title: Nvec_25hpf_GSK_CAGEseq_rep2

status: Public on Apr 10 2026

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

description: Library name: STELLA5mC47

data_processing:
EM-seq data was mapped to the reference genome using BS-seeker2 with Bowtie2 as a back-end aligner. The resulting bam file was then deduplicated with Sambamba, and the methylation calling done with CGmapTools.
RNA-seq data was mapped against the reference transcriptome using Kallisto with default parameters.
ATAC-seq data was mapped to the reference genome using chromap (--preset atac), the resulting BEDPE was used as input for MACS3 callpeaks function (-g 2.7e8 -q 0.05 -B). All peaks were merged using BEDTOOLS merge function, and insert sites were counted using the featureCounts function in the SUBREAD package, requiring 20% read overlap (--fracOverlap 0.2).
Oxford Nanopore data was basecalled using Dorado (0.7.2) with the model 5mCG_5hmCG, sup model, mapped directly to the reference genome. Methylation calls where extracted using modkit with default parameters. Haplotype tags on the bam file were obtained using WhatsHap.
Raw CAGE reads were demultiplexed using standard Illumina processing pipelines. Adapter sequences and low-quality reads were trimmed and filtered using Trim Galore! (v0.6.7, Babraham Bioinformatics) with default settings, after which the G added during the reverse transcription step was removed with cutadapt (v4.6). Quality-filtered reads were aligned to the reference genome using STAR (v5.1.0), ensuring that the 5' end of each read was correctly mapped to its genomic location. Alignments were filtered to retain only primary, uniquely mapped reads with a mapping quality greater than 20.
Assembly: GCF_932526225.1
Supplementary files format and content: CGmap files are described in the BS-Seeker2 github repository: https://github.com/BSSeeker/BSseeker2?tab=readme-ov-file#44-bs_seeker2-call_methylationpy
Supplementary files format and content: Processed mRNA-seq data shows est_counts values obtained from Kallisto Quant function against the reference transcriptome, summarised per gene.
Supplementary files format and content: NarrowPeak files are described in MACS3 documentation (https://macs3-project.github.io/MACS/docs/narrowPeak.html). ATACseq.all_peaks.counts.tsv is the output of featureCounts, where each peak (defined as chr:start-end) is a row and each sample is a column.
Supplementary files format and content: Modkit bedmethyl format is described here: https://github.com/nanoporetech/modkit?tab=readme-ov-file#description-of-bedmethyl-output
Supplementary files format and content: TagCluster for CAGE seq data are described in the CAGEr package. Bigwigs are coverage normalised read counts divided per strand: plus or minus.

organism: Nematostella vectensis

source_name: 25 hpf gastrulae

growth_protocol: Nematostella juveniles and adults were housed in glass dishes containing 15‰ artificial sea water at 19 °C and fed freshly hatched Artemia nauplii three to five times a week, with weekly water changes. Spawning induced following previously established protocols. The gelatinous mass surrounding the eggs was removed using 4% L-cysteine (Sigma-Aldrich, #1.02838), after which eggs were washed and fertilized. Embryos were cultured in 6-well plates at 22°C for consistent developmental staging. Primary polyps metamorphosed were initially fed mashed nauplii until they can ingest intact nauplii and then transferred to larger glass dishes for further growth and maturation.

extract_protocol:
Monarch Genomic DNA Purification Kit (New England Biolabs, #T1030)
mRNA-seq / EM-seq / OmniATAC-seq / Oxford Nanopore Ligation kit (SQK-LSK114) / CAGE-seq

treatment_protocol: For multi-omic profiling, fertilized zygotes produced by pooled gametes of multiple males and females were split into two wells containing either 5 μM GSK-3484862 (MedChemExpress, #HY-135146) or equivalent amount of DMSO (0.1%) as the control. Three independent biological replicates for both treatment and control were prepared using different broodstocks. After 25 hours, gastrula-stage embryos were washed and harvested for DNA, RNA, and nucleus extraction.

value: 25 hpf gastrulae

value: Whole embryo

value: Massachussets


status: Public on Apr 11 2026

type: SRA

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

country: USA

institute: Genentech

description: Library name: ENU29013Inpp5dB6G2RN527_G2_neuro2008rep_S39_R1_2367728791

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the mouse reference genome GRCm38 using GSNAP 74. Only uniquely mapping reads were carried forward to downstream analysis. Sample quality was further assessed on a per-plate basis based on total read counts, percentage of reads mapping to the reference genome, and percentage of reads mapping to exons. Reads predominantly mapped to transcript 3’ ends, as expected from the library preparation method.
Assembly: GRCm38

molecule: total RNA

organism: Mus musculus

source_name: Whole brain

growth_protocol: Founder C57BL/6NCrl males were treated with 3 x 100 mg/kg ENU (Sigma) and mutations bred to homozygosity in three generations. Generation 3 mice were collected usually between 8-12 weeks old, and an ear notch for DNA and brain samples were collected. Typically, 12 siblings from each pedigree were screened.

extract_protocol:
To homogenize the tissue, RNAlater was removed, and a 5 mm stainless steel bead (Qiagen) and 1.6 mL of Qiazol (Qiagen) was added. The tissue was homogenized using a Tissue Lyser II (Qiagen) for at least 30 minutes until a homogenous solution was confirmed. 400 µL of the homogenate solution was transferred into a new tube and allowed to sit for 5 minutes before adding 100 µL of chloroform (Sigma). The homogenate-chloroform mixture was shaken vigorously, allowed to stand for 2 minutes before centrifugation for 5 minutes at 4°C and 1000 x g. The top clear layer was removed and stored at -80 °C. For RNA extraction, 120 µL was transferred into a QIAgen S-block and processed on the QIAcube using the RNeasy 96 QIAcube HT Kit.
cDNA fragment libraries were constructed using the SMART-Seq® v4 3’ DE Kit (Takara Bio) following manufacturer’s recommendations, with minor modifications. Total RNA samples were processed in batches of 1152, distributed across twelve 96-well plates. For each sample, 4 ng total RNA was used as input for cDNA synthesis, then amplified for 8 cycles, with each sample in a row receiving a unique in-line index. Amplified cDNAs within a row were then combined into a 12-plex pool, cleaned up with Ampure XP beads (Beckman Coulter) and quantified using the Qubit HS DNA assay kit (Thermo Fisher Scientific). For each of the 96 cDNA pools generated from 12 plates, 400 pg were carried into Nextera XT library preparations (Illumina Inc.), each assigned with one of the 96 unique combinations of Forward and Reverse HT Index Primers included in the SMART-Seq® v4 3’ DE kit. After Ampure XP clean up and Qubit quantification, the 96 pools were combined in an equimolar manner to generate a 1152-plex Illumina library.  This library was concentrated with Ampure XP beads, quantified with Qubit and assessed on the TapeStation with the High Sensitivity D1000 assay (Agilent Technologies).

treatment_protocol: Mice were euthanized by cervical dislocation, then whole brains were collected. Each cerebellum was removed and the remaining brain matter was transferred to RNAlater and stored at 4C for up to 5 days.

tag: tissue

value: Whole brain

tag: partofsubset

value: TRUE

value: Inpp5d S308X


title: Nvec_25hpf_GSK_CAGEseq_rep1

description: Library name: STELLA5mC46

tag: cell type

tag: genotype

tag: treatment


title: Nvec_25hpf_WT_CAGEseq_rep1

description: Library name: STELLA5mC44

value: No treatment


title: Nvec_25hpf_WT_CAGEseq_rep2

description: Library name: STELLA5mC45


title: PAM, PU.1 knockdown, CUT&Tag, replicate 2

city: Yangzhou

first: Juan

last: Yang

address: 大学南路88号

department: College of Veterinary Medicine

country: China

institute: Yangzhou University

description: Library name: PAM, PU.1 knockdown, CUT_Tag, replicate 2

library_source: genomic

data_processing:
Raw reads were trimmed with Trim Galore v0.6.5. Clean reads were aligned to the reference genome (Sscrofa11.1) using Bowtie v2.3.5 with default settings. The PCR duplicates for each dataset were removed using the rmdup function of samtools v1.2. The data reproducibility between biological replicates was confirmed, then reads from replicates were pooled together for further analysis Peak calling was performed with MACS v2.2.7.1 with --keep-dup all. The called peaks were further cleaned by removing those overlap ENCODE Blacklist V2 regions. Differential binding analysis was performed using v3.4.11 with settings: minOverlap= 1, summits= 250, method=DBA_EDGER. Overlap of peaks were performed using the window function from BEDTools v2.29.2.
Assembly: Sscrofa11.1
Supplementary files format and content: Standardized peak files containing genomic coordinates, peak summit positions, and statistical significance information.
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Sus scrofa

source_name: PAM

extract_protocol:
CUT&Tag assay was performed using NovoNGS CUT&Tag 4.0 High-Sensitivity Kit (for Illumina, Novoprotein scientific Inc., Cat #N259-YH01).
The CUT&Tag  libraries were constructed using the Illumina NovaSeq X Plus platform. During library preparation, target region fragmentation and adapter ligation were mediated by Tn5 transposase, followed by 150 bp paired-end sequencing on the NovaSeq X Plus platform.

tag: cell line

value: PAM

value: porcine alveolar macrophages

value: SPI1-siRNA 24 hours

tag: chip antibody


title: PAM, PU.1, CUT&Tag, replicate 2

description: Library name: PAM, PU.1, CUT_Tag, replicate 2


title: PAM, NC, CUT&Tag, replicate 2

description: Library name: PAM, NC, CUT_Tag, replicate 2

value: NC 24 hours


title: PAM, NC, CUT&Tag, replicate 1

description: Library name: PAM, NC, CUT_Tag, replicate 1


title: PAM, PU.1 knockdown, CUT&Tag, replicate 1

description: Library name: PAM, PU.1 knockdown, CUT_Tag, replicate 1


title: Sample 82, iMGL KO with treatment None

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description: Library name: batch1_GPR34KO1_iMGLs_techrep4

data_processing:
Quantification was performed with Salmon (v1.6.0) with the arguments -l A --posBias --seqBias --gcBias --validate Mapping, with the fullgenome as decoys.
Data was loaded into R with tximport and processed with DESeq2 and other packages.
Assembly: GrCH38
Supplementary files format and content: Count matrix

molecule: polyA RNA

organism: Homo sapiens

source_name: in vitro

growth_protocol: Human iPSC-derived microglia-like cells were differentiated from CRISPR edited WTC11 iPSC lines. iPSCs were maintained on matrigel-coated plates in Essential 8 medium with daily media changes and passaged every 4-6 days. Hematopoietic differentiation was initiated at ~80% confluence via embryoid body formation and culture in defined HPC media with stage-specific cytokine supplement under hypoxic (5% O₂) then normoxic (20% O₂) conditions. Hematopoietic progenitors were harvested at day 10, cryopreserved, and subsequently differentiated into iMGLs in defined media containing M-CSF, IL-34, and TGFB-1, with later supplementation of CD200 and CX3CL1. Cells were maintained at 37°C with 5% CO₂, fed every 2 days, and used for experiments at day 40 of differentiation.

