title: SARS-CoV2_NSP14-mut passage 3 in VERO-AT cells

city: San Antonio

first: Yan

last: Xiang

state: TX

address: 7703 FLOYD CURL DR

department: Microbiology, Immunology and Molecular Genetics

institute: UT Health San Antonio

description: Library name: P3_NSP14-mut-VERO-AT

data_processing:
Sequencing reads were mapped to the reference genome using minimap2
Per-position read depth was calculated using samtools
Variants were called from samtools mpileup by quantifying reference and alternate base counts at each position, followed by filtering based on sequencing quality, minimum coverage thresholds, and a minimum alternate allele frequency of 1.5%.
Assembly: recombinant SARS-CoV-2 genome included in the supplemental file
Supplementary files format and content: reference gemone in fasta format
Supplementary files format and content: reference GTF file
Supplementary files format and content: excel file containg read depth of every samples
Supplementary files format and content: excel file containg error rate per position of every samples
Supplementary files format and content: excel file containg SNP frequency of every samples

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Vero cells expressing ACE2 and Tmprss2

growth_protocol: Five micrograms of SARS-CoV-2 BAC DNA was transfected into Vero-NP cells in 6-well plates using Lipofectamine 3000 transfection reagent (Invitrogen). After 4 hours, the transfection medium was replaced with DMEM containing 5% FBS. Cells were incubated at 37 °C with 5% CO₂ for 3–21 days, after which the tissue culture supernatant was collected and designated passage 0 (P0). Subsequent passages were generated by infecting fresh Vero-NP or Vero-AT cells with 500 µL of virus from the previous passage.

extract_protocol:
Culture supernatants from serial passages of recombinant SARS-CoV-2 in Vero-NP or Vero-AT cells were processed for RNA extraction using TRIzol LS reagent (Invitrogen) according to the manufacturer’s instructions.
The extracted RNA was converted into sequencing libraries and subjected to paired-end deep sequencing (100 or 150 bp reads) with NovaSeq 6000 system

value: Vero cells expressing ACE2 and Tmprss2

tag: timepoint

value: passage 3


title: AS041_L1f

status: Public on Jun 15 2026

type: RNA

city: Lørenskog

first: Hilde

middle: Loge

last: Nilsen

address: Sykehusveien 25

country: Norway

institute: Akershus University Hospital

hyb_protocol: Amplification and labelling efficiency were controlled on the NanoDrop. The cRNA quality was assessed by measuring the RNA absorbance ratio 260nm/280nm. The specific activity of labeled cRNA (pmol Cy3 per ug cRNA) was defined to be 6 or above according to the Agilent recommendations.

scan_protocol: Standard Illumina Protocol

data_processing: Expression signals were normalized with the limma R package. Control probes were removed before processing. Background correction was done with the backgroundCorrect function, using the normexp method and offset 16. Hence the lowest possible normalized expression value is log2(16) = 4. Batch correction was done using the normalizeBetweenArrays function, using the quantile method.

molecule: total RNA

organism: Homo sapiens

source_name: Gut epithelium, P, Rectum

label_protocol: mRNA amplification, labelling, and hybridization were done following the manufacturer’s instructions (Agilent One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling). In short, 50 ng RNA was amplified and labelled with Cy3 using the Low Input Quick Amp Labeling Kit, one-color (product number 5190-2331), and the labelled cRNA was purified using the Qiagen RNeasy Mini Kit.

extract_protocol: Total RNA was isolated using AllPrep kit (Qiagen, Hilden, Germany). The tissue biopsies were homogenized in Buffer RLT using a 5 mm steal bead in the FastPrep-24 Classic Instrument (MP Biomedicals, Irvine, CA, USA) at 6 m/s for 40 sec. The samples were centrifuged and the lysate transferred to new tubes. Further processing was according to the manufacture’s protocol. RNA concentration was measured using the QiaCubeNanoDrop ND-1000 spectrophotometer (Qiagen). The RNA quality, indicated by the RNA integrity number (RIN), was assessed with an Agilent 2100 Bioanalyser, Agilent 2100 Expert software and Agilent RNA 6000 Nano Kit (Agilent Technologies Inc., Santa Clara, CA, USA). RNA samples with RIN number below 7.0 were excluded.

tag: tissue

value: gut epithelium

tag: status

value: Progressor

tag: segment

value: Rectum

tag: inflammation

tag: neoplasia


title: BJ_EV_4

type: SRA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

description:
Library name: Sample 20
Cells were transduced with an empty vector lentivirus (MOI: 3) and cultured for 8 days - replicate 4

library_source: transcriptomic

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed BBDuk from BBTools (v38.76)
Trimmed FASTQ files were aligned to human reference genome hg38 (Ensembl v104) using STAR software (v2.7.0f_0328).
featureCounts in R package Subread (v2.10.5) was used to generate gene counts
Assembly: hg38 (Ensembl v104)
Supplementary files format and content: text files containing counts

source_name: BJ

extract_protocol:
Total RNA was extracted using TriPure™ Isolation Reagent (Sigma-Aldrich), following the manufacturer's instructions with phenol-chloroform extraction.
Libraries were constructed using theTruSeq Stranded Total RNA Library prep kit according to manufacturer’s protocol (Illumina).

