title: Home cagedl mouse-single cell 5hmC cerebral

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

description:
cerebral_cmb_counts.txt
cerebral_cmb_metadata.txt

data_processing:
The SPEED datasets in this study were generated in paired-end format. Read 1 contains one segment of barcode in the 5’terminal (barcode 1) and following genomic DNA fragment. Read 2 carries three barcode segments from the 5’terminal sequentially (barcode 3/ barcode 2/ barcode 1). The data processing pipeline was modified from previous study14.
1). Data pre-processing. Sequencing quality of raw read was examined by FastQC (v0.11.9). Raw SPEED data reads were subjected to FastQC (v0.11.9) for checking sequencing quality and trimmed adaptors by Trimmomatic (v 0.38) under PE mode (-phred33 ILLUMINACLIP: TruSeq3-PE-2. fa: 2:30:10 TRAILING:3 SLIDINGWINDOW: 4:20 MINLEN:50).
2). Barcode identification and removal. Each full-length barcode was composed of 3 segments (barcode 1/ barcode 2/ barcode 3). To ensure the completeness, both read 1 and read 2 were used in barcode identification by BarcodeIdentification_v1.2.0.jar with the default parameters 2 and the barcode was added behind the read name. Finally, reads contain all the three barcode segments were filter for following analyses. In generally, around 75% reads were labeled by full-length barcode. To prevent the inclusion of extra barcode sequences at the 3' end of read 1, the second-round barcode-removing was performed by cutadapt (v 1.18) with parameters ‘-j 15 -m 50 -a "file: Split-Pool-jx_3barcode_rev. fa"’.
3). Mapping to genome and PCR duplicates removal. For mESC, mouse cerebral and cerebellar cortex SPEED data, read 1 in each SPEED library underwent two round barcode-removing (described above) were mapped on mm10 reference genome using Bowtie2 (v 2.3.5), and parameter ‘--trim5 11’ was set to remove barcodes on 5’terminal. Uniquely mapped reads were filtered and sorted by genome coordinates using samtools (v 1.9). The barcode strings on read names were stored in bam file tag ‘CB: Z:’. PCR duplicates were marked by the same start/end position and the same barcode and were removed in the following analysis. In analysis of mESC and hSC mixed library, reads were simultaneously mapped to both hg38 and mm10, and the aforementioned analyses were repeated. Subsequently, reads mapped to hg38 and mm10 were counted separately from deduplicated BAM files for each barcode to verify the single-nuclei labeling validity of SPEED library.
4).5hmC peak calling. The 5hmC-enriched regions in each sample were identified as peaks via MACS2 (v 2.1.2) with parameters ‘-f BAM -g mm -q 0.01 --nomodel --extsize 400 --max-gap 500 --keep-dup all’. The peaks in mouse brain and cerebellum are combined for DHMR analyses. The peaks were annotated by ‘annotatePeaks.pl’ in HOMER (v 4.10) with the default parameter.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cerebral cortex

extract_protocol:
1) Nuclei isolation or extraction Cells or purified nuclei were crosslinked with formaldehyde and lysised with lysis buffer.
2) DNA fragmentation SDS and Triton X-100 were used to isolate and permeabilize nuclei. DNA fragmentation was performed by HpyCH4V in 0.1% Triton, 0.2% Tween-20, 0.2% NP-40, and PBS in to get the DNA fragment size range with 200-500bp.
3) DNA End-repair The dA-tailing process was initiated by adding dA tailing buffer to the nuclei, composed of nuclease-free H2O, dA-tail reaction buffer, and Klenow fragment.
4) Barcode in nuclei ligation The isolated nuclei, DPM barcoded tag and ligation mix ( 2 × Instant Sticky-end Ligase Master Mix, 5 × Quick Ligase Buffer, and 1,2-propanediol) were loaded into each well of a 96-well plate. The 96 well plate was subjected to meticulous mixing at 20 °C, allowing the ligation reaction to progress over a duration of 2 hour. After incubation, the in-nuclei DNA ligation was stopped. The contents of each well were transferred into new tube and washed.The nuclei were next performed second and third rounds of ODD and TERMINAL barcode ligation.
5) DNA reverse crosslinking The ligated-nuclei were reverse crosslinked  with 5 × Proteinase K Buffer and Proteinase K. Then, ligated-DNA was purified by DNA clean & concentrator kit.
6) 5hmC labeling and library construction 5hmC labeling and enrichment procedures follow the published protocols13, 14. Following the reaction, DNA substrates were purified by using the DNA Clean & Concentrator Kit and subsequently reconstituted in H2O.
Library construction was performed according to manufacturer’s recommendations for NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

value: cerebral cortex


title: rtgill.imz.3.C04

status: Public on Jan 01 2025

type: SRA

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description:
Library name: rtgill.imz.3.C04
Cell lysate
imz.counts.txt
imz.lib.7_S1.C04.expression.values

library_source: transcriptomic

data_processing:
RNA-seq Analysis Portal (RAP; Qiagen)
Raw RNA Sequencing fastq files were submitted to QIAGEN’s RNA-seq Analysis Portal (RAP) (QIAGEN). First, raw files were demultiplexed to yield individual reads files for each sample (well) and then mapped to the rainbow trout genome (Omyk_1.0.105) to yield raw counts.
The counts were submitted to ExpressAnalyst for differential expression analysis and benchmark dose response analysis
Assembly: Omyk_1.0.105
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Oncorhynchus mykiss

source_name: RTgill-W1 imz rep 3 conc 6

growth_protocol: Cells were grown in Thermo Scientific™ BioLite™ Cell Culture Treated 100 mm Petri dishes containing 10 ml of complete culture medium (Leibovitz L-15 culture medium supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin), at 21°C.

extract_protocol:
OECD Test Guideline 249 for RTgill-W1 cell exposures, and QIAseq UPXome RNA Library Kits (QIAGEN) for library preparation
QIAseq UPXome RNA Library Kits (QIAGEN) protocol  for library preparation

tag: cell line

tag: cell type

value: Rainbow trout gill

tag: treatment


title: TCR d15 WT #4

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

country: USA

institute: Genentech

description: TCR

data_processing:
10X immune profiling single-cell RNA sequencing data were processed with our in-house pipeline. Briefly, the expression library, the feature barcode library, and the TCR library were first demultiplexed followed by alignment to the mouse reference genome (GRCm38) using Cell Ranger (version 6.0.1). A gene by cell barcode matrix was generated for the gene expression library and a similar matrix was generated for each TotalSeq™-C antibodies (Cd44, Cd39, and Klrg1) and each dCODE™ Dextramer® (for peptides NP396, GP33, Human CMV, and GP276).
Seurat (version 4.0.4) was used for all downstream analysis. Cells with detected genes between 200 and 3000, and with less than 5% mitochondrial mapped reads were kept for downstream analysis. Wildtype, day 15, replicate #3 was removed from further analysis as it showed strong batch effects. Initial clustering showed contamination of B and/or myeloid cells. To address this issue, we used an iterative process where we first performed clustering, identified and removed B/myeloid cells, followed by another round of clustering until majority of contaminating cells were removed. After filtering, we detected  56,550 cells across the whole dataset. We next performed Seurat’s Canonical Correlation Analysis (CCA) to integrate the dataset across day 15 and day 22. During the scaling step, we also regressed out the difference between G2M and S phase scores to maintain the difference between cycling and non-cycling cells. After normalizing the integrated data, we performed linear dimensionality reduction using PCA. We ranked the principal components (PCs) by the amount of variance explained by each and found that after the first 15 PCs the explained variance plateaus. To visualize the data in two-dimensional space, Uniform Manifold Approximation and Projection (UMAP) was performed using the first 15 PCs. We then used the UMAP dimensions to determine the nearest neighbor of each cell and perform clustering by setting the resolution parameter to 0.6. Marker genes for each cluster were determined using FindAllMarkers function (only.pos = T and logfc.threshold = 0.25). We first identified the naïve CD8 T cell clusters using marker genes per cluster. Automatic annotation of other non-naïve clusters was performed using SingleR and using virus specific CD8+ T cells from an LCMV infection model as a reference dataset. Gene set enrichment analysis was performed using fgsea. Briefly, for each cluster, the genes were ranked using a Wilcoxon rank sum test and genes enriched in the Stk40 knockout samples were searched against MSigDB categories: hallmark gene sets (H), curated gene sets (C2), motif gene sets (C3:TFT Legacy), GO gene sets (C5), and immunologic gene sets (C7).
Genome_build: mm10

organism: Mus musculus

source_name: Spleen

extract_protocol:
For chronic LCMV infections, mice were infected with 2 x 106 PFU of LCMV clone 13 intravenously and depleted of CD4 T cells in two doses of anti-CD4 (clone GK1.5): 500ug i.v. 4 days prior to infection and 250ug i.p. 3 days post infection. CD8+ T cells were magnetically purified from spleens of CD4CreER; Stk40loxp/loxp (Stk40 ko) and CD4+/+; Stk40loxp/loxp (WT) LCMV-cl13 infected mice at d15 and d22 after infection. LCMV-specific cells were enriched using Dextramer labeling followed by Miltenyi magnetic purification with anti-PE microbeads. Dextramer labeling was carried out in accordance with Immudex protocol.
Cell capture and scRNAseq-, feature-, and TCRseq- library constructions were carried out using the 10X Chromium Controller and the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) in accordance with the manufacture’s protocol (CG000330 Rev A). Prior to loading into the chromium controller, cells were washed once with PBS and resuspended in PBS at 700-1200 cells/ul for a target cell recovery of 7000 cells.

tag: background

tag: age

value: 7-9 weeks

tag: genotype

value: wild type


title: Home caged mouse-single cell 5hmC cerebellar input

country: China

description:
cerebellar_cmb_counts.txt
cerebellar_cmb_metadata.txt

library_source: genomic

molecule: genomic DNA

source_name: cerebellar cortex

tag: tissue

value: cerebellar cortex

value: WT


title: SH-1_Day4

city: Beijing

first: Hsiang-Ying

last: Lee

address: No.5 Yiheyuan Road

institute: Peking University

data_processing:
After checking data quality using FastQC (version 0.11.7), the paired-end reads were mapped to the hg19 human reference genome by Hisat2 (version 2.1.0).
Read counts were estimated with HTSeq (version 0.12.4).
The reads counts were normalized to TPM (transcription per million).
The DESeq2 package was used to identify differentially expressed genes.
Motif enrichment was performed using Homer software54 with “-start -400 -end 100” parameters.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

molecule: polyA RNA

organism: Homo sapiens

source_name: cord blood

growth_protocol: The cells were maintained in two staged culture medium in humidified atmosphere with 5%CO2 at 37C

extract_protocol:
RNA was  harvested using TRIzol. For RNA-seq, the quality was evaluated using an Agilent 2100 Bioanalyzer. 1 μg of total RNA was used to prepare RNA-seq libraries.
RNA libraries for RNA-seq were prepared using Illumina mRNA-seq Library Prep Kit following manufacturer’s protocols

treatment_protocol: The cell culture system was divided two stages: amplification stage (0-4 days): The cells were cultured in SFEM II medium containing CC100 cytokine and 2% Penicillin streptomycin at a concentration of 105 cells/mL for 4 days. Differentiation stage (5-14 days): Cells were cultured in IMDM-based red differentiation medium containing 5 ng/mL rIL-, 3,100 ng/mL rhSCF and 6 U/mL rhEpo.

