title: female Poecilia latipinna 10, whole brain, Mm treatment


title: female Poecilia latipinna 8, whole brain, Ff treatment

status: Public on Jul 01 2023

type: SRA

city: Austin

first: Rebecca

middle: L

last: Young

state: TX

address: 2415 Speedway #C0930, Patterson Lab 607A

country: USA

institute: University of Texas at Austin

library_source: transcriptomic

data_processing:
Libraries were demultiplexed using a custom python script. Raw 101 bp reads were trimmed to remove low quality base pairs (Phred quality score < 20), reads with few contiguous high-quality base pairs (fewer than 30 bp) using a python script.
python script (http://genomics-pubs.princeton.edu/prv/resources/scripts/TQSfastq.py)
Adapter sequences were trimmed using the program cutadapt (https://cutadapt.readthedocs.io/en/stable/).
To evaluate the quality of the trimmed reads, we ran FastQC (Andrew, 2010) using TACC (Texas Advanced Computing, The University of Texas at Austin).
Reads were pseudoaligned to the Sailfin molly Poecilia latipinna (assembly GCA_001443285.1, retrieved from Ensembl January 2019) with Kallisto (version 0.43.0) using the single-end reads option with a length of 100bp (-l 100), standard deviation of 20 (-s 20).
Assembly: GCA_001443285.1
Supplementary files format and content: tab-delimited Kalisto abundance text files include estimated counts and transcripts per million

molecule: total RNA

organism: Poecilia latipinna

source_name: whole brain

growth_protocol: Fish were maintained in semi-natural on-campus outdoor ponds at the Brakenridgen Field Laboratory at the University of Texas, Austin

extract_protocol:
Immediately following the 30-minute behavioral trial, focal females were immediately decapitated, whole brains were removed and individually immersed in RNAlater solution (Applied Biosystems, Carlsbad, CA, USA) at 4˚ Celsius with gentle shaking for 24 hours, then stored at -80 C (without RNAlater) for subsequent RNA profiling. 1-4 μg of total RNA were used as input for RNA library preparation and sequencing.
RNA libraries for RNA-seq were prepared using Illumina’s TruSeq mRNA Sample Prep Kit.

treatment_protocol: Sexually experienced P. latipinna females were collected from a semi-natural environment and socially isolated for two weeks to ensure sexual receptivity. Each female was subjected to short-term (30min) non-contact dichotomous choice assays. Females were randomly assigned to one of two social choice treatment groups (mate preference with male stimuli to female shoaling partner with female stimuli) without a non-social control. Focal females made preference decisions based on stimuli size differences in both treatments.Each focal female was acclimatized in an opaque cylinder for 5 minutes in the central neutral zone before being released. Following release from habituation, focal females were observed for 15 minutes and position and behavior in tank recorded.  After the first 15 minutes of observations, focal females were brought back to the neutral area and placed in the opaque habituation cylinder while the stimulus fish were switched to opposite sides to ensure that our preference measures were directed at a specific fish rather than a location preference in our experimental tank. Following the stimulus switch, focal females were observed for an additional 15 minutes.

tag: tissue

value: whole brain

tag: preference behavior

value: Ff social context


title: female Poecilia latipinna 12, whole brain, Mm treatment

value: Mm mate choice context


title: female Poecilia latipinna 5, whole brain, Mm treatment


title: female Poecilia latipinna 4, whole brain, Mm treatment


title: female Poecilia latipinna 2, whole brain, Ff treatment


title: Jurkat-1D7_HiC_Rep2

status: Public on May 01 2023

city: New Haven

first: Ya-Chi

last: Ho

state: CT

address: BCMM 349, 295 Congress Ave, BCMM 349

department: Microbial Pathogenesis

institute: Yale University School of Medicine

library_source: genomic

data_processing:
Raw reads were processed using the HiC-Pro 3.0 pipeline with default parameters.
Results were converted to Juicer (.hic) format for further processing and visualization.
Assembly: Hg38 + NL4-3
Supplementary files format and content: .hic, contact matricies at default resolutions for each sample

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

growth_protocol: Jurkat T cells were grown in R10 (RPMI + 10% FBS) at high viability, passaged 1:10 twice weekly.

extract_protocol:
DNA bound to antibody-beads was isolated using a DNA clean and concentrator kit (Zymo Biosciences).
Biotin bound DNA was selecte using streptavadin beads, which were treated with TDE1 (Illumina) to generate a library.

treatment_protocol: Cells were fixed in 2% EM grade PFA for 10 minutes at room temperature with shaking, quenced with 2M glycine to a final concentration of 0.125M, lysed in HiC lysis buffer on ice for 30 minutes, washed twice with HiC lysis buffer, resuspended in an SDS containing buffer. Remaining nuclei were treate with MboI restriction digest over night, followed by ligation at room temperature. Nuclei were then sheered in a Covaris S220 militube. Sheared samples were clarified by centrifugation, precleared with protein A beads, incubated with the antibody overnight, and then collected with additional protein A beads.

value: Blood

tag: cell line

value: Jurkat Cm6

tag: cell type

value: CD4 T cell lymphoma

tag: antibody


title: Jurkat-1G2_HiC_Rep1


title: female Poecilia latipinna 1, whole brain, Ff treatment


title: Jurkat-5F9_HiC_Rep1


title: Jurkat-1D7_HiC_Rep1


title: Jurkat-uninfected_HiC_Rep2


title: Jurkat-uninfected_HiC_Rep1


title: Jurkat-1D7_H3K27AcHiChiP_Rep2

value: Abcam, ab4735


title: Jurkat-1D7_H3K27AcHiChiP_Rep1

value: Abcam, ab4734


title: Jurkat-uninfected_H3K27AcHiChiP_Rep1

value: Abcam, ab4733


title: Jurkat-8B10_H3K27AcHiChiP_Rep2

value: Abcam, ab4732


title: Jurkat-8B10_H3K27AcHiChiP_Rep1

value: Abcam, ab4731


title: Jurkat-5F9_H3K27AcHiChiP_Rep1

value: Abcam, ab4730


title: Jurkat-1G2_H3K27AcHiChiP_Rep1

value: Abcam, ab4729


title: Infected-Jurkat-Pool_hashtags

description:
Infected-Jurkat_atac_fragments.tsv.gz
Mix_CITE_barcodes.tsv.gz
Mix_CITE_features.tsv.gz
Mix_CITE_matrix.mtx.gz

library_source: other

data_processing:
Raw reads were processed using the Cellranger arc pipeline (version 2.0.1) with default parameters, CITE reads were processed with CITE-seq-Count (version 1.4.5).
Assembly: Hg38 + NL4-3
Supplementary files format and content: Matrix files and fragments.tsv files from the cellranger pipeline or CITE-seq-Count, hashkey ~ 1 = 8B10, 2=5F9, 3= 1G2, 4=1D7
Library strategy: Single cell multiome

molecule: protein

extract_protocol:
cDNA, transposed cDNA, and CITE cDNA were extracted according to the 10X multiome protocol with th emodifications described in Mimitou et al.Nat. Biotechnol. 2021.
Libraries were constructed using the 10X multiome protocol with the modificaitons described in Mimitou et al. Nat. Biotechnol. 2021.

treatment_protocol: Dead cells were removed using a bead based kit (STEMCELL Technologies #17899), and hashed using TotalSeq-A antibodies. Each clone was pooled in equal ratios and then lysed on ice with DIG lysis buffer for 5 minutes before washing. Cells werethen loaded into the 10X Chromium controller (10x Genomics) according to the manufacturer protocol.

tag: library type

value: ADT


title: Uninfected-Jurkat_scATAC-seq

description:
Uninfected-Jurkat_atac_fragments.tsv.gz
Uninfected-Jurkat_barcodes.tsv.gz
Uninfected-Jurkat_features.tsv.gz
Uninfected-Jurkat_matrix.mtx.gz


title: Infected-Jurkat-Pool_scATAC-seq

description:
Infected-Jurkat_atac_fragments.tsv.gz
Infected-Jurkat_barcodes.tsv.gz
Infected-Jurkat_features.tsv.gz
Infected-Jurkat_matrix.mtx.gz


title: Uninfected-Jurkat_mRNA-derived-cDNA

molecule: polyA RNA

value: mRNA


title: ATAC_CRISPR_i_sgNT_8B10_Rep3

data_processing:
Raw reads were timmed of the Nextera adpter using cutadapt (version 3.5), mapped using Bowtie2 (version 2.4.4), and used to call peaks with Genrich (version 0.6.1) with options -j -y -r -e chrM -v.
Peaks from all samples were appended, sorted, and merged with bedtools (verison 2.30.0).
DeepTools (version 3.5.1) was used to make bigwig files with bamCoverage (options --binSize 10 --normalizeUsing CPM --ignoreDuplicates)
Assembly: Hg38 + NL4-3
Supplementary files format and content: .bw, bigwig files of genome tracks for ATAC-seq signal from a given sample, resolution of 10bp

extract_protocol:
DNA was isolated using a MinElute PCR cleanup kit (Qiagen #28004) and eluted in 10 L twice. The resulting
The resulting DNA was amplified using NEBNext ULTRA II Q5 master mix (New England Biolabs #M0544X) and Nextera indexing primers for 72°C for 5 minutes, then 98°C for 1 minute, followed by 5 cycles of 98°C for 15 seconds, 63°C for 30 seconds, and 72°C for 1 minute, with a final extension at 72°C for 5 minutes. Additional cycles were added based on qPCR measurements of library amplification for a total of 8–20 cycles per library.

treatment_protocol: cells were lysed on ice for 3 minutes in 50 L ATAC-lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 0.1% NP40, 0.01% digitonin) before the addition of 1mL of ATAC-wash buffer (10 mM Tris-HCl pH 7.4, 10  mM NaCl, 3 mM MgCl2, 0.1% Tween-20). Cells were pelleted at 4°C and then transposed with ATAC-transposition mix (1X TD buffer with 33% PBS, 0.1% Tween-20, 0.01% digitonin, 2.5 L TDE1) at 37°C for 30 minutes.


title: Infected-Jurkat-Pool_mRNA-derived-cDNA


title: ATAC_CRISPR_i_sgNT_8B10_Rep2


title: ATAC_CRISPR_i_sgNT_8B10_Rep1


title: ATAC_CRISPR_i_sgNT_5F9_Rep3


title: cartana_sham_female

status: Public on Jan 17 2024

type: RNA

city: St. Louis

first: Haojia

last: Wu

state: MO

address: 4523 Clayton Ave, MSB Rm 820

institute: Washington University in St Louis

description: ISS by Cartana

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
ISS data processing: ISS data was processed using our in-house pipeline called CellScopes https://github.com/TheHumphreysLab/CellScopes.jl.
Cell segmentation: Cell segmentation was performed using Baysor https://github.com/kharchenkolab/Baysor.
genome assembly: mm10

label: not applicable

organism: Mus musculus

label_protocol: not applicable

extract_protocol: RNA hybridization-based in situ sequencing protocol: Fresh kidneys were incubated in 2-methylbutane (Millipore, Sigma) equilibrated in liquid nitrogen to maintain RNA integrity. Tissues were then stored at −80°C and embedded in cryomolds using OCT (Tissue-Tek 4583) on dry ice. For frozen sectioning, OCT blocks were equilibrated to −18°C, and 10 μm-thick sections were mounted onto the glass slides (1358W; Globe Scientific). Libraries were prepared using the high sensitivity (HS) library preparation kit provided by CARTANA (Sweden) per manufacturer’s instruction. In brief, slides were fixed in freshly prepared formaldehyde diluted in 0.01% DEPC treated PBS, followed by permeabilization in 0.1M HCl (DEPC treated). After dehydration and rehydration in series of alcohol gradients, slides were incubated in RM1-mix (provided by the library kit) overnight at 37°C. Kidney sections were incubated in WB4 (library kit) at 37°C for 30 min. Gene probes were ligated in ligases dissolved in RM2 (library kit) at 37°C for 2 hours. Transcripts were amplified in RM3-mix (library kit) at 30°C overnight. Slides were stained with DAPI for quality control imaging and shipped to 10x Genomics for in situ sequencing.