extract_protocol:
RNA was harvested using Rneasy Plus Mini Kit (Qiagen) from independent wells seeded at 50,000 cells per well. 200 ng of total RNA from each sample was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Kit following manufacturer's instructions

treatment_protocol: At day 40 of differentiation, iMGLs were collected under baseline (untreated) conditions for RNA extraction. In parallel experiments, cells were treated with either PBS (vehicle control) or myelin (6 μg/mL) for 2 hours or 24 hours prior to RNA collection. GPR34 knockout and control (non-targeting CRISPR) lines were processed in parallel under all conditions

value: in vitro

value: in vitro microglia

value: KO

tag: batch


title: Sample 84, iMGL KO with treatment None

description: Library name: batch1_GPR34KO1_iMGLs_techrep6


title: Sample 80, iMGL KO with treatment None

description: Library name: batch1_GPR34KO1_iMGLs_techrep2


title: PAM, PU.1, CUT&Tag, replicate 1

description: Library name: PAM, PU.1, CUT_Tag, replicate 1


title: Sample 77, iMGL CTRL with treatment None

description: Library name: batch1_CTRL1_iMGLs_techrep5

value: CTRL


title: Sample 81, iMGL KO with treatment None

description: Library name: batch1_GPR34KO1_iMGLs_techrep3


title: Sample 79, iMGL KO with treatment None

description: Library name: batch1_GPR34KO1_iMGLs_techrep1


title: pronator teres, male, 23_3-5708-S5-NextRUN5

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

description: Library name: 23_3__pronator_teres__5708__male__S5__NextRUN5

data_processing:
The reads were aligned to the hg38 genome using HISAT2 (v.2.2.1) with GENCODE comprehensive annotation (v.44) and a very-sensitive preset.
Multimapped reads were filtered with samtools (v.1.13) view -q 60 followed by counting the reads-per-gene with featureCounts (v.2.0.6) -s 1.
bedGraph tracks were generated with bedtools (v.2.30.0) genomecov using -bg -5 options to calculate 5'-end coverage.
Assembly: hg38
Supplementary files format and content: File format: tsv, tab-separated plain text files. File contents: the files contain the read counts per gene estimated by featureCounts.
Supplementary files format and content: File format: bedGraph. File contents: aggregated 5' profiles of the mapped CAGE tags, separately for the direct and reverse complementary strands (+ and -).

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted from muscle samples using the RNeasy Fibrous Tissue Kit (Qiagen, Germany) according to the manufacturer’s protocol with minor modifications. 19-30 mg of tissue was homogenized with a mortar and pestle using liquid nitrogen. After that lysis buffer was added, and the lysate was collected into clean tubes. The samples were then incubated with proteinase K solution for 10 minutes at 55°C and centrifuged in an Eppendorf mini spin centrifuge at maximum speed. To precipitate long and short RNAs, one volume of 96% ethanol was added to the supernatant, and all was applied to a column. The column was washed twice with RPE wash buffer, dried, and eluted with nuclease-free water.
Libraries were prepared utilizing the standard nAnT-iCAGE (non-Amplified non-Tagging Illumina Cap Analysis of Gene Expression) protocol described in Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M et al. (2014). Detecting expressed genes using CAGE. In: Miyamoto-Sato E, Ohashi H, Sasaki H, Nishikawa J-I, Yanagawa H (eds) Transcription factor regulatory networks: methods and protocols. Springer, New York, NY, pp 67–85. doi:10.1007/978-1-4939-0805-9_7. 5 μg of total RNA was used as a template for synthesis of the first cDNA strand (nAnT-iCAGE Library Preparation kit DNA form, Yokohama, Japan, and SuperScript III Reverse Transcriptase, Invitrogen, Waltham, MA, USA). Next, RNA/DNA heteroduplexes were biotinylated at 5´-ends (nAnT-iCAGE Library Preparation kit, DNA form, Yokohama, Japan), which allowed selection of the 5´-cap containing molecules with streptavidin beads (Dynabeads M-270 Streptavidin, ThermoFisher Scientific, USA). Then, cDNA was treated with RNase I and H (nAnT-iCAGE Library Preparation kit, DNA form, Japan) and purified using RNACleanUP (Beckman Coulter, Brea, CA, USA). Next, linkers were ligated to the 5′and 3′ ends (nAnT-iCAGE Library Preparation kit, DNAform, Japan) of the cap-trapped cDNA. The 5′- linker employed contained recognition sites for the XmaJI restriction endonuclease (nAnT-iCAGE Library Preparation kit, DNA form, Japan) and the MmeI class II restriction enzyme (nAnT-iCAGE Library Preparation kit, DNA form, Japan), as well as a barcode for multiplexing. The 3′- linker contained a recognition site of the XbaI restriction enzyme (nAnT-iCAGE Library Preparation kit, DNAform, Japan). Treatment with these restriction enzymes yielded short CAGE tags to which a sequencing primer was ligated. In the final stage, a second cDNA strand was synthesized from these short CAGE tags (nAnT-iCAGE Library Preparation kit, DNAform, Japan). The concentration of the resulting libraries was determined by the PicoGreen Assay in a GloMax® Multi Detection System (Promega, Madison, WI, USA), and the libraries were validated using real-time PCR (KAPA Library Quantification Kits Illumina, KAPA Biosystems, Wilmington, MA, South Africa). The sequencing on a either Hiseq2500, Nextseq 550, or Novaseq6000 platform (Illumina, San Diego, CA, USA).

treatment_protocol: Tissue samples were fixed in RNA-later solution (Invitrogen), stored at +4C overnight, and then stored at -80C until RNA isolation.

value: skeletal muscle

tag: muscle short_id

tag: muscle short_latin_name

value: m. pronator teres

tag: muscle full_latin_name

value: Musculus pronator teres caput humerale, Musculus pronator teres caput ulnare

tag: body part

value: Upper limbs

tag: replicate id

tag: person id

tag: Sex

value: male


title: pronator quadratus, male, 23_2_e2-5879-S4-NextRUN4

description: Library name: 23_2_e2__pronator_quadratus__5879__male__S4__NextRUN4

value: m. pronator quadratus

value: Musculus pronator quadratus


title: Sample 76, iMGL CTRL with treatment None

description: Library name: batch1_CTRL1_iMGLs_techrep4


title: Sample 78, iMGL CTRL with treatment None

description: Library name: batch1_CTRL1_iMGLs_techrep6


title: Sample 75, iMGL CTRL with treatment None

description: Library name: batch1_CTRL1_iMGLs_techrep3


title: Sample 83, iMGL KO with treatment None

description: Library name: batch1_GPR34KO1_iMGLs_techrep5


title: Sample 73, iMGL CTRL with treatment None

description: Library name: batch1_CTRL1_iMGLs_techrep1


title: Sample 46, iMGL KO with treatment None

description: Library name: 22NYCHLT4_1_0462199258_KO1_NoMyelin4_G4


title: Sample 74, iMGL CTRL with treatment None

description: Library name: batch1_CTRL1_iMGLs_techrep2


title: Sample 48, iMGL KO with treatment None

description: Library name: 22NYCHLT4_1_0462199258_KO1_NoMyelin6_G6


title: Sample 44, iMGL KO with treatment None

description: Library name: 22NYCHLT4_1_0462199258_KO1_NoMyelin2_E11


title: tail tip

city: Seattle

first: Avery

last: Angell Swearer

state: Washington

address: UW Box 357350, 1705 NE Pacific St.

department: Biochemistry

institute: University of Washington

description: Library name: un0dpa

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed thorugh CellRanger v9.01 Count and Aggregate to generate the filtered_feature_bc_matrix file. This file was processed using the Seurat v3.1 pipeline  in R Studio v4.4.3. Cells expressing < 200 genes were removed from downstream analysis, with a mitochondrial RNA read cutoff of 25%. The data was normalized then scaled by Sample and nFeature_RNA before clustering. Data was integrated by Sample using RPCA Integration. Three poor quality clusters indicated by a high percentage of cells with abnormally low UMI count (nFeature < 500) were manually removed. Cell cycle was predicted as previously described. Cell types were annotated using common cell markers as well as via analysis of differentially expressed cluster markers to generate the tail_final.rds. The neural dataset was subset based on the expression of sox2, pax6, and tubb2b in neural progenitors and/or neurons. The neural subset was re-normalized, scaled by Sample and nFeature_RNA, then integrated by Sample with RPCA. Five clusters were manually removed based on their presence in only one sample (1 cluster), their expression of sclerotome and/or muscle markers (3 clusters), or abnormally low UMI count (nFeature < 500) (1 cluster) to generate the neural_final.rds file.
Assembly: To generate the reference genome, the Xenopus tropicalis v10.0 reference genome and gene models were downloaded from Xenbase
Supplementary files format and content: The filtered_feature_bc_matrix folder is directly from the CellRanger output
Supplementary files format and content: The tail_final.rds file to be opened in Seurat. It contains clearly labeled columns detailing the Sample along with complete cell annotations.
Supplementary files format and content: The neural_final.rds file to be opened in Seurat, with the neural specific subset from the tail. It contains clearly labeled columns detailing the Sample along with complete cell annotations.

organism: Xenopus tropicalis

source_name: tail

extract_protocol:
Tail tissues were collected within 30 minutes of amputation and added to a vial with 72 µl trypLE (ThermoFisher Scientific:12604013) and 3 µl 100 mg/mL collagenase P (ROCHE:11213857001) for every 100 tail tissues. Samples were moved to a 28C water bath for dissociation and triturated with a p200 every 5 minutes until dissociated fully and no chunks was visible (30-60 minutes). To quench the reaction, 150 µl of ice cold 10% FBS was added for every 100 tail tissues. Samples were then spun down for 5 minutes at 1000xg. Supernatant was disposed and cells were resuspended in 300 µl 10% FBS for FACS. For each sample, 22-294 tadpoles were used (tail tip: 294 tadpoles; un1dpa: 222 tadpoles; un3dpa: 133 tadpoles; un7dpa: 22 tadpoles; mid-trunk: 294 tadpoles; 1dpa: 208 tadpoles; 3dpa: 144 tadpoles; 7dpa: 25 tadpoles). Tail tip and mid-trunk tissues were collected from the same specimens.  Cell sorting and collecting were performed with an Aria III Cell Sorter (BD Biosciences) and a 70 µm nozzle as previously described.32 Live singlets were sorted for based size and granularity with FSC and SSC. For GFP gate setting, initial setting was done with positive control transgenic Xtr.Et(eef1a1:GFP)16FMead tadpoles to test for GFP signal and autofluorescence. Selection areas were drawn to exclude most autofluorescent GFP- cells.
Cells were collected into 500 µl solutions of 1x PBS with 1 mg/ml BSA (NEB:B9200S) and counted with a Countess 3 FL Automated Cell Counter (ThermoFisher Scientific). Single-cell mRNA libraries were prepared using the GEM-X single cell 3’ v4 kit (10x Genomics), with a target capture of 10,000 cells. Quality control and quantification assays were performed using a Qubit fluorometer (Thermofisher) and a Screentape Assay (Agilent). Libraries were sequenced on an Illumina NextSeq2000 using a 100 cycle, P4 XLEAP-SBS™ kit. Each sample was sequenced to an average read depth of 226 million total reads, which resulted in an average read depth of ~28,000 reads/cell after normalization.

treatment_protocol: Tadpoles were anesthetized with 0.05% MS-222 in 1/9x MR and tested for response to touch prior to amputation surgery. Once fully anesthetized, a sterilized scalpel was used to amputate and collect intended tissue.

value: tail

value: tail tip


title: Bladder_1

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: Library name: Sample 4

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm39 (Ensembl release 109) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: mm39
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: bladder

extract_protocol:
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and max. 10ng used of total RNA was used as input for SMART-Seq® v4 Ultra® Low Input RNA Kit following manufacture’s protocol (Takara Bio).