value: cord blood

value: Erythroblasts

value: MED16 knockdown

tag: time

value: Day 4

value: erythroid differentiation


title: SCR-2_Day4


title: rtgill.imz.2.H04

description:
Library name: rtgill.imz.2.H04
Cell lysate
imz.counts.txt
imz.lib.2_S1.H04.expression.values

source_name: RTgill-W1 imz rep 2 conc 1


title: TCR d15 WT #3

description: TCR


title: TCR d15 WT #2

description: TCR


title: Home caged mouse-single cell 5hmC cerebellar


title: rtgill.imz.3.A04

description:
Library name: rtgill.imz.3.A04
Cell lysate
imz.counts.txt
imz.lib.7_S1.A04.expression.values

source_name: RTgill-W1 imz rep 3 conc 8


title: SCR-1_Day4


title: rtgill.imz.3.E04

description:
Library name: rtgill.imz.3.E04
Cell lysate
imz.counts.txt
imz.lib.7_S1.E04.expression.values

source_name: RTgill-W1 imz rep 3 conc 4


title: Fear conditioned mouse-single cell 5hmC cerebral input


title: SH-1_Day0

value: HSPCs

value: Day 0


title: HTO d22 KO #4

description: HTO

value: Stk40 knock out


title: Fear conditioned mouse-single cell 5hmC cerebral


title: SH-2_Day0


title: Fear conditioned mouse-single cell 5hmC cerebellar input


title: rtgill.imz.2.E04

description:
Library name: rtgill.imz.2.E04
Cell lysate
imz.counts.txt
imz.lib.2_S1.E04.expression.values

source_name: RTgill-W1 imz rep 2 conc 4


title: Fear conditioned mouse-single cell 5hmC cerebellar


title: rtgill.imz.2.F04

description:
Library name: rtgill.imz.2.F04
Cell lysate
imz.counts.txt
imz.lib.2_S1.F04.expression.values

source_name: RTgill-W1 imz rep 2 conc 3


title: Home caged mouse-single cell 5hmC cerebral input


title: TCR d15 WT #1

description: TCR


title: D4CD34_MED16_R2

data_processing:
Raw ChIP-seq data were trimmed using trim_galore (version 0.4.4_dev) and the cleaned reads were mapped to the hg19 human genome using Bowtie2 (version 2.3.4.1).
Duplicated reads and low-quality reads (MAPQ < 30) were removed using the Picard tool (http:
The bigwig files were generated using bamCoverage and normalized using RPKM (Reads Per Kilobase per Million) in 10 bp bins.
The results were visualized using IGV software. MACS2 was used for peak calling with default parameters for all samples.
Peaks were annotated using the R package ChIPseeker, and co-localization analysis was performed using deeptools.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
106 cells were collected for the assay. 27 µL 37% formaldehyde was added to each sample in a centrifuge tube, followed by incubation at 10 min at room temperature (RT). 110 µL 10X Glycine solution was added, followed by incubation for 5 min at RT and centrifugation at 4000 rpm for 5 min. The supernatant was removed and the cells were washed with 1 mL PBS. The cells were centrifuged at 4°C at 4000 rpm for 5 min and the supernatant was discarded. The cell pellet was resuspended with 100 µL 1X MDB (50 mM Tris‐HCl, pH 8.0, 2 mM CaCl2, 0.2 % Triton X‐100) and 1.5 µL 1X MNase, followed by incubation at 37°C for 5 min, after which 10 µL of 10X Stop buffer (110 mM Tris‐HCl pH 8.0, 55 mM EDTA) was added to stop the reaction. 110 µL 2X RIPA was added to the sample, and the sample was left on ice for 2 min. The sample was subjected to sonic shearing (20w for 2 min). The samples were spun for 15 mins in a microfuge at top speed at 4°C. The supernatant containing chromatin was moved to a fresh pre‐cooled tube (1.5 mL low bind), which was stored at -80°C. Protein A and Protein G beads (Sigma) were mixed (1:1), pre-washed and re-suspended with an equal volume of 1X RIPA. 100 µL of chromatin was pre-cleaned with 15 µL pre-washed beads for 1 h at 4°C, after which 1-2 µg antibody was added to each IP sample. The samples were incubated at 4°C overnight, 15 µL protein A+G beads were added per IP, and the samples were incubated 2‐3 h with rotation at 4°C. RIPA and LiCl wash buffers were prepared and supplemented with protease inhibitors (1:1000). All subsequent washes were performed with rotation at 4°C for 5 mins. The washes were performed as follows: 5 washes with 150 µL RIPA buffer + 1 wash with 150 µL LiCl wash buffer + 1 wash with 150 µL cold TE. The Elution/Digestion buffer for each sample contained 45 µL TE, 5 µL 5M NaCl, and 2.5 µL Proteinase K. Each bead pellet was resuspended in 50 µL Elution/Digestion buffer and incubated with shaking (1200 rpm) at 65°C for 4-6 h. Each sample was separated, the protein A+G beads were discarded, and DNA was recovered with 1.2X NGS beads (Vazyme).
A subsequent PCR step was used to add an additional index to the fragments. Two biological replicates per sample were sequenced using a HiSeq X-Ten (PE150, Illumina) by Novogene (Beijing).

tag: chip antibody


title: SCR-2_Day0


title: HTO d22 KO #3

description: HTO


title: SCR-1_Day0


title: HTO d22 KO #1

description: HTO


title: rtgill.imz.2.D04

description:
Library name: rtgill.imz.2.D04
Cell lysate
imz.counts.txt
imz.lib.2_S1.D04.expression.values

source_name: RTgill-W1 imz rep 2 conc 5


title: HTO d22 KO #2

description: HTO


title: macrophages,VSV-8h-2

city: 济南

first: 辉

middle: 家

last: 僮

address: 济南趵突泉街道文化西路44号

institute: 山东大学

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
mm10
Assembly: C57/6J
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus

source_name: primary cell

growth_protocol: Macrophages were maintained in DMEM supplemented with 10% fetal bovine serum (FBS)and antibiotics in humidified atmosphere with 5% C02 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Macrophages was infected SeV (MOI:1) for 8 hours, VSV (MOI:1) for 8 hours post confluent cells, HSV-1(MOI:10) for 4 hours post confluent cells.

value: primary cell

value: macrophages

value: wt

value: VSV


title: HTO d22 WT #4

description: HTO


title: D4CD34_MED16_R1


title: rtgill.imz.2.C04

description:
Library name: rtgill.imz.2.C04
Cell lysate
imz.counts.txt
imz.lib.2_S1.C04.expression.values

source_name: RTgill-W1 imz rep 2 conc 6

value: Rainbow trout gill


title: macrophages,VSV-8h-3

address: 济南趵突泉街道文化西路44号


title: rtgill.imz.2.G04

description:
Library name: rtgill.imz.2.G04
Cell lysate
imz.counts.txt
imz.lib.2_S1.G04.expression.values

source_name: RTgill-W1 imz rep 2 conc 2


title: D0CD34_MED16_R2


title: rtgill.imz.2.B04

description:
Library name: rtgill.imz.2.B04
Cell lysate
imz.counts.txt
imz.lib.2_S1.B04.expression.values

source_name: RTgill-W1 imz rep 2 conc 7


title: macrophages,VSV-8h-1

address: 济南趵突泉街道文化西路44号


title: HTO d22 WT #3

description: HTO

value: 7-9 weeks


title: rtgill.imz.1.H04

description:
Library name: rtgill.imz.1.H04
Cell lysate
imz.counts.txt
imz.lib.11_S1.H04.expression.values

source_name: RTgill-W1 imz rep 1 conc 1


title: macrophages,SeV-8h-3

address: 济南趵突泉街道文化西路44号

value: SeV


title: D0CD34_MED16_R1


title: rtgill.imz.1.G04

description:
Library name: rtgill.imz.1.G04
Cell lysate
imz.counts.txt
imz.lib.11_S1.G04.expression.values

source_name: RTgill-W1 imz rep 1 conc 2


title: D4CD34SHI_SPT16_R2

value: SPT16 (BioLegend, Cat.#607002)


title: macrophages,SeV-8h-2

address: 济南趵突泉街道文化西路44号


title: HTO d22 WT #1

description: HTO

value: wild type


title: HTO d22 WT #2

description: HTO


title: rtgill.imz.1.F04

description:
Library name: rtgill.imz.1.F04
Cell lysate
imz.counts.txt
imz.lib.11_S1.F04.expression.values

source_name: RTgill-W1 imz rep 1 conc 3


title: D4CD34SHI_SPT16_R1

value: cord blood


title: macrophages,SeV-8h-1

address: 济南趵突泉街道文化西路44号


title: HTO d15 KO #4

description: HTO


title: macrophages,US-3

address: 济南趵突泉街道文化西路44号

value: US


title: rtgill.imz.1.E04

description:
Library name: rtgill.imz.1.E04
Cell lysate
imz.counts.txt
imz.lib.11_S1.E04.expression.values

source_name: RTgill-W1 imz rep 1 conc 4


title: D4CD34SCR_SPT16_R2

value: WT


title: rtgill.imz.1.D04

description:
Library name: rtgill.imz.1.D04
Cell lysate
imz.counts.txt
imz.lib.11_S1.D04.expression.values

source_name: RTgill-W1 imz rep 1 conc 5


title: HTO d15 KO #2

description: HTO

source_name: Spleen


title: D4CD34SCR_SPT16_R1

source_name: cord blood

value: Day 4


title: HTO d15 KO #3

description: HTO


title: macrophages,US-1

address: 济南趵突泉街道文化西路44号


title: HTO d15 KO #1

description: HTO


title: rtgill.imz.2.A04

description:
Library name: rtgill.imz.2.A04
Cell lysate
imz.counts.txt
imz.lib.2_S1.A04.expression.values

source_name: RTgill-W1 imz rep 2 conc 8


title: D4CD34_RUNX1_R2

value: RUNX1 (Abcam, Cat.#23980)

value: erythroid differentiation


title: rtgill.imz.1.C04

description:
Library name: rtgill.imz.1.C04
Cell lysate
imz.counts.txt
imz.lib.11_S1.C04.expression.values

source_name: RTgill-W1 imz rep 1 conc 6


title: macrophages,HSV-1-4h-3

address: 济南趵突泉街道文化西路44号


title: D4CD34_RUNX1_R1


title: rtgill.imz.1.A04

description:
Library name: rtgill.imz.1.A04
Cell lysate
imz.counts.txt
imz.lib.11_S1.A04.expression.values

source_name: RTgill-W1 imz rep 1 conc 8


title: HTO d15 WT #3

description: HTO


title: D0CD34_RUNX1_R2

value: Day 0


title: rtgill.gly.3.H03

description:
Library name: rtgill.gly.3.H03
Cell lysate
gly.counts.txt
gly.lib.6_S1.H03.expression.values

source_name: RTgill-W1 gly rep 3 conc 1


title: macrophages,US, control-3

address: 济南趵突泉街道文化西路44号


title: HTO d15 WT #2

description: HTO


title: D0CD34_RUNX1_R1


title: D4CD34_shMED16_R2

data_processing:
The adaptors were removed from the raw ATAC-seq paired data for day 0 and day 4 using trim_galore software with default parameters.
Trimmed cleaned reads were aligned to human reference genome hg19 using Bowtie2 (version 2.3.4.1) with default parameters and converted to bam files using samtools.
ATAC-seq peaks were identified using MACS2 with the following parameters: “-q 0.05 --nomodel --shift -100 --extsize 200”.
The signal enrichment plot around the TSS of all protein coding genes was generated using deeptools.
The example tracks were visualized using IGV software. The motifs of ATAC-seq peaks were enriched using Homer.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
~105 shSCR and shMED16 samples at day 0 and day 4 cultured CD34+ cells were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 8 mM MgCl2 and NP-40) on ice for 5 min to extract nuclei. The cells were centrifuged at 500 g for 5 min to remove the supernatant. The nuclei were incubated with the Tn5 transposome and corresponding buffer at 37°C for 30 min (Vazyme, Cat. # 11 TD501). The stop buffer was added to the reaction to terminate the tagmentation.  DNA Clean Beads were used to purify DNA.
A subsequent PCR step was used to add an additional index to the fragments. Two biological replicates per sample were sequenced using a HiSeq X-Ten (PE150, Illumina) by Novogene (Beijing).

value: erythroblasts

value: MED16 knockdown


title: HTO d15 WT #1

description: HTO


title: macrophages,HSV-1-4h-1

address: 济南趵突泉街道文化西路44号

value: primary cell

value: macrophages


title: macrophages,US-2

address: 济南趵突泉街道文化西路44号

value: wt


title: rtgill.gly.3.F03

description:
Library name: rtgill.gly.3.F03
Cell lysate
gly.counts.txt
gly.lib.6_S1.F03.expression.values

source_name: RTgill-W1 gly rep 3 conc 3

value: Rainbow trout gill


title: D4CD34_shMED16_R1


title: RNA d22 KO #4

description: RNA

value: 7-9 weeks

value: Stk40 knock out


title: macrophages,US, control-1

address: 济南趵突泉街道文化西路44号


title: RNA d22 KO #3

description: RNA


title: D4CD34_shSCR_R2


title: rtgill.imz.1.B04

description:
Library name: rtgill.imz.1.B04
Cell lysate
imz.counts.txt
imz.lib.11_S1.B04.expression.values

source_name: RTgill-W1 imz rep 1 conc 7


title: END_D39

city: Gainesville

first: Daria

last: Neyroud

state: FL

address: 1275 Center Drive

institute: University of Florida

description:
END_DIAvsSHAM_DIA_DEG.xlsx
END_D39

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package (2_1.6.3).
P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR)
Assembly: mouse reference genome GRCm38 mm10
Supplementary files format and content: xlsx files include log2 fold changes, redcounts, fpkm and padj values

source_name: Diaphragm muscle

growth_protocol: KPC FC1245 cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum, 1% penicillin and 1% streptomycin at 37°C in a 5% CO2 humidified chamber.