tag: genotype

tag: Sex

value: female

tag: surgery

value: sham

value: Kidney


title: ATAC_CRISPR_i_sgNT_5F9_Rep1


title: ATAC_CRISPR_i_sgNT_1G2_Rep3


title: ATAC_CRISPR_i_sgNT_5F9_Rep2


title: ATAC_CRISPR_i_sgNT_1G2_Rep2


title: ATAC_CRISPR_i_sgNT_1G2_Rep1


title: ATAC_CRISPR_i_sgNT_1D7_Rep2


title: ATAC_CRISPR_i_sgNT_1D7_Rep3


title: cartana_sham_male

description: ISS by Cartana

value: male


title: ATAC_CRISPR_i_sgNT_1D7_Rep1


title: female Poecilia latipinna 9, whole brain, Ff treatment

value: whole brain

value: Ff social context


title: female Poecilia latipinna 19, whole brain, Ff treatment


title: ATAC_CRISPR_i_sgHIV_8B10_Rep3

value: Blood

value: Jurkat Cm6


title: ATAC_CRISPR_i_sgHIV_8B10_Rep2

value: CD4 T cell lymphoma


title: ATAC_CRISPR_i_sgHIV_8B10_Rep1


title: ATAC_CRISPR_i_sgHIV_5F9_Rep3


title: female Poecilia latipinna 7, whole brain, Ff treatment


title: ATAC_CRISPR_i_sgHIV_5F9_Rep2


title: female Poecilia latipinna 6, whole brain, Mm treatment

value: Mm mate choice context


title: ATAC_CRISPR_i_sgHIV_5F9_Rep1


title: ATAC_CRISPR_i_sgHIV_1G2_Rep3


title: ATAC_CRISPR_i_sgHIV_1G2_Rep2


title: female Poecilia latipinna 3, whole brain, Mm treatment


title: ATAC_CRISPR_i_sgHIV_1D7_Rep3


title: ATAC_CRISPR_i_sgHIV_1G2_Rep1


title: ATAC_CRISPR_i_sgHIV_1D7_Rep2


title: ATAC_CRISPR_i_sgHIV_1D7_Rep1


title: ATAC_CRISPR_a_sgNT_8B10_Rep2


title: ATAC_CRISPR_a_sgNT_8B10_Rep1


title: ATAC_CRISPR_a_sgNT_5F9_Rep2


title: ATAC_CRISPR_a_sgNT_8B10_Rep3


title: ATAC_CRISPR_a_sgNT_1G2_Rep3


title: ATAC_CRISPR_a_sgNT_1G2_Rep2


title: ATAC_CRISPR_a_sgNT_5F9_Rep3


title: ATAC_CRISPR_a_sgNT_1G2_Rep1


title: ATAC_CRISPR_a_sgNT_5F9_Rep1


title: ATAC_CRISPR_a_sgNT_1D7_Rep3


title: ATAC_CRISPR_a_sgNT_1D7_Rep2


title: ATAC_CRISPR_a_sgNT_1D7_Rep1


title: ATAC_CRISPR_a_sgHIV_8B10_Rep3


title: ATAC_CRISPR_a_sgHIV_8B10_Rep2


title: ATAC_CRISPR_a_sgHIV_8B10_Rep1


title: ATAC_CRISPR_a_sgHIV_1G2_Rep3


title: ATAC_CRISPR_a_sgHIV_5F9_Rep1


title: ATAC_CRISPR_a_sgHIV_1G2_Rep2


title: ATAC_CRISPR_a_sgHIV_1G2_Rep1


title: ATAC_CRISPR_a_sgHIV_5F9_Rep3


title: ATAC_CRISPR_a_sgHIV_5F9_Rep2


title: ATAC_CRISPR_a_sgHIV_1D7_Rep2


title: ATAC_CRISPR_a_sgHIV_1D7_Rep1


title: ATAC_CRISPR_a_sgHIV_1D7_Rep3


title: ATAC_Jurkat_Rep3


title: ATAC_Jurkat_Rep2


title: ATAC_Jurkat_Rep1


title: ATAC_8B10_Rep3


title: ATAC_8B10_Rep2


title: ATAC_8B10_Rep1


title: ATAC_5F9_Rep1


title: ATAC_5F9_Rep2


title: ATAC_1D7_Rep3


title: ATAC_1G2_Rep2


title: ATAC_1G2_Rep1


title: 4C_Jurkat_Rep2

data_processing:
Reads were trimmed using Cutadatp (Version 3.5) in paired end mode to remove primer sequences from the 5’ end of reads associated with the target window (Read 1 – NTTCTCTCTCAGGGTCATCCATTCCATG, Read 2 – GAGGGGCGGCGACTGGTGAGTACGCCAAAAATT) and filtered to select only reads with the correct primer sequence using the cutadapt option “--discard-untrimmed”.
Trimmed reads were mapped using Bowtie2 (Version 2.4.4)
Fragement coverage was  quatified across samples using bedtools (version 2.30.0), resuling count file was filtered to remove any row with 0 fragments across all samples.
Bigwig files were generated using DeepTools bamCoverate (version 3.5.1), bin size 10 and otherwise default parameters
Assembly: Hg38 + NL4-3
Supplementary files format and content: 4C_counts.csv - bed file followed by results of bedtools coverage for each sample, .bw - bigwig files of genome tracks for given sample
Library strategy: 4C-Seq

extract_protocol:
DNA was isolated by ehtnol precipitation (1.4mL of 3M sodium acetate and 36mL 100% ethanol were added to 14 mL ligation mixture, frozen at -20 for 4 hours, spun at max speed, wahed twice with 80% ethanol, dired and then resuspended in TE).
1ug of DNA was used to make 8 PCR reactions with NEBNEXT Ultra II Q5 Master Mix and primers targetting the HIV-1 LTR with appended Nextera adapters, program of 98°C for 2 minutes, followed by 30 cycles for 98°C for 10 seconds, 68°C for 30 seconds, 72°C for 1 minute, reducing the annealing temperature by 1°C per cycle until 63°C was reached, with a final extension time of 5 minutes at 72°C. Rections were pooled and then barcoded.

treatment_protocol: Cells were fixed in 2% EM grade PFA for 10 minutes at room temperature with shaking, quenced with 2M glycine to a final concentration of 0.125M, lysed in HiC lysis buffer on ice for 30 minutes, washed twice with HiC lysis buffer, resuspended in an SDS containing buffer. Remaining nuclei were treate with NLAIII restriction digest over night, followed by ligation at room temperature. Nuclei then underwet reverse crosslinking with protinase K at 55C for one hour with 500 rpm shaking, them incubated at 68C overnight. DNA was then phenol-chloroform extracted and and ethanol precipitated before being digested with MluC1 for 4 hours, followed by fresh restriction enzyme and overnight incubation. DNA was then ethnol precipitate and then ligated in dlute conditions to produce circular DNA.


title: ATAC_1D7_Rep2


title: ATAC_1D7_Rep1


title: 4C_Jurkat_Rep1


title: 4C_8B10_Rep2


title: 4C_8B10_Rep1


title: 4C_5F9_Rep2


title: 4C_5F9_Rep1


title: 4C_1G2_Rep1


title: 4C_1G2_Rep2


title: 4C_1D7_Rep2


title: 4C_1D7_Rep1


title: Dr, D949 muscle

status: Public on Jan 16 2023

city: Columbus

first: Genevieve

last: Kendall

state: OH

address: 700 Children's Drive, WA5014

institute: Nationwide Children's Hospital / The Ohio State University

description: alternate title: none

data_processing:
Reads were trimmed with trim galore 0.6.4 and then trimmed to a maxiumum of 150bp
Reads were aligned with STAR 2.7.2b against the zebrafish genome (danRer11) or the mouse genome (mm10)
Reads per gene were counted using HTseq 0.12.4 and the outputs were merged within R
Read counts were normalized in R using EdgeR
All code used in processing is available at https://github.com/MVesuviusC/2022_VGLL2_NCOA2_paper
Assembly: danRer11 or mm10
Supplementary files format and content: geneCountsCombinedDr_norm.txt.gz and geneCountsCombinedDr_norm.txt.gz are tables containing normalized gene counts

organism: Danio rerio

source_name: Normal Back Skeletal Muscle

growth_protocol: Here we describe transgenic zebrafish and mouse allograft models. For our transgenic zebrafish, Gateway cloning was performed to generate CMV-GFP2A-VGLL2NCOA2 and BetaActin-GFP2A-CICDUX4 injection constructs, each containing the human form of the fusion-oncogene. These were injected into zebrafish in combination with Tol2 mRNA at the single cell stage, and fish were monitored for tumor formation. For our mouse allograft models, C2C12 cells were grown in DMEM+20% FBS, and were stably transfected with pcDNA3.1-control or pcDNA3.1-VGLL2NCOA2. Two million cells were injected intramuscularly to generate allograft VGLL2-NCOA2 tumor models.

extract_protocol:
For zebrafish, GFP positive (and thus transgene positive) tumors was extracted and flash frozen. Total RNA was isolated using the QIAGEN Rneasy Microkit. For zebrafish skeletal muscle total RNA was isolated with a QIAGEN Rneasy Minikit using an additional proteinase K step. For mouse allograft models total RNA was isolated using TRIZOL.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Normal Back Skeletal Muscle

value: Wildtype (AB/TL)

tag: age at sac

value: 118 days

tag: transgene

tag: model

value: no transgene


title: Dr, D950 muscle

description: alternate title: none


title: Dr, D951 muscle

description: alternate title: none


title: Dr, D948 muscle

description: alternate title: none


title: ChIP-Seq input 5

status: Public on Nov 21 2022

city: Adelaide

first: Natasha

last: Harvey

state: SA

address: UniSA CRI Building, North Terrace

country: Australia

institute: Centre for Cancer Biology

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the hg19 genome assembly using BWA version 0.7.9a-r786, allowing at most 3 alignments
Peak calling was done by MACS version 1.4
Genome_build: hg19
Supplementary_files_format_and_content: peak files were generates using MACS1.4

source_name: Human lymphatic endothelial cells

extract_protocol:
Refer to Kazenwadel et al, JCI, 2015
Single read – Illumina

value: Human lymphatic endothelial cells

tag: passages

value: 3 and 4

value: HMVEC-dLyAd

tag: chip antibody

value: none (input)


title: ChIP-Seq input 3.5


title: ChIP-Seq FOXC2

description: Control Input 5

value: goat anti-FOXC2 (Abcam, ab5060)


title: ChIP-Seq NFATC1

description: Control Input 5

value: rabbit anti-NFATC1 (Santa Cruz, sc13033X)


title: SRSF7 siRNA 200uM RPTEC rep2

status: Public on Jun 14 2022

description:
c11
RPTEC bulk RNA-seq

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a maximum of one mismatch in the indexing read for sample demultiplexing. RNA-seq reads were then aligned to the mm10 (for mouse) or GRCh38 (for human) with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Raw counts and RPKM were output for downstream analysis.
Assembly: mm10 (GRCm38) and GRCh38
Supplementary files format and content: *csv: Processed files are the raw read counts and RPKM for each gene/sample in comma-separated text format.

source_name: Human primary renal tubular epithelial cells

growth_protocol: Mouse diabetic nephropathy protocol: To establish the model, female db/db mice (BKS.Cg-Dock7m +/+ Leprdb/J from Jackson, BKS background, Lot 642) were subject to left nephrectomy at 5 weeks of age, and at 12 weeks, infected with a renin expressing adeno-associated virus (ReninAAV, 109 genomic copies) to induce hypertension and accelerate disease progression. In addition to the ReninAAV Unx db/db mice, db/m and Unx db/db mice infected with an empty viral vector (LacZ AAV) were included as healthy and diabetic non-hypertensive controls, respectively.