tag: cell line

value: BJ

tag: cell type

value: foreskin fibroblasts

tag: genotype

value: WT

tag: treatment

value: Empty vector (MOI:3)


title: T.aestivum, PolyA RNA-seq, ChineseSpring, mock, root, replicate2

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

country: China

institute: Fudan University

description: Library name: PolyA_RNA-seq_ChineseSpring_mock_root_rep2

data_processing:
PolyA RNA-seq data were cleaned using fastp (version 0.20.1).
SortMeRNA (version 2.1b) was used to remove reads originating from chloroplasts, mitochondria and rRNA.
The remaining clean reads were mapped to the corresponding genome sequences using hisat2 (v2.1.0)
Reads with a mapping quality score < 20 or mapping to multiple positions were eliminated using SAMtools (v1.16.1).
StringTie (v2.1.7) were used for transcript assembly and gene abundance estimation.
Assembly: Triticum urartu (AA, IGDB version 1.0), Aegilops tauschii (DD, Aet_v4.0), Triticum aestivum (AABBDD, IWGSC version 1.0), Hordeum vulgare (HH, IBSC_v2), Secale cereale (Weining.v1.0) , Zea mays (B73_RefGen_v4) and Oryza sativa (MSU7.0)
Supplementary files format and content: tab-delimited text files include locus, FPKM and TPM for transcripts in each sample

molecule: polyA RNA

organism: Triticum aestivum

source_name: root

growth_protocol: Seedlings (above-ground) of common wheat (Triticum aestivum cultivars ‘Chinesespring’‘AK58’ and ‘Fielder’), barley (Hordeum vulgare cultivar ‘Morex’), rye (Secale cereale cultivar ‘Weining’), maize (Zea mays cultivar ‘B73’) and rice (Oryza sativa cultivars ‘ZH11’ and ‘Jap’) were harvested after 9-day growth. The roots, leaf and embryos of three wheat species (Triticum aestivum cultivar ‘Chinese Spring’, Triticum urartu cultivar ‘G1812’ and Aegilops tauschii cultivar ‘AL8-78’) were collected as follows: roots in the Hoagland solution were harvested after 9-day growth; the fresh immature embryos were isolated 14 days post anthesis; leaf were were harvested after 9-day growth.

extract_protocol:
Nuclei were isolated from 1 mL tissue powder solubilized in 20 mL ice-cold Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextron T40, 20 mM HEPES, pH7.4, 10 mM MgCl2, 0.75% Triton X-100, 0.5 mM EDTA, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF). The mixture was incubated on ice for 5 min, then filtered through 110 µm nylon mesh and a 40 µm cell strainer. The crude nuclei were spun down at 3,500 g for 5 min at 4°C, followed by washes with 150 µL of resuspension buffer (50% Glycerol, 0.5 mM EDTA, 25 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor) and 300 µL of wash buffer (25 mM Tris-HCl, pH 7.5, 300 mM NaCl, 1 M urea, 0.5 mM EDTA, 1% Tween 20, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor). Again, the obtained nuclei were washed with another 150 µL of resuspension buffer and 150 µL of wash buffer. CB RNA was extracted from washed nuclei using TRIzol reagent and subjected to genomic DNA removal by TURBOTM DNase (Life Technologies). After purification with RNA Clean & ConcentratorTM-5 kit (Zymo Research, R1013), ~1 µg CB RNA was subjected to rRNA depletion by a riboPOOL kit (siTOOLs Biotech, PanPlant-10 nmol) and polyA RNA removal by oligo (dT) beads (NEB, S1419). PolyA RNA was enriched from total RNA by oligo(dT) beads. Purified CB RNA and PolyA RNA were transformed into cDNA libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765) and sequenced on an Illumina NovaSeq platform.
RNA-seq

value: root


title: AS041_IV

source_name: Gut epithelium, P, Sigmoideum

value: Sigmoideum


title: Lung 12

description:
Library name: Sample 30
Lung nuclei pooled from three Doxorubicin-treated mice, 4 days after treatment – replicate 3

library_source: transcriptomic single cell

data_processing:
Pre-processing of sequencing results and generation of count matrices was performed using the Cell Ranger version 9.0.0 (10x Genomics) with prebuilt annotation platform GRCm39-2024-A.
Assembly: GRCm39
Supplementary files format and content: filtered_feature_bc_matrix including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files

organism: Mus musculus

source_name: Lung

extract_protocol:
Before tissue extraction, lungs were perfused by injecting PBS through the right ventricle. The extracted pieces were frozen in liquid nitrogen. For kidney samples, half of a frozen mouse kidney was minced on dry ice and homogenized in 5 ml of ice-cold homogenization buffer until no visible chunks remained. Samples from 3 mice were pooled. A 200 µl aliquot of the pooled homogenate was mixed with 400 µl of cold lysis buffer from the Minute™ Single Nucleus Isolation Kit (Invent Biotechnologies) and processed according to the manufacturer's protocol. Nuclei were filtered, centrifuged, washed, and resuspended in PBS containing 1% BSA and 0.2 U/µl RNase inhibitor. Nuclei concentration was measured with Trypan Blue and adjusted to 700–1200 nuclei/µl. For lung samples, the protocol was similar, but only ~50 mg of frozen lung tissue was used for homogenization.
The single-nucleus libraries were prepared with Single Cell 3' v4 (polyA) chemistry  (10x Genomics).