extract_protocol:
Muscle tissues were homogenized in Trizol  and RNA was extracted with phenol/chloroform protocol. After DNAse treatment, 1 μg of RNA was retro-transcribed using the SuperScript IV Reverse Transcriptase kit (Thermofisher) according to the manufacturer guidelines.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

treatment_protocol: The pancreas of ten-week-old male C57BL/6J mice was surgically exposed and 0.25 x 10E6 cells diluted in 50 μl of sterile PBS (KPC group) or 50 μl of sterile PBS (Sham group) were orthotopically injected

value: Diaphragm muscle

tag: strain

value: KPC tumor-bearing at humane-endpoint


title: HTO d15 WT #4

description: HTO

value: wild type


title: RNA d22 KO #2

description: RNA


title: D4CD34_shSCR_R1

value: cord blood


title: rtgill.gly.3.C03

description:
Library name: rtgill.gly.3.C03
Cell lysate
gly.counts.txt
gly.lib.6_S1.C03.expression.values

source_name: RTgill-W1 gly rep 3 conc 6


title: END_D38

description:
END_DIAvsSHAM_DIA_DEG.xlsx
END_D38


title: END_D37

description:
END_DIAvsSHAM_DIA_DEG.xlsx
END_D37


title: macrophages,HSV-1-4h-2

address: 济南趵突泉街道文化西路44号

source_name: primary cell


title: rtgill.gly.3.B03

description:
Library name: rtgill.gly.3.B03
Cell lysate
gly.counts.txt
gly.lib.6_S1.B03.expression.values

source_name: RTgill-W1 gly rep 3 conc 7


title: RNA d22 WT #4

description: RNA


title: RNA d22 KO #1

description: RNA


title: rtgill.gly.3.A03

description:
Library name: rtgill.gly.3.A03
Cell lysate
gly.counts.txt
gly.lib.6_S1.A03.expression.values

source_name: RTgill-W1 gly rep 3 conc 8


title: macrophages,US, control-2

address: 济南趵突泉街道文化西路44号

value: US


title: D14_D35

description:
D14_DIAvsSHAM_DIA_DEG.xlsx
D14_D35

value: KPC tumor-bearing 14 days after KPC cell orthotopic injection


title: rtgill.gly.3.G03

description:
Library name: rtgill.gly.3.G03
Cell lysate
gly.counts.txt
gly.lib.6_S1.G03.expression.values

source_name: RTgill-W1 gly rep 3 conc 2


title: D0CD34shSCR_ATACseq_R2

value: HSPCs

value: WT


title: RNA d22 WT #3

description: RNA


title: rtgill.gly.2.H03

description:
Library name: rtgill.gly.2.H03
Cell lysate
gly.counts.txt
gly.lib.10_S1.H03.expression.values

source_name: RTgill-W1 gly rep 2 conc 1


title: D0CD34shSCR_ATACseq_R1

value: erythroid differentiation


title: rtgill.gly.3.E03

description:
Library name: rtgill.gly.3.E03
Cell lysate
gly.counts.txt
gly.lib.6_S1.E03.expression.values

source_name: RTgill-W1 gly rep 3 conc 4


title: RNA d22 WT #2

description: RNA


title: D14_D34

description:
D14_DIAvsSHAM_DIA_DEG.xlsx
D14_D34


title: rtgill.gly.2.G03

description:
Library name: rtgill.gly.2.G03
Cell lysate
gly.counts.txt
gly.lib.10_S1.G03.expression.values

source_name: RTgill-W1 gly rep 2 conc 2


title: RNA d22 WT #1

description: RNA

source_name: Spleen


title: D15-IDH1-3RNA-Seq

city: zhengzhou

first: li

last: mengjia

address: Science Road 100, Zhengzhou, Henan, 450001, P.R.

institute: zhengzhou university

data_processing:
The useful Perl script was used to filter the original data (Raw Data)
Reads Count for each gene in each sample was counted by HTSeq v0.6.0,
FPKM (Fragments Per Kilobase Million Mapped Reads) was then calculated to estimate the expression level.
DESeq2 version 1.6.3 (https://bioconductor.org/packages/3.0/bioc/html/DESeq2.html) are package for Identifying Differentially Expressed Genes (DEGs) from data.
Gene Ontology (http://geneontology.org/) and Kyoto Encyclopedia of Genes and Genomes (http://www.kegg.jp/) were used to make function enrichment analysis. Gene Set Enrichment Analysis (GSEA) was performed using GSEA version 4.1.0 software (http://www.gsea-msigdb.org/gsea/downloads.jsp).
Assembly: compare data to the reference genome by using HISAT2 which download from ENSEMBL database (http://www.ensembl.org/index.html, human genome build GRCh38.87).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: early erythroid cells, IDH1-shRNA, day 15

growth_protocol: CD34+ cells were purified from cord blood by using the magnetic-activated cell sorting magnetic beads system, according to the manufacturer’s instructions. The purity of isolated CD34+ cells was 95% to 98%. The cell culture procedure was comprised of 3 phases, Composition of the base culture medium was Iscove’s Modified Dulbecco’s Medium, 2% human peripheral blood plasma, 3% human AB serum, 200 mg/mL Holohuman transferrin, 3 IU/mL heparin, and 10 mg/mL insulin. In the first phase (day 0 to day 6), CD34+ cells at a concentration of 105 /mL were cultured in the presence of 10 ng/mL stem cell factor, 1 ng/mL IL-3, and 3 IU/mL erythropoietin. In the second phase (day 7 to day 11), IL-3 does not need to be added into the culture medium. In the third phase that lasted until day 21, the cell concentration was adjusted to 106 /mL on day 11 and to 5×106/mL on day 15, respectively, the medium for this phase was the base medium plus 3 IU/mL erythropoietin, and the concentration of transferrin was adjusted to 1 mg/mL. The cells were cultured at 37°C in the presence of 5% CO2.

extract_protocol:
RNA was extracted and reverse transcribed into cDNA.
The cDNA libraries were prepared using NovaSeq 5000/6000 S4 Reagent Kit (#A00358, Illumina) and sequenced on an Illumina X-ten (E00487, Illumina).

treatment_protocol: The day of getting CD34+ cells was recorded as day 0. Lentivirus human CD34+ transduction at day 2.

value: erythroid cells

value: IDH1 knockdown

value: D15 cultured of erythroid cells


title: D12_D31

description:
D12_DIAvsSHAM_DIA_DEG.xlsx
D12_D31

value: KPC tumor-bearing 12 days after KPC cell orthotopic injection


title: rtgill.gly.2.F03

description:
Library name: rtgill.gly.2.F03
Cell lysate
gly.counts.txt
gly.lib.10_S1.F03.expression.values

source_name: RTgill-W1 gly rep 2 conc 3


title: rtgill.gly.3.D03

description:
Library name: rtgill.gly.3.D03
Cell lysate
gly.counts.txt
gly.lib.6_S1.D03.expression.values

source_name: RTgill-W1 gly rep 3 conc 5


title: D0CD34shMED16_ATACseq_R2

source_name: cord blood

value: MED16 knockdown


title: D15-IDH1-2RNA-Seq


title: rtgill.gly.2.E03

description:
Library name: rtgill.gly.2.E03
Cell lysate
gly.counts.txt
gly.lib.10_S1.E03.expression.values

source_name: RTgill-W1 gly rep 2 conc 4

value: Rainbow trout gill


title: RNA d15 KO #4

description: RNA

value: 7-9 weeks


title: RNA d15 KO #3

description: RNA

value: Stk40 knock out


title: RNA d15 KO #2

description: RNA


title: D15-IDH1-1RNA-Seq


title: rtgill.gly.2.C03

description:
Library name: rtgill.gly.2.C03
Cell lysate
gly.counts.txt
gly.lib.10_S1.C03.expression.values

source_name: RTgill-W1 gly rep 2 conc 6


title: rtgill.gly.2.D03

description:
Library name: rtgill.gly.2.D03
Cell lysate
gly.counts.txt
gly.lib.10_S1.D03.expression.values

source_name: RTgill-W1 gly rep 2 conc 5


title: D12_D28

description:
D12_DIAvsSHAM_DIA_DEG.xlsx
D12_D28

source_name: Diaphragm muscle

value: Diaphragm muscle


title: D15-Luci-3RNA-Seq

source_name: early erythroid cells, Luciferase-shRNA, day 15

value: Control


title: rtgill.gly.2.B03

description:
Library name: rtgill.gly.2.B03
Cell lysate
gly.counts.txt
gly.lib.10_S1.B03.expression.values

source_name: RTgill-W1 gly rep 2 conc 7


title: D15-Luci-1RNA-Seq


title: D12_D29

description:
D12_DIAvsSHAM_DIA_DEG.xlsx
D12_D29


title: D10_D27

description:
D10_DIAvsSHAM_DIA_DEG.xlsx
D10_D27

value: KPC tumor-bearing 10 days after KPC cell orthotopic injection


title: rtgill.gly.2.A03

description:
Library name: rtgill.gly.2.A03
Cell lysate
gly.counts.txt
gly.lib.10_S1.A03.expression.values

source_name: RTgill-W1 gly rep 2 conc 8


title: RNA d15 WT #3

description: RNA

value: wild type


title: RNA d15 KO #1

description: RNA


title: D0CD34shMED16_ATACseq_R1

value: cord blood


title: D10_D35

description:
D10_DIAvsSHAM_DIA_DEG.xlsx
D10_D35


title: early erythroid cells, IDH1-shRNA, day 15 2

data_processing:
DiffBind identifies statistically significant differentially accessible regions using the DEseq2 version 1.6.3 (https://bioconductor.org/packages/3.0/bioc/html/DESeq2.html) with default parameters
The ATAC peak/region <1000bp from the nearest TSS was designated as the promoter.
Overrepresented motif analysis was performed by Hypergeometric Optimization of Motif Enrichment (HOMER) tool Homer version 4.11 (http://homer.ucsd.edu/homer/)
DESeq2 version 1.6.3 (https://bioconductor.org/packages/3.0/bioc/html/DESeq2.html) are package for Identifying Differentially Expressed Genes (DEGs) from data.
Gene Ontology (http://geneontology.org/) and Kyoto Encyclopedia of Genes and Genomes (http://www.kegg.jp/) were used to make function enrichment analysis. Gene Set Enrichment Analysis (GSEA) was performed using GSEA version 4.1.0 software (http://www.gsea-msigdb.org/gsea/downloads.jsp).
Assembly: compare data to the reference genome by using HISAT2 which download from ENSEMBL database (http://www.ensembl.org/index.html, human genome build GRCh38.87).
Supplementary files format and content: Broad Peak

source_name: erythroid cells

extract_protocol:
The  transposition  reaction  was  performed  with  Tn5  transposase  and  the transposed DNA was purified and amplified using a Zymo DNA clean and concentrator-5 kit (Zymo#D4014) to generate sequencing  libraries. .
The cDNA libraries were prepared using NovaSeq 5000/6000 S4 Reagent Kit (#A00358, Illumina) and sequenced on an Illumina X-ten (E00487, Illumina).

value: erythropoiesis


title: D8_D22

description:
D8_DIAvsSHAM_DIA_DEG.xlsx
D8_D22

value: KPC tumor-bearing 8 days after KPC cell orthotopic injection


title: D8_D21

description:
D8_DIAvsSHAM_DIA_DEG.xlsx
D8_D21


title: D10_D24

description:
D10_DIAvsSHAM_DIA_DEG.xlsx
D10_D24


title: D14_D33

description:
D14_DIAvsSHAM_DIA_DEG.xlsx
D14_D33

value: KPC tumor-bearing 14 days after KPC cell orthotopic injection


title: RNA d15 WT #2

description: RNA


title: rtgill.gly.1.G03

description:
Library name: rtgill.gly.1.G03
Cell lysate
gly.counts.txt
gly.lib.1_S1.G03.expression.values

source_name: RTgill-W1 gly rep 1 conc 2


title: early erythroid cells, IDH1-shRNA, day 15 1


title: RNA d15 WT #1

description: RNA


title: D15-Luci-2RNA-Seq


title: D8_D20

description:
D8_DIAvsSHAM_DIA_DEG.xlsx
D8_D20


title: P15216_225_wt_D7

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

data_processing:
Processed using nc-core at scilife labs stockholm. (https://github.com/nf-core/rnaseq)
Star mapping
Deseq2 pipeline for differential analysis (https://doi.org/10.1186/s13059-014-0550-8)
Genome_build: MM10
Supplementary_files_format_and_content: table in txt format containing gene counts

source_name: CD4+ T cells

extract_protocol:
Sorted CD4 T cells were flash frozen on ice and RNA was prepared using miRNeasy Mini kit (Qiagen) according to the manufacturer instructions.
cDNA libraries were prepared using SMARTer® Stranded Total RNA-Seq Pico Kit (Takara) and sequenced using Illumina NovaSeq 6000, 2x150 bp paired-end.