extract_protocol:
Total mRNA were isolated from mouse kidney and human RPTECs using a RNA kit from Qiagen (RNeasy Mini prep kit, Cat# 74104).
Total RNA integrity was determined using Agilent 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol:
Drug treatment protocol: Drug treatments were given to mice as follows:  1. Vehicle (drinking water);   2. Lisinopril (An ACE inhibitor, 10 mg/kg/d in the drinking water);    3. Rosiglitazone (A PPARꙋ activator, 0.007% w/w via admix diet, p.o. ~10 mg/kg/d);   4. JNJ-39933673 (A SGLT2 inhibitor, 0.0075% w/w via admix diet, p.o. 1 ~ mg/kg/d);   5. ACEi plus SGLT2i (dosed as before);   6. ACEi plus rosiglitazone (dosed as before). Terminal samples were collected 48 hours and 2 weeks after treatment inception.
In vitro experiment was performed on human primary tubular epithelial cells (RPTEC) purchased from Lonza (cat# CC-2553, lot 0000635750). RPTECs were treated with SRSF7 siRNA (siGenome, cat# M-015909-01-0020) at concentrations of 100 uM and 200 uM. Scrambled siRNA was used as negative control.

value: RPTEC

value: female

tag: treatment

value: SRSF7 siRNA

tag: treatment timepoint

value: 3 days


title: SRSF7 siRNA 200uM RPTEC rep3

description:
c12
RPTEC bulk RNA-seq


title: ChIP-Seq PROX1

description: Control Input 3.5

value: goat anti-PROX1 (AF2727; R&D Systems)


title: SRSF7 siRNA 200uM RPTEC rep1

description:
c10
RPTEC bulk RNA-seq


title: SRSF7 siRNA 100uM RPTEC rep3

description:
c6
RPTEC bulk RNA-seq


title: SRSF7 siRNA 100uM RPTEC rep1

description:
c4
RPTEC bulk RNA-seq


title: siRNA negative control RPTEC rep1

description:
c1
RPTEC bulk RNA-seq

value: Scrambled siRNA


title: SRSF7 siRNA 100uM RPTEC rep2

description:
c5
RPTEC bulk RNA-seq


title: siRNA negative control RPTEC rep2

description:
c2
RPTEC bulk RNA-seq


title: siRNA negative control RPTEC rep3

description:
c3
RPTEC bulk RNA-seq


title: Grp8b db/db+renin+ACEI+JNJ39933673 Kidney rep5

description:
P3109
whole kidney bulk RNA-seq

value: Kidney

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

value: renin AAV + ACEI + JNJ39933673

value: 2 weeks


title: Grp8b db/db+renin+ACEI+JNJ39933673 Kidney rep4

description:
O3108
whole kidney bulk RNA-seq


title: Grp8b db/db+renin+ACEI+JNJ39933673 Kidney rep2

description:
U3106
whole kidney bulk RNA-seq


title: Grp8b db/db+renin+ACEI+JNJ39933673 Kidney rep3

description:
V3107
whole kidney bulk RNA-seq


title: Grp8b db/db+renin+ACEI+JNJ39933673 Kidney rep1

description:
J3105
whole kidney bulk RNA-seq


title: Grp8a db/db+renin+ACEI+JNJ39933673 Kidney rep5

description:
P3104
whole kidney bulk RNA-seq

value: 2 days


title: Grp8a db/db+renin+ACEI+JNJ39933673 Kidney rep3

description:
H3102
whole kidney bulk RNA-seq


title: Grp8a db/db+renin+ACEI+JNJ39933673 Kidney rep4

description:
O3103
whole kidney bulk RNA-seq


title: Grp8a db/db+renin+ACEI+JNJ39933673 Kidney rep2

description:
G3101
whole kidney bulk RNA-seq


title: Grp8a db/db+renin+ACEI+JNJ39933673 Kidney rep1

description:
A3100
whole kidney bulk RNA-seq


title: Grp7b db/db+renin+JNJ39933673 Kidney rep5

description:
N3099
whole kidney bulk RNA-seq

value: renin AAV + JNJ39933673


title: Grp7b db/db+renin+JNJ39933673 Kidney rep4

description:
M3098
whole kidney bulk RNA-seq


title: Grp7a db/db+renin+JNJ39933673 Kidney rep5

description:
N3094
whole kidney bulk RNA-seq


title: Grp7b db/db+renin+JNJ39933673 Kidney rep3

description:
T3097
whole kidney bulk RNA-seq


title: Grp7b db/db+renin+JNJ39933673 Kidney rep2

description:
M3096
whole kidney bulk RNA-seq


title: Grp7a db/db+renin+JNJ39933673 Kidney rep3

description:
P3092
whole kidney bulk RNA-seq


title: Grp7a db/db+renin+JNJ39933673 Kidney rep2

description:
O3091
whole kidney bulk RNA-seq


title: Grp7a db/db+renin+JNJ39933673 Kidney rep4

description:
M3093
whole kidney bulk RNA-seq


title: Grp7b db/db+renin+JNJ39933673 Kidney rep1

description:
I3095
whole kidney bulk RNA-seq


title: Grp7a db/db+renin+JNJ39933673 Kidney rep1

description:
G3090
whole kidney bulk RNA-seq


title: Grp4b db/db+renin+ACEI Kidney rep3

description:
Q3067
whole kidney bulk RNA-seq

source_name: db/db+renin+ACEI

value: renin AAV + ACEI


title: Grp4b db/db+renin+ACEI Kidney rep5

description:
H3069
whole kidney bulk RNA-seq


title: Grp4b db/db+renin+ACEI Kidney rep4

description:
G3068
whole kidney bulk RNA-seq


title: Grp4b db/db+renin+ACEI Kidney rep2

description:
P3066
whole kidney bulk RNA-seq


title: Grp4b db/db+renin+ACEI Kidney rep1

description:
I3065
whole kidney bulk RNA-seq


title: Grp4a db/db+renin+ACEI Kidney rep4

description:
G3063
whole kidney bulk RNA-seq


title: Grp4a db/db+renin+ACEI Kidney rep5

description:
H3064
whole kidney bulk RNA-seq


title: Grp4a db/db+renin+ACEI Kidney rep2

description:
I3061
whole kidney bulk RNA-seq


title: Grp4a db/db+renin+ACEI Kidney rep1

description:
D3060
whole kidney bulk RNA-seq


title: Grp4a db/db+renin+ACEI Kidney rep3

description:
J3062
whole kidney bulk RNA-seq


title: Grp3b db/db+renin Kidney rep5

description:
B3039
whole kidney bulk RNA-seq

source_name: db/db+renin

value: renin AAV


title: Grp3b db/db+renin Kidney rep4

description:
A3038
whole kidney bulk RNA-seq


title: Grp3b db/db+renin Kidney rep3

description:
K3037
whole kidney bulk RNA-seq


title: Grp3b db/db+renin Kidney rep1

description:
B3035
whole kidney bulk RNA-seq


title: Grp3b db/db+renin Kidney rep2

description:
J3036
whole kidney bulk RNA-seq


title: Grp3a db/db+renin Kidney rep4

description:
A3033
whole kidney bulk RNA-seq


title: Grp3a db/db+renin Kidney rep5

description:
B3034
whole kidney bulk RNA-seq


title: Grp3a db/db+renin Kidney rep3

description:
D3032
whole kidney bulk RNA-seq


title: Grp3a db/db+renin Kidney rep1

description:
I3030
whole kidney bulk RNA-seq


title: Grp2 db/db+PBS Kidney rep3

description:
A3026
whole kidney bulk RNA-seq

source_name: db/db+PBS

value: PBS


title: Grp2 db/db+PBS Kidney rep5

description:
C3028
whole kidney bulk RNA-seq


title: Grp2 db/db+PBS Kidney rep1

description:
N3024
whole kidney bulk RNA-seq


title: Grp2 db/db+PBS Kidney rep2

description:
B3025
whole kidney bulk RNA-seq


title: Grp2 db/db+PBS Kidney rep4

description:
B3027
whole kidney bulk RNA-seq


title: Grp1 db/m+PBS Kidney rep5

description:
H3023
whole kidney bulk RNA-seq

source_name: db/m+PBS

value: BKS.Cg-Dock7m +/- Leprdb/J Leprdb- heterozygous


title: Grp1 db/m+PBS Kidney rep4

description:
G3022
whole kidney bulk RNA-seq


title: Grp1 db/m+PBS Kidney rep1

description:
E3019
whole kidney bulk RNA-seq


title: Grp8b db/db+renin+ACEI+JNJ39933673 rep5

description:
snRNA-seq using 10X Chromium
P3109

data_processing:
Illumina data were demultiplexed and the resulting fastq files were processed by the 10X Genomics cellranger pipeline (version 6.0.1). Reads were mapped to mouse genome mm10. Both exonic and intronic reads were incorporated in the final molecule counts.
We used CellBender to remove the ambient RNA contamination. In brief, the unfiltered count matrices sampleID.h5 from cellranger were input into CellBender. CellBender remove-background was run (on cuda mode) with parameters “expected-cells” and “total-droplets-included” were chosen for each dataset based on the total UMI per cell vs. cell barcode curve in accordance with CellBender documentation. Other parameters were left at their default values. The CellBender corrected count matrices were then input to DoubletFinder to remove the potential doublets. We used default parameters to run DoubletFinder except for the nExp, which is estimated based on the total cell number of the sample (nNuc) and a linear regression equation derived from the Demuxlet study, i.e. nExp = nNuc * (0.018+8.4e-06* nNuc).
Genome_build: mm10
Supplementary_files_format_and_content: The hdf5 files contain the count matrix generated by CellRanger for each sample. The count_matrix_combined_after_cellbender.tar.gz file contains the gene-by-cell count matrix for all cells combined after data QC. The metadata.csv file is the meta data (e.g. cell type annotation, mouseID, group ID and the UMAP coordinates) for all high-quality cells included in the analysis.

extract_protocol:
Single nucleus were isolated using a protocol developed from our lab (dx.doi.org/10.17504/protocols.io.nahdab6).
Single nucleus suspensions at a concentration of 1000 nuclei/ul were loaded into the Chromium Controller as per manufacturer instructions, which target 10,000 nuclei per sample. 12 PCR cycles were used for cDNA synthesis. Each library was sequenced using an Illumina NovaSeq instrument, 8 samples per S4 lane, with one 150 bp read located near the 3′ end of the mRNA.
10x chromium 3' kit version 3 chemistry

treatment_protocol:
To establish the model, female db/db mice (BKS.Cg-Dock7m +/+ Leprdb/J from Jackson, BKS background, Lot 642) were subject to left nephrectomy at 5 weeks of age and, at 12 weeks, infected with a renin expressing adeno-associated virus (ReninAAV, 109 genomic copies) to induce hypertension and accelerate disease progression. In addition to the ReninAAV Unx db/db mice, db/m and Unx db/db mice infected with an empty viral vector (LacZ AAV) were included as healthy and diabetic non-hypertensive controls, respectively.
Drug treatments were given to mice as follows:   1. Vehicle (drinking water)  2. Lisinopril (An ACE inhibitor, 10 mg/kg/d in the drinking water),    3. Rosiglitazone (A PPARꙋ activator, 0.007% w/w via admix diet, p.o. ~10 mg/kg/d)  4. JNJ-39933673 (A SGLT2 inhibitor, 0.0075% w/w via admix diet, p.o. 1 ~ mg/kg/d)  5. ACEi plus SGLT2i (dosed as before).   6. ACEi plus rosiglitazone (dosed as before). Terminal samples were collected 48 hours and 2 weeks after treatment inception