treatment_protocol: Activation of CreER or DreER was achieved by intraperitoneal injection of 0.75 mg tamoxifen per 10g body weight  for three days. Tamoxifen was dissolved in corn oil at a concentration of 20mg/mL.

value: bladder

value: arterial smooth muscle cells

value: Tamoxifen


title: Sample 47, iMGL KO with treatment None

description: Library name: 22NYCHLT4_1_0462199258_KO1_NoMyelin5_G5


title: FCR, female, 31-5489-S7-HiRUN42

description: Library name: 31__FCR__5489__female__S7__HiRUN42

value: FCR

value: m. flexor carpi radialis

value: Musculus flexor carpi radialis

value: female


title: palmaris long, female, 23_1-5489-S8-NextRUN17

description: Library name: 23_1__palmaris_long__5489__female__S8__NextRUN17

value: m. palmaris longus

value: Musculus palmaris longus


title: Sample 40, iMGL KO with treatment Myelin2hours

description: Library name: 22NYCHLT4_1_0462199258_KO1_Myelin2hours4_G7

value: in vitro

value: in vitro microglia

value: KO


title: Sample 38, iMGL KO with treatment Myelin2hours

description: Library name: 22NYCHLT4_1_0462199258_KO1_Myelin2hours2_F2


title: Sample 41, iMGL KO with treatment Myelin2hours

description: Library name: 22NYCHLT4_1_0462199258_KO1_Myelin2hours5_G8


title: Sample 39, iMGL KO with treatment Myelin2hours

description: Library name: 22NYCHLT4_1_0462199258_KO1_Myelin2hours3_F3


title: Sample 36, iMGL KO with treatment Myelin24hours

description: Library name: 22NYCHLT4_1_0462199258_KO1_Myelin24hours6_G12


title: Sample 35, iMGL KO with treatment Myelin24hours

description: Library name: 22NYCHLT4_1_0462199258_KO1_Myelin24hours5_G11


title: Sample 34, iMGL KO with treatment Myelin24hours

description: Library name: 22NYCHLT4_1_0462199258_KO1_Myelin24hours4_G10


title: Sample 42, iMGL KO with treatment Myelin2hours

description: Library name: 22NYCHLT4_1_0462199258_KO1_Myelin2hours6_G9


title: Sample 37, iMGL KO with treatment Myelin2hours

description: Library name: 22NYCHLT4_1_0462199258_KO1_Myelin2hours1_F1


title: Sample 43, iMGL KO with treatment None

description: Library name: 22NYCHLT4_1_0462199258_KO1_NoMyelin1_E10


title: Sample 31, iMGL KO with treatment Myelin24hours

description: Library name: 22NYCHLT4_1_0462199258_KO1_Myelin24hours1_F4


title: Sample 27, iMGL KO with treatment DMSO

description: Library name: 22NYCHLT4_1_0462199258_KO1_DMSO3_A6

value: DMSO


title: Sample 30, iMGL KO with treatment DMSO

description: Library name: 22NYCHLT4_1_0462199258_KO1_DMSO6_C6


title: Sample 24, iMGL CTRL with treatment None

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_NoMyelin6_F9

value: CTRL


title: Sample 25, iMGL KO with treatment DMSO

description: Library name: 22NYCHLT4_1_0462199258_KO1_DMSO1_A4


title: Sample 33, iMGL KO with treatment Myelin24hours

description: Library name: 22NYCHLT4_1_0462199258_KO1_Myelin24hours3_F6


title: Sample 23, iMGL CTRL with treatment None

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_NoMyelin5_F8


title: Sample 22, iMGL CTRL with treatment None

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_NoMyelin4_F7


title: Sample 26, iMGL KO with treatment DMSO

description: Library name: 22NYCHLT4_1_0462199258_KO1_DMSO2_A5


title: Sample 18, iMGL CTRL with treatment Myelin2hours

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_Myelin2hours6_F12


title: Sample 19, iMGL CTRL with treatment None

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_NoMyelin1_E1


title: Sample  8, iMGL CTRL with treatment Myelin24hours

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_Myelin24hours2_E8


title: Sample 28, iMGL KO with treatment DMSO

description: Library name: 22NYCHLT4_1_0462199258_KO1_DMSO4_C4


title: Sample 13, iMGL CTRL with treatment Myelin2hours

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_Myelin2hours1_E4


title: Sample 10, iMGL CTRL with treatment Myelin24hours

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_Myelin24hours4_G1


title: Sample 16, iMGL CTRL with treatment Myelin2hours

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_Myelin2hours4_F10


title: Sample 17, iMGL CTRL with treatment Myelin2hours

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_Myelin2hours5_F11


title: Sample 21, iMGL CTRL with treatment None

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_NoMyelin3_E3


title: Sample  9, iMGL CTRL with treatment Myelin24hours

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_Myelin24hours3_E9


title: Sample  5, iMGL CTRL with treatment DMSO

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_DMSO5_C2


title: Sample  7, iMGL CTRL with treatment Myelin24hours

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_Myelin24hours1_E7


title: Sample  6, iMGL CTRL with treatment DMSO

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_DMSO6_C3


title: Sample 11, iMGL CTRL with treatment Myelin24hours

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_Myelin24hours5_G2


title: Sample 20, iMGL CTRL with treatment None

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_NoMyelin2_E2


title: Sample 12, iMGL CTRL with treatment Myelin24hours

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_Myelin24hours6_G3


title: Sample 14, iMGL CTRL with treatment Myelin2hours

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_Myelin2hours2_E5


title: Sample  3, iMGL CTRL with treatment DMSO

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_DMSO3_A3


title: Sample 15, iMGL CTRL with treatment Myelin2hours

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_Myelin2hours3_E6


title: Sample  1, iMGL CTRL with treatment DMSO

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_DMSO1_A1


title: Sample  2, iMGL CTRL with treatment DMSO

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_DMSO2_A2


title: Sample  4, iMGL CTRL with treatment DMSO

description: Library name: 22NYCHLT4_1_0462199258_CTRL1_DMSO4_C1


title: RNA from tonsil, donor 3

city: Rennes

first: Samuel

last: Bastos Serra Trinca

address: 2 avenue du professeur Léon Bernard

country: France

institute: University of Rennes

description: Library name: T3_ISRR

data_processing:
RNAseq data for in silico repertoire reconstruction using TRUST4 algorithm
Assembly: human reference sequences for IG/TR receptors
Supplementary files format and content: Table of clone counts after hierarchical clustering performed on TRUST4 outputs using the Scoper package (version 1.3.0)

source_name: tonsil

extract_protocol:
RNA extracted from memory B cells obtained by magnetic enrichment from a human tonsil
For classical RNA-seq libraries, 1200 ng of total RNA (with RIN over 7) were used for polyA selection and reverse transcription using the Truseq stranded mRNA library kit (Illumina). Sequencing (2x150 bp paired ends) was run on a Novaseq Illumina platform (Macrogen) in order to acquire 15 Gb of throughput per sample.

value: tonsil

value: memory B cells


title: RNA from tonsil, donor 1

description: Library name: T1_ISRR


title: RNA from tonsil, donor 2

description: Library name: T2_ISRR


title: P5132C2_G9 (NDI)

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

description: Library name: P5132C2_G9

data_processing:
FASTQ files were aligned to GENCODE v45 using a STAR (v2.7.9) two-pass alignment and RSEM (v1.3.3).
Assembly: GENCODE v45
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes basic phenotype information for each sample

source_name: colon

extract_protocol:
Qiagen AllPrep MiniKit
VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina

value: colon

value: mucosal biopsy


title: P5163S2_G10 (NDI)

description: Library name: P5163S2_G10


title: P5132R4_G9 (NDI)

description: Library name: P5132R4_G9


title: P5103S2_G11 (NDI)

description: Library name: P5103S2_G11


title: P5103C2_G11 (NDI)

description: Library name: P5103C2_G11


title: P5103R4_G11 (NDI)

description: Library name: P5103R4_G11


title: P5163C2_G10 (NDI)

description: Library name: P5163C2_G10


title: P5163R4_G10 (NDI)

description: Library name: P5163R4_G10


title: P5132S2_G9 (NDI)

description: Library name: P5132S2_G9


title: P5086C2_G18 (NDI)

description: Library name: P5086C2_G18


title: P5089R3_G14 (NDI)

description: Library name: P5089R3_G14


title: P5043C2_G13 (NDI)

description: Library name: P5043C2_G13


title: P5086R4_G18 (NDI)

description: Library name: P5086R4_G18


title: P5043S2_G13 (NDI)

description: Library name: P5043S2_G13


title: P5089S2_G14 (NDI)

description: Library name: P5089S2_G14


title: P5043R4_G13 (NDI)

description: Library name: P5043R4_G13


title: P5089C_G14 (NDI)

description: Library name: P5089C_G14


title: P4974R4_G10 (NDI)

description: Library name: P4974R4_G10


title: P4974C2_G10 (NDI)

description: Library name: P4974C2_G10


title: P4954S2_G16 (NDI)

description: Library name: P4954S2_G16


title: P5086S_G18 (NDI)

description: Library name: P5086S_G18


title: P4954R3_G16 (NDI)

description: Library name: P4954R3_G16


title: P4974S2_G10 (NDI)

description: Library name: P4974S2_G10


title: P4954C2_G16 (NDI)

description: Library name: P4954C2_G16


title: P4923S2_G11 (NDI)

description: Library name: P4923S2_G11


title: P4923C2_G11 (NDI)

description: Library name: P4923C2_G11


title: P4795S2_G6 (NDI)

description: Library name: P4795S2_G6


title: P48162_G12 (NDI)

description: Library name: P48162_G12


title: P4816C2_G12 (NDI)

description: Library name: P4816C2_G12


title: P4774S2_G14 (NDI)

description: Library name: P4774S2_G14


title: P4795R4_G6 (NDI)

description: Library name: P4795R4_G6


title: P4774C2_G14 (NDI)

description: Library name: P4774C2_G14


title: P4765S2_G6 (NDI)

description: Library name: P4765S2_G6


title: P4762S2_G11 (NDI)

description: Library name: P4762S2_G11


title: P4762R4_G11 (NDI)

description: Library name: P4762R4_G11


title: P4712C2_G11 (NDI)

description: Library name: P4712C2_G11


title: P4759R4_G15 (NDI)

description: Library name: P4759R4_G15


title: P4762C_G11 (NDI)

description: Library name: P4762C_G11


title: P4795C2_G6 (NDI)

description: Library name: P4795C2_G6


title: P4759C2_G15 (NDI)

description: Library name: P4759C2_G15


title: P4816R4_G12 (NDI)

description: Library name: P4816R4_G12


title: P4712R4_G11 (NDI)

description: Library name: P4712R4_G11


title: P4712S2_G11 (NDI)

description: Library name: P4712S2_G11


title: P4774R4_G14 (NDI)

description: Library name: P4774R4_G14


title: P4923R4_G11 (NDI)

description: Library name: P4923R4_G11


title: P4759S2_G15 (NDI)

description: Library name: P4759S2_G15


title: P4765C2_G6 (NDI)

description: Library name: P4765C2_G6


title: P4707R3_G9 (NDI)

description: Library name: P4707R3_G9


title: P4707S2_G9 (NDI)

description: Library name: P4707S2_G9


title: P4707C2_G9 (NDI)

description: Library name: P4707C2_G9


title: P4695S2_G16 (NDI)

description: Library name: P4695S2_G16


title: P4691C2_G14 (NDI)