value: wt

tag: disease


title: RNA d15 WT #4

description: RNA


title: SHAM_D15

description:
See below for given comparisons
SHAM_D15

value: Non-tumor bearing


title: rtgill.gly.1.E03

description:
Library name: rtgill.gly.1.E03
Cell lysate
gly.counts.txt
gly.lib.1_S1.E03.expression.values

source_name: RTgill-W1 gly rep 1 conc 4


title: P15216_224_ki_Naive

value: ki

value: Naive


title: rtgill.gly.1.D03

description:
Library name: rtgill.gly.1.D03
Cell lysate
gly.counts.txt
gly.lib.1_S1.D03.expression.values

source_name: RTgill-W1 gly rep 1 conc 5


title: early erythroid cells, Luciferase-shRNA, day 15 2

value: erythroid cells


title: SHAM_D14

description:
See below for given comparisons
SHAM_D14


title: early erythroid cells, Luciferase-shRNA, day 15 1


title: rtgill.gly.1.C03

description:
Library name: rtgill.gly.1.C03
Cell lysate
gly.counts.txt
gly.lib.1_S1.C03.expression.values

source_name: RTgill-W1 gly rep 1 conc 6


title: P15216_223_ko_D7

value: ko


title: P15216_222_ko_Naive


title: IDH1-H3K79me3-3

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

data_processing:
ChIP-seq reads were aligned to the reference genome using Bowtie2 version 2.3.5.1 (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.5.1/), and only uniquely and non-duplicate mapped reads were utilized to perform the downstream analysis.
Reads coverage and depth were calculated by samtools version 1.6 software (https://github.com/samtools/samtools/releases/).
Deeptools version 2.5.7 (https://deeptools.readthedocs.io/en/develop/content/installation.html) were used to generate the correlation plot for all samples including input samples.
Signal track files in Big Wig format were generated using the MACS2 version 2.1.1.20160309 (https://pypi.org/project/MACS2/) pileup function and were normalized to 1 million reads for visualization.
Peaks and annotation were performed using ChIPseeker version 1.20.0 software (https://www.bioconductor.org/packages/3.9/bioc/html/ChIPseeker.html).
Differential analysis between treat and control samples was conducted using DEseq2 version 1.6.3 (https://bioconductor.org/packages/3.0/bioc/html/DESeq2.html) and edgeR version 3.26.8 (https://bioconductor.org/packages/3.9/bioc/html/edgeR.html).
Assembly: GRCh38.87
Supplementary files format and content: bw, broadPeak

extract_protocol:
Sample preparation procedures: cells (20 x 10^6) were collected and washed twice by PBS, then cells were resuspended in 1% formaldehyde, cross-linked and quenched with 125mm glycine in a shaker at 25°C for 10 minutes. Cells were centrifugated 1500×g at 25°C for 5 minutes. The precipitates were suspended using pre-cooled PBS and centrifuged at 1500×g for 5 minutes. Supernatants which around the sediment were removed very carefully.
Firstly, nanodrop, qubit and Agilent 2100 were used to assess the sample quality, including purity, concentration and fragment distribution. For the library building process, DNA fragments were repaired at the end, added with basic group A and sequencing connector; then PCR amplification and fragment screening were used to complete the preparation of the library. The qualified library was ready for sequencing.

value: Tri-Methyl-Histone H3 (Lys79) (E8B3M) Rabbit mAb (CST#74073)


title: rtgill.gly.1.B03

description:
Library name: rtgill.gly.1.B03
Cell lysate
gly.counts.txt
gly.lib.1_S1.B03.expression.values

source_name: RTgill-W1 gly rep 1 conc 7

value: Rainbow trout gill


title: rtgill.gly.1.H03

description:
Library name: rtgill.gly.1.H03
Cell lysate
gly.counts.txt
gly.lib.1_S1.H03.expression.values

source_name: RTgill-W1 gly rep 1 conc 1


title: rtgill.gly.1.F03

description:
Library name: rtgill.gly.1.F03
Cell lysate
gly.counts.txt
gly.lib.1_S1.F03.expression.values

source_name: RTgill-W1 gly rep 1 conc 3


title: rtgill.gly.1.A03

description:
Library name: rtgill.gly.1.A03
Cell lysate
gly.counts.txt
gly.lib.1_S1.A03.expression.values

source_name: RTgill-W1 gly rep 1 conc 8


title: P15216_221_ki_D7


title: IDH1-H3K79me3-2

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

source_name: cord blood


title: P15216_220_ki_Naive


title: IDH1-H3K79me3-1

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: early erythroid cells, Luciferase-shRNA, day 15 3


title: IDH1-H3K27me2-3

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

value: Di-Methyl-Histone H3 (Lys27) (D18C8) XP® Rabbit mAb CST#9728)


title: rtgill.cln.3.H02

description:
Library name: rtgill.cln.3.H02
Cell lysate
cln.counts.txt
cln.lib.6_S1.H02.expression.values

source_name: RTgill-W1 cln rep 3 conc 1


title: P15216_219_ko_D7


title: HuH7D250

type: RNA

city: BARCELONA

first: Mónica

last: Higuera

address: Passeig de la vall d'hebron 119-129

country: Spain

institute: Vall d'hebron Institute de Recerca (VHIR)

description: Gene expression data from HuH7 cell line treated with zinc acexamate

hyb_protocol: Following fragmentation 5.5ug of sscDNA were hybridized for 16h at 45º on GeneChip Clariom S human array plate. Array plate was washed and stained in the Affymetrix Gene Titan multichannel system

scan_protocol: Array plate was scanned using the Gene Titan Multichannel system

data_processing: Raw expression values were obtained from .CEL files and processed using the RMA method in R package to obtain normalized expression values (log2 scale) at the gene level.

label: biotin

source_name: cell line

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocolo from 200 ng total RNA ((Gene chip WT plus kit manual workflow, user guide)

growth_protocol: NUDE Swiss Crl:NU(Ico)-Foxn1nu female mice were injected subcutaneously with 5*106 HuH7 cells for tumor development. When tumors reached 100 mm3 volume, mice were randomly assigned to 2 groups: treated with ZAC (150mg/kg) or vehicle

extract_protocol: Total RNA was performed with Rneasy mini kit (Qiagen)  according to the manufacturer's instructions.

treatment_protocol: One hour after the last dose of treatment, animals were euthanized, and tumors collected and frozen for RNA extraction

value: treated with zinc acexamate


title: rtgill.cln.3.F02

description:
Library name: rtgill.cln.3.F02
Cell lysate
cln.counts.txt
cln.lib.6_S1.F02.expression.values

source_name: RTgill-W1 cln rep 3 conc 3


title: rtgill.cln.3.G02

description:
Library name: rtgill.cln.3.G02
Cell lysate
cln.counts.txt
cln.lib.6_S1.G02.expression.values

source_name: RTgill-W1 cln rep 3 conc 2


title: IDH1-H3K27me2-2

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

value: Di-Methyl-Histone H3 (Lys27) (D18C8) XP® Rabbit mAb (CST #9728)


title: P15216_218_ko_Naive


title: SHAM_D12

description:
See below for given comparisons
SHAM_D12

source_name: Diaphragm muscle

value: Diaphragm muscle


title: IDH1-H3K27me2-1

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

value: Di-Methyl-Histone H3 (Lys27) (D18C8) XP® Rabbit mAb (CST#9728)


title: P15216_216_ki_D7


title: rtgill.cln.3.E02

description:
Library name: rtgill.cln.3.E02
Cell lysate
cln.counts.txt
cln.lib.6_S1.E02.expression.values

source_name: RTgill-W1 cln rep 3 conc 4


title: rtgill.cln.3.D02

description:
Library name: rtgill.cln.3.D02
Cell lysate
cln.counts.txt
cln.lib.6_S1.D02.expression.values

source_name: RTgill-W1 cln rep 3 conc 5


title: IDH1-H3K9me3-3

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

value: cord blood

value: Tri-Methyl-Histone H3 (Lys9) (D4W1U) Rabbit mAb  (CST#13969)


title: HuH7D150


title: P15216_215_ki_Naive


title: rtgill.cln.3.C02

description:
Library name: rtgill.cln.3.C02
Cell lysate
cln.counts.txt
cln.lib.6_S1.C02.expression.values

source_name: RTgill-W1 cln rep 3 conc 6


title: IDH1-H3K9me3-2

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: P15216_214_wt_D7

source_name: CD4+ T cells


title: HuH7D100


title: P15216_217_ki_D7


title: early erythroid cells, IDH1-shRNA, day 15 3

source_name: erythroid cells

value: IDH1 knockdown

value: erythropoiesis


title: AcZn.Zn12

description: Gene expression data from xenograft tumor from mice treated with Zinc acexamate

source_name: tumor

value: xenograft

value: treated with Zinc acexamate


title: rtgill.cln.3.B02

description:
Library name: rtgill.cln.3.B02
Cell lysate
cln.counts.txt
cln.lib.6_S1.B02.expression.values

source_name: RTgill-W1 cln rep 3 conc 7


title: HuH7D0

description: Gene expression data from HuH7 cell line without treatment

value: without treatment


title: AcZn.Zn23


title: IDH1-Input

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: P15216_213_wt_Naive

value: wt

value: Naive


title: rtgill.cln.2.H02

description:
Library name: rtgill.cln.2.H02
Cell lysate
cln.counts.txt
cln.lib.10_S1.H02.expression.values

source_name: RTgill-W1 cln rep 2 conc 1


title: AcZn.Zn10


title: rtgill.cln.3.A02

description:
Library name: rtgill.cln.3.A02
Cell lysate
cln.counts.txt
cln.lib.6_S1.A02.expression.values

source_name: RTgill-W1 cln rep 3 conc 8


title: P15216_212_ko_D7

value: ko


title: mrna sequencing of zebrafish: miR214 PaternalHET gonads 31dpf rep4

city: Mainz

first: René

last: Ketting

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: CrisprCas9 generated using 2 sgRNAs, >F3, crossed toTg(vasa:eGFP)

data_processing:
RNA-sequencing reads were mapped to the zebrafish genome (Zv10) using the aligner STAR (version 2.4.1d). The command-line parameters for the aligner STAR (version 2.4.1d) were: STAR --runMode alignReads --outBAMsortingThreadN 0 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 2 --alignIntronMin 21 --outSAMtype BAM SortedByCoordinate --sjdbOverhang 99 --outSJfilterReads Unique
Read count table was produced with featureCounts (v. 1.4.6) using Ensembl database gene annotation (release 80). The command-line parameters for the featureCounts (v. 1.4.6) were: -Q 1 -O -T 4 -p -P -s 2
Differential expression was performed using the R/Bioconductor package DESeq2
Assembly: danRer10
Supplementary files format and content: Tab-delimited file with the gene counts per sample as generated by featureCounts

organism: Danio rerio

source_name: gonads

growth_protocol: Fish were maintained at 28°C. Unless stated otherwise, in all experiments a mix of AB and TU strain was used. All experiments were carried out according to German animal welfare law (licenses 23 177-07/G 13-5-087 (CRISPR-Cas9 knockouts), 23177-07/A 15-5-001 OES (tail fin clips)).

extract_protocol:
RNA was extracted using Trizol (Invitrogen) together with the RNA isolation RNA Micro- or Miniprep-kits (ZymoResearch).
NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illumina’s standard protocol (Part # 15031047 Rev, E). Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles, Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2,0 Fluorometer (Life technologies). All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC, SR for 1 x 84 cycles plus 7 cycles for the index read.

value: gonads

value: mz 06de, tg(vasa:eGFP)

tag: breed

value: TUE

value: 27 dpf

tag: parental ko

value: PaternalHET

tag: number of_gonads

value: 9 gonads

value: heterozygous mutation for miR-214 from a heterozygous female crossed to a homozygous male


title: mrna sequencing of zebrafish: miR214 PaternalHET gonads 31dpf rep3


title: AcZn.Zn6


title: P15216_211_ko_Naive


title: IDH1-H3K9me3-1

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

value: cord blood

value: erythroid cells


title: P15216_210_wt_D7


title: rtgill.cln.2.G02

description:
Library name: rtgill.cln.2.G02
Cell lysate
cln.counts.txt
cln.lib.10_S1.G02.expression.values

source_name: RTgill-W1 cln rep 2 conc 2

value: Rainbow trout gill


title: rtgill.cln.2.F02

description:
Library name: rtgill.cln.2.F02
Cell lysate
cln.counts.txt
cln.lib.10_S1.F02.expression.values

source_name: RTgill-W1 cln rep 2 conc 3


title: mrna sequencing of zebrafish: miR214 PaternalHET gonads 31dpf rep2


title: AcZn.Zn2


title: P15216_209_wt_Naive


title: mrna sequencing of zebrafish: miR214 PaternalHET gonads 31dpf rep1


title: mrna sequencing of zebrafish: miR214 PaternalKO gonads 31dpf rep4

value: PaternalKO

value: 8 gonads

value: homozygous mutation for miR-214 from a heterozygous female crossed to a homozygous male


title: mrna sequencing of zebrafish: miR214 PaternalKO gonads 31dpf rep3


title: rtgill.cln.2.D02

description:
Library name: rtgill.cln.2.D02
Cell lysate
cln.counts.txt
cln.lib.10_S1.D02.expression.values

source_name: RTgill-W1 cln rep 2 conc 5


title: rtgill.cln.2.E02

description:
Library name: rtgill.cln.2.E02
Cell lysate
cln.counts.txt
cln.lib.10_S1.E02.expression.values

source_name: RTgill-W1 cln rep 2 conc 4


title: P15216_208_ki_D7

value: ki


title: CTL.Zn17

description: Gene expression data from xenograft tumor from mice without treatment

value: xenograft

value: without treatment


title: CTL.Zn19


title: AcZn.Zn4

value: treated with Zinc acexamate


title: P15216_207_ki_Naive

value: Naive


title: Sample_UIC9_5_117_076

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

country: United Kingdom

institute: University of Exeter Medical School

description:
rz_UC_9_5
nup107_mo_tpm_ribozero.tsv.gz

data_processing:
Stranded paired-end polyA+ and ribozero 150 bp RNA-seq reads were aligned to the Xt9.1 genome combined with ERCC spikes using STAR and quantified as transcripts per million (TPM) for each gene with RSEM  using the RSEM-STAR pipeline, with additional options “--seed 1618 --calc-pme --calc-ci --estimate-rspd --paired-end”.
Assembly: Xt9.1
Supplementary files format and content: Tab delimited file with transcripts per million quantifications for all genes. The gene models are the Xenopus tropicalis 9.1 Xenbase models from https://www.xenbase.org/ (a link to the GTF: https://download.xenbase.org/xenbase/Genomics/JGI/Xentr9.1/XENTR_9.1_Xenbase.gtf.gz).