title: Grp1 db/m+PBS Kidney rep2

description:
A3020
whole kidney bulk RNA-seq


title: Grp8b db/db+renin+ACEI+JNJ39933673 rep4

description:
snRNA-seq using 10X Chromium
O3108


title: Grp8b db/db+renin+ACEI+JNJ39933673 rep3

description:
snRNA-seq using 10X Chromium
V3107


title: Grp8b db/db+renin+ACEI+JNJ39933673 rep2

description:
snRNA-seq using 10X Chromium
U3106


title: Grp8a db/db+renin+ACEI+JNJ39933673 rep4

description:
snRNA-seq using 10X Chromium
O3103


title: Grp8a db/db+renin+ACEI+JNJ39933673 rep2

description:
snRNA-seq using 10X Chromium
G3101


title: Grp8a db/db+renin+ACEI+JNJ39933673 rep1

description:
snRNA-seq using 10X Chromium
A3100


title: Grp8b db/db+renin+ACEI+JNJ39933673 rep1

description:
snRNA-seq using 10X Chromium
J3105


title: Grp8a db/db+renin+ACEI+JNJ39933673 rep5

description:
snRNA-seq using 10X Chromium
P3104


title: Grp7b db/db+renin+JNJ39933673 rep5

description:
snRNA-seq using 10X Chromium
N3099


title: Grp7b db/db+renin+JNJ39933673 rep4

description:
snRNA-seq using 10X Chromium
M3098


title: Grp7b db/db+renin+JNJ39933673 rep3

description:
snRNA-seq using 10X Chromium
T3097


title: Grp7a db/db+renin+JNJ39933673 rep5

description:
snRNA-seq using 10X Chromium
N3094


title: Grp7b db/db+renin+JNJ39933673 rep1

description:
snRNA-seq using 10X Chromium
I3095


title: Grp7a db/db+renin+JNJ39933673 rep4

description:
snRNA-seq using 10X Chromium
M3093


title: Grp7a db/db+renin+JNJ39933673 rep3

description:
snRNA-seq using 10X Chromium
P3092


title: Grp7a db/db+renin+JNJ39933673 rep2

description:
snRNA-seq using 10X Chromium
O3091


title: Blood from patient 4 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 2

status: Public on Aug 01 2026

city: Palo Alto

first: Drishti

last: Guin

state: CA

address: 1804 Embarcadero Rd Suite #201

institute: Transcripta Bio

description:
Library name: treated_4mo_2
plasma_oma_conc.csv
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 4

data_processing:
Raw reads were aligned using Kallisto with bootstrapping (number of bootstraps = 100).
Assembly: GRCh38
Supplementary files format and content: Tab separated files containing transcript ID, transcript length, effective length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts (raw counts) and tpm (counts normalized by eff_length)

source_name: blood

growth_protocol: Blood samples were collected from a 12 year old male patient diagnosed with Leigh Syndrome caused by heterozygous NM_003172.4(SURF1):c.312_321delinsAT (p.Pro104_Leu105insTer); NM_003172.4(SURF1):c.574C>T (p.Arg192Trp) mutations in the SURF1 gene. The patient was  enrolled in an approved research protocol (WCG IRB Protocol #2001-01). Blood was collected in PAXgene tubes and shipped at room temperature to the sequencing facility for processing within 24 hours for RNA sequencing. Whole blood samples were collected at approximately 1 month intervals between July 2024 to November 2024.

extract_protocol:
The RNA was extracted using the PAXgene RNA extraction kit.
Barcoded libraries for RNA-seq were prepared with 100 ng of RNA using NEBNext Ultra II RNA Library Prep Kit (NEB, Ipswich, MA) for Illumina with QIAGEN QIAseq FastSelect -rRNA HMR Kit (QIAGEN, Germany) per manufacturer’s protocol.

treatment_protocol: Omaveloxolone was originally prescribed at 50 mg PO, daily and dose was increased to 100 mg PO, daily after 2 months. Concentration of Omaveloxolone in plasma was estimated using mass spectrometry.

value: blood

value: 100 mg Omaveloxolone

tag: time

value: 4 months


title: Blood from patient 4 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 1

description:
Library name: treated_4mo_1
plasma_oma_conc.csv
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 4

tag: tissue


title: Benign_116_1

status: Public on May 26 2026

city: Turku

first: Matti

last: Poutanen

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

description:
Library name: 116_1
1

data_processing:
The reads were base-called using Illumina Bcl2fastq version 1.8.4 base-calling software.
The reads were aligned against the human hg19 reference genome using STAR version 2.4.2a.
Then, reads were assigned to known genes, and the number of reads per gene was counted using the subreads package
Assembly: Illumina iGenome hg19
Supplementary files format and content: Text file containing genewise raw read counts
Supplementary files format and content: csv file containing the anonymized clinical data of the patients

source_name: prostate

extract_protocol:
RNA-sequencing was carried out on fresh-frozen samples, alongside validation samples containing at least 50% Gleason score (GS) ≥6 carcinoma (malignant sample) or morphologically benign prostatic tissue (benign control sample) from the same patient. Samples were homogenized using an Ultra Turrax homogenizer, and total RNA was extracted using NucleoSpin® RNA kit and NucleoSpin® RNA/DNA buffer set (Macherey-Nagel, Düren, Germany). Proper RNA quality was detected using a Fragment Analyzer™ (Advanced Analytical Technologies, Ankeny, IA).
The samples were prepared for sequencing using the Illumina TruSeq Stranded mRNA Sample Preparation Kit and sequenced on the HiSeq 3000 instrument with paired-end chemistry and 100 bp read length.

value: prostate

tag: group

value: Benign

tag: biochemical recurrance

value: No

tag: ggg

tag: pn

value: Unknown


title: Grp6b db/db+renin+ACEI+Rosiglitazone rep4

description:
snRNA-seq using 10X Chromium
L3089

source_name: db/db+renin+ACEI+Rosiglitazone

value: female

value: renin AAV + ACEI + Rosiglitazone


title: Grp6b db/db+renin+ACEI+Rosiglitazone rep3

description:
snRNA-seq using 10X Chromium
K3087

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous


title: Grp6b db/db+renin+ACEI+Rosiglitazone rep2

description:
snRNA-seq using 10X Chromium
L3086

value: 2 weeks


title: Benign_0272_2

description:
Library name: 0272_2
2


title: Grp6a db/db+renin+ACEI+Rosiglitazone rep5

description:
snRNA-seq using 10X Chromium
K3084

value: 2 days


title: Grp6a db/db+renin+ACEI+Rosiglitazone rep3

description:
snRNA-seq using 10X Chromium
N3082


title: Grp6a db/db+renin+ACEI+Rosiglitazone rep4

description:
snRNA-seq using 10X Chromium
L3083


title: Grp6b db/db+renin+ACEI+Rosiglitazone rep1

description:
snRNA-seq using 10X Chromium
F3085


title: Grp7a db/db+renin+JNJ39933673 rep1

description:
snRNA-seq using 10X Chromium
G3090

value: renin AAV + JNJ39933673


title: Grp6a db/db+renin+ACEI+Rosiglitazone rep2

description:
snRNA-seq using 10X Chromium
M3081


title: Grp6a db/db+renin+ACEI+Rosiglitazone rep1

description:
snRNA-seq using 10X Chromium
F3080


title: Grp5b db/db+renin+Rosiglitazone rep5

description:
snRNA-seq using 10X Chromium
J3079

source_name: db/db+renin+Rosiglitazone

value: renin AAV + Rosiglitazone


title: Grp5b db/db+renin+Rosiglitazone rep2

description:
snRNA-seq using 10X Chromium
K3076


title: Grp5b db/db+renin+Rosiglitazone rep3

description:
snRNA-seq using 10X Chromium
R3077


title: Grp5b db/db+renin+Rosiglitazone rep4

description:
snRNA-seq using 10X Chromium
I3078


title: Grp5b db/db+renin+Rosiglitazone rep1

description:
snRNA-seq using 10X Chromium
E3075


title: Grp5a db/db+renin+Rosiglitazone rep3

description:
snRNA-seq using 10X Chromium
L3072


title: Grp5a db/db+renin+Rosiglitazone rep5

description:
snRNA-seq using 10X Chromium
J3074


title: Grp5a db/db+renin+Rosiglitazone rep4

description:
snRNA-seq using 10X Chromium
I3073


title: Grp5a db/db+renin+Rosiglitazone rep1

description:
snRNA-seq using 10X Chromium
E3070


title: Grp4b db/db+renin+ACEI rep5

description:
snRNA-seq using 10X Chromium
H3069

value: renin AAV + ACEI


title: Grp4b db/db+renin+ACEI rep4

description:
snRNA-seq using 10X Chromium
G3068


title: Grp5a db/db+renin+Rosiglitazone rep2

description:
snRNA-seq using 10X Chromium
K3071


title: Grp4b db/db+renin+ACEI rep3

description:
snRNA-seq using 10X Chromium
Q3067


title: Grp4b db/db+renin+ACEI rep2

description:
snRNA-seq using 10X Chromium
P3066


title: Grp4b db/db+renin+ACEI rep1

description:
snRNA-seq using 10X Chromium
I3065


title: Grp4a db/db+renin+ACEI rep4

description:
snRNA-seq using 10X Chromium
G3063


title: Grp4a db/db+renin+ACEI rep5

description:
snRNA-seq using 10X Chromium
H3064


title: Grp4a db/db+renin+ACEI rep3

description:
snRNA-seq using 10X Chromium
J3062


title: Grp4a db/db+renin+ACEI rep2

description:
snRNA-seq using 10X Chromium
I3061


title: Grp4a db/db+renin+ACEI rep1

description:
snRNA-seq using 10X Chromium
D3060


title: Grp3b db/db+renin rep4

description:
snRNA-seq using 10X Chromium
A3038

value: renin AAV


title: Grp3b db/db+renin rep5

description:
snRNA-seq using 10X Chromium
B3039


title: Grp3b db/db+renin rep3

description:
snRNA-seq using 10X Chromium
K3037


title: Grp3b db/db+renin rep2

description:
snRNA-seq using 10X Chromium
J3036


title: Grp3b db/db+renin rep1

description:
snRNA-seq using 10X Chromium
B3035


title: Grp3a db/db+renin rep4

description:
snRNA-seq using 10X Chromium
A3033


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 10

status: Public on Apr 16 2026

description: Library name: CL-10

data_processing:
Custom perl scripts using the FASTX-toolkit and CUTADAPT v. 2.8 were used to remove reads with a homo-polymer run of “A”≥8 bases, retain reads with minimum 20 bases, removal PCR duplicates – defined as sequences sharing the same degenerate header and 20 bases of sequence – and filtered for quality (Phred quality score > 20 for 90% of the nucleotides).
We aligned preprocessed reads using the Burrows-Wheeler Aligner (bwa-mem) and process reads using samtools.
Assembly: Oreochromis niloticus reference (Orenil1.0 Ensembl cdna) and Labroides dimidiatus genome (Accession: PRJNA937036)
Supplementary files format and content: Processed data .counts are raw counts aligned to the Oreochromis niloticus reference
Supplementary files format and content: Processed data .LdimAlign.counts are raw counts aligned to the Labroides dimidiatus genome

organism: Labroides dimidiatus

source_name: Female, forebrain section

extract_protocol:
Total RNA was extracted using Maxwell 16LEV simplyRNA tissue kit (Promega Corporation, Madison, WI, USA) following manufacturer instructions, including DNase treatment. RNA samples were then eluted into 40uL of nuclease-free water.
Libraries are constructed using the University of Texas Genome Sequencing Analysis Facility protocol for 3'tag-seq. Total RNA was fragmented via Mg+ buffer and cDNA was synthesized with poly-dT oligo. cDNA was amplified using PCR and purified with DNA-binding magnetic beads. Sequencing was perfored on an Illumina HiSeq 2000 instrument.

treatment_protocol: Whole heads were transferred into 30 mL conical tubes with RNAlater (ThermoFischer, Waltham, MA, USA) to preserve the integrity of the RNA. The elapsed time between capture and death ranged from 6 to 28 minutes. After 3 hours (on average) in RNAlater, the samples were transferred into O.C.T. Compound (Sakura, Torrance, CA, USA) and flash frozen in liquid nitrogen and shipped to The University of Texas at Austin for RNA isolation.frozen heads were sectioned on a cryostat microtome into 300µm thick slices. The second most rostral slice of the brain, containing pallial areas Dl and Dm (i.e., the putative teleost homologs of the mammalian hippocampus and basolateral amygdala (areas Dl and Dm, respectively), along with partial portions of septal and striatal territories, was collected and stored in 200ul of ice-cold homogenization buffer with 1-thioglycerol (Promega Corporation, Madison, WI, USA) and stored at -80C until further processing.

