title: CB-P4-mirna02

status: Public on Sep 04 2022

city: Nanjing

first: Bo

address: Sipailou 2#

institute: Southeast University

data_processing:
To prepare for deep sequencing, four small RNA libraries (UCMSC-P4, UCMSC-P11, CBMSC-P4, CBMSC-P11) were constructed using Small RNA Expression Kit (Applied Biosystems, Foster City, CA, USA) according to the manufacturer's protocol. Briefly, RNA samples were hybridized and ligated with adapter mix. Then, reverse transcription was performed followed by RNase H digestion and PCR amplification. The PCR products were finally size-selected and purified. Each pool of libraries included three biological repeats. Then, the SOLID V2 sequencing system (Applied Biosystems, Foster City, CA, USA) was performed to generate read counts of nucleotide sequences.
The sequencing results were analyzed by SOLiD system small RNA analysis pipeline tool (RNA2MAP). The raw data were first filtered to remove low quality reads. Then the data were mapped to the Genbank (http://www.ncbi.nlm.nih.gov/genbank) and sequences matching to rRNAs, tRNAs, snoRNAs and scRNAs were discarded. Finally, by mapping to the miRBase database (http://www.mirbase.org), known and novel miRNAs were identified. The total read counts of each sample were normalized to reads per million (RPM).
To perform differential expression analysis, a DEGseq package tool  was applied and the significantly differential miRNAs were identified according to the p-value (< 0.05).

source_name: Umbilical Crod

extract_protocol:
Total RNAs from UCMSCs and CBMSCs at early (passage 4) and late (passage 11) passages were extracted with mirVana miRNA isolation kit (Life Technologies, Gaithersburg, MD, USA) according to the manufacturer's protocol.
Ribo-zero kit for rRNA removal;One-stranded cDNA was synthesized using RNA as a template and six-base random primers; The second-stranded cDNA was synthesised by adding buffer, dNTPs and enzymes, followed by purification of the double-stranded cDNA using VAHTSTM DNA Clean Beads. purification of double-stranded cDNA;Accurate quantification of library concentrations with Qubit, determination of library fragment size distribution with Agilent 2100 Bioanalyzer

value: Umbilical Crod

value: Mesenchymal sem cells


title: UC-P11-mirna03

type: SRA

last: Sun

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: Umbilical Crod Blood

tag: tissue

value: Umbilical Crod Blood

tag: cell type


title: UC-P4-mirna01


title: Fluoxetine_PAG_Rep5

city: Singapore

first: Nirmala

last: Arul Rayan

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: RNAseq

data_processing:
RNA-seq data were aligned to the Rattus norvegicus rn5 genome (Rn5 ENSEMBL) with the STAR aligner. Read counts were concurrently calculated using HTseq
Any dataset that failed the default Fastqc sequencing parameters and < 75% mapping rate was discarded.
Genome_build: Rn5
Supplementary_files_format_and_content: fastq and read count files

molecule: polyA RNA

organism: Rattus norvegicus

source_name: PAG

growth_protocol: Tissue RNA-seq. Brains were removed and frozen immediately on dry ice. Frozen brains were cryosectioned at 250um thickness onto poly-lysine coated slides. The anatomical regions subject to punching were verified using the rat brain atlas of Paxinos and Watson

extract_protocol:
Frozen, pooled brain tissue punches for each region were thawed on ice in 1 ml Trizol. Tissue was then homogenized using a manual glass douncer with 7-15 slow strokes on ice. RNA was extracted from each replicate sample using the Qiagen RNA Mini kit (Qiagen, Cat# 74104) as per the manufacturer’s instructions with on-column DNase I treatment. RNA quality was examined using a Bioanalyzer 2100 (Agilent technologies, Santa Clara, USA). RNA Integrity Number (RIN) values ranged from 7.1 to 10, with a median value of 9.5. cDNA libraries were prepared using 300 ng of total RNA, from 27 regions in every replicate, using the Illumina TruSeq Stranded Total RNA LT set (Illumina, Cat# RS-122-2301). Paired-end, 76 bp read length RNA-seq was carried out on the Illumina HiSeq 2500 at a depth of 20M reads per sample.
llumina TruSeq Stranded Total RNA LT set (Illumina, Cat# RS-122-2301)

treatment_protocol: 2 month old Charles River rats were treated with 18mg/kg body weight of fluoxetine (FT group) or water (Sham group), ad libitum for 6 weeks

tag: brain region name

value: PAG

tag: treatment

value: Fluoxetine


title: Fluoxetine_Raphe_Rep5

description: RNAseq

source_name: Raphe

value: Raphe


title: Fluoxetine_LC_Rep5

description: RNAseq

source_name: LC

value: LC


title: Fluoxetine_VTA_Rep5

description: RNAseq

source_name: VTA

value: VTA


title: Fluoxetine_Arc_Rep5

description: RNAseq

source_name: Arc

value: Arc


title: Fluoxetine_dorCA1_Rep5

description: RNAseq


title: Fluoxetine_venDG_Rep5

description: RNAseq

source_name: venDG

value: venDG


title: Fluoxetine_HB_Rep5

description: RNAseq

source_name: HB

value: HB


title: Fluoxetine_BLA_Rep5

description: RNAseq

source_name: BLA

value: BLA


title: Fluoxetine_venCA1_Rep5

description: RNAseq


title: Fluoxetine_VMH_Rep5

description: RNAseq

source_name: VMH

value: VMH


title: Fluoxetine_SNT_Rep5

description: RNAseq

source_name: SNT

value: SNT


title: Fluoxetine_MPOA_Rep5

description: RNAseq

source_name: MPOA

value: MPOA


title: Fluoxetine_BNST_Rep5

description: RNAseq

source_name: BNST

value: BNST


title: Fluoxetine_NaCcore_Rep5

description: RNAseq

source_name: NaCcore

value: NaCcore


title: Fluoxetine_CMA_Rep5

description: RNAseq

source_name: CMA

value: CMA


title: Fluoxetine_NaCshell_Rep5

description: RNAseq

source_name: NaCshell

value: NaCshell


title: Fluoxetine_InsularCortex_Rep5

description: RNAseq

source_name: InsularCortex

value: InsularCortex


title: Fluoxetine_dorDG_Rep5

description: RNAseq

source_name: dorDG

value: dorDG


title: CB-P11-mirna04

source_name: Umbilical Crod

value: Umbilical Crod

value: Mesenchymal sem cells


title: Fluoxetine_PVN_Rep5

description: RNAseq

source_name: PVN

value: PVN

value: Fluoxetine


title: Fluoxetine_MDT_Rep5

description: RNAseq

source_name: MDT

value: MDT


title: Fluoxetine_CGC_Rep5

description: RNAseq

source_name: CGC

value: CGC


title: Sham _VTA_Rep5

description: RNAseq

source_name: VTA

value: VTA

value: Sham


title: Sham _Raphe_Rep5

description: RNAseq

source_name: Raphe

value: Raphe


title: Fluoxetine_LH_Rep5

description: RNAseq

source_name: LH

value: LH


title: Sham _LC_Rep5

description: RNAseq

source_name: LC

value: LC


title: Sham _PAG_Rep5

description: RNAseq

source_name: PAG

value: PAG


title: Sham _Arc_Rep5

description: RNAseq

source_name: Arc

value: Arc


title: Sham _HB_Rep5

description: RNAseq

source_name: HB

value: HB


title: Sham _venCA1_Rep5

description: RNAseq


title: Fluoxetine_PLC_Rep5

description: RNAseq

source_name: PLC

value: PLC


title: Sham _dorCA1_Rep5

description: RNAseq


title: Sham _venDG_Rep5

description: RNAseq

source_name: venDG

value: venDG


title: Sham _BLA_Rep5

description: RNAseq

source_name: BLA

value: BLA


title: Sham _CMA_Rep5

description: RNAseq

source_name: CMA

value: CMA


title: Fluoxetine_LS_Rep5

description: RNAseq

source_name: LS

value: LS


title: Sham _dorDG_Rep5

description: RNAseq

source_name: dorDG

value: dorDG


title: Sham _LH_Rep5

description: RNAseq


title: Sham _BNST_Rep5

description: RNAseq, raw data files were corrupted for this sample and are not available.