organism: Xenopus tropicalis

source_name: Whole Embryo

growth_protocol: We induced ovulation, performed IVF, and raised embryos in 1/9xMR, We staged X. tropicalis embryos according to Nieuwkoop and Faber.

extract_protocol:
10 ml of an ERCC RNA Spike-In Mix (Thermo Fisher Scientific) was added to 860 ml of DEPC-treated water and then diluted 1:10 into Trizol. 10 embryos per timepoint and condition (UIC and MO) were homogenized in 100 ml of Trizol+Spike-In mixture. Each sample was frozen using ethanol and dry ice and then stored at -80 °C. All samples were processed for RNA extraction at the same time. Following isopropanol precipitation, RNA pellets were resuspended in DEPC-treated water and precipitated with 5M LiCl at 4 °C overnight. This solution was centrifuged at 4 °C, and RNA pellets were washed twice with 70% ethanol. Final RNA products were resuspended in DEPC-treated water (2 ml/embryo).
RNA libraries were prepared for Illumina sequencing using standard polyA+ and RiboZero Illumina protocols

treatment_protocol: Synchronized embryos were generated by IVF. Uninjected controls (UC) and embryos injected with 10ng of the ATG Nup107 morpholino oligo (MO) were raised in 1/9X MR at 25 °C and then 10 embryos were collected from each group at 30 min intervals from stage 6 until stage 12

value: Whole Embryo

value: 9.5 hpf

value: UC

tag: fraction

value: RiboZero RNA


title: P15216_206_wt_D7

value: wt


title: rtgill.cln.2.C02

description:
Library name: rtgill.cln.2.C02
Cell lysate
cln.counts.txt
cln.lib.10_S1.C02.expression.values

source_name: RTgill-W1 cln rep 2 conc 6


title: CTL.Zn14


title: mrna sequencing of zebrafish: miR214 PaternalKO gonads 31dpf rep1

value: gonads

value: mz 06de, tg(vasa:eGFP)

value: TUE

value: 27 dpf

value: 9 gonads


title: rtgill.cln.2.A02

description:
Library name: rtgill.cln.2.A02
Cell lysate
cln.counts.txt
cln.lib.10_S1.A02.expression.values

source_name: RTgill-W1 cln rep 2 conc 8

value: Rainbow trout gill


title: CTL.Zn7


title: Sample_UIC8_5_165_028

description:
rz_UC_8_5
nup107_mo_tpm_ribozero.tsv.gz

value: 8.5 hpf


title: mrna sequencing of zebrafish: miR214 PaternalKO gonads 31dpf rep2

value: PaternalKO

value: homozygous mutation for miR-214 from a heterozygous female crossed to a homozygous male


title: rtgill.cln.2.B02

description:
Library name: rtgill.cln.2.B02
Cell lysate
cln.counts.txt
cln.lib.10_S1.B02.expression.values

source_name: RTgill-W1 cln rep 2 conc 7


title: CTL.Zn1

value: xenograft

value: without treatment


title: Sample_UIC9_141_052

description:
rz_UC_9_0
nup107_mo_tpm_ribozero.tsv.gz

value: 9 hpf


title: P15216_205_wt_Naive

value: Naive


title: mrna sequencing of zebrafish: miR214 maternalHET gonads 31dpf rep4

value: maternalHET

value: 7 gonads

value: heterozygous mutation for miR-214 from a homozygous female crossed to a heterozygous male


title: mrna sequencing of zebrafish: miR214 maternalHET gonads 31dpf rep3


title: rtgill.cln.1.H02

description:
Library name: rtgill.cln.1.H02
Cell lysate
cln.counts.txt
cln.lib.1_S1.H02.expression.values

source_name: RTgill-W1 cln rep 1 conc 1


title: Sample_UIC7_5_118_075

description:
rz_UC_7_5
nup107_mo_tpm_ribozero.tsv.gz

value: Whole Embryo

value: 7.5 hpf

value: UC

value: RiboZero RNA


title: Sample_UIC6_5_166_027

description:
rz_UC_6_5
nup107_mo_tpm_ribozero.tsv.gz

value: 6.5 hpf


title: rtgill.cln.1.E02

description:
Library name: rtgill.cln.1.E02
Cell lysate
cln.counts.txt
cln.lib.1_S1.E02.expression.values

source_name: RTgill-W1 cln rep 1 conc 4


title: P15216_202_wt_D7

source_name: CD4+ T cells

value: wt


title: rtgill.cln.1.G02

description:
Library name: rtgill.cln.1.G02
Cell lysate
cln.counts.txt
cln.lib.1_S1.G02.expression.values

source_name: RTgill-W1 cln rep 1 conc 2

value: Rainbow trout gill


title: P15216_201_wt_Naive


title: Sample_UIC7_142_051

description:
rz_UC_7_0
nup107_mo_tpm_ribozero.tsv.gz

value: 7 hpf


title: mrna sequencing of zebrafish: miR214 maternalKO gonads 31dpf rep4

value: gonads

value: mz 06de, tg(vasa:eGFP)

value: TUE

value: 27 dpf

value: maternalKO

value: 8 gonads

value: homozygous mutation for miR-214 from a homozygous female crossed to a heterozygous male


title: rtgill.cln.1.F02

description:
Library name: rtgill.cln.1.F02
Cell lysate
cln.counts.txt
cln.lib.1_S1.F02.expression.values

source_name: RTgill-W1 cln rep 1 conc 3


title: Sample_UIC6_190_003

description:
rz_UC_6_0
nup107_mo_tpm_ribozero.tsv.gz

value: 6 hpf


title: rtgill.cln.1.D02

description:
Library name: rtgill.cln.1.D02
Cell lysate
cln.counts.txt
cln.lib.1_S1.D02.expression.values

source_name: RTgill-W1 cln rep 1 conc 5


title: Control_RNASeq

city: Taichung

first: Li-Ching

last: Hsieh

address: 145 Xingda Rd.

department: Graduate Institute of Genomics and Bioinformatics

country: Taiwan

institute: National Chung Hsing University

data_processing:
Trimmomatic (Bolger et al., 2014) was employed to remove low-quality reads with a Phred quality score Q (Ewing and Green, 1998) below 20 and to trim Illumina® adaptor sequences, completing the preprocessing of reads prior to assembly.
De novo transcriptome assembly was performed using Trinity (Grabherr et al., 2011) with default settings and a minimum contig length of 200 bases.
Transcriptome expression levels were quantified in terms of Transcripts Per Million (TPM) using eXpress (Roberts and Pachter, 2013), which also estimates the number of reads mapping to each unigene for further differential gene expression analysis.
Differential gene expression analysis was subsequently carried out using edgeR (McCarthy et al., 2012) with the dispersion parameter set to 0.01 and employing the trimmed mean of M-values (TMM) method (Robinson and Oshlack, 2010).
Unigenes displaying an absolute log2-fold-change (|log2FC|) greater than 2 and a false discovery rate (FDR) below 0.001 were identified as significantly differentially expressed genes (DEGs).
Assembly: De novo transcriptome assembly was performed; no reference genome was used.
Supplementary files format and content: Tab-separated values (unigene ID, length, number of reads mapping to each unigene, TPM, annotation) files

organism: Mesembryanthemum crystallinum

source_name: seedling

growth_protocol: Sterilized ice plant (Mesembryanthemum crystallinum L.) seeds were sown in 1X Murashige and Skoog basal medium with vitamins (M519, PhytoTechnology Laboratories, USA) and maintained in a vertical position at 25oC under illumination 16 h 50 μmol m−2 s−1 light/8h dark for 5 days (light-grown seedlings) or continuous darkness at 25oC for 3 days (dark-grown/etiolated seedlings).

extract_protocol:
Total RNA was extracted from 15 seedlings using 1 mL TRIzol reagent (Invitrogen) according to the manufacturer’s instruction.
The library construction involved several steps: initially, mRNA was isolated from total RNA using magnetic beads with poly-T oligonucleotides to target poly-A containing mRNA, followed by heating to fragment the isolated mRNA. This was then reverse transcribed into cDNA using random primers. Adaptors were then attached to both the 3’ and 5’ ends, followed by PCR to amplify the fragments. The PCR-amplified cDNA was assessed with both Experion™ and the Qubit™ 3.0 fluorometer (Invitrogen™, U.S.A.) to ensure that the fragment length and concentration met the requirements for the Illumina® Hiseq 2000 sequencing platform.

treatment_protocol: During the salt treatment time, agar plates were placed at an angle of inclination of 10o and control (liquid MS medium) or salt (MS plus 200 mM NaCl) were added directly to plates to cover the lower part of the roots, but not the upper part of seedlings as described by Chiang et al. (2016).

value: seedling

value: WT

value: liquid MS medium


title: mrna sequencing of zebrafish: miR214 maternalKO gonads 31dpf rep3

value: 9 gonads


title: mrna sequencing of zebrafish: miR214 maternalHET gonads 31dpf rep1

value: maternalHET

value: 7 gonads

value: heterozygous mutation for miR-214 from a homozygous female crossed to a heterozygous male


title: Sample_UIC5_143_050

description:
rz_UC_5_0
nup107_mo_tpm_ribozero.tsv.gz

value: Whole Embryo

value: 5 hpf

value: UC

value: RiboZero RNA


title: Sample_UIC5_5_119_074

description:
rz_UC_5_5
nup107_mo_tpm_ribozero.tsv.gz

value: 5.5 hpf


title: rtgill.cln.1.C02

description:
Library name: rtgill.cln.1.C02
Cell lysate
cln.counts.txt
cln.lib.1_S1.C02.expression.values

source_name: RTgill-W1 cln rep 1 conc 6

value: Rainbow trout gill


title: Sample_UIC4_5_167_026

description:
rz_UC_4_5
nup107_mo_tpm_ribozero.tsv.gz

value: 4.5 hpf


title: Salt_RNASeq

value: liquid MS medium plus 200 mM NaCl


title: CAL-27, sphere, rep3

city: Wuhan

first: Yuantong

last: Liu

state: Hubei

address: Luoyu road

institute: Wuhan University

data_processing:
BGISEQ-500 sequencer.
Clean reads were mapped to the reference genome using HISAT/Bowtie2 tools.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: xls file includes TPM for each sample

extract_protocol:
Total RNA was extracted from the cells using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGI-Shenzhen, China)


title: P15216_204_ko_D7

value: ko


title: rtgill.cln.1.B02

description:
Library name: rtgill.cln.1.B02
Cell lysate
cln.counts.txt
cln.lib.1_S1.B02.expression.values

source_name: RTgill-W1 cln rep 1 conc 7


title: mrna sequencing of zebrafish: miR214 maternalKO gonads 31dpf rep1

source_name: gonads

value: gonads

value: mz 06de, tg(vasa:eGFP)

value: TUE

value: 27 dpf

value: maternalKO

value: homozygous mutation for miR-214 from a homozygous female crossed to a heterozygous male


title: P15216_203_ko_Naive

value: Naive


title: mrna sequencing of zebrafish: miR214 maternalKO gonads 31dpf rep2

value: 9 gonads


title: HUB_DB_008

city: Jena

first: Dennis

middle: de

last: de Bakker

address: Beutenbergstraße 11

institute: FLI

data_processing:
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. (2014) Cell.
(Sample 1,2) Mapped reads were assigned to cells based on barcodes according to the CEL-seq2 protocol (Hashimshony et al., 2016)) In brief, read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier (UMI) and followed by a 24 nt PolyA stretch and a number (<40) of transcript derived bases. Cell specific barcodes are specified in the file "cel-seq2_barcodes.csv", well numbers refer to the 384-well plate in the following ordre: A1 to A24 - B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2, containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded.
(Sample 3,4) Mapped reads were assigned to cells based on barcodes according to the CEL-seq2 protocol (Hashimshony et al., 2016)) In brief, read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier (UMI) and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel-seq2_barcodes.csv".  Read 1 was not used for quantification. Read 2, containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded.
Genome_build: zv9 (with improved 3' annotation, see Junker et al (2014) Cell)
Supplementary_files_format_and_content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.

source_name: Cardiomyocytes of the Zebrafish heart ventricle

extract_protocol:
Live cells were sorted into 384-well plates with Vapor-Lock oil containing a droplet with barcoded primers, spike-in RNA and dNTPs, followed by heat-induced cell lysis and cDNA syntheses using a robotic liquid handler. After cell lysis for 5 minutes at 65C, RT and second strand mixes were distributed with the Nanodrop II liquid handling platform.
Primers consisted of a 24bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific 8bp barcode, the 5' Illumina Truseq small RNA kit adapter and a T7 promoter. After all cells were pooled in one library, the CEL-seq2 protocol was used for librabry prep (Hashimony et al., 2016)

treatment_protocol: Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tg(nppa:mCitrine) cells were subsequently FACS sorted based on mCherry expression in 384 well plates, each well containing 1 cell.