value: Female, forebrain section

value: high density; Clam Gardens


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 6

description: Library name: TUB-6

organism: Labrichthys unilineatus


title: Donor 1, vehicle

city: Chicago

first: Mariana

last: Bustamante Eduardo

state: IL

address: 303 E. Superior St. Lurie 4-220

department: Department of Surgery

institute: Northwestern University

description:
Library name: MBE-1_292-VE
llumina Single Cell 3′ RNA Prep, T10 kit

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using PIPseeker (version 3.3.0). Sequencing reads were aligned to the GRCh38 human genome using the corresponding gene model from the Ensembl database, and a digital expression matrix containing unique molecular identifiers (UMIs) was generated. scRNA-seq analysis was performed using Seurat (version 5.3.1) in R (version 4.4.0).
Assembly: hg 38
Supplementary files format and content: scRNA-seq matrix files generated by pipseeker

source_name: breast

growth_protocol: Breast microstructures were plated in Corning Primaria cell culture plates in vehicle or octanoic acid media, and primary cells were allowed to migrate from the microstructures onto the plate surface over 48 hours.

extract_protocol:
Migratory cells were incubated in 0.05% Trypsin-EDTA (Gibco, #25300054) for 15 minutes, then passed through a 40 µm cell strainer.
A total of 3,400 viable cells/μL were resuspended in Cell Suspension Buffer for library preparation using the Illumina Single Cell 3' RNA Prep, T10 kit (Illumina, #20135691) following the manufacturer’s protocol.

value: breast

value: vehicle


title: Grp3a db/db+renin rep5

description:
snRNA-seq using 10X Chromium
B3034


title: Grp3a db/db+renin rep2

description:
snRNA-seq using 10X Chromium
C3031


title: Grp3a db/db+renin rep1

description:
snRNA-seq using 10X Chromium
I3030


title: Grp3a db/db+renin Kidney rep2

description:
C3031
whole kidney bulk RNA-seq

value: Kidney


title: Grp3a db/db+renin rep3

description:
snRNA-seq using 10X Chromium
D3032


title: Grp2 db/db+PBS rep5

description:
snRNA-seq using 10X Chromium
C3028

value: PBS


title: Grp2 db/db+PBS rep4

description:
snRNA-seq using 10X Chromium
B3027


title: Grp2 db/db+PBS rep6

description:
snRNA-seq using 10X Chromium
A3029


title: Grp1 db/m+PBS Kidney rep3

description:
F3021
whole kidney bulk RNA-seq

value: BKS.Cg-Dock7m +/- Leprdb/J Leprdb- heterozygous


title: Grp2 db/db+PBS rep1

description:
snRNA-seq using 10X Chromium
N3024


title: Grp2 db/db+PBS rep2

description:
snRNA-seq using 10X Chromium
B3025


title: Grp1 db/m+PBS rep5

description:
snRNA-seq using 10X Chromium
H3023


title: Grp2 db/db+PBS rep3

description:
snRNA-seq using 10X Chromium
A3026


title: Grp1 db/m+PBS rep4

description:
snRNA-seq using 10X Chromium
G3022


title: Grp1 db/m+PBS rep3

description:
snRNA-seq using 10X Chromium
F3021


title: Grp1 db/m+PBS rep1

description:
snRNA-seq using 10X Chromium
E3019


title: Takasato organoid

status: Public on Dec 15 2020

description: single cell RNA-seq

data_processing:
Raw reads were demultiplexed using the command “cellranger mkfastq” from the CellRanger toolkit (version 3.0). Read alignment, barcode identification and UMI quantification were completed using the command “cellranger count”.
Genome_build: GRCh38
Supplementary_files_format_and_content: cellranger count

source_name: iPS cells

extract_protocol:
Organoids from Uchimura and Takasato protocols were harvested at day 26 and dissociated into single cells using 0.25% TrypLE. Cells were counted on hemocytometers (InCYTO C-chip) and partitioned into each droplet with a barcoded gel bead using the 10X Chromium instrument (10X Genomics, Pleasanton, CA). Single cell was lysed and RNAs were reverse transcribed into cDNA within each droplet. After breaking the emulsion, cDNAs were amplified and fragmented followed by the addition of Illumina adapters using the Chromium Single Cell 5’ Library & Gel Bead Kit. Samples were indexed and sequenced on the S4 flow cell of NovaSeq 6000 (Illumina).
RNA libraries were prepared for sequencing following the 5' library preparation protocol from 10x Genomics
10x Chromium 5' scRNA-seq library

tag: protocol

value: 10x Genomics 5' library kit

value: Takasato organoid


title: Uchimura organoid

description: single cell RNA-seq

value: Uchimura organoid


title: Grp1 db/m+PBS rep2

description:
snRNA-seq using 10X Chromium
A3020

tag: genotype

value: female


title: ctl_atacseq_2

status: Public on Sep 15 2020

city: Waltham

first: Erin

middle: Amelia

last: Clark

state: MA

address: 415 South St

department: Biology

institute: Brandeis University

description: control

data_processing:
RNA-seq reads mapped by STAR quantified with featureCounts.
RNA-seq reads mapped by STAR. ATAC-seq reads were mapped using Bowtie2 and filtered to get none mitochondrial unique reads (noDupMT).
ATAC-seq peaks were identified using HOMER and IDR.
Differentially expressed genes were identified by Limma. Differential ATAC peaks were indentified using DiffBind.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts (RNA-seq) bw (ATAC-seq)

source_name: RORb-gfp heterozygous mice, P28-30

growth_protocol: In vivo

extract_protocol:
For RNA: Arcturus PicoPure RNA Isolation kit, for ATAC: lysis buffer and Zymo Clean and Concnetrator-5 kit
RNA libraries were prepared by using Ovation Trio RNA-Seq library preparation kit with mouse rRNA depletion. ATAC libraries were prepared as details in Clark, et al. BioProtocols

value: one copy of GFP knocked into RORb locus

value: collected from L4


title: ctl_atacseq_1

description: control


title: P30_ctl_rnaseq_4

source_name: RORb-gfp heterozygous mice, P30

value: collected from L4 S1


title: P30_ctl_rnaseq_2


title: P30_ctl_rnaseq_1


title: P30_ctl_rnaseq_3


title: Grp8a db/db+renin+ACEI+JNJ39933673 rep3

description:
snRNA-seq using 10X Chromium
H3102

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

tag: Sex

value: renin AAV + ACEI + JNJ39933673

value: 2 days


title: P2_ctl_rnaseq_3

source_name: RORb-gfp heterozygous mice, P2


title: P2_ctl_rnaseq_4


title: P2_ctl_rnaseq_2


title: D35PrPzF_Via 2

status: Public on Apr 28 2020

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center

description:
Samples were sequenced on the Illumina NextSeq 500 and the Illumina NovaSeq 6000
Viable cells from normal human prostate tissue peripheral zone

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 3.1.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 3.1.0 was used to generate mapped bam files using default settings combining fastq's from NextSeq 500 and NovaSeq 6000
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5)

source_name: Viable human prostate peripheral zone

extract_protocol:
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 3’ library and gel bead kit v2 according to manufacture’s recommendations
According to 10x Genomics’ protocol, sequenced (R1=26cycles R2=58cycles, i7=8cycles on NextSeq 500) OR (PE150 on NovaSeq 6000)

treatment_protocol: Populations of single-cells dissociated from health prostates from organ donors were isolated by FACS

tag: patient phenotype

value: Donor (Normal)

tag: prostatic zone

value: Peripheral Zone

tag: digestion enzyme

value: 5mg/mL Collagenase I 4hr

tag: facs ab profile

value: Via-


title: D35PrTzF_Via 2

description:
Samples were sequenced on the Illumina NextSeq 500 and the Illumina NovaSeq 6000
Viable cells from normal human prostate tissue transition zone including prostatic urethra

source_name: Viable human prostate transition zone

value: Transition Zone + Urethra


title: D27PrTzF_Via 2


title: D27PrPzF_Via 2


title: P2_ctl_rnaseq_1


title: Grp7b db/db+renin+JNJ39933673 rep2

description:
snRNA-seq using 10X Chromium
M3096

value: renin AAV + JNJ39933673

value: 2 weeks


title: Female.D10UUO.PT.3

status: Public on Sep 21 2019

description: TRAP-seq

data_processing:
Sequencing reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was accessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3.
Genome_build: Ensembl release 76 assembly
Supplementary_files_format_and_content: Raw counts, RPKMs.

source_name: Proximal tubule

extract_protocol: [TRAP-seq protocol]  Kidneys were removed and decapsulated after perfusion with iced-cold PBS. Renal cortex was rapidly dissected and minced on ice. Samples were then transferred to 1 ml of ice-cold extraction buffer for homogenization. Streptavidin Dyanbeads, which were freshly coated with monoclonal anti-GFP antibodies (clone 19C8 and clone 19F7) through biotinylated Protein L, were added to the kidney postmitochondrial supernatants and incubated at 4°C under end-over-end rotation for 4 hours for immunoprecipitation. After that, beads were collected on a magnetic rack, and the unbound fraction of samples were taken. Collected beads were then washed 4 times by high-salt washing buffer. Bound fractions of samples were then extracted by Qiagen RNeasy lysis buffer. All of the bound and unbound fractions of RNA were then purified by RNeasy MinElute Cleanup Kit  with in-column DNase digestion

tag: gender

value: Female

tag: age

tag: disease state

value: day 10 after unilateral ureteral obstruction (UUO) surgery (severe kidney injury model)

value: Proximal tubule


title: Female.D10UUO.PT.2

description: TRAP-seq


title: D17PrTzF_Via 2


title: Female.D5UUO.PT.3

description: TRAP-seq

value: day 5 after unilateral ureteral obstruction (UUO) surgery (moderate kidney injury model)


title: D17PrPzF_Via 2


title: Female.D10UUO.PT.1

description: TRAP-seq


title: Female.D5UUO.PT.2

description: TRAP-seq


title: Female.D5UUO.PT.1

description: TRAP-seq


title: Female.CLK.PT.2

description: TRAP-seq

value: contralateral kidney (healthy control)


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 5

description: Library name: LYR-5

organism: Thalassoma lunare

value: Female, forebrain section


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 4

description: Library name: MEL-4

organism: Halichoeres melanurus


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 5

description: Library name: MEL-5


title: Female.D10UUO.Total.2

description: TRAP-seq

source_name: Total kidney

value: Total kidney


title: Female.CLK.PT.1

description: TRAP-seq


title: Female.D10UUO.Total.1

description: TRAP-seq


title: Female.D5UUO.Total.2

description: TRAP-seq


title: Female.D10UUO.Total.3

description: TRAP-seq


title: Female.D5UUO.Total.3

description: TRAP-seq


title: Female.CLK.Total.3

description: TRAP-seq


title: Female.CLK.Total.2

description: TRAP-seq


title: Male.D5UUO.PT.3

description: TRAP-seq

value: Male


title: Male.D10UUO.PT.1

description: TRAP-seq


title: Male.D5UUO.PT.2

description: TRAP-seq


title: Male.D5UUO.PT.1

description: TRAP-seq


title: Male.CLK.PT.1

description: TRAP-seq


title: Male.CLK.PT.2

description: TRAP-seq


title: Male.D10UUO.Total.3

description: TRAP-seq


title: Male.D10UUO.Total.2

description: TRAP-seq


title: Male.D5UUO.Total.2

description: TRAP-seq


title: Male.CLK.Total.3

description: TRAP-seq


title: Male.CLK.Total.1

description: TRAP-seq


title: Male.CLK.Total.2

description: TRAP-seq


title: MP-736-16

status: Public on Aug 09 2019

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, using Cutadapt-1.2.1 and low-quality (q < 25) sequence, then mapped to mm10 whole genome using TopHat2 (with Bowtie2 settings of 'sensitive') and quantified to RefSeq89 annotation, using strict paired-end compatibility, with requirement of junction reads to match introns, minimum feature overlap of 95%, and minimum reads of 1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include alignment counts per gene for each sample

source_name: WT_Male_Skeletal muscle (quadriceps)

growth_protocol: All the experiments were performed using age-matched, and when possible, littermate controls. The animals were fed with a regular chow diet ad libitum and were housed at an ambient temperature.