value: Lung

tag: Sex

value: male

value: Lung cells

tag: strain

value: Doxo

tag: age

value: 3 months old


title: BJ_EV_3

description:
Library name: Sample 19
Cells were transduced with an empty vector lentivirus (MOI: 3) and cultured for 8 days - replicate 3


title: AS069_III

source_name: Gut epithelium, NP, Descendens

value: Non-progressor

value: Descendens


title: BJ_EV_2

description:
Library name: Sample 18
Cells were transduced with an empty vector lentivirus (MOI: 3) and cultured for 8 days - replicate 2


title: AS069_I

source_name: Gut epithelium, NP, Ascendens

value: Ascendens


title: Lung 11

description:
Library name: Sample 29
Lung nuclei pooled from three Doxorubicin-treated mice, 4 days after treatment – replicate 2


title: T.aestivum, PolyA RNA-seq, ChineseSpring, mock, leaf, replicate2

description: Library name: PolyA_RNA-seq_ChineseSpring_mock_leaf_rep2

source_name: leaf

value: leaf


title: T.aestivum, PolyA RNA-seq, ChineseSpring, mock, leaf, replicate1

description: Library name: PolyA_RNA-seq_ChineseSpring_mock_leaf_rep1


title: AS068_V

source_name: Gut epithelium, NP, Rectum

value: gut epithelium


title: T.aestivum, PolyA RNA-seq, ChineseSpring, mock, root, replicate1

description: Library name: PolyA_RNA-seq_ChineseSpring_mock_root_rep1


title: BJ_OSIS_4

description:
Library name: Sample 16
Cells were treated with 0.5 mM H2O2 for 2 hours and cultured for 8 days - replicate 4

value: Oxidative stress-induced senescence (8 days 0.5 mM H2O2)


title: Lung 10

description:
Library name: Sample 28
Lung nuclei pooled from three Doxorubicin-treated mice, 4 days after treatment – replicate 1


title: T.aestivum,  Chromatin_Bound(CB) RNA-seq, ChineseSpring, mock, root, replicate1

description: Library name: CB_RNA-seq_ChineseSpring_mock_root_rep1

library_source: other

data_processing:
CB RNA-seq data were cleaned using fastp (version 0.20.1).
SortMeRNA (version 2.1b) was used to remove reads originating from chloroplasts, mitochondria and rRNA.
The remaining clean reads were mapped to the corresponding genome sequences using hisat2 (v2.1.0)
Reads with a mapping quality score < 20 or mapping to multiple positions were eliminated using SAMtools (v1.16.1).
For each species, all CB RNA samples were subsampled to match the read count of each sample with the lowest number of reads. The subsampled data were then merged in each species for further analysis. Peak calling were conducted using MACS2 as described for ChIP-seq data processing.
Assembly: Triticum urartu (AA, IGDB version 1.0), Aegilops tauschii (DD, Aet_v4.0), Triticum aestivum (AABBDD, IWGSC version 1.0), Hordeum vulgare (HH, IBSC_v2), Secale cereale (Weining.v1.0) , Zea mays (B73_RefGen_v4) and Oryza sativa (MSU7.0)
Supplementary files format and content: bw files

molecule: other

extract_protocol:
Nuclei were isolated from 1 mL tissue powder solubilized in 20 mL ice-cold Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextron T40, 20 mM HEPES, pH7.4, 10 mM MgCl2, 0.75% Triton X-100, 0.5 mM EDTA, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF). The mixture was incubated on ice for 5 min, then filtered through 110 µm nylon mesh and a 40 µm cell strainer. The crude nuclei were spun down at 3,500 g for 5 min at 4°C, followed by washes with 150 µL of resuspension buffer (50% Glycerol, 0.5 mM EDTA, 25 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor) and 300 µL of wash buffer (25 mM Tris-HCl, pH 7.5, 300 mM NaCl, 1 M urea, 0.5 mM EDTA, 1% Tween 20, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor). Again, the obtained nuclei were washed with another 150 µL of resuspension buffer and 150 µL of wash buffer. CB RNA was extracted from washed nuclei using TRIzol reagent and subjected to genomic DNA removal by TURBOTM DNase (Life Technologies). After purification with RNA Clean & ConcentratorTM-5 kit (Zymo Research, R1013), ~1 µg CB RNA was subjected to rRNA depletion by a riboPOOL kit (siTOOLs Biotech, PanPlant-10 nmol) and polyA RNA removal by oligo (dT) beads (NEB, S1419). PolyA RNA was enriched from total RNA by oligo(dT) beads. Purified CB RNA and PolyA RNA were transformed into cDNA libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765) and sequenced on an Illumina NovaSeq platform.
Chromatin-bound(CB) RNA-seq


title: AS068_I


title: Lung 8

description:
Library name: Sample 26
Lung nuclei pooled from three Doxorubicin-treated mice, 2 days after treatment – replicate 2


title: AS067_V

value: Rectum


title: T.aestivum,  Chromatin_Bound(CB) RNA-seq, ChineseSpring, mock, leaf, replicate2

description: Library name: CB_RNA-seq_ChineseSpring_mock_leaf_rep2


title: BJ_OSIS_2

description:
Library name: Sample 14
Cells were treated with 0.5 mM H2O2 for 2 hours and cultured for 8 days - replicate 2

value: BJ

value: foreskin fibroblasts


title: BJ_OSIS_3

description:
Library name: Sample 15
Cells were treated with 0.5 mM H2O2 for 2 hours and cultured for 8 days - replicate 3

value: WT


title: Lung 7

description:
Library name: Sample 25
Lung nuclei pooled from three Doxorubicin-treated mice, 2 days after treatment – replicate 1


title: BJ_OSIS_1

description:
Library name: Sample 13
Cells were treated with 0.5 mM H2O2 for 2 hours and cultured for 8 days - replicate 1


title: AS067_III


title: T.aestivum,  Chromatin_Bound(CB) RNA-seq, ChineseSpring, mock, leaf, replicate1