tag: Stage

tag: line

value: Adult zebrafish ventricle


title: Sample_UIC8_189_004

description:
rz_UC_8_0
nup107_mo_tpm_ribozero.tsv.gz

value: Whole Embryo

value: 8 hpf


title: Sample_UIC4_191_002

description:
rz_UC_4_0
nup107_mo_tpm_ribozero.tsv.gz

value: 4 hpf

value: UC

value: RiboZero RNA


title: CAL-27, sphere, rep2

tag: cell line


title: mrna sequencing of zebrafish: miR214 maternalHET gonads 31dpf rep2

value: maternalHET

value: 7 gonads

value: heterozygous mutation for miR-214 from a homozygous female crossed to a heterozygous male


title: rtgill.cln.1.A02

description:
Library name: rtgill.cln.1.A02
Cell lysate
cln.counts.txt
cln.lib.1_S1.A02.expression.values

data_processing:
RNA-seq Analysis Portal (RAP; Qiagen)
Raw RNA Sequencing fastq files were submitted to QIAGEN’s RNA-seq Analysis Portal (RAP) (QIAGEN). First, raw files were demultiplexed to yield individual reads files for each sample (well) and then mapped to the rainbow trout genome (Omyk_1.0.105) to yield raw counts.
The counts were submitted to ExpressAnalyst for differential expression analysis and benchmark dose response analysis
Assembly: Omyk_1.0.105
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: RTgill-W1 cln rep 1 conc 8

extract_protocol:
OECD Test Guideline 249 for RTgill-W1 cell exposures, and QIAseq UPXome RNA Library Kits (QIAGEN) for library preparation
QIAseq UPXome RNA Library Kits (QIAGEN) protocol  for library preparation

tag: cell type

value: Rainbow trout gill


title: Sample_UIC3_5_120_073

description:
rz_UC_3_5
nup107_mo_tpm_ribozero.tsv.gz

value: 3.5 hpf

tag: treatment


title: CAL-27, sphere, rep1


title: rtgill.ata.3.G01

description:
Library name: rtgill.ata.3.G01
Cell lysate
ata.counts.txt
ata.lib.6_S1.G01.expression.values

source_name: RTgill-W1 ata rep 3 conc 2


title: rtgill.ata.3.H01

description:
Library name: rtgill.ata.3.H01
Cell lysate
ata.counts.txt
ata.lib.6_S1.H01.expression.values

source_name: RTgill-W1 ata rep 3 conc 1


title: HUB_DB_007


title: CAL-27, parental, rep3


title: CAL-27, parental, rep2


title: Sample_UIC2_5_168_025

description:
rz_UC_2_5
nup107_mo_tpm_ribozero.tsv.gz

source_name: Whole Embryo

value: 2.5 hpf


title: Sample_UIC3_144_049

description:
rz_UC_3_0
nup107_mo_tpm_ribozero.tsv.gz

value: 3 hpf


title: rtgill.ata.3.F01

description:
Library name: rtgill.ata.3.F01
Cell lysate
ata.counts.txt
ata.lib.6_S1.F01.expression.values

source_name: RTgill-W1 ata rep 3 conc 3


title: HUB_DB_003


title: CAL-27, parental, rep1


title: HUB_DB_006


title: rtgill.ata.3.D01

description:
Library name: rtgill.ata.3.D01
Cell lysate
ata.counts.txt
ata.lib.6_S1.D01.expression.values

source_name: RTgill-W1 ata rep 3 conc 5


title: Sample_UIC2_192_001

description:
rz_UC_2_0
nup107_mo_tpm_ribozero.tsv.gz

value: 2 hpf


title: rtgill.ata.3.E01

description:
Library name: rtgill.ata.3.E01
Cell lysate
ata.counts.txt
ata.lib.6_S1.E01.expression.values

source_name: RTgill-W1 ata rep 3 conc 4


title: SCC4, sphere, rep3


title: HUB_DB_005


title: rtgill.ata.3.C01

description:
Library name: rtgill.ata.3.C01
Cell lysate
ata.counts.txt
ata.lib.6_S1.C01.expression.values

source_name: RTgill-W1 ata rep 3 conc 6


title: SCC4, sphere, rep1


title: SCC4, sphere, rep2


title: Sample_UIC12_187_006

description:
rz_UC_12_0
nup107_mo_tpm_ribozero.tsv.gz

value: 12 hpf


title: HUB_DB_001


title: Sample_UIC11_5_116_077

description:
rz_UC_11_5
nup107_mo_tpm_ribozero.tsv.gz


title: rtgill.ata.3.B01

description:
Library name: rtgill.ata.3.B01
Cell lysate
ata.counts.txt
ata.lib.6_S1.B01.expression.values

source_name: RTgill-W1 ata rep 3 conc 7


title: SCC4, parental, rep3


title: HUB_DB_004


title: rtgill.ata.3.A01

description:
Library name: rtgill.ata.3.A01
Cell lysate
ata.counts.txt
ata.lib.6_S1.A01.expression.values

source_name: RTgill-W1 ata rep 3 conc 8


title: Intestinal stem cell, experimental, rep3

city: Halifax

first: Francesca

last: Di Cara

state: Nova Scotia

address: 5850/5980 University Avenue

institute: Dalhousie University

description: Library name: NS.1827.001.UPX_2.ics (paired) C66

data_processing:
1) Qiagen GeneGlobe platform (www.qiagen.com/GeneGlobe ) 2) QIAGEN CLC Genomics Workbench 3) HISAT2, StringTie, Ballgown and Deseq2 pipeline
Assembly: dm6
Supplementary files format and content: tab-delimited text file

organism: Drosophila melanogaster

source_name: intestinal progenitor cells

extract_protocol:
Intestinal stem cell isolation by fluorescence-activated cell sorting (FACS) was adapted from the published protocol article by Dutta et al., 2013. In brief, three biological replicates consisting of 200 fly guts per replicate were dissected in PBS-1X and then immediately transferred into a 1.5 ml microcentrifuge tube containing ice-cold diethylpyrocarbonate (DEPC)-treated water-PBS (400 l). Dissected midguts were then dissociated with 100 l elastase solution (1 mg/ml final concentration) and incubated for 1 hour at 27C in a heating block with shaking at 34 g. Dissociated cells were centrifuged for 20 min at 300 g, at 4C, and the pellets were resuspended in 500 l fresh PBS-DEPC for sorting. 1 l of 1 mg/ml propidium iodide was added, and then dissociated cells were filtered using 25-m filters to remove clumps. Cell suspension was then FACS sorted. GFP+ cells from the esgGFP>w1118 and w1118 (negative control no GFP) midguts flies were sorted out first to set the fluorescence gate. For each of the three biological replicates, about 40,000 GFP+ cells were sorted. RNA was isolated from the FACS-sorted GFP+ cells using a Direct-zol RNA Microprep kit,
library preparation using the QIAseq UPX3 transcriptome for next-generation sequencing paired to the QIAseq UPX 3 trans. 12 (Index 48). Libraries were pooled and quantified using QIAseq library Quant Assay kit and analyzed on a bioanalyzer (Agilent).

value: intestinal progenitor cells


title: Sample_UIC11_140_053

description:
rz_UC_11_0
nup107_mo_tpm_ribozero.tsv.gz

value: 11 hpf


title: Intestinal stem cell, experimental, rep2

description: Library name: NS.1827.001.UPX_2.ics (paired) C65


title: SCC4, parental, rep2


title: Sample_UIC10_5_164_029

description:
rz_UC_10_5
nup107_mo_tpm_ribozero.tsv.gz


title: rtgill.ata.2.H01

description:
Library name: rtgill.ata.2.H01
Cell lysate
ata.counts.txt
ata.lib.10_S1.H01.expression.values

source_name: RTgill-W1 ata rep 2 conc 1


title: SCC4, parental, rep1


title: Sample_UIC10_188_005

description:
rz_UC_10_0
nup107_mo_tpm_ribozero.tsv.gz

value: 10 hpf


title: rtgill.ata.2.G01

description:
Library name: rtgill.ata.2.G01
Cell lysate
ata.counts.txt
ata.lib.10_S1.G01.expression.values

source_name: RTgill-W1 ata rep 2 conc 2


title: Intestinal stem cell, control, rep3

description: Library name: NS.1827.001.UPX_2.ics (paired) C63

value: wildtype


title: Commercial bovine milk powder EV miRNAs

city: St Genès-Champanelle

first: Christine

last: LEROUX

address: Route de Theix

country: France

institute: INRAE

data_processing:
After ttrimming of adaptor sequences and removal of reads containing ambiguous base calls (FASTX-Toolkit, http://hannonlab.cshl.edu/fastx_toolkit/index.html), reads were filtered according to their size (15–40 nt). Reads quantification and annotation were performed using the ncPRO-seq pipeline (Chen et al., 2012).
Assembly: The sequence reads were aligned against the Bos taurus btau 5.0.1 genome and with miRBase_v22.1. Precursors and mature miRNAs were identified using the miRDeep2 core module, miRDeep2.pl (Friedländer et al., 2012).
Supplementary files format and content: tab-delimited text file

organism: Bos taurus

source_name: Milk powder EV

extract_protocol:
RNA extraction performed using a mirVana Total Isolation kit (life Technologies)
Small RNA-Seq libraries were generated using Library prep for small RNA-seq kit (Illumina, San Diego, CA). Acrylamide gel purifications of 140-160 nt amplified cDNA (corresponding to cDNA obtained from small RNA + 120 nt from the adapters) were performed. The final cDNA libraries were checked for quality and quantified using capillary electrophoresis. Libraries were loaded in the flow cell and sequenced as single-end 50 base reads

treatment_protocol: Mil samples were reconstituted from powedrs in warm water, then extracellular vesicles were isolated using SEC

value: Milk powder EV


title: Sample_MO9_5_105_088

description:
rz_MO_9_5
nup107_mo_tpm_ribozero.tsv.gz

value: Whole Embryo

value: 9.5 hpf

value: MO


title: XXGH3

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Data were analyzed using miRDeep2 software utilizing the bovine reference genome bosTau8 (UMD_3.1.1) and miRBase release 22 (all species), after cleaning the adapters and filtering for their size (17-28 nt) using Cutadapt v.3.5. A custom Perl script parse_miRDeep2_outputs.pl was used with the quantifier.pl miRDeep2 module for quantification and the elimination of redundancy between mature microRNAs. Sequences of mature miRNAs identified in other species and the predicted miRNAs were searched in the RumimiR database (v. March 2021) to consider ruminant miRNAs described in the literature but not in the last version of miRBase (v.22).
Assembly: bosTau8 (UMD3.1.1)
Supplementary files format and content: csv file including the 3 butters (B01, B02, B03) data withmiRNA names and sequences

source_name: butter

extract_protocol:
Approximately 1 g of unsalted French commercial butters from three different brands were reduced to powder in liquid nitrogen. RNA was extracted from c.a. 350 mg of butter powder using the miRVana kit (Thermo Fisher Scientific, USA). Double chloroform was added according to the manufacturer’s instruction.
P2783 : Small RNA-Seq librairies were generated from 300 ng of total RNA using TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA), according to manufacturer's instructions. The protocol takes advantage of the natural structure common to most microRNA molecules that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA, first the 3' RNA adapter that is specifically modified to target microRNAs and other small RNAs, then the 5' RNA adapter. Small RNA ligated with 3' and 5' adapters were reverse transcribed and PCR amplified (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 15 sec at 72oC] x 13 cycles; 10 min at 72oC) to create cDNA constructs. Amplified cDNA constructs of 140 to 180 nt were selectively isolated by acrylamide gel purification followed by ethanol precipitation.  The final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: butter


title: rtgill.ata.2.F01

description:
Library name: rtgill.ata.2.F01
Cell lysate
ata.counts.txt
ata.lib.10_S1.F01.expression.values

source_name: RTgill-W1 ata rep 2 conc 3


title: Intestinal stem cell, control, rep2

description: Library name: NS.1827.001.UPX_2.ics (paired) C62


title: rtgill.ata.2.E01

description:
Library name: rtgill.ata.2.E01
Cell lysate
ata.counts.txt
ata.lib.10_S1.E01.expression.values

source_name: RTgill-W1 ata rep 2 conc 4


title: Sample_MO8_177_016

description:
rz_MO_8_0
nup107_mo_tpm_ribozero.tsv.gz

value: 8 hpf

value: RiboZero RNA


title: Sample_MO9_129_064

description:
rz_MO_9_0
nup107_mo_tpm_ribozero.tsv.gz

value: 9 hpf


title: rtgill.ata.2.C01

description:
Library name: rtgill.ata.2.C01
Cell lysate
ata.counts.txt
ata.lib.10_S1.C01.expression.values

source_name: RTgill-W1 ata rep 2 conc 6

value: Rainbow trout gill


title: XXGH1


title: rtgill.ata.2.B01

description:
Library name: rtgill.ata.2.B01
Cell lysate
ata.counts.txt
ata.lib.10_S1.B01.expression.values

source_name: RTgill-W1 ata rep 2 conc 7


title: old_surgery_48h_hippocampus_9

city: Boston

first: Zhuoran

last: Yin

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description:
Library name: FACS99_HP
FACS99_HP