extract_protocol:
Total RNA was extracted from snap-frozen quadriceps muscles (n=4/sex/genotype) using RNeasy mini kit (Qiagen). The quality of total RNA was validated by Bioanalyzer (Agilent Technologies). Approximately 1 µg of RNA per sample was used to construct the cDNA library
RNA libraries were prepared for sequencing using standard Illumina protocols, using the TruSeq stranded mRNA library prep kit (Illumina). The cDNA libraries were quantitated using KAPA library quantification kit for Illumina platforms (Kapa Biosystems). The individual indexed libraries were diluted to 4 nM and pooled in equal quantity and denatured before loading onto the Illumina NextSeq 500. The sequencing was run as paired-end reads (2 × 75 bp per read) with a targeted depth of 60 million paired-end reads per sample.

tag: strain

tag: genotype/variation

value: WT

value: 6 months

value: Skeletal muscle (quadriceps)


title: MP-737-16

tag: tissue


title: MP-733-16


title: MP-732-16


title: MP-728-16


title: MP-729-16


title: MP-724-16


title: KGli1_24h

status: Public on Jun 27 2019

description: Dropseq single cell RNA-seq

data_processing:
Paired-end sequencing reads were processed as previously described using the Drop-Seq Tools v1.12 software available in McCarroll’s lab (http://mccarrolllab.com/dropseq/). Briefly, each cDNA read (read2) was tagged with the cell barcode (the first 12 bases in read 1) and unique molecular identifier (UMI, the next 8 bases in read 1), trimmed of sequencing adaptors and poly-A sequences, and aligned to the mouse reference genome assembly (mm10) using STAR v 2.5.3a. Cell barcodes were corrected for possible bead synthesis errors using the DetectBeadSynthesisErrors program, and then collapsed to core barcodes if they were within an edit distance of 1. Digital gene expression (DEG) matrix was compiled by counting the number of unique UMIs for a given gene (as row) in a given cell (as column).
Genome_build: mm10
Supplementary_files_format_and_content: txt, UMI count matrix

source_name: Kidney Gli1+ cells

extract_protocol:
We used the DropSeq protocol described by Mackosco et al to generate the single cell transcriptomes. In brief, cells were diluted to a concentration of 100 cells/mL, and co-encapsulated with barcoded beads (ChemGenes #Macosko201110), which were diluted to a concentration of 120 beads/mL. Droplets of about 1 nL in size were generated using microfluidic polydimethylsiloxane (PDMS) co-flow devices (FlowJEM Drop-seq chips). Droplets were collected in a 50-mL RNase-free Falcon tube for a total run time of about 15 min. Droplet emulsion was aliquoted into 1 mL each of cells and beads and were broken promptly by perfluorooctanol, following which barcoded beads with captured transcriptomes were washed and spun down at 4 C. Hybridized RNA was reverse transcribed and exonuclease-treated. The beads from one run were then equally distributed into individual PCR tubes with populations of 8,000 beads/tube (~400 cells). PCR tubes were separately amplified for 4+9 PCR cycles, and the PCR products were purified by the addition of 0.6x Agencourt AMPure XP beads (Beckman Coulter #A63881). The quality of the amplified cDNA was evaluated by Bioanalyzer (Agilent 2100) on a High Sensitivity DNA chip. Only cDNA with average insertion size > 1200 bp were used for downstream library preparation and sequencing. cDNA from an estimated 5,000 cells were prepared and tagmented by Nextera XT (Illumina) using 600 pg of cDNA input. cDNA library was amplified (12 cycles) using custom primers as described (Macosko et al., 2015). Amplified libraries were purified with a 0.6x volume of AMPure XP beads and quality was measured by Bioanalyzer. Libraries with average length of ~500-700 bp were submitted to Genome Technology Access Center (GTAC) of Washington University in St. Louis and sequenced on HiSeq 2500 (Illumina).
DropSeq library preparation

treatment_protocol: Gli1+ cells were plated at a concentration of 3 × 105 cells into 10-cm3 dishes and allowed to attach overnight in regular media. The following day, cells were starved in serum-free αMEM media containing 1% pen/strep for 2 h. The cells were then treated with 1 ng/ml TGF-β for either 6 h, 12 h, or 24 h. Control cells without TGF-β were harvested after the 2-h starving period. The cells were harvested with TrypLE Select (Thermo Fisher Scientific) for 10 min at 37°C, and after 10 min, cells were further dispersed by gentle pipetting and filtered through a 40-µm cell strainer (pluriSelect). Single-cell suspension was visually inspected under a microscope, counted by hemocytometer (INCYTO C-chip), and resuspended in PBS + 0.01% BSA.

tag: treatment

value: TGF-beta, 24hrs


title: KGli1_0h

description: Dropseq single cell RNA-seq

value: TGF-beta, 0hr


title: KGli1_6h

description: Dropseq single cell RNA-seq

value: TGF-beta, 6hrs


title: KGli1_12h

description: Dropseq single cell RNA-seq

value: TGF-beta, 12hrs


title: Shiftwork Sham, biological rep 3

status: Public on Apr 23 2019

city: Guelph

first: Tami

last: Martino

address: 50 Stone Road

department: Biomedical Sciences

country: Canada

institute: University of Guelph

hyb_protocol: Following fragmentation, cRNA were hydridized on Affymetrix GeneChip Mouse Gene 2.0 ST arrays, according to manufacturer's instructions. GeneChips were washed and stained on the Gene Atlas platform.

scan_protocol: GeneChips were scanned on the GeneAtlas platform.

data_processing: The data were analyzed with GeneSpring GX software v. 14.9 using default Affymetrix settings.

label: biotin

source_name: Shiftwork Sham Heart

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA.

growth_protocol: The mice were collected at 8 weeks of age (24-hours post-MI surgery) at 6 hours after lights on.

extract_protocol: Total RNA was extracted using the TRIzol method according to manufacturer's instructions.

treatment_protocol: The hearts were collected and snap frozen in liquid nitrogen and stored at -80C.

value: myocardium


title: Shiftwork Sham, biological rep 2


title: Xorna

status: Public on Dec 18 2018

data_processing:
An aliquot of total RNA was then run on a Bioanalyzer Nano RNA chip (Agilent) to confirm RNA integrity score was above 7 for each sample
Trimmomatic was used to filter and trim reads using the following parameters: -phred33 ILLUMINACLIPadapters.fa:3:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
A transcriptome was assembled de novo using Trinity from the reads of each sample/species
de novo assembled contigs were annotated to reference genomes using blastx
Reads were mapped the the annotated de novo assembly using bwa mem
Raw reads were calculated as the sum of transcript counts using SAMtools and Reads Per Million of library size (RPM) were calculated as the reads mapping to de novo assembled contigs  of annotated as the same gene and normalized by the size the size of the library.
Supplementary_files_format_and_content: fasta files including the de novo assembled contigs annotated using closely related reference genomes for each Sample
Supplementary_files_format_and_content: csv files including raw reads and RPMs for each sample

organism: Xenotilapia ornatipinnis

source_name: fore- and mid-brain

extract_protocol:
fore- and mid-brains were rapidly dissected and flash frozen on dry ice or preserved in RNAlater and stored at -80C until RNA was extracted using Trizol
RNA libraries were prepared for sequencing using the NEB small RNA kit (cat #E6160L or #E6160S) Illumina protocols by the University of Texas at Austin Genome Sequencing and Analysis Facility (GSAF)

value: fore- and mid-brain

value: male

tag: state

value: reproductive

tag: number of individuals pooled

tag: annotation genome


title: Mpen

organism: Microtus pennsylvanicus


title: Ri

organism: Ranitomeya imitator


title: het ctrl, bloomington food, repl CB1

city: Bloomington

first: Jason

middle: M

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

institute: Indiana University

description:
Library name: GSF3528-MR04-ctrl-bloomington-repl-CB1
GSF3528_MR04_ctrl_bloomington_repl_CB1

data_processing:
Quantification via Salmon pseudoaligner
Normalization and differential expression via DESeq2
Assembly: BDGP6.32
Supplementary files format and content: tab-separated, transformed log counts from DESeq2

organism: Drosophila melanogaster

source_name: whole animal

growth_protocol: Control (Impl317/+) and Ldh (Impl317/16) mutant eggs were collected on M+Y food. After 40-44hrs, 50 larvae were transferred to each M+Y food plate and BDSC-F Cubes plate, kept at 25ºC.

extract_protocol:
Three biological replicates containing 25 mid-L2 (~60 hours AEL after egg-laying) larvae were collected from both plates and washed twice with ice-cold 1X PBS. Total RNA was extracted from homogenized samples using a RNeasy kit (Qiagen; 74104).
Illumina TruSeq Stranded mRNA Library Kit

value: whole animal

value: heterozygous control (Impl3 17/+)

value: bloomington food

tag: replicate


title: Op

organism: Oophaga pumilio


title: As

organism: Anthus spinoletta


title: Pcal

organism: Peromyscus californicus


title: Kupffer cells, 2h post Sham (control), replicate 4

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description: Library name: SHAM-4

data_processing:
Reads were quality checked with fastQC and no further processing was required
Reads were mapped to the mm39 reference genome with STAR (2.7.10b) and the gencode M30. Read counts were directly obtained using the the featurecounts package
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm39
Supplementary files format and content: tab delimited count matrix with the raw counts per sample

source_name: liver

growth_protocol: All mice were housed in individually ventilated cages at conventional housing conditions (22°C, 14/10h light/dark cycle, dark phase starting at 9 p.m.) in a specific pathogen-free facility. Food (chow diet consisting of 18% proteins, 4.5% fibers, 4.5% fat and 6.3% ashes, Provimi Kliba SA) and water were given at libitum

extract_protocol:
Total RNA was isolated with Aurum Total RNA mini Kit (Bio-Rad) following the manufacturer’s instructions
Library preparation was done using the illumina truseq stranded library kit for sequencing with a Cloudbreak sequencing kit on the element AVITI according the the manufacturer's instructions

treatment_protocol: Mice were subject to CLP or sham surgery and 2 hours later livers were isolated and prepared for FACS to isolate KCs

value: liver

tag: cell type

value: Kupffer cell

tag: genotype

value: WT C57BL/6J

value: Sham


title: Male.D10UUO.PT.3

description: TRAP-seq

value: Male

value: day 10 after unilateral ureteral obstruction (UUO) surgery (severe kidney injury model)

value: Proximal tubule


title: Sham, biological rep 5

status: Public on Nov 30 2018

source_name: Sham Heart


title: Sham, biological rep 4


title: Sham, biological rep 3


title: Normal MI, biological rep 3

source_name: Normal MI Heart


title: Normal MI, biological rep 2


title: Shiftwork MI, biological rep 3

source_name: Shiftwork MI Heart


title: Normal MI, biological rep 1


title: Shiftwork MI, biological rep 2


title: TenxNuc_UUO

status: Public on Oct 13 2018

description:
single nucleus RNA-seq
Processed data file: UUO.dge.txt.gz

data_processing:
We used a newly developed pipeline, zUMIs (Parekh et al., 2018), to process the single cell and single nucleus sequencing data from mouse kidney. In brief, we first filtered out the low-quality barcodes or UMIs based on sequence with the internal read filtering algorithm built in zUMIs. We then used zUMIs to map the filtered reads to mouse reference genome (mm10) using STAR 2.5.3a (two-pass mapping mode). Next, zUMIs quantified the reads uniquely mapped to exonic or intronic reads and inferred the true barcodes that mark cells by fitting a k-dimensional multivariate normal distribution with mclust package. Finally, a UMI count table utilizing both exonic and intronic reads were generated for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: The .txt files report gene-level raw UMI count matrices.  The .txt files' column headers contain barcode sequences.