description: Library name: CB_RNA-seq_ChineseSpring_mock_leaf_rep1


title: LeprCre_aged-injury

status: Public on Jun 16 2026

city: Nagasaki

first: Yuki

last: Matsushita

state: Nagasaki

address: Sakamoto 1-7-1

country: Japan

institute: Nagasaki University

description:
Library name: geo_submission_scRNAseq_AgedAb1_2
aged-injury stroma at 18 months (1 week after surgery)

data_processing:
The sequencing data was first pre-processed using the BD software Seven Bridges.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of EGFP and tdTomato-WPRE to the mouse genome (GRCm39).
Further downstream analysis steps were performed using the Seurat R package (v.5.1).
We filtered out cells with less than 2,000 genes per cell and more than 20% mitochondrial read content.
The downstream analysis steps include normalization (LogNormalize), identification of highly variable genes across the single cells (vst method), scaling with default settings, dimensionality reduction (PCA and UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Assembly: GRCm39
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz

source_name: Femur bone marrow

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. tdTomato+ cells were FACS-isolated. ~30,000 cells per each group were loaded onto the BD Rhapsody HT Xpress (BD Biosciences).
BD Rhapsody HT Xpress (BD Biosciences)

value: Femur bone marrow

value: Bone marrow stromal cells

value: Lepr-cre; R26R-tdTomato

value: 1x bone marrow ablation surgery


title: Lung 6

description:
Library name: Sample 24
Lung nuclei pooled from three Doxorubicin-treated mice, 1 day after treatment – replicate 3

value: Lung

value: male

value: Lung cells


title: BJ_IRIS_4

description:
Library name: Sample 12
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 4

value: Ionizing radiation-induced senescence (8 days 15 Gy)


title: AS067_I

value: Non-progressor


title: T.aestivum,  Chromatin_Bound(CB) RNA-seq, ChineseSpring, embryo, replicate2

description: Library name: CB_RNA-seq_ChineseSpring_embryo_rep2

source_name: embryo

value: embryo


title: Lung 5

description:
Library name: Sample 23
Lung nuclei pooled from three Doxorubicin-treated mice, 1 day after treatment – replicate 2

value: Doxo

value: 3 months old


title: AS096_V

value: gut epithelium

value: Chronic


title: BJ_IRIS_3

description:
Library name: Sample 11
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 3

value: BJ


title: Lung 4

description:
Library name: Sample 22
Lung nuclei pooled from three Doxorubicin-treated mice, 1 day after treatment – replicate 1


title: BJ_IRIS_2

description:
Library name: Sample 10
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 2

value: foreskin fibroblasts


title: AS096_III

value: Descendens


title: T.aestivum, ChIP-seq, H3K9ac, Chinese Spring, root

description: Library name: CS_Root_H3K9ac_rep1

library_source: genomic

data_processing:
The sequencing reads were trimmed with fastp (0.22.0).
The clean reads were aligned with bwa program (version 0.7.17-r1188).
Peaks were called using MACS (v2.1.0.20150731).
Assembly: Aegilops tauschii (DD, Aet_v4.0), Secale cereale (Weining.v1.0)
Supplementary files format and content: peak files

molecule: genomic DNA

source_name: panicle

growth_protocol: Seeds were surface-sterilized via a 10-min incubation in 30% H2O2 and then thoroughly washed five times with distilled water. The seeds were germinated in water for 3 days at 22 °C.The germinated seeds with residual endosperm were transferred to soil  and grown under 16 h light/ 8 h dark condition at 22 °C in greenhouse.

extract_protocol:
The 9-day-old seedlings (above-ground parts) were harvested and directly vacuum-infiltrated with a formaldehyde cross-linking solution for ChIP-seq. More than 10 ng of ChIP DNA extracted from each sample was used to prepare the sequencing samples.
ChIP-seq

value: panicle

tag: chip antibody

value: H3 acetyl-Lys 9 (Upstate)


title: Lung 3

description:
Library name: Sample 21
Lung nuclei pooled from three untreated mice – replicate 3

value: untreated


title: BJ_IRIS_1

description:
Library name: Sample 9
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 1

value: WT


title: AS096_I

value: Ascendens


title: T.aestivum, ChIP-seq, H3K4me3, Chinese Spring, root

description: Library name: CS_Root_H3K4me3_rep1

value: H3 trimethyl-Lys 4 (Abcam)


title: Lung 2

description:
Library name: Sample 20
Lung nuclei pooled from three untreated mice – replicate 2

value: Lung

value: male

value: Lung cells


title: AS095_V

value: Non-progressor

value: Rectum


title: T.aestivum, ChIP-seq, H3K27me3, Chinese Spring, root

description: Library name: CS_Root_H3K27me3_rep1

value: H3 trimethyl-Lys 27 (ABclonal, A2363)


title: BJ_ETIS_4

description:
Library name: Sample 8
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 4

value: Etoposide-induced senescence (8 days 25 µM)


title: Lung 1

description:
Library name: Sample 19
Lung nuclei pooled from three untreated mice – replicate 1

value: 3 months old


title: BJ_ETIS_3

description:
Library name: Sample 7
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 3

value: BJ


title: AS095_IV

source_name: Gut epithelium, NP, Sigmoideum

value: gut epithelium

value: Sigmoideum


title: T.aestivum,lncRNA-seq, ChineseSpring, embryo, replicate1

description: Library name: lncRNA-seq_ChineseSpring_embryo_rep1

data_processing:
lncRNA-seq data were cleaned using fastp (version 0.20.1).
SortMeRNA (version 2.1b) was used to remove reads originating from chloroplasts, mitochondria and rRNA.
The remaining clean reads were mapped to the corresponding genome sequences using hisat2 (v2.1.0)
Reads with a mapping quality score < 20 or mapping to multiple positions were eliminated using SAMtools (v1.16.1).
StringTie (v2.1.7) were used for transcript assembly and gene abundance estimation.
Assembly: Triticum aestivum (AABBDD, IWGSC version 1.0)
Supplementary files format and content: tab-delimited text files include reads FPKM and TPM for each Sample