data_processing:
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
FASTQ files were quantified using the Bulk RNA-seq pipeline published by BCBio at Harvard Medical School (June 2022).
Differential expression analysis was conducted using R (v4.2.1) and DESeq2 (v1.36.0); for each dataset we quantified differential expression between young surgery and young control mice, and between old surgery and old control mice.
Adjusted p-values were determined using the Benjamini-Hochberg procedure and significance cutoffs were set at FDR <= 0.2, log2FC >= |0.58|
Assembly: mm10
Supplementary files format and content: matrix tables with raw gene counts for every sample, divided by brain region and timepoint

source_name: brain

extract_protocol:
1,000 isolated Ly6C–CD11b+Fcrls+ microglia were lysed in 5 ul TCL buffer +1% beta-mercaptoethanol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: region

value: hippocampus

value: microglia

value: WT

value: 20-22 months

value: surgery

tag: timepoint

value: 48 hours


title: Intestinal stem cell, control, rep1

description: Library name: NS.1827.001.UPX_2.ics (paired) C61

value: intestinal progenitor cells

tag: genotype

value: wildtype


title: Sample_MO8_5_153_040

description:
rz_MO_8_5
nup107_mo_tpm_ribozero.tsv.gz

source_name: Whole Embryo

tag: tissue

value: Whole Embryo

value: 8.5 hpf


title: Sample_MO7_5_106_087

description:
rz_MO_7_5
nup107_mo_tpm_ribozero.tsv.gz

tag: time

value: 7.5 hpf

value: MO


title: Intestinal stem cell, experimental, rep1

description: Library name: NS.1827.001.UPX_2.ics (paired) C64


title: rtgill.ata.2.A01

description:
Library name: rtgill.ata.2.A01
Cell lysate
ata.counts.txt
ata.lib.10_S1.A01.expression.values

source_name: RTgill-W1 ata rep 2 conc 8


title: AR KO primary hepatocyte_GCG_input

city: Hangzhou

first: Chen

last: Jie

state: Zhejiang

address: Dunyu Road No.300

department: School of Life Science

institute: Westlake University

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were detected by BGI programs. Low-quality reads include three types, and the read which could be accord with anyone of the three types will be removed:1) The ratio of N in whole read was over 10%; 2) Remove reads in which unknown bases are more than 10%; 3) The ratio of base whose quality was less than 20 was over 10%.
BWA (Burrows-Wheeler Aligner, Version: 0.7.10)is used to do genome alignment after evaluating its performance
The candidate  Peak  region was extended to be long enough for modeling. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a  Peak  when p-value < le-05.MACS (Model-based Analysis for  ChIP -Seq, version: MACS-1.4.2) was used for peak recalling.
Assembly: GCGm39
Supplementary files format and content: bigWig

source_name: Female

growth_protocol: Isloated primary hepatocytes were seeded on the collagen coated plates at 2×10^6 cells/ml(or each samples) with 7.5%FBS M199(100nM dex), after 4h attachment, the medium was replaced with fresh 7.5%FBS medium with dex and maintained for 24 hours,then change to serum free M199(100nM dex) medium, 12h later, treated cells with 100 nM glucagon/Veh for 6hrs and collected the samples for cut& run assay according to the instructions.

extract_protocol:
The cells were fixed with 0.1% formaldehyde for 2 minutes, followed by quenching the cross-linking reaction using a 10× glycine solution. Subsequently, the samples underwent cut&run assay using the CST kit (#86652) as per the provided protocol.
ChIP-Seq libraries were prepared using the MGIEasy Universal DNA Library Prep Set/MGI/1000006986,  (1) DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor. (2) PCR amplification and size selection (usually 100-300bp, including adaptor sequence). (3) Qualified library for sequencing.

value: Female

value: Primary hepatocytes

value: AR KO

value: glucagon 6h


title: Sample_MO7_130_063

description:
rz_MO_7_0
nup107_mo_tpm_ribozero.tsv.gz

value: 7 hpf

value: RiboZero RNA


title: rtgill.ata.2.D01

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

institute: McGill University

description:
Library name: rtgill.ata.2.D01
Cell lysate
ata.counts.txt
ata.lib.10_S1.D01.expression.values

source_name: RTgill-W1 ata rep 2 conc 5

value: Rainbow trout gill


title: old_ctrl_48h_hemisphere_8

description:
Library name: FACS98_HM
FACS98_HM

value: brain

value: hemisphere

value: microglia

value: WT

tag: age

value: control


title: old_surgery_48h_hemisphere_9

description:
Library name: FACS99_HM
FACS99_HM

value: 20-22 months

value: surgery

value: 48 hours


title: AR KO primary hepatocyte_Veh_input

value: vehicle


title: AR KO primary hepatocyte_GCG_ERRα

value: ERRalpha (Abcam)


title: old_ctrl_48h_hippocampus_8

description:
Library name: FACS98_HP
FACS98_HP

value: hippocampus


title: Sample_MO6_5_154_039

description:
rz_MO_6_5
nup107_mo_tpm_ribozero.tsv.gz

value: Whole Embryo

value: 6.5 hpf

value: MO


title: rtgill.ata.1.H01

description:
Library name: rtgill.ata.1.H01
Cell lysate
ata.counts.txt
ata.lib.1_S1.H01.expression.values

source_name: RTgill-W1 ata rep 1 conc 1


title: AR KO primary hepatocyte_Veh_ERRα

value: Female

value: Primary hepatocytes

value: AR KO


title: XXGH2

value: butter


title: rtgill.ata.1.G01

description:
Library name: rtgill.ata.1.G01
Cell lysate
ata.counts.txt
ata.lib.1_S1.G01.expression.values

source_name: RTgill-W1 ata rep 1 conc 2

value: Rainbow trout gill


title: Sample_MO5_5_107_086

description:
rz_MO_5_5
nup107_mo_tpm_ribozero.tsv.gz

value: 5.5 hpf

value: RiboZero RNA


title: WT primary hepatocyte_GCG_input

value: WT

value: glucagon 6h


title: old_ctrl_48h_hemisphere_7

description:
Library name: FACS96_HM
FACS96_HM

value: brain

value: hemisphere

value: microglia

value: 20-22 months

value: control


title: rtgill.ata.1.F01

description:
Library name: rtgill.ata.1.F01
Cell lysate
ata.counts.txt
ata.lib.1_S1.F01.expression.values

source_name: RTgill-W1 ata rep 1 conc 3


title: Sample_MO5_131_062

description:
rz_MO_5_0
nup107_mo_tpm_ribozero.tsv.gz

value: Whole Embryo

value: 5 hpf


title: old_surgery_48h_hippocampus_8

description:
Library name: FACS95_HP
FACS95_HP

value: hippocampus

value: surgery

value: 48 hours


title: Sample_MO4_5_155_038

description:
rz_MO_4_5
nup107_mo_tpm_ribozero.tsv.gz

value: 4.5 hpf

value: MO


title: WT primary hepatocyte_GCG_ERRα

value: Female

value: Primary hepatocytes

value: ERRalpha (Abcam)


title: rtgill.ata.1.E01

description:
Library name: rtgill.ata.1.E01
Cell lysate
ata.counts.txt
ata.lib.1_S1.E01.expression.values

source_name: RTgill-W1 ata rep 1 conc 4

value: Rainbow trout gill


title: rtgill.ata.1.C01

description:
Library name: rtgill.ata.1.C01
Cell lysate
ata.counts.txt
ata.lib.1_S1.C01.expression.values

source_name: RTgill-W1 ata rep 1 conc 6


title: WT primary hepatocyte_Veh_AR

value: AR (Abcam)

value: WT

value: vehicle


title: Sample_MO4_179_014

description:
rz_MO_4_0
nup107_mo_tpm_ribozero.tsv.gz

value: 4 hpf

value: RiboZero RNA


title: Sample_MO3_5_108_085

description:
rz_MO_3_5
nup107_mo_tpm_ribozero.tsv.gz

value: 3.5 hpf


title: old_ctrl_48h_hippocampus_7

description:
Library name: FACS96_HP
FACS96_HP

value: brain

value: microglia

value: 20-22 months

value: control


title: WT primary hepatocyte_Veh_ERRα


title: rtgill.ata.1.B01

description:
Library name: rtgill.ata.1.B01
Cell lysate
ata.counts.txt
ata.lib.1_S1.B01.expression.values

source_name: RTgill-W1 ata rep 1 conc 7


title: rtgill.ata.1.A01

description:
Library name: rtgill.ata.1.A01
Cell lysate
ata.counts.txt
ata.lib.1_S1.A01.expression.values

source_name: RTgill-W1 ata rep 1 conc 8


title: old_surgery_48h_hemisphere_7

description:
Library name: FACS93_HM
FACS93_HM

value: hemisphere

value: surgery

value: 48 hours


title: young_ctrl_48h_hemisphere_4

description:
Library name: FACS90_HM
FACS90_HM

value: 3-5 months


title: young_ctrl_48h_hippocampus_4

description:
Library name: FACS90_HP
FACS90_HP

value: hippocampus


title: WT primary hepatocyte_Veh_input

value: Female

value: Primary hepatocytes


title: old_surgery_48h_hippocampus_7

description:
Library name: FACS93_HP
FACS93_HP


title: Sample_MO3_132_061

description:
rz_MO_3_0
nup107_mo_tpm_ribozero.tsv.gz

value: Whole Embryo

value: 3 hpf

value: MO


title: WT primary hepatocyte_GCG_AR

value: AR (Abcam)

value: WT

value: glucagon 6h


title: Sample_MO6_178_015

description:
rz_MO_6_0
nup107_mo_tpm_ribozero.tsv.gz

value: 6 hpf

value: RiboZero RNA


title: dsDouble-kd_R3

city: Valencia

first: Jordi

last: Planells

state: Valencia

address: Doctor Moliner, 50 street

department: Biologia celular, biologia funcional y antropologia fisica

institute: Universitat de València

description: ATAC from tagmented DNA extracted from Double-kd (Rrp6+Dis3) S2 cells

data_processing:
Read file QC: Paired-end sequencing files were analyzed with FastQC, summarized with MultiQC, included in the nf-core atac-seq processing pipeline
Adapter clipping, quality trimming and filtering: Adapters were trimmed with Trim Galore! included in the nf-core atac-seq processing pipeline
Genome alignment: Reads were aligned to dm6 genome with bwa, multimapping reads were kept, included in the nf-core atac-seq processing pipeline
Read count extraction: Peak calling (narrow_peaks) was performed with MACS2 using default values, included in the nf-core atac-seq processing pipeline
Assembly: BDGP6 (dm6)
Supplementary files format and content: consensus_peaks_all_samples.bed

source_name: S2 cell line

growth_protocol: Drosophila melanogaster Schneider 2 (S2) cells were cultured at 28 °C in Schneider’s medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 50 μg/ml streptomycin and 50 U/ml penicillin (Gibco).

extract_protocol:
50.000 cells were centrifuged (500 x g, 5 min, 4ºC), washed in ice-cold PBS and lysed in cold lysis buffer. Nuclei were then pelleted and used as input material for tagmentation.
All the samples consist of biological triplicates. Tagmentation and library preparation was performed according to Buenrostro et al. 2015 and Yu et al. 2018. using Nextera DNA library kit (FC-121-1030). Libraries were sequenced in NextSeq500, obtaining paired-end, unstranded 37 cycles reads.

treatment_protocol: The MegaScript RNAi kit was used to produce dsRNA for RNAi experiments. Primer sequences are listed in Suppl. Table S1. Cells were incubated with dsRNAs complementary to GFP (control), Rrp6, Dis3, or both (double knockdown condition) for 48 hours at 28°C. The treatment was repeated once more at 48 hours and cells were harvested 96 hours after the initial transfection. All experiments were carried out in biological triplicates.

