeasy Plant kit (Qiagen, Germany).
Genomic DNA Sonicated to 100-300 bp fragments and purified with MiniElute PCR Purification Kit (Qiagen, Germany), incubated at 20 ℃ after add End Repair Mix. Then purified and added a single ‘A’ nucleotide to the 3’ ends of the blunt fragments, purified again and add Methylated Adapter to the 5’ and 3’ ends of each fragment. Then fragments with 300bp-400bp size-range were purified with QIAquick Gel Extraction kit (Qiagen, Germany) and subjected to bisulfite treatment by using Methylation-Gold kit (ZYMO). Followed with PCR and gel purification (350bp-400bp range fragments were selected). Qualified libraries sequenced pair end on the NovaSeq 6000 system.

treatment_protocol: 3 plants from msh1 memory revertant, 2 plants from non-reverant (full-sibs of reverant), and 3 msh1 memory control plants were sequenced. Leaves at bolting were flash freezed in liquid nitrogen.  Tissues were ground by motor and pestle in liquid nitrogen.

tag: replicate type

value: biological rep 2

value: rosette leaves

tag: developmental stage

value: bolting


title: Rev_4

description: msh1 memory revertant

value: biological rep 1


title: NR_4

description: Non-reverant


title: Rev_5

description: msh1 memory revertant


title: Rev_6

description: msh1 memory revertant

value: biological rep 3


title: day 7- only RA treated cells between day 3-5  [R7-Rep2]


title: 105_3

value: SBxSB

value: Hot

value: larval