growth_protocol: Seedlings (above-ground) of common wheat (Triticum aestivum cultivars ‘ChineseSpring’‘AK58’ and ‘Fielder’), barley (Hordeum vulgare cultivar ‘Morex’), rye (Secale cereale cultivar ‘Weining’), maize (Zea mays cultivar ‘B73’) and rice (Oryza sativa cultivars ‘ZH11’ and ‘Jap’) were harvested after 9-day growth. The roots, leaf and embryos of three wheat species (Triticum aestivum cultivar ‘Chinese Spring’, Triticum urartu cultivar ‘G1812’ and Aegilops tauschii cultivar ‘AL8-78’) were collected as follows: roots in the Hoagland solution were harvested after 9-day growth; the fresh immature embryos were isolated 14 days post anthesis; leaf were were harvested after 9-day growth.

extract_protocol:
RNA was extracted from Chinese Spring immature embryo (powder 10-16 days), using standard protocols. 2μg total RNA (rRNA depleted) were used to prepare lncRNA-seq.
lncRNA-seq

value: embryo


title: Kidney 18

description:
Library name: Sample 18
Kidney nuclei pooled from three Doxorubicin-treated mice, 12 days after treatment – replicate 3

source_name: Kidney

value: Kidney

value: Kidney cells

value: Doxo


title: AS095_I

value: Ascendens

value: Chronic active


title: BJ_ETIS_2

description:
Library name: Sample 6
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 2

value: foreskin fibroblasts

value: WT


title: Z.mays, PolyA RNA-seq, B73, replicate2

description: Library name: PolyA_RNA-seq_maize_B73_rep2

organism: Zea mays

source_name: 9-day-old seedling

value: 9-day-old seedling


title: Kidney 17

description:
Library name: Sample 17
Kidney nuclei pooled from three Doxorubicin-treated mice, 12 days after treatment – replicate 2

value: male


title: BJ_ETIS_1

description:
Library name: Sample 5
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 1


title: AS086_V

value: Non-progressor

value: Rectum


title: Z.mays, PolyA RNA-seq, B73, replicate1

description: Library name: PolyA_RNA-seq_maize_B73_rep1


title: Kidney 16

description:
Library name: Sample 16
Kidney nuclei pooled from three Doxorubicin-treated mice, 12 days after treatment – replicate 1


title: AS086_III

value: Descendens


title: Z.mays, Chromatin_Bound(CB) RNA-seq, B73, replicate2

description: Library name: CB_RNA-seq_maize_B73_rep2


title: BJ_P_4

description:
Library name: Sample 4
Cells were cultured for 8 days in DMSO-containing media - replicate 4

value: Control proliferating cells


title: Kidney 15

description:
Library name: Sample 15
Kidney nuclei pooled from three Doxorubicin-treated mice, 6 days after treatment – replicate 3

value: 3 months old


title: BJ_P_3

description:
Library name: Sample 3
Cells were cultured for 8 days in DMSO-containing media - replicate 3

value: BJ


title: AS086_I

value: gut epithelium


title: shRen_Tead1_1

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute on Aging

description: Library name: Sample 2

data_processing:
Adapter and quality trimming were performed using Cutadapt. Reads were aligned to the mm10 genome and a repeat-masked E. coli genome (used as spike-in) using Bowtie2. Reads with inserts <120 bp mapped to mm10 were extracted (deepTools), and a scaling factor based on the E. coli spike-in was used to generate normalized bigWig files. Peak calling was performed using Genrich using the following parameters: q 1e-4  -a 700. For cumulative distribution frequency (CDF) analysis, TEAD1 signals at categorized peaks (based on RNA-Seq regulation, downregulated, upregulated or not-regulated) were associated with the nearest TSS using BEDtools, and plotted with ggecdf (ggpubr).
Assembly: mm10
Supplementary files format and content: bigWig files for each sample
Library strategy: CUT&Run