description: Library name: P4691C2_G14


title: P4695C2_G16 (NDI)

description: Library name: P4695C2_G16


title: P4695R4_G16 (NDI)

description: Library name: P4695R4_G16


title: P4605S2_G8 (NDI)

description: Library name: P4605S2_G8


title: P4691R4_G14 (NDI)

description: Library name: P4691R4_G14


title: P4765R3_G6 (NDI)

description: Library name: P4765R3_G6


title: P4691S2_G14 (NDI)

description: Library name: P4691S2_G14


title: P4587S2_G6 (NDI)

description: Library name: P4587S2_G6


title: P4605C2_G8 (NDI)

description: Library name: P4605C2_G8


title: P4504C2_G17 (NDI)

description: Library name: P4504C2_G17


title: P4500S2_G14 (NDI)

description: Library name: P4500S2_G14


title: P4524C2_G16 (NDI)

description: Library name: P4524C2_G16


title: P4504R4_G17 (NDI)

description: Library name: P4504R4_G17


title: P4524R4_G16 (NDI)

description: Library name: P4524R4_G16


title: P4587R4_G6 (NDI)

description: Library name: P4587R4_G6


title: P4587C2_G6 (NDI)

description: Library name: P4587C2_G6


title: P4524S2_G16 (NDI)

description: Library name: P4524S2_G16


title: P4504S2_G17 (NDI)

description: Library name: P4504S2_G17


title: P4494S2_G6 (NDI)

description: Library name: P4494S2_G6


title: P4500C2_G14 (NDI)

description: Library name: P4500C2_G14


title: P4500R4_G14 (NDI)

description: Library name: P4500R4_G14


title: P4494R4_G6 (NDI)

description: Library name: P4494R4_G6


title: P4494C2_G6 (NDI)

description: Library name: P4494C2_G6


title: P4473R4_G15 (NDI)

description: Library name: P4473R4_G15


title: P4473S2_G15 (NDI)

description: Library name: P4473S2_G15


title: P4459R4_G4_mix (NDI)

description: Library name: P4459R4_G4_mix


title: P4473C2_G15 (NDI)

description: Library name: P4473C2_G15


title: P44592_G4 (NDI)

description: Library name: P44592_G4


title: P4437C2_G17 (NDI)

description: Library name: P4437C2_G17


title: P4437R4_G17 (NDI)

description: Library name: P4437R4_G17


title: P4437S2_G17 (NDI)

description: Library name: P4437S2_G17


title: P4459C2_G4 (NDI)

description: Library name: P4459C2_G4


title: P4417R4_G17 (NDI)

description: Library name: P4417R4_G17


title: P4361R4_G13 (NDI)

description: Library name: P4361R4_G13


title: P4361S2_G13 (NDI)

description: Library name: P4361S2_G13


title: P4337R4_G16 (NDI)

description: Library name: P4337R4_G16


title: P4417S2_G17 (NDI)

description: Library name: P4417S2_G17


title: P4417C2_G17 (NDI)

description: Library name: P4417C2_G17


title: P4364_S2 (NDI)

description: Library name: P4364_S2


title: P4337C2_G16 (NDI)

description: Library name: P4337C2_G16


title: P4346C_G3 (NDI)

description: Library name: P4346C_G3


title: P4364R4_G10 (NDI)

description: Library name: P4364R4_G10


title: P4321S2_G16 (NDI)

description: Library name: P4321S2_G16


title: P4364C_G10 (NDI)

description: Library name: P4364C_G10


title: P4337S2_G16 (NDI)

description: Library name: P4337S2_G16


title: P4361C2_G13 (NDI)

description: Library name: P4361C2_G13


title: P4321R4_G16 (NDI)

description: Library name: P4321R4_G16


title: P4346S_G3 (NDI)

description: Library name: P4346S_G3


title: P4346R4_G3 (NDI)

description: Library name: P4346R4_G3


title: P4312R4_G2 (NDI)

description: Library name: P4312R4_G2


title: P4312S2_G2 (NDI)

description: Library name: P4312S2_G2


title: P4309S2_G6 (NDI)

description: Library name: P4309S2_G6


title: P4288S2_G14 (NDI)

description: Library name: P4288S2_G14


title: P4288R4_G14 (NDI)

description: Library name: P4288R4_G14


title: P4278S2_G15 (NDI)

description: Library name: P4278S2_G15


title: P4239C_G2 (NDI)

description: Library name: P4239C_G2


title: P4278R4_G15 (NDI)

description: Library name: P4278R4_G15


title: P4288C2_G14 (NDI)

description: Library name: P4288C2_G14


title: P4241S2_G3 (NDI)

description: Library name: P4241S2_G3


title: P4211R4_G12 (NDI)

description: Library name: P4211R4_G12


title: P4241R4_G3 (NDI)

description: Library name: P4241R4_G3


title: P4312C_G2 (NDI)

description: Library name: P4312C_G2


title: P4211C2_G12 (NDI)

description: Library name: P4211C2_G12


title: P4309R4_G6 (NDI)

description: Library name: P4309R4_G6


title: P4199R4_G9 (NDI)

description: Library name: P4199R4_G9


title: P4199C2_G9 (NDI)

description: Library name: P4199C2_G9


title: P4239S_G2 (NDI)

description: Library name: P4239S_G2


title: P4239R4_G2 (NDI)

description: Library name: P4239R4_G2


title: P4278C2_G15 (NDI)

description: Library name: P4278C2_G15


title: P4241C_G3 (NDI)

description: Library name: P4241C_G3


title: P4211S2_G12 (NDI)

description: Library name: P4211S2_G12


title: P4309C2_G6 (NDI)

description: Library name: P4309C2_G6


title: P4182R4_G12 (NDI)

description: Library name: P4182R4_G12


title: P4182S2_G12 (NDI)

description: Library name: P4182S2_G12


title: P4321C2_G16 (NDI)

description: Library name: P4321C2_G16


title: P4199S2_G9 (NDI)

description: Library name: P4199S2_G9


title: P4171S2_G16 (NDI)

description: Library name: P4171S2_G16


title: P4182C2_G12 (NDI)

description: Library name: P4182C2_G12


title: P4171R4_G16 (NDI)

description: Library name: P4171R4_G16


title: P4171C2_G16 (NDI)

description: Library name: P4171C2_G16


title: Clev4277S_G7 (NDI)

description: Library name: Clev4277S_G7


title: P4066S_G2 (NDI)

description: Library name: P4066S_G2


title: Clev4223S_G6 (NDI)

description: Library name: Clev4223S_G6


title: P4066R3_G2 (NDI)

description: Library name: P4066R3_G2


title: P4066C2_G2 (NDI)

description: Library name: P4066C2_G2


title: Clev4277R_G7 (NDI)

description: Library name: Clev4277R_G7


title: Clev4202R_G3 (NDI)

description: Library name: Clev4202R_G3


title: Clev4193S_G2 (NDI)

description: Library name: Clev4193S_G2


title: Clev4193C_G2 (NDI)

description: Library name: Clev4193C_G2


title: Clev4193R_G2 (NDI)

description: Library name: Clev4193R_G2


title: Clev4183R_G5 (NDI)

description: Library name: Clev4183R_G5


title: Clev4208R_G5 (NDI)

description: Library name: Clev4208R_G5


title: Clev4223C_G6 (NDI)

description: Library name: Clev4223C_G6


title: Clev4183S_G5 (NDI)

description: Library name: Clev4183S_G5


title: Clev4208C_G5 (NDI)

description: Library name: Clev4208C_G5


title: Clev4173C_G3 (NDI)

description: Library name: Clev4173C_G3


title: Clev4208S_G5 (NDI)

description: Library name: Clev4208S_G5


title: Clev4223R_G6 (NDI)

description: Library name: Clev4223R_G6


title: Clev4183C_G5 (NDI)

description: Library name: Clev4183C_G5


title: Clev4202S_G3 (NDI)

description: Library name: Clev4202S_G3


title: Clev4277C_G7 (NDI)

description: Library name: Clev4277C_G7


title: Clev4173R_G3 (NDI)

description: Library name: Clev4173R_G3


title: Clev4202C_G3 (NDI)

description: Library name: Clev4202C_G3


title: Clev4146S_G4 (NDI)

description: Library name: Clev4146S_G4


title: Clev4173S_G3 (NDI)

description: Library name: Clev4173S_G3


title: Clev4146C_G4 (NDI)

description: Library name: Clev4146C_G4


title: Sample 45, iMGL KO with treatment None

description: Library name: 22NYCHLT4_1_0462199258_KO1_NoMyelin3_E12


title: Clev4146R_G4 (NDI)

description: Library name: Clev4146R_G4


title: W3

city: Chicago

first: Asia

last: Owais

state: IL

address: 840 S Wood Street

department: Cardiology

institute: University of Illinois at Chicago

description: Library name: sample 3

data_processing:
Raw FASTQ files were uploaded to Biojupies (https://maayanlab.cloud/biojupies) for analysis. Human genome build 38
Assembly: hg38
Supplementary files format and content: normalized gene expression values in .xls format

source_name: iPSC-derived atrial cardiomyocytes

growth_protocol: iPSC-aCMs were maintained in Cardiomyocyte maturation medium prior to RNA extraction

extract_protocol:
RNA was isolated using Trizol and QC-ed by bioAnalyzer (Agilent 2100)
RNA-seq libraries were generated using an Illumina TruSEQ-like protocol (provided by Illumina).

value: iPSC-derived atrial cardiomyocytes

value: cardiomyocyte

value: WT

value: atrial cardiomyocyte diffferentiation


title: Sample 32, iMGL KO with treatment Myelin24hours

description: Library name: 22NYCHLT4_1_0462199258_KO1_Myelin24hours2_F5


title: Clev4125R_G2 (NDI)

description: Library name: Clev4125R_G2


title: Clev4048R_G4 (NDI)

description: Library name: Clev4048R_G4


title: Clev4105R_G3 (NDI)

description: Library name: Clev4105R_G3


title: Clev4124S_G7 (NDI)

description: Library name: Clev4124S_G7


title: Clev4124C_G7 (NDI)

description: Library name: Clev4124C_G7


title: Clev4125S_G2 (NDI)

description: Library name: Clev4125S_G2


title: Clev4048C_G4 (NDI)

description: Library name: Clev4048C_G4


title: Clev4048S_G4 (NDI)

description: Library name: Clev4048S_G4


title: M3

description: Library name: sample 6


title: Clev4124R_G7 (NDI)

description: Library name: Clev4124R_G7


title: M2

description: Library name: sample 5


title: W2

description: Library name: sample 2


title: Clev4105C_G3 (NDI)

description: Library name: Clev4105C_G3


title: M1

description: Library name: sample 4


title: PATR1-3

city: Ankara

first: Efe

last: Dalli

address: Dogol Street

country: Turkey

institute: Ankara University

description: Library name: Tep242

data_processing:
Quality control of raw paired-end reads was performed using FastQC (v0.11.9).
Adaptor sequences and low-quality bases were removed using Cutadapt (v3.5).
Cleaned reads were aligned to the WBcel235 reference genome using STAR (v2.7.11b) in two-pass mode with Ensembl gene annotations.
Sorted BAM files were generated and gene-level read counts were obtained using STAR's quant mode.
Assembly: WBcel235
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample.