source_name: BNST

value: BNST


title: Sham _MPOA_Rep5

description: RNAseq

source_name: MPOA

value: MPOA


title: Sham _LS_Rep5

description: RNAseq


title: Fluoxetine_MS_Rep5

description: RNAseq

source_name: MS

value: MS

value: Fluoxetine


title: Sham _SNT_Rep5

description: RNAseq

source_name: SNT

value: SNT

value: Sham


title: Sham _NaCshell_Rep5

description: RNAseq

source_name: NaCshell

value: NaCshell


title: Sham _NaCcore_Rep5

description: RNAseq

source_name: NaCcore

value: NaCcore


title: Sham _VMH_Rep5

description: RNAseq

source_name: VMH

value: VMH


title: Fluoxetine_ILC_Rep5

description: RNAseq

source_name: ILC

value: ILC


title: Sham _ILC_Rep5

description: RNAseq


title: Sham _PLC_Rep5

description: RNAseq


title: Sham _InsularCortex_Rep5

description: RNAseq

source_name: InsularCortex

value: InsularCortex


title: Fluoxetine_Raphe_Rep4

description: RNAseq

source_name: Raphe

value: Raphe


title: Sham _MS_Rep5

description: RNAseq


title: Sham _CGC_Rep5

description: RNAseq

source_name: CGC

value: CGC


title: Fluoxetine_PAG_Rep4

description: RNAseq

source_name: PAG

value: PAG


title: Fluoxetine_VTA_Rep4

description: RNAseq

source_name: VTA

value: VTA


title: Fluoxetine_venDG_Rep4

description: RNAseq

source_name: venDG

value: venDG


title: Fluoxetine_dorCA1_Rep4

description: RNAseq


title: Fluoxetine_CMA_Rep4

description: RNAseq

source_name: CMA

value: CMA


title: Fluoxetine_SNT_Rep4

description: RNAseq


title: Fluoxetine_BLA_Rep4

description: RNAseq

source_name: BLA

value: BLA


title: Fluoxetine_LC_Rep4

description: RNAseq

source_name: LC

value: LC


title: Fluoxetine_venCA1_Rep4

description: RNAseq


title: Fluoxetine_HB_Rep4

description: RNAseq

source_name: HB

value: HB


title: Fluoxetine_Arc_Rep4

description: RNAseq

source_name: Arc

value: Arc

value: Fluoxetine


title: Fluoxetine_MPOA_Rep4

description: RNAseq

source_name: MPOA

value: MPOA


title: Fluoxetine_PVN_Rep4

description: RNAseq

source_name: PVN

value: PVN


title: Sham _MDT_Rep5

description: RNAseq

source_name: MDT

value: MDT

value: Sham


title: Sham _PVN_Rep5

description: RNAseq


title: Fluoxetine_NaCshell_Rep4

description: RNAseq

source_name: NaCshell

value: NaCshell


title: Fluoxetine_MDT_Rep4

description: RNAseq


title: Fluoxetine_VMH_Rep4

description: RNAseq

source_name: VMH

value: VMH


title: Fluoxetine_dorDG_Rep4

description: RNAseq

source_name: dorDG

value: dorDG


title: Fluoxetine_LH_Rep4

description: RNAseq

source_name: LH

value: LH


title: Fluoxetine_MS_Rep4

description: RNAseq

source_name: MS

value: MS


title: Fluoxetine_BNST_Rep4

description: RNAseq

source_name: BNST

value: BNST


title: Fluoxetine_LS_Rep4

description: RNAseq

source_name: LS

value: LS


title: Fluoxetine_CGC_Rep4

description: RNAseq

source_name: CGC

value: CGC


title: Fluoxetine_NaCcore_Rep4

description: RNAseq

source_name: NaCcore

value: NaCcore


title: Sham _PAG_Rep4

description: RNAseq

source_name: PAG

value: PAG


title: Fluoxetine_ILC_Rep4

description: RNAseq

source_name: ILC

value: ILC


title: Sham _venCA1_Rep4

description: RNAseq


title: Sham _Arc_Rep4

description: RNAseq

value: Arc


title: Fluoxetine_PLC_Rep4

description: RNAseq

source_name: PLC

value: PLC

value: Fluoxetine


title: Sham _dorCA1_Rep4

description: RNAseq


title: Sham _SNT_Rep4

description: RNAseq

source_name: SNT

value: SNT


title: Sham _LC_Rep4

description: RNAseq

source_name: LC

value: LC


title: Sham _dorDG_Rep4

description: RNAseq

value: Sham


title: Sham _venDG_Rep4

description: RNAseq

source_name: venDG

value: venDG


title: Sham _BLA_Rep4

description: RNAseq

source_name: BLA

value: BLA


title: Sham _HB_Rep4

description: RNAseq

source_name: HB

value: HB


title: Fluoxetine_InsularCortex_Rep4

description: RNAseq

source_name: InsularCortex

value: InsularCortex


title: Sham _VTA_Rep4

description: RNAseq

source_name: VTA

value: VTA


title: Sham _VMH_Rep4

description: RNAseq

source_name: VMH

value: VMH


title: Sham _MPOA_Rep4

description: RNAseq

source_name: MPOA

value: MPOA


title: Sham _MDT_Rep4

description: RNAseq

source_name: MDT

value: MDT


title: Sham _BNST_Rep4

description: RNAseq

source_name: BNST

value: BNST


title: Sham _PVN_Rep4

description: RNAseq

source_name: PVN

value: PVN


title: Sham _CMA_Rep4

description: RNAseq

source_name: CMA

value: CMA


title: Sham _Raphe_Rep4

description: RNAseq

source_name: Raphe

value: Raphe


title: Sham _LS_Rep4

description: RNAseq

source_name: LS

value: LS


title: Sham _NaCcore_Rep4

description: RNAseq

source_name: NaCcore

value: NaCcore


title: Sham _NaCshell_Rep4

description: RNAseq

source_name: NaCshell

value: NaCshell


title: Sham _InsularCortex_Rep4

description: RNAseq


title: Sham _MS_Rep4

description: RNAseq

source_name: MS

value: MS


title: Sham _PLC_Rep4

description: RNAseq

source_name: PLC

value: PLC

value: Sham


title: Sham _ILC_Rep4

description: RNAseq

source_name: ILC

value: ILC


title: Fluoxetine_SNT_Rep3

description: RNAseq

source_name: SNT

value: SNT

value: Fluoxetine


title: Sham _CGC_Rep4

description: RNAseq

source_name: CGC

value: CGC


title: Sham_SNT_Rep3

description: RNAseq


title: Fluoxetine_LC_Rep3

description: RNAseq

source_name: LC

value: LC


title: Fluoxetine_VTA_Rep3

description: RNAseq

source_name: VTA

value: VTA


title: Fluoxetine_ARC_Rep3

description: RNAseq

source_name: ARC

value: ARC


title: Fluoxetine_Raphe_Rep3

description: RNAseq


title: Fluoxetine_venCA1_Rep3

description: RNAseq


title: Sham _LH_Rep4

description: RNAseq

source_name: LH

value: LH


title: Fluoxetine_venDG_Rep3

description: RNAseq

source_name: venDG

value: venDG


title: Fluoxetine_PAG_Rep3

description: RNAseq

source_name: PAG

value: PAG


title: Fluoxetine_HB_Rep3

description: RNAseq

source_name: HB

value: HB


title: Fluoxetine_CMA_Rep3

description: RNAseq

source_name: CMA

value: CMA


title: Fluoxetine_dorCA1_Rep3

description: RNAseq


title: Fluoxetine_dorDG_Rep3

description: RNAseq

source_name: dorDG

value: dorDG


title: Fluoxetine_VMH_Rep3

description: RNAseq

source_name: VMH

value: VMH


title: Fluoxetine_LH_Rep3

description: RNAseq


title: Fluoxetine_PVN_Rep3

description: RNAseq

source_name: PVN

value: PVN


title: Fluoxetine_MDT_Rep3

description: RNAseq

source_name: MDT

value: MDT


title: Fluoxetine_BNST_Rep3

description: RNAseq

source_name: BNST

value: BNST


title: Fluoxetine_BLA_Rep3

description: RNAseq

source_name: BLA

value: BLA


title: Fluoxetine_MS_Rep3

description: RNAseq

source_name: MS

value: MS


title: Fluoxetine_NaCshell_Rep3

description: RNAseq

source_name: NaCshell

value: NaCshell

value: Fluoxetine


title: Fluoxetine_NaCcore_Rep3

description: RNAseq

source_name: NaCcore

value: NaCcore


title: Sham_LC_Rep3

description: RNAseq

source_name: LC

value: LC

value: Sham


title: synovial tissue of dogs affected with Osteoarthritis, OA40

city: Fujisawa

first: Atsushi

last: Yamazaki

department: Department of Veterinary Medicine, College of Bioresource and Sciences

country: Japan

institute: Nihon University

data_processing:
The sequencing adapters are ligated to the RNA molecules, which act as primer binding sites during reverse transcription and PCR amplification. Adenylated single strand DNA 3' adapter followed by a 5' adapter is ligated to the small RNAs using a ligating enzyme such as T4 RNA ligase 2. The adapters are also designed to capture small RNAs with 5' phosphate groups which is characteristic of microRNAs, rather than RNA degradation products with 5' hydroxyl group.
miRNA fragments with ligated adapters are converted to cDNA fragments which are later used in the sequencing reaction. There are many commercial kits using some form of reverse transcriptase in order to carry out this step. PCR is then performed to amplify the pool of cDNA sequences.
The amplified cDNA fragments are run on agarose gel and the band containing the molecules corresponding to the miRNA fragments with ligated adapters are cut out for subsequent sequencing (library size is ranged from 145 bp to 160 bp)
cDNA fragments are sequenced by the read length using sequence by synthesis method on the illumina platform.
After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads.
rRNA removed reads are sequentially aligned to reference genome, miRBase v22.1 to classify known miRNAs prediction is performed by miRDeep2.
Assembly: miRBase v22.1
Supplementary files format and content: tab-delimited text file includes RPM and Read count for each Sample

organism: Canis lupus familiaris

source_name: synovial tissue of stifle joint

extract_protocol:
RNA was harvested using miRneasy Mini kit (Qiagen). 1.0ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Small RNA Library Prep Kit following manufacturer's protocols.

value: synovial tissue of stifle joint

tag: disease state

value: Osteoarthritis caused by lateral patella luxation

tag: Sex

value: female

tag: age

value: non steroidal anti inflammatory drugs


title: synovial tissue of dogs affected with Osteoarthritis, OA32

value: Osteoarthritis caused by cranial cruciate ligament rupture

value: male

tag: condition

value: neutered


title: Fluoxetine_InsularCortex_Rep3

description: RNAseq

source_name: InsularCortex

value: InsularCortex


title: synovial tissue of normal dogs, N3

value: Normal


title: Fluoxetine_CGC_Rep3

description: RNAseq

source_name: CGC

value: CGC


title: synovial tissue of dogs affected with Osteoarthritis, OA26


title: Fluoxetine_ILC_Rep3

description: RNAseq

source_name: ILC

value: ILC


title: synovial tissue of normal dogs, N1


title: Sham _PAG_Rep3

description: RNAseq

source_name: PAG

value: PAG


title: Fluoxetine_PLC_Rep3

description: RNAseq

source_name: PLC

value: PLC


title: Sham _VTA_Rep3

description: RNAseq

source_name: VTA

value: VTA


title: Sham _venCA1_Rep3

description: RNAseq


title: Sham _venDG_Rep3

description: RNAseq

source_name: venDG

value: venDG


title: Fluoxetine_LS_Rep3

description: RNAseq

source_name: LS

value: LS

value: Fluoxetine


title: dFOXO-null_male_totalsmall_06d_rep2

city: Waltham

first: Siobhan

last: Gartland

state: MA

address: 415 SOUTH STREET

department: Biology

country: USA

institute: Brandeis University

description:
d94_m_ts_06do_rep2
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index32

data_processing:
Galaxy web platform (usegalaxy.org (Afgan, Baker et al. 2018)) and the Mississippi server sponsored by the ARTbio bioinformatics facility of the Institut de Biologie Paris Seine based at the University Pierre & Marie Curie
Adapters were removed using the application Trim Galore! designed by Felix Krueger on default settings and inputting the adapter sequence GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT to remove it.
The trimmed sequence files were processed through the Reverse-Complement application.
These trimmed and reverse complimented files were then size selected using Filter FASTQ (Blankenberg, Gordon et al. 2010) to filter out reads longer than 25 nt and filtered to only include 21 nt reads for transposon siRNA analysis
Reads were mapped to the dm6 genome or an in-house FASTA of spike-ins (Gainetdinov, Colpan et al. 2018), known Drosophila transposons, mature miRNAs, and miR* strands using sR_bowtie (Langmead, Trapnell et al. 2009) set to match and report all valid alignments with 1 mismatch allowed
Alignments were quantified using featureCounts (Liao, Smyth et al. 2014). miRNAs, miR* strands, and transposons with an average of less than 5 reads across the libraries were removed from analysis to avoid noise using DEBrowser v1.18.2 (Kucukural, Yukselen et al. 2019)
Replicates were averaged together.
Libraries were normalized by total mapped reads as adapted from described (Czech, Malone et al. 2008, Czech, Zhou et al. 2009)
Assembly: dm6
Supplementary files format and content: prenormalization files are tab delimited files composed of featureCounts outputs
Supplementary files format and content: Normalized files are tab delimited files normalized as percent of total reads mapped

organism: Drosophila melanogaster

source_name: whole body

growth_protocol: Flies were kept at 25°C, fed banana agar, and flipped weekly. Males and females of the same genotype were kept together. Young and old of the same genotype and replicate were siblings.