extract_protocol:
Tumor-bearing livers were minced and digested in 15 mL of 1× PBS containing 7.5 mg Pronase, 7.5 mg Collagenase P, and 1.5 mg DNase I using a C Tube (Miltenyi Biotec) and the gentleMACS Octo Dissociator (Miltenyi) for 45 minutes at 100 rpm and 37 °C. Following digestion, the cell suspension was filtered through a 100 µm cell strainer and washed with an appropriate volume of Advanced DMEM/F12 (AdDMEM/F12) medium. Red blood cell lysis was performed using the Red Blood Cell Lysis Solution (Miltenyi, #130-094-183), followed by debris removal (Miltenyi, #130-109-398) and dead cell removal (Miltenyi, #130-090-101) according to the manufacturer’s protocols. Cells were then incubated with Fc receptor blocking reagent (Miltenyi) for 10 minutes on ice. Tumor cells were labeled with anti-EpCAM-APC antibody (eBioscience, #17-5791-82; 1:100) for 30 minutes on ice. After washing, cells were incubated with anti-APC microbeads (Miltenyi) for an additional 30 minutes. Labeled cells were then loaded onto LS columns (Miltenyi) and processed according to the manufacturer’s instructions. Positively labeled EpCAM⁺ cells were eluted and further processed for downstream applications.
Following EpCAM enrichment, tumor cells were counted and resuspended at a concentration of 2 × 106 cells in wash buffer (20 mM HEPES, pH 7.5; 150 mM NaCl; 0.5 mM spermidine; protease inhibitor cocktail). For each CUT&RUN reaction, 2 × 105 cells were used. Cells were incubated with 10 µL of activated Concanavalin A-coated magnetic beads (Polysciences) for 10 minutes at room temperature on a hula mixer with constant agitation. Following bead binding, samples were placed on a magnetic stand to remove the supernatant. Bead-bound cells were resuspended in 100 µL of antibody buffer (20 mM HEPES, pH 7.5; 150 mM NaCl; 0.5 mM spermidine; 0.01% [w/v] digitonin; 2 mM EDTA; protease inhibitor), and primary antibodies were added as follows: anti-YAP1 ( Cell Signaling Technology, #14074), anti-TEAD1 (Cell Signaling Technology, #12292), anti-H3K27Ac (Abcam, ab4729), and anti-H3K4me1 (Cell Signaling Technology, #5326). A species-matched IgG was used as a negative control. Samples were incubated overnight at 4°C on a hula mixer set at a 50° tilt and 1 RPM. The next day, samples were washed twice with digitonin wash buffer (20 mM HEPES, pH 7.5; 150 mM NaCl; 0.5 mM spermidine; 0.01% digitonin; protease inhibitor). Protein A/G-MNase (pAG-MNase; 1 µg/mL) was added in digitonin wash buffer, and samples were incubated for 1 hour at 4°C with gentle agitation. After incubation, cells were washed three times with digitonin wash buffer and twice with low-salt buffer (20 mM HEPES, pH 7.5; 0.5 mM spermidine; 0.01% digitonin). Nuclease activation was performed by transferring the samples to calcium-containing buffer (3.5 mM HEPES, pH 7.5; 10 mM CaCl₂; 0.01% digitonin; protease inhibitor) and incubating on ice for 1 hour with continuous mixing. Cleaved DNA fragments were released by incubation at 37°C for 30 minutes in STOP buffer (170 mM NaCl; 20 mM EGTA; 0.01% digitonin; 50 µg/mL RNase A; 25 µg/mL Glycogen Blue). Supernatants were collected, and DNA was purified by phenol-chloroform extraction. Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645) following the manufacturer’s protocol. Library quality was assessed using the Fragment Analyzer (Agilent Technologies), and equimolar pooling of libraries was performed. Pooled libraries were gel purified, quantified on an Agilent 2100 Bioanalyzer, and sequenced as 75 bp single-end reads on an Illumina NextSeq 500 platform.

value: shRen

tag: cut&run antibody


title: T.aestivum,  Chromatin_Bound(CB) RNA-seq, ChineseSpring, embryo, replicate1

description: Library name: CB_RNA-seq_ChineseSpring_embryo_rep1

value: embryo


title: Z.mays, Chromatin_Bound(CB) RNA-seq, B73, replicate1

description: Library name: CB_RNA-seq_maize_B73_rep1


title: BJ_P_2

description:
Library name: Sample 2
Cells were cultured for 8 days in DMSO-containing media - replicate 2


title: Kidney 14

description:
Library name: Sample 14
Kidney nuclei pooled from three Doxorubicin-treated mice, 6 days after treatment – replicate 2

value: Kidney

value: Kidney cells


title: AS082_V


title: H1299, miR-9-5p overexpression, 4

city: Ioannina

first: Evangelos

last: Kolettas

address: School of Medicine, University of Ioannina, University Campus, 45110 ioannina, Greece

department: School of Medicine

country: Greece

institute: University of Ioannina

description:
Library name: H1299 miR-9-5p 4
H1299_MIR9_12
H1299 normalised counts.xlsx

data_processing:
Quality was assessed with FastQC. To identify differentially expressed genes, sequencing reads were mapped to the human genome using HISAT2 with the reverse strand option. HTseq-count was used in reverse mode for counting reads falling inside genes. Differential gene expression analysis was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: xlsx files containing normalised gene counts for A549 and H1299 samples. Rows correspond to genes and columns correspond to individual samples.

growth_protocol: 4 x 10^6 cells in 200 μl of PBS were subcutaneously inoculated into immunocompromised NSG (NOD-SCID-IL2Rgamma) mice aged 5 weeks. Each animal was inoculated bilaterally, with modified cells (left side for control Twl-PGKgfp-H1 A549 and H1299 and right side for TwI-miR-9-5p A549 and H1299 cells, n = 9 per cell line). Mice were sacrificed after 4 and 6 weeks for H1299 and A549 respectively after cell inoculation. The isolated tumours were weighed and immediately snap-frozen in liquid nitrogen then stored at -80°C for RNA isolation.

extract_protocol:
4 biological samples (tumour xenografts) were selected from A549 and H1299 for RNA-Seq analysis. For total RNA isolation from tumours grown from control and miR-9-5p A549 and H1299 cells, mortar and pestle disruption with liquid nitrogen was used to grind tissue into fine powder. For each sample, 50 mg of tissue was lysed with 700 μl QIAzol lysis reagent. Total RNA was extracted  using the miRNEASY kit (Qiagen).
RNASeq library preparation was carried out with the NEBNext Ultra II directional library prep kit for Illumina.