value: dsDouble-kd


title: Sample_MO2_5_156_037

description:
rz_MO_2_5
nup107_mo_tpm_ribozero.tsv.gz

value: 2.5 hpf


title: old_surgery_48h_hemisphere_8

description:
Library name: FACS95_HM
FACS95_HM

value: brain

value: hemisphere

value: microglia

value: 20-22 months


title: rtgill.dmso.6.H10

address: 21,1111 Lakeshore Blvd, Apt #2

description:
Library name: rtgill.dmso.6.H10
Cell lysate
dmso.counts.txt
dmso.9_DMSO_col10_S1.H10.expression.values

source_name: RTgill-W1 ctrl rep 39

value: ctrl

value: Rainbow trout gill


title: dsDouble-kd_R2


title: old_surgery_48h_hippocampus_6

description:
Library name: FACS89_HP
FACS89_HP

value: hippocampus

value: surgery

value: 48 hours


title: rtgill.ata.1.D01

description:
Library name: rtgill.ata.1.D01
Cell lysate
ata.counts.txt
ata.lib.1_S1.D01.expression.values

source_name: RTgill-W1 ata rep 1 conc 5


title: rtgill.dmso.6.G10

description:
Library name: rtgill.dmso.6.G10
Cell lysate
dmso.counts.txt
dmso.9_DMSO_col10_S1.G10.expression.values

source_name: RTgill-W1 ctrl rep 38


title: dsDouble-kd_R1


title: old_ctrl_48h_hippocampus_6

description:
Library name: FACS88_HP
FACS88_HP

value: control


title: rtgill.dmso.6.F10

description:
Library name: rtgill.dmso.6.F10
Cell lysate
dmso.counts.txt
dmso.9_DMSO_col10_S1.F10.expression.values

source_name: RTgill-W1 ctrl rep 37


title: Sample_MO12_175_018

description:
rz_MO_12_0
nup107_mo_tpm_ribozero.tsv.gz

value: Whole Embryo

value: 12 hpf

value: MO


title: old_surgery_48h_hemisphere_6

description:
Library name: FACS89_HM
FACS89_HM

source_name: brain

value: WT


title: dsDis3_R3

description: ATAC from tagmented DNA extracted from GFP-kd S2 cells. Control condition


title: dsDis3_R2


title: rtgill.dmso.6.D10

description:
Library name: rtgill.dmso.6.D10
Cell lysate
dmso.counts.txt
dmso.9_DMSO_col10_S1.D10.expression.values

source_name: RTgill-W1 ctrl rep 35


title: Sample_MO10_5_152_041

description:
rz_MO_10_5
nup107_mo_tpm_ribozero.tsv.gz

source_name: Whole Embryo

value: RiboZero RNA


title: dsDis3_R1


title: Sample_MO11_5_104_089

description:
rz_MO_11_5
nup107_mo_tpm_ribozero.tsv.gz


title: old_ctrl_48h_hemisphere_6

description:
Library name: FACS88_HM
FACS88_HM


title: rtgill.dmso.6.E10

description:
Library name: rtgill.dmso.6.E10
Cell lysate
dmso.counts.txt
dmso.9_DMSO_col10_S1.E10.expression.values

source_name: RTgill-W1 ctrl rep 36


title: young_surgery_48h_hippocampus_4

description:
Library name: FACS87_HP
FACS87_HP

value: 3-5 months


title: Sample_MO10_176_017

description:
rz_MO_10_0
nup107_mo_tpm_polyA.tsv.gz

value: 10 hpf


title: rtgill.dmso.6.B10

description:
Library name: rtgill.dmso.6.B10
Cell lysate
dmso.counts.txt
dmso.9_DMSO_col10_S1.B10.expression.values

source_name: RTgill-W1 ctrl rep 33


title: dsRrp6_R3

description: ATAC from tagmented DNA extracted from Rrp6-kd S2 cells


title: Sample_MO11_128_065

description:
rz_MO_11_0
nup107_mo_tpm_ribozero.tsv.gz

value: 11 hpf


title: dsRrp6_R2


title: old_ctrl_48h_hippocampus_5

description:
Library name: FACS86_HP
FACS86_HP

value: brain


title: young_surgery_48h_hemisphere_4

description:
Library name: FACS87_HM
FACS87_HM

value: hemisphere

value: microglia


title: old_ctrl_48h_hemisphere_5

description:
Library name: FACS86_HM
FACS86_HM

value: 20-22 months


title: rtgill.dmso.6.C10

description:
Library name: rtgill.dmso.6.C10
Cell lysate
dmso.counts.txt
dmso.9_DMSO_col10_S1.C10.expression.values

source_name: RTgill-W1 ctrl rep 34

value: ctrl

value: Rainbow trout gill


title: Sample_UIC9_5_309_268

description:
PA_UC_9_5
nup107_mo_tpm_polyA.tsv.gz

value: 9.5 hpf

value: UC

value: PolyA+ RNA


title: dsRrp6_R1


title: Sample_MO2_180_013

description:
rz_MO_2_0
nup107_mo_tpm_ribozero.tsv.gz

value: Whole Embryo

value: 2 hpf


title: rtgill.dmso.5.H11

description:
Library name: rtgill.dmso.5.H11
Cell lysate
dmso.counts.txt
dmso.4_DMSO_col11_S1.H11.expression.values

source_name: RTgill-W1 ctrl rep 31


title: young_surgery_48h_hippocampus_3

description:
Library name: FACS85_HP
FACS85_HP

value: hippocampus

value: surgery

value: 48 hours


title: dsGFP_R3

description: ATAC from tagmented DNA extracted from GFP-Control S2 cells

value: dsGFP


title: rtgill.dmso.5.G11

description:
Library name: rtgill.dmso.5.G11
Cell lysate
dmso.counts.txt
dmso.4_DMSO_col11_S1.G11.expression.values

source_name: RTgill-W1 ctrl rep 30


title: Sample_UIC8_381_196

description:
PA_UC_8_0
nup107_mo_tpm_polyA.tsv.gz

value: 8 hpf


title: dsGFP_R2


title: young_surgery_48h_hemisphere_3

description:
Library name: FACS85_HM
FACS85_HM

value: WT

value: 3-5 months


title: young_ctrl_48h_hippocampus_3

description:
Library name: FACS84_HP
FACS84_HP

value: brain

value: control


title: rtgill.dmso.5.F11

description:
Library name: rtgill.dmso.5.F11
Cell lysate
dmso.counts.txt
dmso.4_DMSO_col11_S1.F11.expression.values

source_name: RTgill-W1 ctrl rep 29


title: young_ctrl_48h_hemisphere_3

description:
Library name: FACS84_HM
FACS84_HM

value: hemisphere

value: microglia


title: rtgill.dmso.5.E11

description:
Library name: rtgill.dmso.5.E11
Cell lysate
dmso.counts.txt
dmso.4_DMSO_col11_S1.E11.expression.values

source_name: RTgill-W1 ctrl rep 28

value: ctrl

value: Rainbow trout gill


title: Sample_UIC7_5_310_267

description:
PA_UC_7_5
nup107_mo_tpm_polyA.tsv.gz

value: 7.5 hpf

value: UC


title: old_surgery_48h_hippocampus_5

description:
Library name: FACS83_HP
FACS83_HP

value: 20-22 months


title: dsDouble-kd_chromatin_associated_(0-500bp_fraction) S29_C4S

description:
dsDouble-kd_chromatin_associated_(0-500bp_fraction)
chromatin-associated RNA (0-500bp fraction)
RNA extracted from the 0-500bp chromatin fraction in Double-kd S2 cells. Replicate 1. This sample together with S20_C4L, correspond to C4_merged_chromatin_fractions column in each processed data file

data_processing:
Read file QC: Total reads were analysed with FastQC and visually inspected to make sure each sequenced sample met the adequate quality standards.
Adapter clipping, quality trimming and filtering: Adapters were trimmed with cutadapt and trimmomatic
Genome alignment: Raw sequences were aligned to the Ensembl drosophila genome using TopHat
Read count extraction: Read counts per gene were extracted with featureCounts
Filtering by expression and normalization: DESeq2 outlier removal, low count filtering, and normalization.
Assembly: BDGP6 (dm6)
Supplementary files format and content: Tab-delimited text file containing the featureCounts raw read count matrix

extract_protocol:
Total RNA was extracted using Trizol (Ambion) and ethanol precipitated following standard procedures. For chromatin-associated RNA extraction,S2 cells were crosslinked with formaldehyde for 10 min at RT and the cross-linking was stopped by addition of 1 M glycine for 10 additional min. RNA was isolated with Trizol (Ambion) The cells were then collected and resuspended in Buffer 1 (50 mM Hepes pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0,25% Triton X100 and cOmplete protease inhibitors) and incubated for 10’ at 4 °C, followed by centrifugation at 4 °C and 500g. The pellet was resuspended in cold Buffer 2 (200 mM Nacl, 1 mM EDTA, 0,5 mM EGTA, 10 mM Tris pH 8 and cOmplete protease inhibitors) and centrifuged again. Finally, chromatin was resuspended in Buffer 3 (1 mM EDTA, 0,5 mM EGTA and 10 mM Tris pH 8 and cOmplete protease inhibitors). Chromatin was fragmented using a Bioruptor sonicator (Diagenode) with 25 high intensity sonication 30’’ on/off pulses. RNA was isolated with Trizol (Ambion)
RNA-seq experiments consisted of biological triplicates, but the total RNA samples were pooled and sequenced together. Before RNA-sequencing, and in order to obtain adequate sequencing coverage for RNAs over such a broad size range, the RNA preparations were fractionated using AMPure XP paramagnetic beads (Agilent technologies) at a concentration of 0,6X to select RNAs larger than 500 nt and 1,6X to select caRNAs smaller than 500 nt. The 0-500 nt caRNAs were directly submitted to ribosomal depletion and library preparation, whereas caRNAs >500 nt were first fragmented by sonication. The NEBNext rRNA Depletion kit was used for ribosomal RNA depletion. Single-end strand-specific libraries were prepared using NEBNext Ultra RNA library Prep Kit for Illumina (NEB) according to the manufacturer's instructions. Samples were sequenced in a Illumina NextSeq 500 sequencer aiming for a depth of 15 million reads in average per sample with a length of 80 nucleotides per read

value: dsDouble knockdown (Rrp6+Dis3)


title: Sample_UIC6_5_358_219

description:
PA_UC_6_5
nup107_mo_tpm_polyA.tsv.gz

value: Whole Embryo

value: 6.5 hpf

value: PolyA+ RNA


title: dsRrp6_chromatin_associated_(0-500bp_fraction) S26_C2S

description:
dsRrp6_chromatin_associated_(0-500bp_fraction)
chromatin-associated RNA (0-500bp fraction)
RNA extracted from the 0-500bp chromatin fraction in Rrp6-kd S2 cells. Replicate 3. This sample together with S18_C2L, correspond to C2_merged_chromatin_fractions column in each processed data file

value: dsRrp6 knockdown


title: dsDis3_chromatin_associated_(0-500bp_fraction) S28_C3S

description:
dsDis3_chromatin_associated_(0-500bp_fraction)
chromatin-associated RNA (0-500bp fraction)
RNA extracted from the 0-500bp chromatin fraction in Dis3-kd S2 cells. Replicate 3. This sample together with S19_C3L, correspond to C3_merged_chromatin_fractions column in each processed data file

value: dsDis3 knockdown


title: rtgill.dmso.6.A10

description:
Library name: rtgill.dmso.6.A10
Cell lysate
dmso.counts.txt
dmso.9_DMSO_col10_S1.A10.expression.values

source_name: RTgill-W1 ctrl rep 32


title: old_surgery_48h_hemisphere_5

description:
Library name: FACS83_HM
FACS83_HM

value: WT

value: surgery

value: 48 hours


title: Sample_UIC9_333_244

description:
PA_UC_9_0
nup107_mo_tpm_polyA.tsv.gz

value: 9 hpf


title: rtgill.dmso.5.B11

description:
Library name: rtgill.dmso.5.B11
Cell lysate
dmso.counts.txt
dmso.4_DMSO_col11_S1.B11.expression.values

source_name: RTgill-W1 ctrl rep 25


title: Sample_UIC6_382_195

description:
PA_UC_6_0
nup107_mo_tpm_polyA.tsv.gz

value: 6 hpf


title: Sample_UIC5_5_311_266

description:
PA_UC_5_5
nup107_mo_tpm_polyA.tsv.gz

value: 5.5 hpf


title: young_ctrl_48h_hippocampus_2

description:
Library name: FACS82_HP
FACS82_HP

value: brain

value: hippocampus

value: microglia

value: 3-5 months

value: control


title: dsDouble-kd_chromatin_associated_(0-500bp_fraction) S24_B4S

description:
dsDouble-kd_chromatin_associated_(0-500bp_fraction)
chromatin-associated RNA (0-500bp fraction)
RNA extracted from the 0-500bp chromatin fraction in Double-kd S2 cells. Replicate 2. This sample together with S16_B4L, correspond to B4_merged_chromatin_fractions column in each processed data file

source_name: S2 cell line

value: dsDouble knockdown (Rrp6+Dis3)


title: dsGFP_chromatin_associated_(0-500bp_fraction) S25_C1S

description:
dsGFP_chromatin_associated_(0-500bp_fraction)
chromatin-associated RNA (0-500bp fraction)
RNA extracted from the 0-500bp chromatin fraction in GFP-Control S2 cells. Replicate 3. This sample together with S17_C1L, correspond to C1_merged_chromatin_fractions column in each processed data file

value: dsGFP knockdown (control)


title: Sample_UIC5_335_242

description:
PA_UC_5_0
nup107_mo_tpm_polyA.tsv.gz

value: Whole Embryo

value: 5 hpf

value: UC


title: rtgill.dmso.5.A11

description:
Library name: rtgill.dmso.5.A11
Cell lysate
dmso.counts.txt
dmso.4_DMSO_col11_S1.A11.expression.values

source_name: RTgill-W1 ctrl rep 24

value: ctrl

value: Rainbow trout gill


title: young_surgery_48h_hippocampus_2

description:
Library name: FACS81_HP
FACS81_HP

value: WT

value: surgery


title: Sample_UIC8_5_357_220

description:
PA_UC_8_5
nup107_mo_tpm_polyA.tsv.gz

value: 8.5 hpf

value: PolyA+ RNA


title: Sample_UIC7_334_243

description:
PA_UC_7_0
nup107_mo_tpm_polyA.tsv.gz

value: 7 hpf


title: dsGFP_R1

value: dsGFP