organism: Caenorhabditis elegans

source_name: whole body

extract_protocol:
Poly A enrichment by magnetic beads
Watchmaker mRNA Library Prep

value: whole body


title: W1

description: Library name: sample 1


title: UNC5-3

description: Library name: Tep239


title: PATR1-2

description: Library name: Tep241


title: PATR1-1

description: Library name: Tep240


title: UNC5-2

description: Library name: Tep238


title: UNC5-1

description: Library name: Tep237


title: WT-2

description: Library name: Tep235


title: WT-3

description: Library name: Tep236


title: WT-1

description: Library name: Tep234


title: Co-cultured_Test (19BBz-RAB5) biol rep 4

city: Philadelphia

first: Kaitlin

middle: Adele

last: Read

state: Pennsylvania

address: 3600 Civic Center Blvd, Bldg 421, Rm 8-184

institute: University of Pennsylvania

data_processing:
Data trimming, filtering, alignment, and DESeq2 were performed by BGI Genomics. Preprocessing was performed using SOAPnuke (v1.5.2; https://github.com/BGI-flexlab/SOAPnuke). Mapping was performed using HISAT2 (v2.0.4) and Bowtie2 (v2.2.5). DEseq2 analysis was performed using version 1.44.0. Final filtering to remove low-copy-number genes was performed using Microsoft Excel.
Assembly: GRCh38/hg38
Supplementary files format and content: The processed data file is provided as a Microsoft Excel document, containing both normalized read counts and information from DESeq2 analysis (performed independently for each set of samples). Data for the first set of samples (D9) is provided on one tab, and the second set of samples (co-cultured) is provided on a second tab.

source_name: CD3+CAR+ human CD4 and CD8 T cells

extract_protocol:
RNA was isolated by BGI genomics using the Qiagen RNeasy Plus kit.
As provided by the company that performed the sequencing (BGI Genomics): 1) mRNA enrichment and purification: 1) Oligo dT Selection (mRNA enrichment): Use oligo dT beads to enrich mRNA with poly A tail. 2) RNA fragment and reverse transcription: Fragment the RNA and first-strand cDNA was generated using random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP. 3) End repair, add A and adaptor ligation: The synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments. 4) PCR amplification: Prior to PCR amplification, the dUTP-marked strand is selectively degraded by Uracil-DNA-Glycosylase(UDG). The remaining strand is amplified to generate a cDNA library suitable for sequencing. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer. 5) Single strand separation and cyclization: Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) DNA nanoball synthesis.

value: CD3+CAR+ human CD4 and CD8 T cells


title: Co-cultured_Test (19BBz-RAB5) biol rep 2


title: Co-cultured_Test (19BBz-RAB5) biol rep 1


title: Co-cultured_Test (19BBz-RAB5) biol rep 3


title: D9_Test (19BBz-RAB5) biol rep 4


title: Co-cultured_Control (19BBz-tEGFR) biol rep 4


title: Co-cultured_Control (19BBz-tEGFR) biol rep 2


title: D9_Test (19BBz-RAB5) biol rep 2


title: D9_Control (19BBz-tEGFR) biol rep 3


title: Co-cultured_Control (19BBz-tEGFR) biol rep 1


title: D9_Control (19BBz-tEGFR) biol rep 4


title: D9_Control (19BBz-tEGFR) biol rep 1


title: Co-cultured_Control (19BBz-tEGFR) biol rep 3


title: D9_Test (19BBz-RAB5) biol rep 1


title: CosMx, slide_11

type: RNA

city: Houston

first: Salvador

last: Alonso

state: Texas

address: 1400 Holcombe Blvd, FC10.3030

department: GI Medical Oncology

institute: MD Anderson Cancer Center

description: FFPE tissue slides were submitted for in situ hybridization using the CosMx platform

hyb_protocol: The hybridized samples were then processed following the manufacturer’s protocol

scan_protocol: After hybridization, tissue slides were imaged using the CosMx system, capturing immunofluorescence images and individual RNA transcript location

data_processing:
Image processing and transcript localization were performed using NanoString’s pipeline, which includes cell segmentation, transcript quantification, and spatial mapping. Cell segmentation was performed based on nuclear and membrane staining
Cell clustering and cell typing, gene set enrichment analysis, differential gene expression, spatial transcriptomic images, heatmaps, and volcano plots were generated using Seurat, Prism and Illustrator
Processed Data File: expression_matrix_Alonso.csv

label: 1000-plex RNA panel

source_name: colorectal cancer

label_protocol: Antibodies used for immunofluorescence included CD298/B2M membrane marker mix, panCK, CD45, and DAPI (Nanostring).

growth_protocol: formalin-fixed, paraffin-embedded (FFPE) tissue sections (5 µm thick) were obtained from 30 patient samples and mounted onto glass slides.

extract_protocol: FFPE sections underwent deparaffinization and rehydration

value: colorectal cancer

tag: disease state

value: Metastatic


title: D9_Control (19BBz-tEGFR) biol rep 2


title: D9_Test (19BBz-RAB5) biol rep 3


title: CosMx, slide_10

treatment_protocol: FFPE sections underwent deparaffinization and rehydration


title: CosMx, slide_5


title: CosMx, slide_8


title: CosMx, slide_13


title: CosMx, slide_12


title: CosMx, slide_4


title: CosMx, slide_7


title: CosMx, slide_3


title: CosMx, slide_6


title: CosMx, slide_1


title: CosMx, slide_2


title: Rag2, Kidney, WT [K6]

city: Jerusalem

first: Itamar

last: Harel

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: sample K6

data_processing:
Quality control and adapter trimming of the fastq sequence files were performed with FastQC (v0.11.8), fastx-toolkits (v0.0.13), Trim Galore! (v0.6.4), and Cutadapt (3.4). Options were set to remove Illumina TruSeq adapters and end sequences to retain high-quality bases with phred score > 20 and a remaining length > 20 bp. Successful processing was verified by re-running FastQC. Reads was mapped and quantified to the killifish genome Nfu_20140520 using STAR 2.7.6a. Differential gene expression between rag2 mutant and WT fish was performed using the edgeR package (v3.32.1).
Assembly: Nfu_20140520
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Nothobranchius furzeri

source_name: Kidney

growth_protocol: Fish were grown at 28°C in a central filtration recirculating system with a 12 h light/dark cycle at the Hebrew University of Jerusalem (Aquazone ltd, Israel). Fish were fed with live Artemia until the age of 2 weeks (#109448, Primo), and starting week 3, fish were fed three times a day on weekdays (and once a day on weekends), with GEMMA Micro 500 Fish Diet (Skretting Zebrafish, USA), supplemented with Artemia once a day.

extract_protocol:
Head kidney was isolated as described in (Astre et al. 2022)
Library preparation was performed using KAPA mRNA HyperPrep Kit (ROCHE-08105936001) according to the recommended protocols. Library quantity and pooling were measured by Qubit (dsDNA HS, Q32854), Size selection at 4% agarose gel. Library quality was measured by Tape Station (HS, 5067-5584). Libraries were sequenced by NextSeq 2000 P2, 100 cycle,75 bp single-end (Illumina, 20024906) with ~40 million reads per sample.

value: Kidney

tag: age

value: 5 months

value: Male


title: Rag2, Kidney, WT [K1]

description: sample K1

tag: tissue


title: Multiome, 24hr Flu, ATAC, Human

city: CINCINNATI

first: William

last: Zacharias

state: OH

address: 3333 BURNET AVE

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: 10X-Zacharias-William-Hufluganoid24hr-20240822-Multiv1-ATAC
Human_24hr_Flu_filtered_feature_bc_matrix.h5

library_source: genomic single cell

data_processing:
Multiome files were demultiplexed using Cellranger mkfastq then processed using the Cell Ranger Arc pipeline.
Assembly: Custom - GRCm39 with PR8 IAV / GRCh38 with PR8 IAV
Supplementary files format and content: Cell Ranger Arc output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: Seurat object: mouse_minseqe_submission_ready.rds, human_minseqe_submission_ready.rds

source_name: Lung

extract_protocol:
Nuclei isolated from flu-exposed and control AEOs at 8, 16, and 24hours were encapsulated in Gel-Beads-in emulsion (GEMs) using the Next-GEM Chromium Single Cell Multiome ATAC + Gene Expression Library & Gel Bead Kit v1 on the 10xChromium.
Standard institutional library preparation protocol for Illumina sequencing at CCMC

value: Lung

value: Organoid

value: Flu

tag: timepoint


title: Multiome, 24hr Control, ATAC, Human

description:
Library name: 10X-Zacharias-William-Huganoidcon24hr-20240822-Multiv1-ATAC
Human_24hr_Control_filtered_feature_bc_matrix.h5

tag: cell type

value: Control


title: Multiome, 16hr Flu, GEX, Human

description: Library name: 10X-Zacharias-William-Hufluganoid16hr-20240821-Multiv1-GEX-hg

molecule: nuclear RNA


title: Rag2, Kidney, KO [K3]

description: sample K3

tag: genotype

value: rag2 KO


title: Rag2, Kidney, WT [K5]

description: sample K5


title: Rag2, Kidney, KO [K2]

description: sample K2


title: Multiome, 16hr Flu, ATAC, Human

description:
Library name: 10X-Zacharias-William-Hufluganoid16hr-20240821-Multiv1-ATAC
Human_16hr_Flu_filtered_feature_bc_matrix.h5

tag: treatment


title: Multiome, 8hr Control, ATAC, Human

description:
Library name: 10X-Zacharias-William-Huganoidcon8hr-20240822-Multiv1-ATAC
Human_8hr_Control_filtered_feature_bc_matrix.h5


title: Multiome, 16hr Control, ATAC, Human

description:
Library name: 10X-Zacharias-William-Huganoidcon16hr-20240821-Multiv1-ATAC
Human_16hr_Control_filtered_feature_bc_matrix.h5


title: Rag2, Kidney, KO [K4]

description: sample K4


title: Multiome, 8hr Flu, GEX, Human

description: Library name: 10X-Zacharias-William-Hufluganoid8hr-20240822-Multiv1-GEX-hg


title: Multiome, 16hr Control, GEX, Human

description: Library name: 10X-Zacharias-William-Huganoidcon16hr-20240821-Multiv1-GEX-hg


title: Multiome, 8hr Control, GEX, Human

description: Library name: 10X-Zacharias-William-Huganoidcon8hr-20240822-Multiv1-GEX-hg


title: AZ06, 4 timepoints pool, cell hashtag CMO

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 2720 S Moody Ave

department: Department of Biology Medical Engineering

institute: Oregon Health Science University

description:
Library name: 55197_55199_AZ06_hashtag
10x Genomics

data_processing:
Raw sequences were processed and aligned to the GRChg38 genome using 10x Genomics’ CellRanger “multi” pipeline with default settings.
Assembly: GRCh38
Supplementary files format and content: raw unfiltered matrix files for the pools
Supplementary files format and content: CSV of CMO-cell assignment

source_name: Peripheral blood

extract_protocol:
Peripheral blood was collected from patients treated with AZD4573 at the prespecified timepoints noted above. PBMCs were isolated using standard Ficoll-Hypaque technique (Amersham). Red blood cells were lysed using ACK buffer (Thermo Fisher Scientific). PBMCs were viably frozen for subsequent analysis.
Upon thawing, PMBCs were washed and single cells were labeled with Cell Multiplexing Oligos (CMOs) (CellPlex Kit Set A, 1000261) (10x Genomics) according to the manufacturer’s instructions. Labeled samples were pooled in desired ratios. Cell concentration and viability of the pooled sample was determined using a TC20TM Automated Cell Counter (Bio-Rad). A total of 10,000 cells were targeted per pooled sample. Each sample pool was loaded into a different lane of a 10x chip (Chromium Next GEM Chip G Single Cell Kit, 1000127). cDNA libraries were generated using the Single Cell 3’ Library & Gel Bead kit version 3.1 (1000121). Indexed sequencing libraries were constructed using the reagents in the library Construction Kit (10xGenomics, 1000190). The barcode sequencing libraries were sequenced on the NovaSeq 6000 platform (Illumina) with paired-end sequencing and dual indexing. A total of 28, 10, 10 and 101 cycles were run for Read 1, i7 index, i5 index and Read 2, respectively.