value: Human lung cancer cell line

value: Cells grown as tumour xenografts in NOD-SCID-IL2Rgamma mice


title: Kidney 13

description:
Library name: Sample 13
Kidney nuclei pooled from three Doxorubicin-treated mice, 6 days after treatment – replicate 1

value: Doxo


title: WT1

city: Suzhou

first: Qiang

last: Shan

address: No. 100, Chongwen Road

institute: Suzhou Institute of Systems Medicine

description: Library name: WT1

data_processing:
CLC Genomics Workbench v 11.0.1
Seguence reads were trimmed for adaptor sequence/low-quality sequence using CLc genomicbenchwork (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 fraction0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: bigwig, narrowpeak( except for input sample)

source_name: lung

extract_protocol:
WT or Tle3–/– cells were sorted on 14 dpi. Three biological replicates for each cell type, and 50,000 cells for each replicate were used to prepare ATACseq libraries as previously described. Briefly, the sorted cell pellets were washed and treated in lysis buffer for 3 min on ice. The extracted nuclei were resuspended in transposition mix containing 2.5 µl Transposase (Illumina) and incubated at 37oC for 30 min. The products were purified with MinElute Reaction Cleanup Kit (Qiagen), and then amplified by PCR for 13 cycles with barcoded Nextera primers (Illumina). DNA fragments in the range of 150-1,000 bp were recovered from 2% E-Gel EX Agarose Gels (Invitrogen/ThermoFisher Scientific).
The libraries were quantified using a KAPA Library Quantification kit and sequenced on Illumina HiSeq 4000 sequencing systems in paired end 150 bp reads at the Admera Health.

value: lung

value: Tissue resident memory cells

value: WT

value: mice intranasal infection with WSN-GP33


title: BJ_P_1

description:
Library name: Sample 1
Cells were cultured for 8 days in DMSO-containing media - replicate 1

value: foreskin fibroblasts


title: AS082_III

value: Non-progressor

value: Descendens


title: scRNA-seq of HNSCC-patient-derived peripheral blood CD8+ T cells; 2A

city: Bethesda

first: Cem

last: Sievers

address: 10 Center Drive

institute: NIH

description: Library name: 2A_GEX

data_processing:
The resulting fastq files were processed using cellranger multi (version 8.1.0).
Supplementary files format and content: Cellranger output files:  sample_id_filtered_feature_bc_matrix.h5, sample_id_clonotypes.csv, sample_id_filtered_contig_annotations.csv, sample_id_vdj_contig_info.pb

source_name: peripheral blood

extract_protocol:
CD8+ peripheral blood T cells were isolated from fresh PBMC using the EasySep Human CD8+ T cell Isolation Kit (Stemcell Technologies) per manufacturer recommendations. 3x105 cells suspended in PRMI-1640-based media supplemented with 10% fetal bovine serum (FBS), 5 mM glutamine and 25 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) were plated in a 12 well tissue culture plate and cultured for 4 days in the presence or absence of Human T-Activator CD3/28 Dynabeads (Thermo Fisher) used per manufacturer recommendations. After culture, cells were harvested, magnetic stimulation beads were removed, and cells were subjected to capture for single cell RNA- and TCR-sequencing.
Cells were mixed with barcoded gelbeads and 5′ GEM Kit v2 reagents (10X Genomics), and single-cell capture was performed. Following reverse transcription, cDNA was amplified, and gene expression libraries were constructed according to the manufacturer’s recommendations. Each fragmented DNA library was loaded into a sequencing lane on a NovaSeq X Plus (Illumina) and was sequenced with pair-end reads of 75 bp.

value: peripheral blood

value: CD8+ T cells

value: mixed

value: treatment-naïve


title: BMMSC_IRIS_3

description:
Library name: Sample 35
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 3

source_name: BMMSC

value: BMMSC

value: Bone marrow mesenchymal stem cells

value: Ionizing radiation-induced senescence (8 days 15 Gy)


title: H1299, miR-9-5p overexpression, 3

description:
Library name: H1299 miR-9-5p 3
H1299_MIR9_11
H1299 normalised counts.xlsx

value: Human lung cancer cell line


title: Kidney 12

description:
Library name: Sample 12
Kidney nuclei pooled from three Doxorubicin-treated mice, 4 days after treatment – replicate 3

value: Kidney

value: male

value: Kidney cells

value: 3 months old


title: LC037_II

value: gut epithelium

value: Ascendens


title: sgRNA replicate 2

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 W 10th Street, HS5000

department: Center for Computational Biology and Bioinformatics

institute: Indiana School of Medicine

library_source: genomic single cell

data_processing:
The cellranger multi algorithm of Cell Ranger 7.0 (http://support.10xgenomics.com/) was used to process the sequence data
Assembly: hg38
Supplementary files format and content: Chrm_381_liu_rep12Merged_replalcgenes.rds: R data file with Seurat object containing single nucleus RNA sequencing counts in cells with single sgRNA feature labels

extract_protocol:
10X Genomics Chromium X
The libraries were constructed following the 10X Genomics protocol for Chromium NEXT GEM Single Cell 5’ HT Reagent Kits (Dual Index) with Feature Barcode technology for CRISPR Screening

value: neuroblastoma


title: TREND,SLC43A2sg,1

first: Honglin

last: Tang

address: 866 Yuhangtang Road

institute: Zhejiang  University

description:
Library name: Sample4
Column name in TPM.matrix_All_Samples.txt:SLC_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
TPM were calculated using protocol. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Tumor

extract_protocol:
etinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tumor

value: tumor-infiltrating lymphocytes

value: Lymphocytes

value: SLC43A2 knockdown

value: Tail vein injection


title: H1299, miR-9-5p overexpression, 2

description:
Library name: H1299 miR-9-5p 2
H1299_MIR9_7
H1299 normalised counts.xlsx

value: Cells grown as tumour xenografts in NOD-SCID-IL2Rgamma mice


title: Kidney 11

description:
Library name: Sample 11
Kidney nuclei pooled from three Doxorubicin-treated mice, 4 days after treatment – replicate 2