source_name: Kidney

extract_protocol:
[Single cell dissociation protocol] Kidney from a C57BL/6 mouse was minced into 1 mm pieces with a razor blade and incubated at 37 ˚C in enzyme dissociation buffer containing 250 U/ml Liberase (Roche) and 40 U/ml DNase I. After 10 min, the solution was transferred to a Miltenyi C-tube and the gentleMACS D1 program was run (Miltenyi). Cells were further digested for additional 10 min with trituration, and the reaction was stopped by adding 10% fetal bovine serum. The dissociated cells were pelleted by centrifugation (500 g, 5 min), washed twice, passed through a 35 µM FACS tube (Falcon) and pelleted again by centrifugation (500 g, 5 min). Cells were resuspended in PBS+1%BSA and purified by FACS with optimal gates set for side scatter and forward scatter.
[Nuclei extraction protocol] Nuclei were isolated with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with protease inhibitor (Roche #5892791001) and RNase inhibitor (Promega #N2615, Life Technologies #AM2696). Samples were cut into <2 mm pieces and homogenized using a Dounce homogenizer (Kimble Chase #885302-0002) in 2ml of ice-cold Nuclei EZ Lysis buffer and incubated on ice for 5 min with an additional 2ml of lysis buffer. The homogenate was filtered through a 40-µm cell strainer (pluriSelect #43-50040-51) and then centrifuged at 500 x for 5 min at 4 ºC. The pellet was resuspended and washed with 4 ml of the buffer and incubated on ice for 5 min. After another centrifugation, the pellet was resuspended with Nuclei Suspension Buffer (1x PBS, 0.07% BSA, 0.1% RNase inhibitor), filtered through a 20-µm cell strainer (pluriSelect 43-50020-50) and counted. We used the inDrops protocol developed by Klein et al to generate single nucleus transcriptome.
[Dropseq protocol] We used the DropSeq protocol described by Mackosco et al to generate the single cell transcriptomes
[sNuc-Dropseq protocol] We adapted the DropSeq platform to profile single nucleus with the methods reported by Hu et al  (Mol Cell, 2017)
[DroNcSeq protocol] We used soft lithography techniques to fabricate the DroNc-seq silicon master microfluidic devices. DroNc was performed as previously described by Habib et al (Nature Methods, 2017)
[sNuc-10x protocol] We followed the guideline provided by the manufacturer (10x Genomics) to generate single nucleus transcriptomes
RNA libraries were prepared for sequencing using standard Dropseq and 10X Chromium procedure
single cell/nucleus RNA-seq

tag: protocol

value: Single nucleus isolation

tag: disease state (group)

value: Day14 UUO

tag: platform

value: TenxNuc


title: DroNcSeq_healthy

description:
single nucleus RNA-seq
Processed data file: Healthy.combined.dge.txt.gz

value: Healthy

value: DroNcSeq


title: TenxNuc_healthy


title: sNucDropseq_healthy

value: sNucDropseq


title: Shiftwork Sham, biological rep 5

value: myocardium


title: Moch

organism: Microtus ochrogaster

value: fore- and mid-brain

tag: Sex

value: male

value: reproductive


title: Dropseq_healthy

description:
single cell RNA-seq
Processed data file: Healthy.combined.dge.txt.gz

value: Single cell dissociation

value: DropSeq


title: Xspil

organism: Xenotilapia spiloptera


title: Morizane_ES_lane1

description:
single cell RNA-seq
processed data file: Morizane_ES.dge.txt.gz

data_processing:
DropSeq: Paired-end sequencing reads were processed as previously described using the Drop-Seq Tools v1.12 software available in McCarroll’s lab (http://mccarrolllab.com/dropseq/). Briefly, each cDNA read (read2) was tagged with the cell barcode (the first 12 bases in read 1) and unique molecular identifier (UMI, the next 8 bases in read 1), trimmed of sequencing adaptors and poly-A sequences, and aligned to the human (GRCh38) or a concatenation of the mouse and human (for the species-mixing experiment) reference genome assembly using STAR v 2.5.3a. Cell barcodes were corrected for possible bead synthesis errors using the DetectBeadSynthesisErrors program, and then collapsed to core barcodes if they were within an edit distance of 1. Digital gene expression (DEG) matrix was compiled by counting the number of unique UMIs for a given gene (as row) in a given cell (as column).
sNuc-10X Chromium: We used a newly developed pipeline, zUMIs (Parekh et al., 2018), to process the single nucleus sequencing data from human adult kidney. In brief, we first filtered out the low-quality barcodes or UMIs based on sequence with the internal read filtering algorithm built in zUMIs. We then used zUMIs to map the filtered reads to human reference genome (GRCh38) using STAR 2.5.3a (two-pass mapping mode). Next, zUMIs quantified the reads uniquely mapped to exonic or intronic reads and inferred the true barcodes that mark cells by fitting a k-dimensional multivariate normal distribution with mclust package. Finally, a UMI count table utilizing both exonic and intronic reads were generated for downstream analysis. The whole data processing was executed by running the script on a HPC cluster with the following example script: bash zUMIs-master.sh -f R1.fastq.gz -r R2.fastq.gz -c 1-16 -m 17-26 -l 98 -n Human_kidney -g GRCh38_ref_genome -a GRCh38_ref_genes.gtf -p 30
Genome_build: hg19

extract_protocol:
Nuclei extraction protocol: Nuclei were isolated with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with protease inhibitor (Roche #5892791001) and RNase inhibitor (Promega #N2615, Life Technologies #AM2696). Samples were cut into <2 mm pieces and homogenized using a Dounce homogenizer (Kimble Chase #885302-0002) in 2ml of ice-cold Nuclei EZ Lysis buffer and incubated on ice for 5 min with an additional 2ml of lysis buffer. The homogenate was filtered through a 40-µm cell strainer (pluriSelect #43-50040-51) and then centrifuged at 500 x for 5 min at 4 ºC. The pellet was resuspended and washed with 4 ml of the buffer and incubated on ice for 5 min. After another centrifugation, the pellet was resuspended with Nuclei Suspension Buffer (1x PBS, 0.07% BSA, 0.1% RNase inhibitor), filtered through a 20-µm cell strainer (pluriSelect 43-50020-50) and counted.
RNA libraries were prepared for sequencing using standard Dropseq and 10X Chromium procedure

treatment_protocol:
Organoid differentiation protocol: We used the protocols established by Takasato et al (Takasato protocol) and Morizane et al (Morizane protocol) to differentiate iPS and hES cells into kidney organoids.
Organoid dissociation and Dropseq protocol: Organoids were dissociated into single cell using TrypLE for 5-10 min at 37C with shaking. We used the DropSeq protocol described by Mackosco et al to generate the single cell transcriptomes

tag: tissue/cell type

value: Organoid

tag: differentiation protocol

value: Morizane

tag: time point


title: Morizane_iPS_Batch3_lane2

description:
single cell RNA-seq
processed data file: Morizane_iPS_Batch3.dge.txt.gz


title: Morizane_iPS_Batch3_lane1


title: Takasato_ES_Batch2_lane1

description:
single cell RNA-seq
processed data file: Takasato_ES.dge.txt.gz

value: Takasato


title: Takasato_ES_Batch1_lane2


title: Takasato_ES_Batch2_lane2


title: Takasato_ES_Batch1_lane1


title: Takasato_iPS_Batch3_lane2

description:
single cell RNA-seq
processed data file: Takasato_iPS_Batch3.dge.txt.gz


title: Takasato_iPS_Batch3_lane1


title: Human_kidney_rep2

description:
single nucleus RNA-seq
processed data file: Human_kidney_snRNA.dge.txt.gz

value: Human kidney

tag: age

value: Age 62

value: 10X Chromium


title: Human_kidney_rep1


title: Takasato_iPS_day34

description:
single cell RNA-seq
processed data file: Takasato_iPS_day34.dge.txt.gz


title: Takasato_iPS_day26

description:
single cell RNA-seq
processed data file: Takasato.iPS.timecourse.txt.gz


title: Takasato_iPS_day19


title: Takasato_iPS_day12


title: Takasato_iPS_day7


title: Takasato_iPS_day0


title: Morizane_iPS_Batch2

description:
single cell RNA-seq
processed data file: Morizane_iPS_Batch1_2.dge.txt.gz


title: Morizane_iPS_Batch1


title: BDNF_inhibitor_batch2_rep2

description:
single cell RNA-seq
processed data file: BDNF_inhibitor.dge.txt.gz


title: BDNF_inhibitor_batch2_rep1


title: Takasato_iPS_Batch1

description:
single cell RNA-seq
processed data file: Takasato_iPS_Batch1_2.dge.txt.gz


title: Takasato_iPS_Batch2


title: BDNF_inhibitor_batch1


title: Shiftwork MI, biological rep 1

tag: strain


title: Isocortex.VISp@L6_glu_56L rep3

status: Public on Jul 20 2018

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

data_processing:
Illumina Casava and BCL2FASTQ1.8.3 were used for basecalling
Sequenced reads were trimmed for NuGEN and Illumina adaptor sequences using cutadapt v1.7.1 with parameters --overlap=7 --minimum-length=30. Ribosomal RNA, mitochondrial and phiX sequences were filtered using bowtie2 v2.1.0 with default parameters. Remaining reads were then mapped to mm10 genome using STAR v2.4.0i with parameters  --chimSegmentMin 15 --outFilterMismatchNmax 3.
Uniquely mapped reads were assigned to genes using HTSeq v0.6.1p1 with parameter -s no -m intersection-nonempty and using wgEncodeGencodeVM4Basic annotation downloaded from UCSC with ERCC information added.
Supplementary_files_format_and_content: tab deliminated files include raw counts for each sample
Genome_build: mm10

source_name: Isocortex (VISp@L6)

extract_protocol:
Acutely extracted brain was sliced at 300um thickness, digested with pronase for 1 hour at RT, triturated and GFP labeled cells were sorted manually. RNA was extracted using PicoPure kit (ThermoFisher, KIT0204).
Extracted RNA was amplified using Ovation RNA-Seq System V2 (NuGEN, #7102). 1~1.5 ug of the amplified material was used for library construction using Encore NGS Multiplex System (NuGEN, #0314).
adapters: truseq

tag: tissue

value: Isocortex (VISp@L6)

tag: region

tag: age (postnatal day)

value: M

tag: weight (g)

tag: num_cells (# of sorted cells in the sample)

tag: ercc5 (10^-5 dilution of ercc in ul)

tag: ercc_mix (ercc mix used)


title: Isocortex.VISp@L6_glu_56L rep4


title: Isocortex.VISp@L6_glu_56L rep2


title: Biopsy tube4 part4

status: Public on Jun 19 2018

description:
single cell RNA-seq
Renal biopsy was minced into small pieces and incubated in freshly prepared dissociation buffer containing 0.25% trypsin and 40U/ml DNase I. Dissociated cells were harvested every 10 min by filtering the cell suspension through a 70 µm cell strainer (pluriSelect) into 10% FBS buffer on ice. The residual biopsy tissue trapped on the cell strainer was dissociated once again with 1 mL dissociation buffer for 10 min, passed through cell strainer into the same FBS buffer from the first collection. We repeated this dissociation procedure three times until most of the tissue had been dissociated into single cells (total dissociation time was 30 min). Finally, cells were collected by centrifugation at 400 g for 5 min, resuspended in inDrop cell suspension buffer (9% Optiprep) and strained by a 40 µm cell mesh (pluriSelect) to further remove cell clumps and large fragments.
InDrop was performed as previous described. In brief, cells were diluted into 60,000 cells/mL in 9% Optiprep buffer. Single cell encapsulation was carried out using an inDrop instrument and microfluidic chip manufactured by 1CellBio. In total, four tubes of cells with an estimate of 1,000 cells/tube were collected. Library preparation was performed according to the protocol provided by the manufacturer. We used low PCR cycles (8-9 cycles) to amplify the libraries from this sample. Libraries were sequenced by HiSeq 2500 and NextSeq with a sequencing depth of 50K reads/cell.

data_processing:
Pair-end reads were processed by a newly developed inDrop computational pipeline (https://github.com/hms-dbmi/dropEst). In brief, cell barcodes and UMIs from the library were extracted from read1 by the dropTag program and added to the names of the transcript reads, resulting in a new fastq file for read alignment. We used STAR (version 2.5.3a) to map the high quality reads to the human genome (GRCh38). Only reads that were uniquely mapped to the genome (~70% of the total reads) were used for UMIs counts. We next ran the dropEst program to estimate the accurate molecular counts, which generated a UMI count matrix for each gene in each cell.
Supplementary_files_format_and_content: counts

source_name: Transplant kidney

extract_protocol:
RNA libraries were prepared for sequencing using standard inDrops procedure
Single cell RNA-seq

value: inDrop

value: 21 yrs


title: Biopsy tube4 part3


title: Biopsy tube4 part2


title: Isocortex.VISp@L6_glu_56L rep1


title: Morizane_ES_lane2


title: Biopsy tube4 part1


title: Human_kidney_sNucInDrop

description: single nucleus RNA-seq

data_processing:
We used a newly developed pipeline, dropEst, to process the sNuc-inDrop data. In brief, we first filtered out the bad quality reads and extract the cell barcodes and UMIs from the library using the dropTag program (./droptag -c configs/indrop_v1_2.xml Barcode.reads.fastq.gz cDNA.reads.fastq.gz). We then mapped the filtered reads to human reference genome (GRCh38) using STAR 2.5.3a with the parameters: --genomeDir genome_index_dir --runThreadN 30 --readFilesCommand zcat --sjdbGTFfile path_to_gtf_file --outSAMtype BAM Unsorted --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --sjdbOverhang 44 --twopassMode Basic --readFilesIn filtered.reads.fastq.gz). Finally, we quantified the reads uniquely mapped to exonic or intronic reads with the dropEst program (./dropest -m -g path_to_gtf -L ie -c configs/indrop_v1_2.xml STAR.Aligned.out.bam), and build a UMI counts matrix for each gene using both exonic and intronic reads.