value: Peripheral blood

value: Peripheral blood mononuclear cells

tag: subject status

value: MCL patient receiving AZD4573


title: Multiome, 8hr Flu, ATAC, Human

description:
Library name: 10X-Zacharias-William-Hufluganoid8hr-20240822-Multiv1-ATAC
Human_8hr_Flu_filtered_feature_bc_matrix.h5


title: AZ01, 4 timepoints pool, cell hashtag CMO

description:
Library name: 55196_55198_AZ01_hashtag
10x Genomics


title: AZ06, 4 timepoints pool, GEX

description:
Library name: 55197_55199_AZ06
10x Genomics


title: AZ01, 4 timepoints pool, GEX

description:
Library name: 55196_55198_AZ01
10x Genomics


title: Pt37_C1D8 scmultiome- scATAC

city: New Delhi

first: Veena

last: Kochat

state: New Delhi

address: Aruna Asaf Ali Marg

department: Stem Cell Biology Lab

country: India

institute: National Institute of Immunology

description: Library name: Pt37_C1D8_ATAC

data_processing:
Initially, the raw multiome data comprising both gene expression and chromatin accessibility fragments were processed using 10x Genomics Cell Ranger ARC. The scRNAseq data from multiple samples were imported using import10xFeatureMatrix. For the ATAC modality, low-quality cells defined as those with TSS enrichment less than 5, fewer than 2,500 fragments, or missing RNA UMIs were filtered out. Cell barcodes were used to match and integrate scRNA-seq and scATAC-seq data in ArchR, retaining only shared cells using subsetArchRProject(). Gene expression data were incorporated with matched RNA constraints, and iterative LSI was applied separately to both RNA and ATAC matrices for dimensionality reduction. A combined low-dimensional embedding was then generated followed by UMAP visualization and clustering. Differential gene activity gene score matrix and chromatin accessibility peak matrix were identified, peaks calling was performed using MACS2. Subsequently, motif enrichment analysis was conducted using ENCODE and HOMER annotations to identify transcription factor binding patterns across clusters.
Assembly: GRCh38
Supplementary files format and content: atac_fragments.tsv.gz
Supplementary files format and content: atac_fragments.tsv.gz.tbi
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: atac_peaks.bed
Supplementary files format and content: per_barcode_metrics.csv

source_name: PBMCs

extract_protocol:
From cryopreserved PBMCs, nuclei were isolated using the Chromium Nuclei Isolation Kit from 10X genomics (PN-1000493) based on the manufacturer's protocol.
Single nuclei suspensions were processed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (10x Genomics, PN: 1000283) platform following the manufacturer’s protocol, generating paired ATAC and gene expression libraries for each sample.

value: PBMCs

tag: individual

value: APX005M + Pembrolizumab

tag: time


title: Pt32_BL scmultiome- scATAC

description: Library name: Pt32_BL_ATAC

value: BL


title: Pt37_BL scmultiome- scATAC

description: Library name: Pt37_BL_ATAC


title: Pt32_C1D8 scmultiome- scATAC

description: Library name: Pt32_C1D8_ATAC


title: Pt37_C2D1 scmultiome- scATAC

description: Library name: Pt37_C2D1_ATAC


title: Pt28_C2D1 scmultiome- scATAC

description: Library name: Pt28_C2D1_ATAC


title: Pt37_C1D3 scmultiome- scATAC

description: Library name: Pt37_C1D3_ATAC


title: Pt28_C1D8 scmultiome- scATAC

description: Library name: Pt28_C1D8_ATAC


title: Pt28_C1D3 scmultiome- scATAC

description: Library name: Pt28_C1D3_ATAC


title: Pt32_C1D3 scmultiome- scATAC

description: Library name: Pt32_C1D3_ATAC


title: Pt28_BL scmultiome- scATAC

description: Library name: Pt28_BL_ATAC


title: Pt37_C1D8 scmultiome- scRNA

description: Library name: Pt37_C1D8_GEX


title: P4605R4_G8 (NDI)

description: Library name: P4605R4_G8

value: colon

value: mucosal biopsy


title: Pt32_C2D1 scmultiome- scATAC

description: Library name: Pt32_C2D1_ATAC


title: Pt32_C2D1 scmultiome- scRNA

description: Library name: Pt32_C2D1_GEX


title: Pt37_BL scmultiome- scRNA

description: Library name: Pt37_BL_GEX


title: PATL1-2

description: Library name: Tep513

data_processing:
Quality control of raw paired-end reads was performed using FastQC (v0.11.9).
Adaptor sequences and low-quality bases were removed using Cutadapt (v3.5).
Cleaned reads were aligned to the GRCh38 reference genome using STAR (v2.7.11b) in two-pass mode with Ensembl gene annotations.
Sorted BAM files were generated and gene-level read counts were obtained using STAR's quant mode.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample.

source_name: Human fibroblast

value: Human fibroblast


title: HCF1-2

description: Library name: Tep510

value: control


title: PATL1-3

description: Library name: Tep514


title: Pt37_C1D3 scmultiome- scRNA

description: Library name: Pt37_C1D3_GEX


title: Pt32_C1D8 scmultiome- scRNA

description: Library name: Pt32_C1D8_GEX


title: HCF1-3

description: Library name: Tep511


title: Pt37_C2D1 scmultiome- scRNA

description: Library name: Pt37_C2D1_GEX


title: Pt28_C1D8 scmultiome- scRNA

description: Library name: Pt28_C1D8_GEX


title: HCF1-1

description: Library name: Tep509


title: Pt32_C1D3 scmultiome- scRNA

description: Library name: Pt32_C1D3_GEX


title: Pt28_C1D3 scmultiome- scRNA

description: Library name: Pt28_C1D3_GEX


title: PATL1-1

description: Library name: Tep512


title: TPH1KO_S16

city: Paris

first: Benedicte

last: Oules

address: 123 bvd Port Royal

institute: INSERM Université Paris Cité

description:
Library name: 224364_S10_m2_skin_TPH1KO_S16
Column name in NGS23-004_ensemblGRCm38r101_skin_deseq2_NormalizedMatrix: S10_m2_skin_TPH1KO_S16

data_processing:
Fastq files were then aligned using STAR algorithm (version 2.7.6a)
Key parameters included: --twopassMode Basic, --sjdbOverhang 74, and --outFilterType BySJout. Output BAM files were sorted by coordinate (--outSAMtype BAM SortedByCoordinate). Unmapped reads were retained (--outSAMunmapped Within). Transcriptome alignments were also generated using --quantMode TranscriptomeSAM
Reads were count using RSEM (v.1.31)
Gene expression levels were normalized as transcripts per million (TPM)
We used the standard DESeq2 normalization method (DESeq2’s median of ratios with the DESeq function), with a pre-filter of reads and genes (reads uniquely mapped on the genome, or up to 10 different loci with a count adjustement, and genes with at least 10 reads in at least 3 different samples).
Assembly: Ensembl release 101, GRCm38
Supplementary files format and content: tsv file of normalized matrix

source_name: skin

extract_protocol:
Total RNA was extracted from dorsal skin using the Rneasy Mini Kit (Qiagen)
Librairies were prepared using the NEBNext Ultra RNA Library Prep Kit

value: skin

value: TPH1 knockout


title: Pt32_BL scmultiome- scRNA

description: Library name: Pt32_BL_GEX


title: Pt28_C2D1 scmultiome- scRNA

description: Library name: Pt28_C2D1_GEX


title: Whole larva, 24 h exposure, DMSO, rep C

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

institute: United States Environmental Protection Agency

description: Library name: FCP_DEX_0_C

data_processing:
Base calling: Base calling was done by Illumina Real Time Analysis (v3.4.4)
Demultiplex: Output was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0
Indexing: The fathead minnow reference genome (assembly GCA_016745375.1; Martinson et al., 2022) was indexed with STAR (v2.7.10a). The following sample specific parameters were used to generate the genome index: --genomeSAindexNbases 13 --sjdbOverhang 99.
Assign counts: HTSeq (v2.0.1) was used to assign counts to each gene. FastQC and MultiQC (v1.12) were used to assess quality control metrics of the processed reads.  Counts to each gene were parsed, and count data for each exposure condition written to a single tab-delimited matrix file with samples arranged as columns and genes arranged in rows.
Filter counts: Raw counts were first screened to see if any exhibited total counts <2M, and a boxplot of log10 raw counts (+1) for each sample was generated to look for samples with unusual counts distribution. Lowly expressed genes were removed from the raw count matrices using edgeR’s (Robinson et al., 2010) built-in filtering function, filterByExpr(), in version 3.40.2; namely, genes with < 15 reads across all samples and < 10 reads in 70% of samples in the smallest group (treatment or control) were filtered out.
Count normalization and filtering: Library normalization factors for the filtered count matrices were calculated using the trimmed mean of M-values method via the edgeR function calcNormFactors(). Filtered counts were then normalized by read depth using th counts per million (CPM) method. CPM values were then transformed with log2 with a pseudo-count of 1 added to prevent taking the log of a negative count value. PCA was performed on the normalized count values for outlier detection. Samples were removed as outliers based on visual inspection of the PCA plots as sample replicate size did not allow for robust statistical methods to be used.
Assembly: GCA_016745375.1
Supplementary files format and content: *.txt file raw count matrix
Supplementary files format and content: *.txt file count matrix with all filtering, normalization and quality control filters applied. Header rows provide unique sample ID and expsoure concentrations.

organism: Pimephales promelas

extract_protocol:
Total RNA was extracted from pooled homogenates using the Zymo Research Direct-zol-96 RNA kit (Zymo Research). The protocol has been adapted to the Biomek i5 to yield 40 µL of total RNA. The quantity and quality of total RNA was observed using a NanoDrop Eight (Thermo Fisher Scientific; Waltham, MA, USA), prior to storage at -80 ºC.
Libraries were prepared using the Lexogen QuantSeq 3' mRNA-Seq V2 Library Prep Kit with Unique Dual Index (UDI) and QuantSeq Unique Molecular Identifier (UMI) module following manufacturer's recommendations.