extract_protocol:
RNA was extracted from 40 whole flies with Trizol reagent (Invitrogen) and sized selected to 19 to 35 nt fragments using 17% 19:1 acrylamide:bisacrylamide urea gels (National Diagnostics).
Gels were sliced from 19-35 nt, crushed, and eluted overnight in 500 µl 0.3 M sodium acetate with rotation.
20 µg of glycogen and small RNA spike ins (Gainetdinov, Colpan et al. 2018) were added to the supernatant before it was precipitated with 750 µl isopropanol at -20 °C for 1 hour, centrifuged at 15,000 rpm for 30 minutes at 4 °C, washed in 80% EtOH, air dried, and resuspended in 50 µl H2O.
Small RNA libraries were constructed using the NEBNext® Small RNA Library Prep Set for Illumina®(New England Biolabs).

value: whole body

tag: strain

value: wDah

tag: genotype

value: 6 days


title: dFOXO-null_male_totalsmall_31d_rep2

description:
d94_m_ts_31do_rep2
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index48

value: 31 days


title: wDah_male_totalsmall_31d_rep2

description:
wDa_m_ts_31do_rep2
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index46


title: wDah_female_totalsmall_31d_rep2

description:
wDa_f_ts_31do_rep2
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index45

value: female


title: Sham _dorCA1_Rep3

description: RNAseq

value: Sham


title: dFOXO-null_female_totalsmall_06d_rep2

description:
d94_f_ts_06do_rep2
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index31


title: Sham _dorDG_Rep3

description: RNAseq

source_name: dorDG

value: dorDG


title: dFOXO-null_female_totalsmall_31d_rep2

description:
d94_f_ts_31do_rep2
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index47


title: wDah_male_totalsmall_06d_rep2

description:
wDa_m_ts_06do_rep2
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index30

value: male


title: wDah_female_totalsmall_06d_rep2

description:
wDa_f_ts_06do_rep2
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index29


title: Sham _HB_Rep3

description: RNAseq

source_name: HB

value: HB


title: Sham _BLA_Rep3

description: RNAseq

source_name: BLA

value: BLA


title: Sham _CMA_Rep3

description: RNAseq

source_name: CMA

value: CMA


title: dFOXO-null_female_totalsmall_31d_rep1

description:
d94_f_ts_31do_rep1
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index39


title: wDah_male_totalsmall_31d_rep1

description:
wDa_m_ts_31do_rep1
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index38


title: dFOXO-null_male_totalsmall_31d_rep1

description:
d94_m_ts_31do_rep1
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index40


title: synovial tissue of normal dogs, N2

value: synovial tissue of stifle joint

value: Normal


title: wDah_female_totalsmall_31d_rep1

description:
wDa_f_ts_31do_rep1
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index37


title: Sham _Raphe_Rep3

description: RNAseq

source_name: Raphe

value: Raphe


title: Sham _VMH_Rep3

description: RNAseq

source_name: VMH

value: VMH


title: Sham _MDT_Rep3

description: RNAseq

source_name: MDT

value: MDT


title: Sham _LH_Rep3

description: RNAseq

source_name: LH

value: LH


title: dFOXO-null_male_totalsmall_05d_rep1

description:
d94_m_ts_05do_rep1
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index36

value: whole body

value: 5 days


title: Sham _PVN_Rep3

description: RNAseq

source_name: PVN

value: PVN


title: dFOXO-null_female_totalsmall_05d_rep1

description:
d94_f_ts_05do_rep1
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index35

value: wDah


title: Sham _BNST_Rep3

description: RNAseq

source_name: BNST

value: BNST


title: wDah_female_totalsmall_05d_rep1

description:
wDa_f_ts_05do_rep1
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index33

value: female


title: Sham _NaCcore_Rep3

description: RNAseq

source_name: NaCcore

value: NaCcore

value: Sham


title: wDah_male_Ago1IP_35d_exp2

description:
wDa_m_A1_35do_exp2
IP_sample_index19_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

data_processing:
Galaxy web platform (usegalaxy.org (Afgan, Baker et al. 2018)) and the Mississippi server sponsored by the ARTbio bioinformatics facility of the Institut de Biologie Paris Seine based at the University Pierre & Marie Curie
Adapters were removed using the application Trim Galore! designed by Felix Krueger on default settings and inputting the adapter sequence GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT to remove it.
The trimmed sequence files were processed through the Reverse-Complement application.
These trimmed and reverse complimented files were then size selected using Filter FASTQ (Blankenberg, Gordon et al. 2010) to filter out reads longer than 25 nt and filtered to only include 21 nt reads for transposon siRNA analysis
Reads were mapped to the dm6 genome or an in-house FASTA of spike-ins (Gainetdinov, Colpan et al. 2018), known Drosophila transposons, mature miRNAs, and miR* strands using sR_bowtie (Langmead, Trapnell et al. 2009) set to match and report all valid alignments with 1 mismatch allowed
Alignments were quantified using featureCounts (Liao, Smyth et al. 2014). miRNAs, miR* strands, and transposons with an average of less than 5 reads across the libraries were removed from analysis to avoid noise using DEBrowser v1.18.2 (Kucukural, Yukselen et al. 2019)
Replicates were averaged togather
Libraries were normalized by total mapped reads as adapted from described (Czech, Malone et al. 2008, Czech, Zhou et al. 2009)
Assembly: dm6
Supplementary files format and content: prenormalization files are tab delimited files composed of featureCounts outputs
Supplementary files format and content: Normalized files are tab delimited files normalized as percent of total reads mapped

extract_protocol:
40 whole flies were homogenized in 500 µl of chilled lysis buffer (Kadener, Menet et al. 2009). Lysates were incubated on ice for 10 minutes and centrifuged at 15,000 rpm for 15 minutes at 4 °C.
For the Ago1 immunoprecipitation 4 µl of BRD-GP-3 and 4 µl BRD-GP-4 were added to 100 µl of lysate. For the Ago2 immunoprecipitation, the same was done with BRD-GP-5 and BRD-GP-6. Lysates with antibody were incubated with rotation for 1 hour at 4 °C.
50 µl of 25% slurry Pierce protein A/G magnetic agarose (Thermo Fisher) were prepared for each IP. The magnetic agarose was washed in 1 ml of lysis buffer three times before being resuspended in the original volume.
40 µl of slurry were aliquoted into new tubes, supernatant was removed, and the lysates with antibody were added. Lysates and magnetic agarose were incubated overnight with rotation at 4 °C.
Agarose was washed five times for 5 minutes in 500 µl of lysis buffer at 4 °C before elution for RNA extraction with Trizol
Small RNA libraries were constructed using the NEBNext® Small RNA Library Prep Set for Illumina®(New England Biolabs).

value: male

tag: ip antibody

value: anti-Ago1 (BRD-GP-3 BRD-GP-4)

value: 35 days


title: wDah_male_Ago2IP_35d_exp2

description:
wDa_m_A2_35do_exp2
IP_sample_index20_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: anti-Ago2 (BRD-GP-5 BRD-GP-6)


title: Sham _LS_Rep3

description: RNAseq

value: LS


title: Sham _InsularCortex_Rep3

description: RNAseq

source_name: InsularCortex

value: InsularCortex


title: Sham _NaCshell_Rep3

description: RNAseq

source_name: NaCshell

value: NaCshell


title: wDah_male_Ago2IP_05d_exp2

description:
wDa_m_A2_05do_exp2
IP_sample_index18_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt


title: Sham _CGC_Rep3

description: RNAseq

source_name: CGC

value: CGC


title: wDah_female_Ago2IP_35d_exp2

description:
wDa_f_A2_35do_exp2
IP_sample_index16_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt


title: Sham _ILC_Rep3

description: RNAseq

source_name: ILC

value: ILC


title: wDah_female_Ago2IP_05d_exp2

description:
wDa_f_A2_05do_exp2
IP_sample_index14_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: whole body


title: Sham _PLC_Rep3

description: RNAseq

source_name: PLC

value: PLC


title: wDah_female_Ago1IP_35d_exp2

description:
wDa_f_A1_35do_exp2
IP_sample_index15_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

source_name: whole body


title: wDah_male_Ago1IP_05d_exp2

description:
wDa_m_A1_05do_exp2
IP_sample_index17_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: 5 days


title: Fluoxetine_LC_Rep1

description: RNAseq

source_name: LC

value: LC

value: Fluoxetine


title: wDah_female_Ago1IP_05d_exp2

description:
wDa_f_A1_05do_exp2
IP_sample_index13_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: wDah

value: female


title: dFOXO-null_female_Ago2IP_35d_exp2

description:
d94_f_A2_35do_exp2
IP_sample_index11_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt


title: dFOXO-null_male_Ago2IP_35d_exp2

description:
d94_m_A2_35do_exp2
IP_sample_index12_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt


title: dFOXO-null_female_Ago2IP_05d_exp2

description:
d94_f_A2_05do_exp2
IP_sample_index10_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt


title: dFOXO-null_male_Ago2IP_05d_exp2

description:
d94_m_A2_05do_exp2
IP_sample_index06_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt


title: Sham_SNT_Rep1

description: RNAseq

source_name: SNT

value: SNT

value: Sham


title: Sham _MPOA_Rep3

description: RNAseq

source_name: MPOA

value: MPOA


title: wDah_male_totalsmall_05d_rep1

description:
wDa_m_ts_05do_rep1
totalsmallRNA_mappedtomiRNAstransposons_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_normalized.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_prenormalization.txt
totalsmallRNA_mappedtomiRNAstransposons_21nt_normalized.txt
totalsmallRNA_mappedtodm6_prenormalization.txt
totalsmallRNA_mappedtodm6_normalized.txt
Total_small_sample_index34

value: male


title: Fluoxetine_SNT_Rep1

description: RNAseq


title: Sham_LC_Rep1

description: RNAseq


title: Fluoxetine_Raphe_Rep1

description: RNAseq

value: Raphe


title: dFOXO-null_male_Ago1IP_35d_exp2

description:
d94_m_A1_35do_exp2
IP_sample_index08_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: anti-Ago1 (BRD-GP-3 BRD-GP-4)

value: 35 days


title: Fluoxetine_PAG_Rep1

description: RNAseq

source_name: PAG

value: PAG


title: Sham _MS_Rep3

description: RNAseq

source_name: MS

value: MS


title: dFOXO-null_female_Ago1IP_35d_exp2

description:
d94_f_A1_35do_exp2
IP_sample_index07_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt


title: Fluoxetine_VTA_Rep1

description: RNAseq

source_name: VTA

value: VTA


title: Fluoxetine_venCA1_Rep1

description: RNAseq


title: Fluoxetine_ARC_Rep1

description: RNAseq

source_name: ARC

value: ARC


title: dFOXO-null_female_Ago1IP_05d_exp2

description:
d94_f_A1_05do_exp2
IP_sample_index05_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: whole body


title: dFOXO-null_male_Ago2IP_35d_exp1

description:
d94_m_A2_35do_exp1
IP_sample_index20_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: anti-Ago2 (BRD-GP-5 BRD-GP-6)


title: Fluoxetine_venDG_Rep1

description: RNAseq

source_name: venDG

value: venDG


title: dFOXO-null_male_Ago1IP_35d_exp1

description:
d94_m_A1_35do_exp1
IP_sample_index19_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt


title: dFOXO-null_female_Ago2IP_35d_exp1

description:
d94_f_A2_35do_exp1
IP_sample_index18_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt


title: Fluoxetine_dorCA1_Rep1

description: RNAseq

value: Fluoxetine


title: dFOXO-null_female_Ago1IP_35d_exp1

description:
d94_f_A1_35do_exp1
IP_sample_index17_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: wDah


title: dFOXO-null_male_Ago2IP_05d_exp1

description:
d94_m_A2_05do_exp1
IP_sample_index16_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: 5 days


title: Fluoxetine_dorDG_Rep1

description: RNAseq

source_name: dorDG

value: dorDG


title: dFOXO-null_male_Ago1IP_05d_exp1

description:
d94_m_A1_05do_exp1
IP_sample_index15_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt


title: Fluoxetine_BLA_Rep1

description: RNAseq

source_name: BLA

value: BLA


title: dFOXO-null_female_Ago2IP_05d_exp1

description:
d94_f_A2_05do_exp1
IP_sample_index14_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: female


title: Fluoxetine_CMA_Rep1

description: RNAseq

source_name: CMA

value: CMA


title: dFOXO-null_female_Ago1IP_05d_exp1

description:
d94_f_A1_05do_exp1
IP_sample_index13_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt


title: wDah_male_Ago2IP_35d_exp1

description:
wDa_m_A2_35do_exp1
IP_sample_index12_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: male


title: wDah_male_Ago1IP_35d_exp1

description:
wDa_m_A1_35do_exp1
IP_sample_index11_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: anti-Ago1 (BRD-GP-3 BRD-GP-4)


title: Fluoxetine_VMH_Rep1

description: RNAseq

source_name: VMH

value: VMH


title: Fluoxetine_MDT_Rep1

description: RNAseq

source_name: MDT

value: MDT


title: Fluoxetine_PVN_Rep1

description: RNAseq

source_name: PVN

value: PVN


title: Fluoxetine_BNST_Rep1

description: RNAseq

source_name: BNST

value: BNST


title: wDah_female_Ago2IP_35d_exp1

description:
wDa_f_A2_35do_exp1
IP_sample_index10_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: 35 days


title: wDah_female_Ago1IP_35d_exp1

description:
wDa_f_A1_35do_exp1
IP_sample_index09_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: whole body


title: dFOXO-null_male_Ago1IP_05d_exp2

description:
d94_m_A1_05do_exp2
IP_sample_index09_exp2
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt


title: Fluoxetine_MS_Rep1

description: RNAseq

value: MS


title: Fluoxetine_LS_Rep1

description: RNAseq

source_name: LS

value: LS


title: wDah_male_Ago2IP_05d_exp1

description:
wDa_m_A2_05do_exp1
IP_sample_index08_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

source_name: whole body

value: anti-Ago2 (BRD-GP-5 BRD-GP-6)


title: wDah_male_Ago1IP_05d_exp1

description:
wDa_m_A1_05do_exp1
IP_sample_index07_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: wDah


title: Fluoxetine_HB_Rep1

description: RNAseq

source_name: HB

value: HB

value: Fluoxetine


title: Fluoxetine_NaCcore_Rep1

description: RNAseq, raw data files were corrupted for this sample and are not available.

source_name: NaCcore

value: NaCcore


title: wDah_female_Ago1IP_05d_exp1

description:
wDa_f_A1_05do_exp1
IP_sample_index05_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: female

value: 5 days


title: Fluoxetine_NaCshell_Rep1

description: RNAseq

source_name: NaCshell

value: NaCshell


title: Fluoxetine_InsularCortex_Rep1

description: RNAseq

source_name: InsularCortex

value: InsularCortex


title: Fluoxetine_ILC_Rep1

description: RNAseq

source_name: ILC

value: ILC


title: Fluoxetine_LH_Rep1

description: RNAseq

source_name: LH

value: LH


title: PA01-rep4

city: kunming

first: Yi-Cheng

last: Ma

email: 290361200@qq.com, mayc@ynu.edu.cn

state: yunnan

address: NO.2 North Cuihu Road

institute: Yunnan University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 2*150 bp paired-end reads were generated.
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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads.
Differential expression analysis of two conditions/groups (four biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value.The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and log2(Fold change) of 1 were set as the threshold for significantly differential expression.
Assembly: Caenorhabditis elegans WBcel235
Supplementary files format and content: xlsx files include RPKM values for each Sample

organism: Caenorhabditis elegans

growth_protocol: Worms were maintained on nematode growth media (NGM) and fed with E. coli OP50 at 20°C

extract_protocol:
Bacteria were removed and worms were natural precipitation by M9 buffer , flash frozen on dry ice, and RNA was harvested using Trizol reagent.A total amount of 3 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: P. aeruginosa PA01 or E. coli OP50  was incubated on PGS plates first for 24 h at 37ºC and then for 24 h at 25ºC.  Mid-L4 animals were transferred onto the  PGS plates at 25°C and harvesting worms after 12 hours.

value: P. aeruginosa PA01 exposure

value: wild type

tag: developmental stage


title: Fluoxetine_CGC_Rep1

description: RNAseq

source_name: CGC

value: CGC


title: PA01-rep3


title: PA01-rep2


title: Fluoxetine_PLC_Rep1

description: RNAseq

source_name: PLC

value: PLC


title: Sham_VTA_Rep1

description: RNAseq

source_name: VTA

value: VTA

value: Sham


title: OP50-rep3

value: E. coli OP50 exposure


title: Sham_PAG_Rep1

description: RNAseq

source_name: PAG

value: PAG


title: Sham_Raphe_Rep1

description: RNAseq

source_name: Raphe

value: Raphe


title: Sham_venCA1_Rep1

description: RNAseq


title: OP50-rep1


title: Sham_venDG_Rep1

description: RNAseq

source_name: venDG

value: venDG


title: PA01-H4K8ac-rep3-Input

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: Caenorhabditis elegans WBcel235
Supplementary files format and content: xlsx files include Peak values for each Sample

molecule: genomic DNA

extract_protocol:
The worms were exposed to P. aeruginosa PA01 on PGS plates at 25 °C for 12 hours. After three washes in M9 buffer, animals were resuspended in PBS, frozen immediately in liquid nitrogen followed by storage at -80 °C. After cell lysis, the chromatin was sheared into 0.2- to 1-kb fragments. The soluble chromatin fraction was immunoprecipitated using antibodies specific for H4K5ac (Abcam, ab51997) or H4K8ac (Abcam, ab45166).
ChIP-seq libraries were prepared using the NEBNext UltraDNA library prep kit (New England Biolabs) and single-end sequenced on an Illumina HiSeq6000.

treatment_protocol: P. aeruginosa PA01 was incubated on PGS plates first for 24 h at 37ºC and then for 24 h at 25ºC.  Mid-L4 animals were transferred onto the  PGS plates at 25°C and harvesting worms after 12 hours.

tag: chip antibody


title: OP50-rep2


title: PA01-rep1


title: Sham_HB_Rep1

description: RNAseq

value: HB


title: PA01-H4K8ac-rep2-Input


title: wDah_female_Ago2IP_05d_exp1

description:
wDa_f_A2_05do_exp1
IP_sample_index06_exp1
AgoIP_mappedtomiRNAstransposons_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_normalized.txt
AgoIP_mappedtomiRNAstransposons_21nt_prenormalization.txt
AgoIP_mappedtomiRNAstransposons_21nt_normalized.txt
AgoIP_mappedtodm6_prenormalization.txt
AgoIP_mappedtodm6_normalized.txt

value: whole body

value: wDah

value: female

value: anti-Ago2 (BRD-GP-5 BRD-GP-6)


title: Sham_dorCA1_Rep1

description: RNAseq


title: Sham_dorDG_Rep1

source_name: dorDG

value: dorDG


title: PA01-H4K5ac-rep3-Input


title: Sham_CMA_Rep1

description: RNAseq

source_name: CMA

value: CMA


title: PA01-H4K5ac-rep2-Input

value: P. aeruginosa PA01 exposure


title: OP50-rep4

value: wild type


title: PA01-H4K5ac-rep1-Input


title: Sham_LH_Rep1

value: LH


title: Sham_VMH_Rep1

source_name: VMH

value: VMH


title: Sham_MDT_Rep1

description: RNAseq

source_name: MDT

value: MDT


title: PA01-H4K8ac-rep2-IP

value: anti-H4K8ac (abcam, ab45166)


title: PA01-H4K8ac-rep1-IP


title: PA01-H4K8ac-rep3-IP


title: Sham_PVN_Rep1

description: RNAseq

source_name: PVN

value: PVN

value: Sham


title: PA01-H4K5ac-rep3-IP

value: anti-H4K5ac (abcam, ab51997)


title: Sham_MS_Rep1

description: RNAseq

source_name: MS

value: MS


title: PA01-H4K5ac-rep1-IP


title: Liver, DDC diet, 0 day and 7 days, n=2 each and pooled sequencing [10X_Myeloidcells]