Raw data format and content: In the GEO/SRA submission, R2 is the cell barcode and UMI reads. R1 is the transcript reads (biological reads). For inDrop single cell RNA-seq data processing, the cell barcode and UMI were extracted from read 2, and then appended to read 1 so we can quantify the transcripts for each gene in each cell.
Supplementary_files_format_and_content: UMI counts matrix for each gene using both exonic and intronic reads

source_name: Human kidney

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (Sigma #NUC-101) supplemented with protease inhibitor (Roche #5892791001) and RNase inhibitor (Promega #N2615, Life Technologies #AM2696). Samples were cut into <2 mm pieces and homogenized using a Dounce homogenizer (Kimble Chase #885302-0002) in 2ml of ice-cold Nuclei EZ Lysis buffer and incubated on ice for 5 min with an additional 2ml of lysis buffer. The homogenate was filtered through a 40-µm cell strainer (pluriSelect #43-50040-51) and then centrifuged at 500 x for 5 min at 4 ºC. The pellet was resuspended and washed with 4 ml of the buffer and incubated on ice for 5 min. After another centrifugation, the pellet was resuspended with Nuclei Suspension Buffer (1x PBS, 0.07% BSA, 0.1% RNase inhibitor), filtered through a 20-µm cell strainer (pluriSelect 43-50020-50) and counted. We used the inDrops protocol developed by Klein et al to generate single nucleus transcriptome.
RNA libraries were prepared for sequencing using standard inDrops procedure

value: 70 years

value: inDrops


title: Biopsy tube3


title: Cell383

status: Public on Apr 24 2018

data_processing: The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script. The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 3.0.4.b. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Sailfish version 0.6.3. was used to produce isoform estimated counts.

source_name: Mouse kidney

extract_protocol:
Kidney dissociation protocol: Mice were euthanized and perfused with sterile PBS via the left ventricle and the kidneys were placed in PBS with 5% FBS. After thoroughly mincing the tissue/organ using a sterile scalpel (Feather), the tissue/organ was placed in gentleMACS C Tubes (Miltenyi Biotec) containing 1.5ml DMEM (Life Technologies) with 0.1mg/ml Liberase TL (Roche). The tissue was then dissociated using the D program of the gentleMacs dissociator (Miltenyi Biotec) followed by 30 min incubation at 37°C.
FACS-seq protocol: Single cell sorting was performed at the Siteman Flow Cytometry Core (Washington University) using an iCyt Synergy sorter (Sony). Single cells were sorted directly into 10x lysis buffer (Clontech) in 96well PCR plates. Data were analyzed by using Flow Jo software (Version 9.6.2, Tree Star Inc).  96-well plates with single cell in each well were sealed and sent to the sequencing core at Washington University in St Louis (Genome Technology Access Center, GTAC). RNA from individual wells were processed with the Clonetech Smarter system and ligated with unique barcodes. Each plate was then pooled into one library and the resulting pools were then ligated to adapters containing unique 7bp index sequences so that samples originating from a single plate can be identified by Illumina conventional indexing strategies and each individual well is defined by barcoades sequenced on the first read of a paired end read pair. All plates were pooled into a single library and subjected to Illumina sequencing (HiSeq2500 2x50bp).
RNA libraries were prepared for sequencing using standard FACS-seq procedure

value: Single cell FACS-seq

value: 8 wks

tag: cell population

tag: batch


title: Biopsy tube1

tag: protocol


title: Biopsy tube2


title: Cell384


title: Female.CLK.PT.3

description: TRAP-seq

tag: gender

value: Female

tag: disease state

value: contralateral kidney (healthy control)

value: Proximal tubule


title: Cell382


title: Female.CLK.Total.1

description: TRAP-seq

value: Total kidney


title: Female.D5UUO.Total.1

description: TRAP-seq

value: day 5 after unilateral ureteral obstruction (UUO) surgery (moderate kidney injury model)


title: Male.D10UUO.PT.4

description: TRAP-seq

value: Male

value: day 10 after unilateral ureteral obstruction (UUO) surgery (severe kidney injury model)


title: Male.D10UUO.PT.2

description: TRAP-seq


title: Male.CLK.PT.3

description: TRAP-seq


title: Male.D5UUO.PT.4

description: TRAP-seq


title: Male.CLK.PT.4

description: TRAP-seq


title: Cell380


title: Cell381


title: Cell379


title: Male.D10UUO.Total.4

description: TRAP-seq


title: Cell378


title: Cell377


title: Cell376


title: Cell375


title: Cell373


title: Male.CLK.Total.4

description: TRAP-seq


title: Male.D5UUO.Total.3

description: TRAP-seq


title: Male.D5UUO.Total.4

description: TRAP-seq


title: Male.D10UUO.Total.1

description: TRAP-seq


title: Cell374


title: Cell370


title: Cell372


title: Cell371


title: Male.D5UUO.Total.1

description: TRAP-seq


title: Cell366


title: Cell367


title: Cell369


title: Cell368


title: Cell365


title: Cell364


title: Cell363


title: Cell362


title: Cell360


title: Sham, biological rep 1

value: myocardium


title: Cell358


title: Cell359


title: Cell357


title: MP-725-16

tag: genotype/variation

value: 6 months

tag: Sex

value: Skeletal muscle (quadriceps)


title: Cell354


title: Cell355


title: Cell353


title: Cell361


title: Cell352


title: Cell351


title: Cell350


title: Cell356


title: Cell348


title: Cell349


title: Cell345


title: Cell346


title: Cell344


title: Cell347


title: Cell343


title: Cell342


title: Cell340


title: Shiftwork Sham, biological rep 4


title: Cell341


title: Cell338


title: Cell337


title: Cell336


title: Cell339


title: Cell334


title: Cell331


title: Cell335


title: Cell332


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title: Cell282


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title: Cell253


title: Cell251


title: Cell252


title: Cell308


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title: Cell143


title: Cell142


title: Cell140


title: Cell141


title: Cell139


title: Cell138


title: Pman

organism: Peromyscus maniculatus

value: fore- and mid-brain

value: male

tag: state

value: reproductive

tag: number of individuals pooled

tag: annotation genome


title: Cell137

tag: age


title: Cell136


title: Cell135


title: Cell134


title: Cell133


title: Cell130


title: Cell128


title: Cell127


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title: Cell14


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title: Cell6


title: Cell5


title: Cell37


title: Cell3


title: Cell4


title: Cell2


title: Cell1


title: Cell25


title: Cell28


title: male a

status: Public on Oct 18 2000

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description:
Whole adult male minus gonads (12-24 hours post-eclosion) Drosophila melanogaster of the genotype y w[67c1]
Keywords = soma, male, sex

source_name: y w[67c1]/Y male


title: testis b

description: Testis dissected from adult (12-24 hours post-eclosion) Drosophila melanogaster of the genotype y w67c1.

source_name: y w[67c1]/Y testis


title: testis a

description:
Testis dissected from adult (12-24 hours post-eclosion) Drosophila melanogaster of the genotype y w[67c1].
Keywords = gonad, male, sex


title: Foreskin Fibroblasts

status: Public on Sep 28 2000

type: SAGE

anchor: NlaIII

city: Bern

first: Marc

last: Kenzelmann

address: Friedbuhlstrasse 51

department: Molecular Genome Analysis

country: Switzerland

institute: Institute of Medical Microbiology, University of Bern

description:
Primary human foreskin fibroblasts at passages 15-18, cultured in Eagles Minimal Essential Medium (MEM) supplemented with penicillin and 10% fetal calf serum (FCS).
Confluent cells serum starved for 3 days with MEM containing 1% FCS. 85% of cells in G0/G1 phase of cell cycle.
mRNA was isolated using a direct mRNA extraction kit.
Keywords = fibroblast, cultured, cell cycle synchronized

organism: Homo sapiens

source_name: mRNA of untreated foreskin fibroblasts


title: HCMV-infected foreskin fibroblasts

description:
Primary human foreskin fibroblasts at passages 15-18, cultured in Eagles Minimal Essential Medium (MEM) supplemented with penicillin and 10% fetal calf serum (FCS).
Confluent cells serum starved for 3 days with MEM containing 1% FCS.
85% of cells in G0/G1 cell cycle phase.
Cells infected at a multiplicity of infection (m.o.i.) of 5 with human cytomegalovirus (HCMV) strain AD169 infectious particles (virions) for 90 min at 37°Celsius.
mRNA isolated using a direct mRNA extraction kit.
Keywords = human cytomegalovirus, AD169, virions, HCMV-infected foreskin fibroblasts

source_name: mRNA of HCMV-infected human foreskin fibroblasts


title: Cell10

organism: Mus musculus


title: Cell8


title: Cell58


title: Cell55


title: Cell53


title: Cell45


title: Cell40


title: Cell36


title: Cell109


title: Dp

city: Austin

first: Rebecca

last: Young

address: 2415 Speedway #C0930, Patterson Lab 607A

institute: University of Texas at Austin

organism: Prunella modularis

tag: tissue


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 4

description: Library name: BLA-4

data_processing:
Custom perl scripts using the FASTX-toolkit and CUTADAPT v. 2.8 were used to remove reads with a homo-polymer run of “A”≥8 bases, retain reads with minimum 20 bases, removal PCR duplicates – defined as sequences sharing the same degenerate header and 20 bases of sequence – and filtered for quality (Phred quality score > 20 for 90% of the nucleotides).
We aligned preprocessed reads using the Burrows-Wheeler Aligner (bwa-mem) and process reads using samtools.
Assembly: Oreochromis niloticus reference (Orenil1.0 Ensembl cdna) and Labroides dimidiatus genome (Accession: PRJNA937036)
Supplementary files format and content: Processed data .counts are raw counts aligned to the Oreochromis niloticus reference
Supplementary files format and content: Processed data .LdimAlign.counts are raw counts aligned to the Labroides dimidiatus genome

organism: Hemigymnus melapterus

source_name: Female, forebrain section

extract_protocol:
Total RNA was extracted using Maxwell 16LEV simplyRNA tissue kit (Promega Corporation, Madison, WI, USA) following manufacturer instructions, including DNase treatment. RNA samples were then eluted into 40uL of nuclease-free water.
Libraries are constructed using the University of Texas Genome Sequencing Analysis Facility protocol for 3'tag-seq. Total RNA was fragmented via Mg+ buffer and cDNA was synthesized with poly-dT oligo. cDNA was amplified using PCR and purified with DNA-binding magnetic beads. Sequencing was perfored on an Illumina HiSeq 2000 instrument.

value: Female, forebrain section