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: DMSO Negative Control


title: Whole larva, 24 h exposure, DMSO, rep B

description: Library name: FCP_DEX_0_B

tag: age

tag: tissue

tag: Sex

value: Great Lakes Toxicology & Ecology Division

tag: treatment


title: WT_S11

description:
Library name: 224376_S4_m2_skin_WT_S11
Column name in NGS23-004_ensemblGRCm38r101_skin_deseq2_NormalizedMatrix: S4_m2_skin_WT_S11

tag: genotype

value: WT


title: TPH1KO_S15

description:
Library name: 224392_S9_m2_skin_TPH1KO_S15
Column name in NGS23-004_ensemblGRCm38r101_skin_deseq2_NormalizedMatrix: S9_m2_skin_TPH1KO_S15


title: Pt28_BL scmultiome- scRNA

description: Library name: Pt28_BL_GEX

value: PBMCs

tag: individual

value: APX005M + Pembrolizumab

tag: time

value: BL


title: TPH1KO_S14

description:
Library name: 224388_S7_m2_skin_TPH1KO_S14
Column name in NGS23-004_ensemblGRCm38r101_skin_deseq2_NormalizedMatrix: S7_m2_skin_TPH1KO_S14

value: skin

value: TPH1 knockout


title: TPH1KO_S13

description:
Library name: 224384_S6_m2_skin_TPH1KO_S13
Column name in NGS23-004_ensemblGRCm38r101_skin_deseq2_NormalizedMatrix: S6_m2_skin_TPH1KO_S13


title: WT_S10

description:
Library name: 224372_S3_m2_skin_WT_S10
Column name in NGS23-004_ensemblGRCm38r101_skin_deseq2_NormalizedMatrix: S3_m2_skin_WT_S10


title: WT_S9

description:
Library name: 224368_S2_m2_skin_WT_S9
Column name in NGS23-004_ensemblGRCm38r101_skin_deseq2_NormalizedMatrix: S2_m2_skin_WT_S9


title: Whole larva, 24 h exposure, 0.006 uM fluticasone propionate, rep C

description: Library name: FCP_6_C

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name

value: Fluticasone Propionate (DTXSID8045511)


title: WT_S12

description:
Library name: 224380_S5_m2_skin_WT_S12
Column name in NGS23-004_ensemblGRCm38r101_skin_deseq2_NormalizedMatrix: S5_m2_skin_WT_S12


title: Nvec_Sperm_GSK_Nanopore

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

institute: Queen Mary University of London

description: Library name: STELLA5mC43

data_processing:
EM-seq data was mapped to the reference genome using BS-seeker2 with Bowtie2 as a back-end aligner. The resulting bam file was then deduplicated with Sambamba, and the methylation calling done with CGmapTools.
RNA-seq data was mapped against the reference transcriptome using Kallisto with default parameters.
ATAC-seq data was mapped to the reference genome using chromap (--preset atac), the resulting BEDPE was used as input for MACS3 callpeaks function (-g 2.7e8 -q 0.05 -B). All peaks were merged using BEDTOOLS merge function, and insert sites were counted using the featureCounts function in the SUBREAD package, requiring 20% read overlap (--fracOverlap 0.2).
Oxford Nanopore data was basecalled using Dorado (0.7.2) with the model 5mCG_5hmCG, sup model, mapped directly to the reference genome. Methylation calls where extracted using modkit with default parameters. Haplotype tags on the bam file were obtained using WhatsHap.
Raw CAGE reads were demultiplexed using standard Illumina processing pipelines. Adapter sequences and low-quality reads were trimmed and filtered using Trim Galore! (v0.6.7, Babraham Bioinformatics) with default settings, after which the G added during the reverse transcription step was removed with cutadapt (v4.6). Quality-filtered reads were aligned to the reference genome using STAR (v5.1.0), ensuring that the 5' end of each read was correctly mapped to its genomic location. Alignments were filtered to retain only primary, uniquely mapped reads with a mapping quality greater than 20.
Assembly: GCF_932526225.1
Supplementary files format and content: CGmap files are described in the BS-Seeker2 github repository: https://github.com/BSSeeker/BSseeker2?tab=readme-ov-file#44-bs_seeker2-call_methylationpy
Supplementary files format and content: Processed mRNA-seq data shows est_counts values obtained from Kallisto Quant function against the reference transcriptome, summarised per gene.
Supplementary files format and content: NarrowPeak files are described in MACS3 documentation (https://macs3-project.github.io/MACS/docs/narrowPeak.html). ATACseq.all_peaks.counts.tsv is the output of featureCounts, where each peak (defined as chr:start-end) is a row and each sample is a column.
Supplementary files format and content: Modkit bedmethyl format is described here: https://github.com/nanoporetech/modkit?tab=readme-ov-file#description-of-bedmethyl-output
Supplementary files format and content: TagCluster for CAGE seq data are described in the CAGEr package. Bigwigs are coverage normalised read counts divided per strand: plus or minus.

source_name: Sperm

extract_protocol:
Monarch Genomic DNA Purification Kit (New England Biolabs, #T1030)
mRNA-seq / EM-seq / OmniATAC-seq / Oxford Nanopore Ligation kit (SQK-LSK114) / CAGE-seq

value: Sperm

tag: cell type

value: Massachussets

value: Gametes of GSK treated individual


title: ADAR1 #1

city: Gosselies

first: Denis

middle: LJ

last: Lafontaine

state: Hainaut

address: Av Profs Jeneer & Brachet, 12

country: Belgium

institute: Universite libre de Bruxelles

description: Library name: DLRMS057

data_processing:
The RiboMethSeq was conducted exactly as described in Marchand et al. 201635 for data in Supplementary Figure S7. Analysis: Adapter sequences were trimmed from raw reads using Trimmomatic v0.39 with the following parameters: LEADING:30, TRAILING:30, SLIDINGWINDOW:4:15, AVGQUAL:30, and MINLEN:17. Quality control of the raw and trimmed reads was assessed using FastQC (v0.11.9). Alignment to the reference rRNA sequence was done by Bowtie2 (v2.3.5.1), with default parameters. Sorting, indexing and extraction of mapped reads was done using Samtools (v1.15.1), with option -F 4 to exclude the unmapped reads. Subsequent analysis was conducted using R: the quantification of ribosomal RNA (rRNA) 2′-O-Me residues was performed using the RNAmodR.RiboMethSeq package (v1.18.0), the final processed data were exported using the writexl (v1.5.0) package, display output were generated with the Prism software (v10.3.0).
Assembly: The rRNA reference sequence used are 18S: NR_003286.4; 5.8S: NR_003285.2; and 28S: NR_003287.4
Supplementary files format and content: RMS_FS7.xlsx

source_name: PaTu

extract_protocol:
Total RNA was harvested in 200 μL 1X Buffer RLT (QIAGEN, 79216) and isolated using the QIAGEN RNeasy Mini Kit (74104), followed by 1 hr of DNase treatment using TURBO DNase (ThermoFisher, AM2238). DNase-digested RNA was then further purified with the Zymo RNA Clean and Concentrator-25 kit (R1017).
RNA was hydrolyzed in bicarbonate buffer and the reaction was stopped by ethanol precipitation. The resulting fragments were then end-repaired and converted into an Illumina library using the NEB Next Small RNA Library Prepkit (Bioke, E7300S), according to the manufacturer’s protocol.

tag: cell line

value: PaTu


title: ADAR2 #1

description: Library name: DLRMS059


title: ADAR1 #2

description: Library name: DLRMS058


title: Whole larva, 24 h exposure, DMSO, rep A

description: Library name: FCP_DEX_0_A

value: larvae

value: whole body

value: not determined

value: -80 deg C

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units


title: Whole larva, 24 h exposure, 0.006 uM fluticasone propionate, rep B

description: Library name: FCP_6_B

tag: age

tag: tissue

tag: Sex

value: Great Lakes Toxicology & Ecology Division

value: μM

tag: nominal conc

tag: nominal conc_units

tag: treatment


title: Nvec_F1_Gastrula_UntreatedxUntreated_Nanopore

description: Library name: STELLA5mC41

source_name: 25 hpf gastrulae

value: 25 hpf gastrulae

value: Whole embryo

tag: genotype

value: No treatment


title: SCR

description: Library name: DLRMS056


title: Whole larva, 24 h exposure, 0.006 uM fluticasone propionate, rep A

description: Library name: FCP_6_A

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name

value: Fluticasone Propionate (DTXSID8045511)


title: Nvec_F1_Juvenile_GSKxUntreated_Nanopore

description: Library name: STELLA5mC42

source_name: Whole animal

value: Whole animal

tag: cell type

value: Massachussets

value: No treatment (F1 of GSK treated individuals)


title: Nvec_Sperm_MO_EMseq_rep1

description: Library name: STELLA5mC39

data_processing:
EM-seq data was mapped to the reference genome using BS-seeker2 with Bowtie2 as a back-end aligner. The resulting bam file was then deduplicated with Sambamba, and the methylation calling done with CGmapTools.
RNA-seq data was mapped against the reference transcriptome using Kallisto with default parameters.
ATAC-seq data was mapped to the reference genome using chromap (--preset atac), the resulting BEDPE was used as input for MACS3 callpeaks function (-g 2.7e8 -q 0.05 -B). All peaks were merged using BEDTOOLS merge function, and insert sites were counted using the featureCounts function in the SUBREAD package, requiring 20% read overlap (--fracOverlap 0.2).
Oxford Nanopore data was basecalled using Dorado (0.7.2) with the model 5mCG_5hmCG, sup model, mapped directly to the reference genome. Methylation calls where extracted using modkit with default parameters. Haplotype tags on the bam file were obtained using WhatsHap.
Raw CAGE reads were demultiplexed using standard Illumina processing pipelines. Adapter sequences and low-quality reads were trimmed and filtered using Trim Galore! (v0.6.7, Babraham Bioinformatics) with default settings, after which the G added during the reverse transcription step was removed with cutadapt (v4.6). Quality-filtered reads were aligned to the reference genome using STAR (v5.1.0), ensuring that the 5' end of each read was correctly mapped to its genomic location. Alignments were filtered to retain only primary, uniquely mapped reads with a mapping quality greater than 20.
Assembly: GCF_932526225.1
Supplementary files format and content: CGmap files are described in the BS-Seeker2 github repository: https://github.com/BSSeeker/BSseeker2?tab=readme-ov-file#44-bs_seeker2-call_methylationpy
Supplementary files format and content: Processed mRNA-seq data shows est_counts values obtained from Kallisto Quant function against the reference transcriptome, summarised per gene.
Supplementary files format and content: NarrowPeak files are described in MACS3 documentation (https://macs3-project.github.io/MACS/docs/narrowPeak.html). ATACseq.all_peaks.counts.tsv is the output of featureCounts, where each peak (defined as chr:start-end) is a row and each sample is a column.
Supplementary files format and content: Modkit bedmethyl format is described here: https://github.com/nanoporetech/modkit?tab=readme-ov-file#description-of-bedmethyl-output
Supplementary files format and content: TagCluster for CAGE seq data are described in the CAGEr package. Bigwigs are coverage normalised read counts divided per strand: plus or minus.
Library strategy: EM-seq

value: Sperm

value: Gametes of Morpholine injected individual


title: Nvec_Sperm_GSK_EMseq_rep2

description: Library name: STELLA5mC37

value: Gametes of GSK treated individual


title: Whole larva, 24 h exposure, 0.06 uM fluticasone propionate, rep B

description: Library name: FCP_60_B

value: larvae

value: whole body

value: not determined

value: -80 deg C

value: USA:Minnesota, Duluth

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: Nvec_Sperm_GSK_EMseq_rep3

description: Library name: STELLA5mC38


title: Whole larva, 24 h exposure, 0.06 uM fluticasone propionate, rep C

description: Library name: FCP_60_C

tag: age

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM


title: Nvec_F1_Gastrula_GSKxUntreated_Nanopore

description: Library name: STELLA5mC40

tag: tissue

value: 25 hpf gastrulae

value: Whole embryo


title: Mock

description: Library name: DLRMS055

tag: cell line

value: PaTu


title: Nvec_Sperm_GSK_EMseq_rep1

description: Library name: STELLA5mC36

tag: genotype

tag: treatment


title: Nvec_Sperm_Control_EMseq_rep2

description: Library name: STELLA5mC35

value: No treatment


title: Whole larva, 24 h exposure, 0.06 uM fluticasone propionate, rep A

description: Library name: FCP_60_A

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

tag: Sex

value: Great Lakes Toxicology & Ecology Division

tag: nominal conc

tag: nominal conc_units

value: Fluticasone Propionate (DTXSID8045511)


title: Nvec_F1_MO_25hpf_RNAseq_rep2

description:
Library name: STELLA5mC33
Nvec_Complete_Gene_Counts.tsv

tag: cell type

value: Massachussets

value: No treatment (F1 of Morpholino injected individuals)


title: S250801

city: Wuhan

first: fangyu

last: wang

state: Hubei

address: Donghu Road, No. 115, Wuchang District

institute: Wuhan university

description: Library name: S250801

data_processing:
RNAseq fastq files were pre-processed with Cellranger.
Assembly: hg38
Supplementary files format and content: matrix table with raw gene counts for every gene and every cell

source_name: Glioma

extract_protocol:
Separating one part of human GBM tissue, the RNA isolation was performed using the RNAiso Plus (TAKARA, 9109) according to the manufacturer’s instructions. RNA quality was evaluated spectrophotometrically, and the RNA integrity was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, no.E7775). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and sequenced with paired-end reads on an Illumina NovaSeq 6000 (Illumina).