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

description:
10X Genomics
10X_Myeloidcells

library_source: transcriptomic single cell

data_processing:
For 10X dataset, sequencing reads were aligned to the mouse reference genome (mm10) and estimated cell-containing partitions and associated UMI using the Cell Ranger (v6.0.1) single-cell software suite. For Smart-seq2 dataset, nine pair-end libraries, each containing sequencing reads from dozens of single cells, were constructed. For each library, the template switch oligo (TSO) sequences were trimmed by cutadapt (v1.14) (Martin, 2011), and the low-quality bases at 3’ end of reads were trimmed by trimmomatic (v0.36) (Bolger et al., 2014). After that, demultiplex was done by fastx toolkit (v0.0.13) (http://hannonlab.cshl.edu/fastx_toolkit).
Since we introduced UMI in our Smart-seq2 protocol, we then tagged the UMI sequence to the read name of each sequence by umi_tools (Smith et al., 2017). Thus, we got tagged FASTQ files for every assessed cell. As the read2 was mainly composed of polyA sequences, we aligned only read1 of individual FASTQ files to mm10 using STAR aligner (v2.5.2b) (Dobin et al., 2013).
Htseq-count (v0.6.0) (Anders et al., 2015) were used to get UMI count table for Smart-seq2 data.
The Seurat (v4.0.1) (Satija et al., 2015; Stuart et al., 2019) R package was employed to perform scRNA-Seq data analysis.
Assembly: mm10
Supplementary files format and content: UMI_SparseMatrix_Hepatocyte.rds: UMI count matrix of all processed hepatocytes (R object, sparse matrix, please loaded by "readRDS" function in R)
Supplementary files format and content: UMI_SparseMatrix_MyeloidCells.rds: UMI count matrix of all myoleid cells (R object, sparse matrix, please loaded by "readRDS" function in R)
Supplementary files format and content: metadata_Hepatocyte.txt: cell annotation for hepatocyte
Supplementary files format and content: metadata_MyeloidCells.txt: cell annotation for myoleid cells
Supplementary files format and content: cellBarcode_batch1_Z101-Z104.fasta: barcode needed for demulplexing smart-seq2 FASTQ data (Z101 to Z104)
Supplementary files format and content: cellBarcode_batch2_L1-L4.fasta: barcode needed for demulplexing smart-seq2 FASTQ data (L1 to L4)
Supplementary files format and content: cellBarcode_batch2_L5.fasta: barcode needed for demultiplexing smart-seq2 FASTQ data (L5)

organism: Mus musculus

source_name: Liver

extract_protocol:
We collected primary hepatocytes via perfusion as reported from normal (Rosa26-mTmG mice for denoting normal liver-derived cells based on mTomato expression, n=2) and DDC-injured (WT mice, n=2) liver, and performed pooled 10X Chromium scRNA-seq (10X genomics Methods). In Smart-seq2 protocols, we used Sox9-EGFP mice to trace hepatocyte-derived Sox9-positive LPLC in injured liver (n=2 for each group). Injured hepatocytes and LPLC from DDC-injured livers were isolated by sorting GFP- or GFP+ hepatocytes by the BD influx cell sorter based on size/granularity and GFP expression. We also isolated and enriced macrophages via  anti-F4/80 (Ebioscience, 13-4801-82, 1:200) staining. After MACS based on anti-Biotin Microbeads (Miltenyi, 130-105-637) using AutoMACS Pro for enriched macrophages, 10,210 non-parenchymal cells from normal livers (Rosa26-mTmG mice, n=2) and DDC-injured (WT mice, n=2) livers were pooled and sequenced on Novaseq lanes by Novagene AIT.
For 10X pipeline, isolated hepatocytes or enriched macrophages were processed using the Chromium Single Cell 30 (v3 Chemistry) platform (10X Genomics, Pleasanton, CA). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. For Smart-seq2, single hepatocyte was placed into the lysis buffer by the mouth pipette. The reverse transcription reaction was performed with 25 nt oligo (dT) primer anchored with an 8 nt cell-specific barcode and 8 nt unique molecular identifiers (UMI). After the first-strand synthesis, the second-strand cDNA was synthesized, and the cDNA was amplified by 14 cycles of PCR. The amplified cDNA of single cells was then pooled together for the following steps. Biotinylated pre-indexed primers were used to further amplify the PCR product by an additional 4 cycles of PCR to introduce biotin tags to the 3’ ends of the amplified cDNAs. Approximately 300 ng cDNA was sheared to approximately 300 bp by Covaris S2, and the 3’ terminal of the cDNA was captured by Dynabeads® MyOne Streptavidin C1 beads (Thermo Fisher). The RNA-seq library was constructed using a Kapa Hyper Prep Kit (Kapa Biosystems) and subjected to 150 bp paired-end sequencing on an Illumina HiSeq 4000 platform (sequenced by Annoroad).

value: Liver

tag: cell line

value: primary cells

value: Macrophages/Monocytes

value: Rosa26-mTmG (normal diet) and WT (DDC diet)

value: DDC diet for 0 day and 7 days


title: Liver, DDC diet with CLO treatment, 0 day and 7 days, n=2 each and pooled sequencing [10X_CLO_Hepatocytes]

description:
10X Genomics
10X_CLO_Hepatocytes

value: Hepatocytes


title: Sham_NaCcore_Rep1

description: RNAseq

source_name: NaCcore

value: NaCcore


title: Sham_LS_Rep1

description: RNAseq

source_name: LS

value: LS


title: PA01-H4K5ac-rep2-IP

value: P. aeruginosa PA01 exposure

value: wild type


title: PA01-H4K8ac-rep1-Input


title: Sham_BLA_Rep1

source_name: BLA

value: BLA


title: Liver, DDC diet, 0 day and 7 days, n=2 each and pooled sequencing [10X_Hepatocytes]

description:
10X Genomics
10X_Hepatocytes


title: Sham_InsularCortex_Rep1

description: RNAseq

source_name: InsularCortex

value: InsularCortex


title: Sham_CGC_Rep1

description: RNAseq

source_name: CGC

value: CGC


title: Sham_ILC_Rep1

description: RNAseq

source_name: ILC

value: ILC


title: Sham_PLC_Rep1

source_name: PLC

value: PLC

value: Sham


title: scWAT_GC_CT_1

city: Dresden

first: Holger

last: Henneicke

address: Fetscherstraße 105

country: Germany

institute: Center for Regenerative Therapies Dresden (CRTD)

data_processing:
Basic quality control of the resulting sequencing reads was performed using FastQC, and RNA-SeQC [version 1.1.8].
Reads were aligned to the mm10 reference genome using GSNAP [version 2018-07-04].
The Ensembl gene annotation [Mus musculus; version 98] was used for splice site detection.
Uniquely aligned reads per gene were counted using FeatureCounts [version 1.6.3] and the respective Ensembl annotation.
Assembly: mm10
Supplementary files format and content: They are tab-separated txt files (one for each tissue) with the output from FeatureCounts, where each row represents a gene and the columns contain the gene information followed by the sample counts.

source_name: subcutaneous WAT

extract_protocol:
Adipose tissues were cryosectioned and specific areas were collected by laser capture microdissection into micro-tubes. Total RNA was isolated using “RNeasy Micro Kit” (Qiagen, Germany).
~2 ng of total RNA for each sample was used for library construction using SMARTSeq2 protocol in DRESDEN-concept Genome Center Dresden.

value: subcutaneous WAT

value: male

tag: temperature

value: GC


title: scWAT_GC_CT_3


title: scWAT_GC_CT_4


title: scWAT_Ctrl_CT_3

value: Ctrl


title: Sham_BNST_Rep1

source_name: BNST

value: BNST


title: FT-LC-Rep2

data_processing:
BWA aligner was used to align raw fastq file to rat genome (rn5)
Dfilter (Kumar et al., Nature Biotechnology, 2013) was used to call peaks using region-specific ChIP-seq files and whole brain control input.
Union of peaks from different brain regions was made and the read-count on those peaks were taken in different brain region
Genome_build: rn5
Supplementary_files_format_and_content: The processed file contain peaks call from Dfilter

source_name: Rat-brain-LC

growth_protocol: Brains were removed and frozen immediately on dry ice. Frozen brains were cryosectioned at 250um thickness onto poly-lysine coated slides. The anatomical regions subject to punching were verified using Nissl-staining of slide sections and the rat brain atlas of Paxinos and Watson

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody.
Libraries were prepared according to Quail et al. 2008-https://doi.org/10.1038/nmeth.1270. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR-amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: 2-months old Charles River rats were treated with 18 mg/kg body weight of fluoxetine (FT group) or water (Sham group), ad libitum for 6 weeks

value: 2 months

value: brain

tag: brain region

value: LC

value: Treatment with Fluoxetine

tag: chip-antibody

value: H3K27ac active motif cat#39133 Lot no.16612005


title: Sham_MPOA_Rep1

description: RNAseq

source_name: MPOA

value: MPOA


title: scWAT_Ctrl_CT_2

tag: tissue


title: FT-Snt-Rep2

source_name: Rat-brain-Snt

value: Snt


title: scWAT_Ctrl_CT_1


title: scWAT_Ctrl_CT_5


title: scWAT_GC_CT_5


title: scWAT_Ctrl_CT_4


title: scWAT_GC_RT_5


title: FT-PAG-Rep2

source_name: Rat-brain-PAG

value: PAG


title: FT-VTA-Rep2

source_name: Rat-brain-VTA

value: VTA


title: FT-arc-Rep2

source_name: Rat-brain-arc

value: arc


title: FT-venCA1-Rep2


title: FT-venDG-Rep2

source_name: Rat-brain-venDG

value: venDG


title: Sham_NaCshell_Rep1

description: RNAseq

source_name: NaCshell

value: NaCshell

value: Sham


title: FT-dorCA1-Rep2


title: FT-dorDG-Rep2

source_name: Rat-brain-dorDG

value: dorDG


title: scWAT_GC_RT_3

value: subcutaneous WAT

value: male

value: GC


title: scWAT_Ctrl_RT_4

value: Ctrl


title: scWAT_GC_RT_1


title: scWAT_GC_RT_2


title: scWAT_Ctrl_RT_3


title: FT-Raphe-Rep2

source_name: Rat-brain-Raphe

value: 2 months

value: brain

value: Raphe


title: FT-CMA-Rep2

source_name: Rat-brain-CMA

value: CMA

value: Treatment with Fluoxetine

value: H3K27ac active motif cat#39133 Lot no.16612005


title: scWAT_Ctrl_RT_1


title: Liver, DDC diet, 7 days [Smart_seq2_Hepatocytes_Z104]

description:
Smart_seq2
Smart_seq2_Hepatocytes_Z104

source_name: Liver

value: Liver

value: primary cells

tag: cell type

value: Hepatocytes

value: DDC diet for 7 days


title: Liver, DDC diet, 7 days [Smart_seq2_Hepatocytes_Z103]

description:
Smart_seq2
Smart_seq2_Hepatocytes_Z103


title: Liver, DDC diet, 0 day and 7 days [Smart_seq2_Hepatocytes_Z102]

description:
Smart_seq2
Smart_seq2_Hepatocytes_Z102

value: DDC diet for 0 day and 7 days


title: FT-LH-Rep2

source_name: Rat-brain-LH

value: LH


title: Liver, DDC diet, 0 days, n=1  for all normal diet in Smart_seq2 method [Smart_seq2_Hepatocytes_Z101]

description:
Smart_seq2
Smart_seq2_Hepatocytes_Z101

value: DDC diet for 0 day


title: scWAT_GC_RT_4

value: subcutaneous WAT


title: goWAT_GC_CT_5

source_name: gonadal WAT

value: gonadal WAT

value: male


title: FT-BLA-Rep2

source_name: Rat-brain-BLA

value: BLA


title: Liver, DDC diet, 7 days [Smart_seq2_Hepatocytes_L4]

description:
Smart_seq2
Smart_seq2_Hepatocytes_L4


title: goWAT_GC_CT_4

value: GC


title: goWAT_GC_CT_3


title: Liver, DDC diet, 3 days [Smart_seq2_Hepatocytes_L2]

description:
Smart_seq2
Smart_seq2_Hepatocytes_L2

value: DDC diet for 3 days


title: FT-VMH-Rep2

source_name: Rat-brain-VMH

value: 2 months

value: brain

value: VMH


title: FT-BNST-Rep2

source_name: Rat-brain-BNST

value: BNST

value: Treatment with Fluoxetine

value: H3K27ac active motif cat#39133 Lot no.16612005


title: goWAT_GC_CT_2


title: Liver, DDC diet, 3 days and 7 days [Smart_seq2_Hepatocytes_L5]

description:
Smart_seq2
Smart_seq2_Hepatocytes_L5

value: Liver

value: primary cells

value: Hepatocytes

value: DDC diet for 3 days and 7 days


title: Liver, DDC diet, 3 days [Smart_seq2_Hepatocytes_L1]

description:
Smart_seq2
Smart_seq2_Hepatocytes_L1


title: FT-LS-Rep2

source_name: Rat-brain-LS

value: LS


title: K-NSCs-3

city: yichang

first: yafeng

last: lv

address: No. 8, Daxue Road, Xiling District, Yichang City

institute: China Three Gorges University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp [1] (version 0.18.0). The parameters were as follow:1) removing reads containing adapters;2) removing reads containing more than 10% of unknown nucleotides (N);3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 [2] (version 2.2.8) was used for mapping reads to ribosome  RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation
An index of the reference genome was built, and aired-end clean reads were mapped to the reference genome using HISAT2. 2.4[3] with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1[4][5] in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software.
RNAs differential expression analysis was performed by DESeq2[6] software between two different groups (and by edgeR[7] between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts
Assembly: GRCH38/hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: skin

growth_protocol: iPSCs cultured under feeder-free conditions in Essential 8 ™ Medium on vitronectin.

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

treatment_protocol: We started with high-quality human iPSCs cultured under feeder-free conditions, such as in Essential 8 ™ Medium on vitronectin. When the iPSCs reached ~70–80% confluency, they are dislodged to generate cell clumps. NSC culture medium was added to vitronectin coated 6-well plates . Conical tubes containing iPSC suspensions were gently shaken, and then the iPSCs were seeded into wells at a density of 2.5 × 105 iPSCs/well. The plates were moved in several quick back-and-forth and side-to-side motions to disperse the cells across the surface and then gently placed in a CO2 incubator. On days 2 and 4, remove any non-neural differentiated colonies and add 5 mL of pre-warmed complete PSC Neural Induction Medium into each well.. On day 6 of neural induction, the cells reached near maximal confluence. On day 7 of neural induction, the NSCs (P0) were harvested and expanded. Of note, after dissociating the NSCs, overnight treatment with the ROCK inhibitor Y27632 was required at the time of plating to prevent cell death during both expansion and differentiation.

value: Globoid Cell Leukodystrophy

value: skin

value: NSCs

value: GALC mutation


title: scWAT_Ctrl_RT_2

source_name: subcutaneous WAT

value: subcutaneous WAT

value: male

value: Ctrl


title: FT-NaCcore-Rep2

source_name: Rat-brain-NaCcore

value: 2 months

value: brain

value: NaCcore


title: K-NSCs-1


title: FT-MDT-Rep2

source_name: Rat-brain-MDT

value: MDT

value: Treatment with Fluoxetine


title: goWAT_Ctrl_CT_5

value: gonadal WAT


title: goWAT_GC_CT_1

value: GC


title: K-NSCs-2


title: AF-NSCs-2

value: Normal Control

value: WT


title: FT-NaCshell-Rep2

source_name: Rat-brain-NaCshell

value: NaCshell

value: H3K27ac active motif cat#39133 Lot no.16612005


title: goWAT_Ctrl_CT_2


title: K-iPSCs-3

value: Globoid Cell Leukodystrophy

value: skin

value: iPSCs


title: AF-iPSCs-1


title: AF-NSCs-1

value: NSCs


title: goWAT_Ctrl_CT_4

value: male


title: AF-NSCs-3


title: FT-PLC-Rep2

source_name: Rat-brain-PLC

value: PLC


title: AF-iPSCs-2


title: FT-ILC-Rep2

source_name: Rat-brain-ILC

value: 2 months

value: ILC


title: K-iPSCs-1

value: GALC mutation


title: AF-iPSCs-3


title: goWAT_Ctrl_CT_3

value: Ctrl


title: goWAT_Ctrl_CT_1


title: BLAS cells expressing wild type Tat [blas_tat_3]

city: Villejuif

first: Anna

last: Schwager

state: Please Select

address: 39 114 Rue Edouard Vaillant

department: CNRS UMR9018

country: France

institute: Institut Gustave Roussy

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence by Novogene in-house scripts.
Trimmed sequencing reads were mapped to the human genome (assembly GRCh38.p10) using HISAT2 (version 2.0.5).
Read counting was performed using featureCounts in a strand-specific mode. GENCODE v26 gene annotation (ALL) was used.
Assembly: GRCh38.p10
Supplementary files format and content: csv file with raw counts for each sample

source_name: BLAS

growth_protocol: BLAS cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 2% glucose, 2 mM L-Glutamine, 1 mM Pyruvate and 1× penicillin/streptomycin antibiotics (all from Gibco, Thermo Fisher Scientific, Waltham, Massachusetts, USA). Jurkat T cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% D-glucose, 1M HEPES Buffer solution, 100 mM sodium pyruvate, 1x penicillin/streptomycin antibiotics (all from Gibco).

extract_protocol:
Total RNA from BLAS cells was isolated using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany) following manufacturer's instructions. 3 ug of total RNA was sent for the construction of sequencing libraries.
RNA-seq libraries were prepared using the Agilent SureSelect Automated Strand-Specific RNA Library Prep using the manufacturer's protocol.

value: BLAS

value: lymphoblastoid B-cells

value: expressing WT Tat

value: no

tag: time

value: Day 0


title: FT-MS-Rep2

source_name: Rat-brain-MS

value: brain

value: MS

tag: treatment

value: Treatment with Fluoxetine


title: Liver, DDC diet, 3 days and 7 days, n=2  for all DDC3d/7d in Smart_seq2 method [Smart_seq2_Hepatocytes_L3]

description:
Smart_seq2
Smart_seq2_Hepatocytes_L3

value: Liver

value: primary cells

value: Hepatocytes

value: DDC diet for 3 days and 7 days


title: BLAS cells expressing wild type Tat [blas_tat_2]


title: K-iPSCs-2

tag: disease state

value: Globoid Cell Leukodystrophy

value: skin

value: iPSCs


title: goWAT_GC_RT_5

value: gonadal WAT

tag: Sex

value: male

value: GC


title: FT-InsularCortex-Rep2

source_name: Rat-brain-InsularCortex

tag: age

value: 2 months

value: InsularCortex

value: H3K27ac active motif cat#39133 Lot no.16612005


title: FT-CGC-Rep2

source_name: Rat-brain-CGC

value: CGC


title: goWAT_GC_RT_4


title: Sham-Snt-Rep2

source_name: Rat-brain-Snt

value: brain

value: Snt

value: untreated


title: Sham-LC-Rep2

source_name: Rat-brain-LC

value: LC


title: BLAS cells expressing mutated Tat [blas_tatc22g_3]

value: BLAS

value: lymphoblastoid B-cells

value: expressing Tat C22G

value: no

value: Day 0


title: BLAS cells expressing mutated Tat [blas_tatc22g_2]


title: BLAS cells expressing wild type Tat [blas_tat_1]

value: expressing WT Tat


title: BLAS cells expressing mutated Tat [blas_tatc22g_1]


title: BLAS cells, control  [blas_2]

value: WT


title: BLAS cells, control  [blas_1]


title: goWAT_GC_RT_3

source_name: gonadal WAT

value: gonadal WAT

value: male


title: NC-2

city: Suzhou

first: Wenzhuo

last: Zhuang

state: Jiangsu

address: Ren Ai Road 199

department: Department of Cell Biology, School of Biology & Basic Medical Sciences

institute: Soochow University

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each genewere obtained by htseq-count. DEGs were identified using the DESeq( 2012) R package  functions estimateSizeFactors and nbinomTest. GO enrichmentand KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
If it was transcript-level quantification, FPKM and read counts value of each transcript (protein_coding) was calculated using bowtie2 and eXpress . DEGs were identified using the DESeq (2012) functions estimateSizeFactors and nbinomTest. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
The reads were reassembled using StringTie . Then gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software.The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofile
Genome_build: hisat2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: LP-1 cells

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego,CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or Illumina HiSeq X Ten) and 125bp/150bp paired-end reads were generated.

tag: sirna

value: Ctrl

value: myeloma


title: Sham-Raphe-Rep2

source_name: Rat-brain-Raphe

value: 2 months

value: Raphe

value: H3K27ac active motif cat#39133 Lot no.16612005


title: shSRSF1-1


title: BLAS cells, control  [blas_3]


title: NC-1


title: shSRSF1-2


title: goWAT_Ctrl_RT_3

tag: strain


title: Sham-PAG-Rep2

source_name: Rat-brain-PAG

value: brain

value: PAG


title: RNA-Seq of sus scrofa: cell population from blastocyst seeding [Type_D2]

city: Seoul

first: Chang-Kyu

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

data_processing:
The paired-end sequencing was performed using an Illumina NovaSeq 6000
Using FastQC, sequences were filtered and quality of reads were analyzed
RPKM and TPM were calculated from nuber of read counts
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: raw counts of sequencing reads and processed read counts including RPKM

organism: Sus scrofa

source_name: Seeding colonies of porcine blastocyst

growth_protocol: Day 7 blastocysts were attached on the murine fetal fibroblast and cultured for 14 days. Four cell types were isolated under conditioned porcine embryonic stem cell medium.