value: Glioma

value: WT


title: Nvec_Sperm_Control_EMseq_rep1

description: Library name: STELLA5mC34

value: Sperm


title: S250729

description: Library name: S250729


title: Whole larva, 24 h exposure, 0.003 uM fluticasone propionate, rep C

description: Library name: FCP_3_C

value: larvae

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

tag: birth location


title: Nvec_F1_MO_25hpf_RNAseq_rep1

description:
Library name: STELLA5mC32
Nvec_Complete_Gene_Counts.tsv

value: 25 hpf gastrulae

value: Whole embryo


title: Nvec_F1_MO_25hpf_ATACseq_rep2

description:
Library name: STELLA5mC29
ATACseq.all_peaks.counts.tsv


title: SSB.Teniposide.20.B6

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

institute: Huaqiao University

description: Library name: SSB.Teniposide.20.B6

data_processing:
SSiNGLe method: The genomic site mapping was performed the same way as in the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) with the two additional filtering steps. One, PCR duplicates were removed. Two, a read-pair was used only if the first base of the read 2 aligned to the reference sequence. The coordinate of  the first aligning base of the read 2 was assigned as the position of the SSB site.
Assembly: hg19(GRCh37) for the human reads mapping
Supplementary files format and content: All BED files contain coordinates of SSBs mapped to human genomes. The 5th columns show the number of reads representing the SSBs.

extract_protocol:
Three million human chronic myeloid leukemia K562 cells were seeded at 1 million cells per 1 ml of culture medium in each well of 6-well plates. The cells were grown in RPMI 1640 (Gibco, Billings, MT, USA) supplemented with 10% heat-inactivated fetal bovine serum (ExCell Bio, Montevideo, Uruguay) and 1% penicillin-streptomycin (Gibco) at 37 oC in 5% CO2. After 16 h, the cells were separately treated with 0.1%DMSO, 100 μM etoposide (AbMole), 100 μM teniposide (Merck), 10 μM mitoxantrone (Merck), 10 μM m-amsacrine hydrochloride (Merck), 10 μM pixentrone, 0.1 μM, 1 μM, 10 μM, 20 μM or 100 μM doxorubicin (Merck), and 20 μM epirubicin (Selleck) for 1 hour. All drugs were dissolved in DMSO, and each treatment was done in three independent biological replicas. After the drug treatment, DNA was isolated with the TIANamp Genomic DNA Kit (TIANGEN Biotech, DP304) according to the manufacturer’s protocol
SSiNGLe method

value: chronic myelogenous leukemia cell line

value: treated with 20 μM teniposide

tag: batch

value: 1 hr


title: SSB.Teniposide.20.B4

description: Library name: SSB.Teniposide.20.B4


title: SSB.Teniposide.1.B6

description: Library name: SSB.Teniposide.1.B6

value: treated with 1 μM teniposide


title: Nvec_F1_MO_25hpf_EMseq_rep1

description: Library name: STELLA5mC30


title: Whole larva, 24 h exposure, 0.003 uM fluticasone propionate, rep B

description: Library name: FCP_3_B

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

value: Fluticasone Propionate (DTXSID8045511)


title: SSB.Teniposide.1.B5

description: Library name: SSB.Teniposide.1.B5

tag: cell line

tag: treatment


title: Nvec_F1_MO_25hpf_EMseq_rep2

description: Library name: STELLA5mC31

tag: tissue

tag: genotype

value: Massachussets

value: No treatment (F1 of Morpholino injected individuals)


title: SSB.Teniposide.20.B5

description: Library name: SSB.Teniposide.20.B5

tag: cell type


title: Nvec_F1_GSK_25hpf_RNAseq_rep1

description:
Library name: STELLA5mC26
Nvec_Complete_Gene_Counts.tsv

value: No treatment (F1 of GSK treated individuals)


title: Whole larva, 24 h exposure, 0.003 uM fluticasone propionate, rep A

description: Library name: FCP_3_A

tag: strain

tag: dev stage

value: larvae

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

value: Great Lakes Toxicology & Ecology Division

tag: nominal conc

tag: nominal conc_units


title: Nvec_F1_MO_25hpf_ATACseq_rep1

description:
Library name: STELLA5mC28
ATACseq.all_peaks.counts.tsv

value: 25 hpf gastrulae

value: Whole embryo


title: Whole larva, 24 h exposure, 0.034 uM fluticasone propionate, rep C

description: Library name: FCP_34_C

tag: age

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

tag: birth location


title: Nvec_F1_GSK_25hpf_RNAseq_rep2

description:
Library name: STELLA5mC27
Nvec_Complete_Gene_Counts.tsv


title: Whole larva, 24 h exposure, 0.034 uM fluticasone propionate, rep B

description: Library name: FCP_34_B

value: GLTED-Duluth-wt

tag: breeding method

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units


title: Nvec_F1_GSK_25hpf_EMseq_rep1

description: Library name: STELLA5mC24

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: SSB.Teniposide.1.B4

description: Library name: SSB.Teniposide.1.B4

tag: cell line

value: chronic myelogenous leukemia cell line

value: treated with 1 μM teniposide

tag: batch

value: 1 hr


title: Nvec_F1_GSK_25hpf_EMseq_rep2

description: Library name: STELLA5mC25


title: Nvec_F1_GSK_25hpf_ATACseq_rep2

description:
Library name: STELLA5mC23
ATACseq.all_peaks.counts.tsv


title: Whole larva, 24 h exposure, 0.034 uM fluticasone propionate, rep A

description: Library name: FCP_34_A

tag: strain

value: 5-6 dpf

tag: dev stage

tag: Sex

tag: store cond

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

value: μM

tag: nominal conc

tag: nominal conc_units


title: Nvec_F1_GSK_25hpf_ATACseq_rep1

description:
Library name: STELLA5mC22
ATACseq.all_peaks.counts.tsv

value: Massachussets

value: No treatment (F1 of GSK treated individuals)


title: Nvec_Egg_GSK_EMseq_rep2

description: Library name: STELLA5mC21

source_name: Eggs

value: Eggs

value: Gametes of GSK treated individual


title: SSB.Teniposide.10.B6

description: Library name: SSB.Teniposide.10.B6

value: treated with 10 μM teniposide


title: Whole larva, 24 h exposure, 0.019 uM fluticasone propionate, rep C

description: Library name: FCP_19_C

tag: age

value: larvae

value: whole body

value: not determined

value: -80 deg C

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: birth location

tag: breeding method

value: Great Lakes Toxicology & Ecology Division

value: Fluticasone Propionate (DTXSID8045511)


title: Nvec_Egg_Control_EMseq_rep1

description: Library name: STELLA5mC18

tag: tissue

tag: cell type

value: No treatment


title: Sample 29, iMGL KO with treatment DMSO

city: Cambridge

first: Joshua

last: Levin

address: 75 Ames St

institute: Broad Institute

description: Library name: 22NYCHLT4_1_0462199258_KO1_DMSO5_C5

data_processing:
Quantification was performed with Salmon (v1.6.0) with the arguments -l A --posBias --seqBias --gcBias --validate Mapping, with the fullgenome as decoys.
Data was loaded into R with tximport and processed with DESeq2 and other packages.
Assembly: GrCH38
Supplementary files format and content: Count matrix

source_name: in vitro

extract_protocol:
RNA was harvested using Rneasy Plus Mini Kit (Qiagen) from independent wells seeded at 50,000 cells per well. 200 ng of total RNA from each sample was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Kit following manufacturer's instructions

value: in vitro

value: in vitro microglia

tag: genotype

value: KO

tag: treatment

value: DMSO


title: Nvec_25hpf_GSK_RNAseq_rep1

description:
Library name: STELLA5mC15
Nvec_Complete_Gene_Counts.tsv

value: 25 hpf gastrulae

value: Whole embryo


title: Nvec_25hpf_GSK_RNAseq_rep3

description:
Library name: STELLA5mC17
Nvec_Complete_Gene_Counts.tsv

value: Massachussets


title: Whole larva, 24 h exposure, 0.19 uM fluticasone propionate, rep C

description: Library name: FCP_191_C

value: GLTED-Duluth-wt

value: 5-6 dpf

value: USA:Minnesota, Duluth

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM


title: SSB.Teniposide.10.B5

description: Library name: SSB.Teniposide.10.B5

tag: cell line

value: chronic myelogenous leukemia cell line

value: treated with 10 μM teniposide

tag: batch

value: 1 hr


title: Nvec_Egg_GSK_EMseq_rep1

description: Library name: STELLA5mC20

value: Eggs

value: Gametes of GSK treated individual


title: Clev4105S_G3 (NDI)

description: Library name: Clev4105S_G3

data_processing:
FASTQ files were aligned to GENCODE v45 using a STAR (v2.7.9) two-pass alignment and RSEM (v1.3.3).
Assembly: GENCODE v45
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes basic phenotype information for each sample

source_name: colon

value: colon

value: mucosal biopsy


title: SSB.Teniposide.10.B4

description: Library name: SSB.Teniposide.10.B4


title: Clev4125C_G2 (NDI)

description: Library name: Clev4125C_G2


title: SSB.Teniposide.100.B6

description: Library name: SSB.Teniposide.100.B6

value: treated with 100 μM teniposide


title: Whole larva, 24 h exposure, 0.019 uM fluticasone propionate, rep A

description: Library name: FCP_19_A

source_name: whole body

tag: strain

tag: dev stage

value: larvae

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

value: Great Lakes Toxicology & Ecology Division

tag: nominal conc

tag: nominal conc_units

value: Fluticasone Propionate (DTXSID8045511)


title: Nvec_Egg_Control_EMseq_rep2

description: Library name: STELLA5mC19

value: Massachussets

value: No treatment


title: Nvec_25hpf_GSK_EMseq_rep3

description: Library name: STELLA5mC14

value: 25 hpf gastrulae

value: Whole embryo


title: SSB.Teniposide.100.B5

description: Library name: SSB.Teniposide.100.B5

value: chronic myelogenous leukemia cell line


title: Nvec_25hpf_GSK_RNAseq_rep2

description:
Library name: STELLA5mC16
Nvec_Complete_Gene_Counts.tsv


title: Nvec_25hpf_GSK_EMseq_rep2

description: Library name: STELLA5mC13