extract_protocol:
Total RNA was extracted using proper kit (Invirustech, South Korea, Cat#; IVF3001)
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing was used to prepare samples for running

value: embryo originated cells

tag: cell population

value: D; Mesoderm-like cells


title: Sham-venCA1-Rep2

value: untreated


title: RNA-Seq of sus scrofa: cell population from blastocyst seeding [Type_D1]


title: Sham-venDG-Rep2

source_name: Rat-brain-venDG

value: venDG


title: Sham-VTA-Rep2

source_name: Rat-brain-VTA

value: VTA


title: goWAT_GC_RT_1

value: GC


title: goWAT_Ctrl_RT_2


title: RNA-Seq of sus scrofa: cell population from blastocyst seeding [Type_D]


title: Sham-dorCA1-Rep2


title: RNA-Seq of sus scrofa: cell population from blastocyst seeding [Type_C1]

value: C; Trophectoderm-like cells


title: goWAT_Ctrl_RT_1


title: RNA-Seq of sus scrofa: cell population from blastocyst seeding [Type_C2]


title: Sham-DorDG-Rep2

source_name: Rat-brain-DorDG

value: DorDG


title: RNA-Seq of sus scrofa: cell population from blastocyst seeding [Type_C]


title: RNA-Seq of sus scrofa: cell population from blastocyst seeding [Type_B2]

value: B; Primitive endoderm-like cells


title: goWAT_GC_RT_2

value: gonadal WAT

value: male


title: goWAT_Ctrl_RT_4

value: Ctrl


title: iBAT_GC_CT_4

source_name: interscapular BAT

value: interscapular BAT


title: RNA-Seq of sus scrofa: cell population from blastocyst seeding [Type_B1]


title: Sham-CMA-Rep2

source_name: Rat-brain-CMA

value: 2 months

value: CMA


title: iBAT_GC_CT_3


title: Sham-BLA-Rep2

source_name: Rat-brain-BLA

value: brain

value: BLA

value: H3K27ac active motif cat#39133 Lot no.16612005


title: RNA-Seq of sus scrofa: cell population from blastocyst seeding [Type_B]

value: embryo originated cells


title: RNA-Seq of sus scrofa: cell population from blastocyst seeding [Type_A2]

value: A; Epiblast-like cells


title: RNA-Seq of sus scrofa: cell population from blastocyst seeding [Type_A1]


title: Sham-VMH-Rep2

source_name: Rat-brain-VMH

value: VMH

value: untreated


title: iBAT_GC_CT_2

value: GC


title: RRB1527

description:
10x Genomics Gene Expression*3'v2
venDG2021_countmatrix.csv.gz

data_processing:
RNA-seq data were aligned to the Rattus norvegicus rn5 genome (Rn5 ENSEMBL) and processed using Cell Ranger (10x Genomics) pipeline
Seurat v3 pipeline
Genome_build: Rn5
Supplementary_files_format_and_content: fastq and count matrix

growth_protocol: Tissue single-cell RNA-seq. Brains were removed and transported on ice in ice cold PBS. The brain was placed on brain slicer moulds and sectioned closer to the hippocampal planes. Dorsal dentate gyrus and ventral dentate gyrus regions were micropunched across 5-6 planes. The anatomical regions subject to punching were verified using the rat brain atlas of Paxinos and Watson.

extract_protocol:
10x Genomics Chromium snRNA-seq was performed on nuclei extracted from dorsal dentate gyrus (dorDG) and ventral dentate gyrus (venDG) regions of control and fluoxetine-treated rats (6 weeks of fluoxetine treatment). All rats were male. Cell-types were identified by unsupervised clustering and differential gene expression was performed between cases and controls for each cell-type cluster. The library preparation was performed with the Chromium Single Cell 3’ Reagent Kits v2. Paired-end sequencing with single-indexing was performed on the HiSeq Illumina 4000. FastQ files were produced with Cellranger v2.1.0 mkfastq. Alignments and gene counts were generated with Cellranger v2.1.0 count.
10x Chromium Single Cell 3’ Reagent Kit v2

tag: sample name

tag: single cell library id

tag: brain region_replicate

tag: treatmeant

value: FT


title: RRB1526


title: Sham-LH-Rep2

source_name: Rat-brain-LH

value: LH


title: RRB1525


title: Sham-MDT-Rep2

source_name: Rat-brain-MDT

value: MDT


title: RRB1524


title: iBAT_GC_CT_5

tag: temperature


title: RRB1523

description:
10x Genomics Gene Expression*3'v2
dorDG2021_countmatrix.csv.gz


title: iBAT_Ctrl_CT_5


title: RRB1522


title: Sham-MPOA-Rep2

source_name: Rat-brain-MPOA

tag: brain region

value: MPOA


title: iBAT_Ctrl_CT_4

value: male


title: RRB1521


title: RRB1520


title: Sham-BNST-Rep2

source_name: Rat-brain-BNST

value: BNST

tag: chip-antibody


title: iBAT_Ctrl_CT_3

tag: tissue

value: interscapular BAT

value: Ctrl


title: RRB1519

value: Sham


title: RRB1518


title: RRB1517


title: Sham-MS-Rep2

source_name: Rat-brain-MS

value: 2 months

value: brain

value: MS


title: Sham-LS-Rep2

source_name: Rat-brain-LS

value: LS

value: H3K27ac active motif cat#39133 Lot no.16612005


title: RNA-Seq of sus scrofa: cell population from blastocyst seeding [Type_A]

tag: cell type

value: embryo originated cells

value: A; Epiblast-like cells


title: RRB1516


title: iBAT_Ctrl_CT_2


title: Sham-NaCcore-Rep2

source_name: Rat-brain-NaCcore

value: NaCcore

value: untreated


title: RRB1514


title: iBAT_Ctrl_CT_1


title: RRB1513


title: iBAT_GC_CT_1

value: GC


title: iBAT_GC_RT_5


title: RRB1511

value: FT


title: RRB1512


title: Sham-NaCshell-Rep2

source_name: Rat-brain-NaCshell

value: NaCshell


title: iBAT_GC_RT_4

value: male


title: Sham-InsularCortex-Rep2

source_name: Rat-brain-InsularCortex

value: InsularCortex


title: RRB1510


title: RRB1509


title: RRB1508


title: iBAT_GC_RT_3

value: interscapular BAT


title: RRB1507


title: iBAT_GC_RT_2


title: Sham-ILC-Rep2

source_name: Rat-brain-ILC

value: ILC


title: Sham-CGC-Rep2

source_name: Rat-brain-CGC

value: CGC


title: RRB1506


title: iBAT_GC_RT_1


title: RRB1515

value: Sham


title: RRB1505


title: RRB1504


title: Sham+FT-Input4-Rep1

value: 2 months

value: brain

value: none (input)


title: Sham-PLC-Rep2

source_name: Rat-brain-PLC

value: PLC

value: H3K27ac active motif cat#39133 Lot no.16612005


title: iBAT_Ctrl_RT_2

value: Ctrl


title: iBAT_Ctrl_RT_3


title: RRB1502


title: RRB1503


title: RRB1501


title: RRB1499


title: iBAT_Ctrl_RT_1


title: Sham+FT-Input2-Rep1


title: RRB1498


title: RRB1497


title: RRB1500


title: RRB1496


title: Sham+FT-Input1-Rep1


title: RRB1495


title: RRB1491


title: FT-LC-Rep1

source_name: Rat-brain-LC

value: LC

value: Treatment with Fluoxetine


title: RRB1492


title: FT-Snt-Rep1

source_name: Rat-brain-Snt

value: Snt


title: RRB1494

value: FT


title: RRB1493


title: RRB1490


title: RRB1489


title: Sham+FT-Input3-Rep1

value: untreated


title: FT-PAG-Rep1

source_name: Rat-brain-PAG

value: PAG


title: RRB1488


title: Bulk RNA-seq E4_Old_Bulk RNA-seq rep5

city: Lexington

first: Lance

middle: A

last: Johnson

state: KY

address: 760 Press Ave, HKRB 135

department: Physiology/Sanders-Brown Center on Aging

institute: University of Kentucky

data_processing:
Raw FASTQ data and H&E images were processed by the Space Ranger v1.3.0 (10X Genomics) pipeline. Illumina base call (BCL) files from the sequencing instrument were converted to FASTQ format for each sample using the mkfastq. Visium spatial expression libraries were analyzed with the count command. Image alignment to predefined spots was performed by the fiducial alignment grid of the tissue image to determine the orientation and position of the input image. Sequencing reads were aligned to the mm10 reference genome using STAR (v2.5.1b) aligner. Gene expression profiling in each spot was performed with UMI and 10X barcode information.
Assembly: mm10
Supplementary files format and content: Count txt files

source_name: Brain

extract_protocol:
The mirroring hemisphere (right) from brains processed for scRNAseq were immediately placed in OCT compound (Fisher HealthCare Tissue Plus O.C.T. Compound Clear 4585) and gently lowered into isopentane (Sigma Aldrich 2-Methylbutane M32631) in a beaker surrounded by dry ice (isopentane chilled to approximately -70°C). Brains were submerged for 60 seconds, placed on dry ice, wrapped in aluminum foil, and stored at -80°C until sectioning. Prepared brain hemispheres were cryosectioned to 10 μm thick coronal sections at approximately Bregma -2.00 mm. Serial 10 μm sections immediately rostral and caudal to the section mounted on the Visium Spatial Gene Expression slide (10X Genomics) were collected for immunohistochemistry. Optimal tissue permeabilization time was determined using the manufacturer’s optimization protocols (10X Genomics, Visium Spatial Tissue Optimization), and accordingly, experimental tissues were permeabilized for 18 min for Visium Spatial Gene Expression analysis. Prior to library preparation, tissue sections were methanol-fixed, stained with hematoxylin and eosin (H&E), and imaged on a Nikon NiU microscope with Fi3 color camera. Sections were then permeabilized and processed to obtain cDNA libraries, which were subsequently prepared according to the manufacturer’s protocol (https://support.10xgenomics.com/spatial-gene-expression/libraryprep).
Sample libraries were constructed using Next GEM automated 3’ reagents (10X Genomics, v3.1) following manufacturer’s suggested protocol (#CG000286 Rev B). Final library quantification and quality check was performed using BioAnalyzer (Agilent), and sequencing performed on a NovaSeq 6000 S4 flow cell, 150 bp Paired-End sequencing (Novogene).

value: Brain

value: Brain cells

tag: genotype


title: Bulk RNA-seq E4_Young_Bulk RNA-seq rep2

tag: treatment


title: Bulk RNA-seq E4_Old_Bulk RNA-seq rep4


title: FT-Raphe-Rep1

source_name: Rat-brain-Raphe

value: Raphe


title: Bulk RNA-seq E4_Young_Bulk RNA-seq rep3


title: Bulk RNA-seq E3_Young_Bulk RNA-seq rep2


title: RRB1486


title: RRB1485


title: Bulk RNA-seq E3_Young_Bulk RNA-seq rep1


title: FT-arc-Rep1

source_name: Rat-brain-arc

value: arc


title: Bulk RNA-seq E3_Old_Bulk RNA-seq rep3


title: FT-venCA1-Rep1


title: Illumina_Day4 replicate 1

city: Rehovot

first: Bareket

last: Dassa

address: 234 Herzl st.

department: Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

data_processing:
Raw reads were analyzed using the UTAP transcriptome analysis pipeline [Kohen, R., et al]. Initially, reads were trimmed using cutadapt to remove TruSeq adaptors (with the parameters: -times 2 -q 20 -m 25). Reads were mapped to the genome (mm10, GenCode annotation) using STAR (v2.4.2a) with the parameters –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic
Counting reads on genes was done using htseq-count using mm10 Gencode annotation (downloaded from iGenomes UCSC)
Genome_build: mm10
Supplementary_files_format_and_content: htseq gene counts

source_name: Embryonic Stem Cells

growth_protocol: Embryoid bodies (Ebs) where generated by 4 days incubation of single cell suspension (35000 cells/ml) of R1 mouse  embryonic stem (mES) cells in 5 ml mES growth medium (DMEM, 15% FBS, L-Glutamine, Non-Essential Amino Acids) and named sample undiff,  then for 4 days, 2-beta-Mercaptoethanol, without Lif in 6 cm low cell binding dishes.

extract_protocol:
RNA was extracted with an RNeasy Mini kit (Qiagen)
1 microgram of total RNA was processed using the Illumina TruSeq RNA Sample Preparation Kit v2 protocol and 700ng for the Illumina TruSeq Strand Specific total RNA with RiboZero Gold protocol (Illumina). Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of 9 samples on three lanes. Libraries were prepared using protocols RTA (1.17.21.3) and HCS (2.0.12.0).

treatment_protocol: Four-day-old Ebs where treated for 4 days with 2mM Retinoic Acid (RA) (Retinoic Acid, Sigma R2625). The day of RA addition corresponds to the sample name day 0. Day 4 corresponds to the sample that had been treated for 4 days with RA.

tag: cell line

value: Embryoid bodies


title: RRB1479


title: Bulk RNA-seq E4_Mid_Bulk RNA-seq rep3


title: FT-venDG-Rep1

source_name: Rat-brain-venDG

value: 2 months

value: venDG


title: Illumina_Undiff replicate 2


title: Bulk RNA-seq E3_Mid_Bulk RNA-seq rep3


title: FT-HB-Rep1

source_name: Rat-brain-HB

value: brain

value: HB


title: RRB1487

value: Sham


title: FT-VTA-Rep1

source_name: Rat-brain-VTA

value: VTA

value: H3K27ac active motif cat#39133 Lot no.16612005


title: RRB1478


title: FT-dorCA1-Rep1

value: Treatment with Fluoxetine


title: RRB1477


title: RRB1484


title: Illumina_Undiff replicate 1


title: RRB1476


title: Bulk RNA-seq E4_Old_Bulk RNA-seq rep3


title: Bulk RNA-seq E3_Mid_Bulk RNA-seq rep2


title: FT-dorDG-Rep1

source_name: Rat-brain-dorDG

value: dorDG


title: Bulk RNA-seq E3_Old_Bulk RNA-seq rep2


title: RRB1475


title: delta_2C-CM 2D Sample 10

city: Cambridge

first: Vincent

last: Butty

address: 77 Massachusetts Avenue Bldg 68-317A

department: Biology / Koch Institute / Bioengineering / CEHS

institute: Massachusetts Institute of Technology

data_processing:
Reads were aligned against hg19 (Feb. 2009) using bwa mem v. 0.7.12-r1039 with flags –t 16 –f, and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5´ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using bedtools v. 2.25.0. In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against hg19, and read density across genomic features were estimated for RNA-Seq-specific quality control metrics.
For mapping and quantitation, reads were scored against GRCh38/ENSEMBL 101 annotation using Salmon v.1.3 with flags quant -p 8 -l ISR –validateMappings [PATRO2017]. The resulting  quant.sf files were imported into the R statistical environment using the tximport library (tximport function, option “salmon”), and gene-level counts and transcript per-milllion (TPM) estimates were calculated at gene level.
Assembly: hg38 (ENSEMBL 101)
Supplementary files format and content: Tab-delimited text file with tx_import-processed Salmon quantification files, collapsed as counts/ gene and log2TPM/gene.

source_name: iPSC-derived cardiomyocytes

growth_protocol: hiPSC were seeded onto 12-well plates at 60,000 cells/well and maintained  until they reached 60% confluence. On days 0 – 2 of differentiation, cells were cultured with RPMI (Cat. # 11875093, Thermo Fisher Scientific) supplemented with B27 minus insulin (Cat. # A1895601, Thermo Fisher Scientific) and 6µM CHIR99021 (Cat. # 72054, Stem Cell Technologies). Cells were replenished with RPMI/B27(-insulin) on day 3, then cultured with RPMI/B27(-insulin) supplemented with 5µM IWR1-endo (Cat. # 2564, Stem Cell Technologies) on days 4 and 5.  From days 6 – 12, cells were maintained in RPMI/B27(-insulin) with media changes every 48 hours. Lactate selection was performed on day 12 for 48hrs with RPMI supplemented with 5mM sodium lactate (Cat. # L7022, MilliporeSigma).

extract_protocol:
RNA was extracted with Trizol (Thermo Fisher) followed by a column based purification (Zymo Research). Eluates were stored at -80C prior to sequencing.
One microliter of undiluted total RNA was incubated with 10ul of NEB Dynabeads for polyaA+ RNA selection, eluted, and fragmented in 12ul. Illumina libraries were constructed using NEB Ultra II protocol; 5ul of the fragmented solution using half the amount of reagent and 1,2 PrD instead of enhancer in the ligation step, with 16 PCR cycles of final amplification and duplex barcoding. Libraries were quantified using the Fragment Analyzer and qPCR before being sequenced on an Illumina NextSeq 500 using 75-bp paired-end reads.

treatment_protocol: iPSC-CMs in each sample were isolated using both positive and negative selection columns (Miltenyi).

value: iPSC-derived cardiomyocytes

tag: iPSc line

value: WTC-11 AAVS1Cas9/+

value: RBPMS2 -/-


title: delta_2C-CM 2D Sample 9


title: FT-BLA-Rep1

source_name: Rat-brain-BLA

tag: age

value: BLA


title: FT-CMA-Rep1

source_name: Rat-brain-CMA

value: CMA


title: Illumina_Day4 replicate 2


title: delta_2C-CM 2D Sample 8


title: RRB1474


title: Bulk RNA-seq E4_Mid_Bulk RNA-seq rep2

value: Brain

value: Brain cells


title: Bulk RNA-seq E4_Mid_Bulk RNA-seq rep1


title: RRB1473


title: delta_2C-CM 2D Sample 7


title: FT-VMH-Rep1

source_name: Rat-brain-VMH

value: VMH


title: FT-LH-Rep1

source_name: Rat-brain-LH

value: 2 months

value: LH


title: Bulk RNA-seq E4_Old_Bulk RNA-seq rep2


title: RRB1472


title: WTC-CM 2D -Sample 6

value: wild type (unedited)


title: RRB1471


title: delta_2C-CM 2D Sample 6


title: FT-MDT-Rep1

source_name: Rat-brain-MDT

value: brain

value: MDT


title: Bulk RNA-seq E3_Old_Bulk RNA-seq rep1


title: RRB1470

value: Sham


title: WTC-CM 2D -Sample 5


title: Bulk RNA-seq E4_Young_Bulk RNA-seq rep1


title: FT-BNST-Rep1

source_name: Rat-brain-BNST

value: BNST

value: H3K27ac active motif cat#39133 Lot no.16612005


title: RRB1468


title: WTC-CM 2D -Sample 3


title: WTC-CM 2D -Sample 4


title: FT-PVN-Rep1

source_name: Rat-brain-PVN

value: PVN

value: Treatment with Fluoxetine


title: RRB1469


title: Bulk RNA-seq E4_Old_Bulk RNA-seq rep1


title: FT-MPOA-Rep1

source_name: Rat-brain-MPOA

value: MPOA


title: RRB1467

value: FT


title: RRB1466


title: Bulk RNA-seq E3_Mid_Bulk RNA-seq rep1

source_name: Brain


title: FT-LS-Rep1

source_name: Rat-brain-LS

value: LS


title: Control,  PBMCs treated with HFn-Cur 3

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differental expression analysis for mRNA and lncRNA was performed using R package DESeq2
Assembly: HG19
Supplementary files format and content: counts, FPKMs, TPMs

source_name: F67, HFn, CUR

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were prepared by centrifugation. Peripheral blood was layered (density=1.077) and centrifuged at 950g for 30 min. After isolation on a Ficoll-Histopaque layer (Sigma, Italy), cell viability was assayed by a trypan blue exclusion test and the cells were used for RNA extraction.

extract_protocol:
Samples were homogenized and total RNA was isolated by Trizol® reagent(Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quntified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA ntegrity number of ≥8 were subjected to deep sequencing.
Sequencing libraries were prepared by the Illumina TruSeq Stranded Total RNA kit (Illumina) using 500-ng total RNA (Illumina) and by the Lexogen SENSE Total RNA-Seq Library Prep Kit using 500-ng total RNA (Lexogen). Qualities of sequencing libraries were assessed with 4200 TapeStation with the DNA1000 reagnt kit. RNA processing has been carried out using Illumina NextSeq 500 Sequencing.

treatment_protocol: PBMCs were independently treated for 48 h with Hfn-BDC (10 μM). The experiment is composed by 4 different condition: AD not treated (AD NT), Controls not treated (CTR NT), AD treated with HfnBDC (AD HfnBDC) and controls treated with HfnBDC (CTR HfnBDC). After treatment, cell viability was assayed by a trypan blue exclusion test.

tag: individual

tag: disease state

value: Control

value: Blood

value: PBMC

value: HFn-Cur


title: Control,  PBMCs treated with HFn-Cur 2

source_name: M70, HFn, CUR


title: FT-NaCcore-Rep1

source_name: Rat-brain-NaCcore

value: 2 months

value: NaCcore


title: FT-NaCshell-Rep1

source_name: Rat-brain-NaCshell

value: NaCshell


title: AD patient,  PBMCs treated with HFn-Cur 4

source_name: F76, HFn, CUR

value: AD


title: RRB1464


title: AD patient,  PBMCs treated with HFn-Cur 3

source_name: F59, HFn, CUR


title: RRB1462


title: FT-InsularCortex-Rep1

source_name: Rat-brain-InsularCortex

value: brain

value: InsularCortex


title: RRB1461


title: RRB1460


title: FT-PLC-Rep1

source_name: Rat-brain-PLC

value: PLC


title: Control,  PBMCs treated with HFn-BDC 4

source_name: M69, HFn, BDC

value: HFn-BDC


title: RRB1459

value: Sham


title: RRB1465


title: Control,  PBMCs treated with HFn-BDC 3

source_name: F67, HFn, BDC


title: Control,  PBMCs treated with HFn-Cur 4

source_name: M69, HFn, CUR


title: Control,  PBMCs treated with HFn-Cur 1

source_name: F53, HFn, CUR