value: Doxo


title: AS082_I

value: Non-progressor


title: H1299, miR-9-5p overexpression, 1

description:
Library name: H1299 miR-9-5p 1
H1299_MIR9_6
H1299 normalised counts.xlsx


title: AS081_V

value: Rectum


title: sgRNA replicate 1


title: Kidney 10

description:
Library name: Sample 10
Kidney nuclei pooled from three Doxorubicin-treated mice, 4 days after treatment – replicate 1


title: BMMSC_ETIS_3

description:
Library name: Sample 31
Cells were cultured for 8 days in 50 µM etoposide-containing media - replicate 3

value: BMMSC

value: Bone marrow mesenchymal stem cells

value: WT

value: Etoposide-induced senescence (8 days 50 µM)


title: cDNA replicate 2


title: H1299, control, 4

description:
Library name: H1299 control 4
H1299_TWI-HI_12
H1299 normalised counts.xlsx

value: Human lung cancer cell line

value: control (Twl-PGKgfp-H1 )


title: Kidney 9

description:
Library name: Sample 9
Kidney nuclei pooled from three Doxorubicin-treated mice, 2 days after treatment – replicate 3

value: Kidney

value: male

value: Kidney cells

value: 3 months old


title: AS081_III

value: gut epithelium

value: Descendens


title: BMMSC_ETIS_1

description:
Library name: Sample 29
Cells were cultured for 8 days in 50 µM etoposide-containing media - replicate 1


title: PolyA-RNA_FKT_BamMut 38h-heat-shock, bam, rep 1

city: Risskov

first: Thomas

middle: Høgsbro

last: Grønbæk

address: Broloftet 5, 4.tv

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description: Library name: Sample_45

data_processing:
RNA and sRNAseq: RNA reads were demultiplexed and trimmed for standard illumina adapter sequences including 4 random nucleotides from each end.
cutntag: Paired-end illumina reads were adapter-trimmed using Trim Galore for standard illumina adapters.
Assembly: dm6, r6.63
Supplementary files format and content: SLX-19644_totalRNA_RNAseq_GeTMM_TE_sense.xlsx, R17585_TOsK_MZ-piwiaub_dKD_TE_GeTMM_sense.xlsx, R18168_GeTMM_gene.xlsx,  R18168_GeTMM_TE_sense.xlsx, SLX-17461_GeTMM_gene.xlsx. All xlsx file with RNAseq reads mapping to TE consensus sequences in sense orientation or to whole transcriptiome. Mapped to the Drosophila transcriptome using STAR, allowing 2 mismatches and uniquely mapped reads were used for downstream analysis. Gene expression quantification was normalized using Gene length corrected TMM using edgeR (v3.34.0).
Supplementary files format and content: R16775_1kb_tiles_RNA_mappers_sum-PlusMinus.xlsx. xlsx file, Small RNAseq mapping to 1kb tiles. Not accounting for orientation (summed). Reads were mapped to the Drosophila genome using Bowtie allowing 0 MM and only uniquely mapping reads. Read coverage was quantified over non-overlapping 1 kb genomic windows using bedtools and normalized to 10 million uniquely mapping reads.
Supplementary files format and content: CutnTag_avg_GeTMM_TE_consensus_unistrand.xlsx. Xlsx file, cutntag reads mapping to TE consensus sequence unistrand. Mapped to the Drosophila transcriptome using Bowtie, allowing 0 mismatches and uniquely mapped reads were used for downstream analysis. Gene expression quantification was normalized using Gene length corrected TMM using edgeR (v3.34.0).
Supplementary files format and content: CutnTag_bam_Table_for_heatmap_log2CPMadd1_single_TE_insertions.xlsx. Xlsx table of cutntag reads mapping to 50bp windows 500bp +/- to all identified single TE insertions in log2 counts per million (CPM). Reads were mapped to in-house ONT long-read assembled D. melanogaster genome from MTD-GAL4; white-sh fly cross using Bowtie2 with concordant-only alignment. The resulting alignments were coordinate-sorted and duplicate marking was done using samtools. Finally reads were filtered for only paired alignments with MAPQ ≥ 30 and no duplicates. Bigwig tracks (all mappers and unique mappers) were generated per sample using deeptools bamCoverage (bin size 10 bp, CPM normalization). Bigwig tracks were intersected with TE insertion coordinates (CutnTag_single_TE_insertions_table.xlsx) from long read DNA sequencing and Cut&Tag data for info on how these were called).
Supplementary files format and content: CutnTag_single_TE_insertions_table.xlsx. Xlsx file of single TE insertions and genome coordinates. TE annotation in long-read genome assembly was done using EDTA v. 2.2 with Drosophila consensus TE library supplied as the reference. TE annotation with CUT&Tag data was done using ngs_te_mapper2 v. 1.0.2. Briefly, the reads from CUT&Tag experiments were used to search for TE insertions by means of finding reads spanning TE consensus sequence and flanking long-read genome assembly sequence at candidate insertion sites. To call an insertion, we required the detection of reads spanning the TE and the flanking genome at both ends of the TE. Insertions identified this way were then pooled for the same fly line and then we analyzed only TE insertions present – but not necessarily homozygous – across every experimental cross in our CUT&Tag analyses.

organism: Drosophila melanogaster

source_name: bam mutant ovarian cysts

growth_protocol: D. melanogaster strains were crossed and reared for experiments at 25°C and 70% humidity with 12:12 hrs light/dark cycle in vials containing standard medium. Before dissection, the flies were fed extra yeast and kept with 3-5 males to support ovary development. The day before dissection, the flies were transferred to a fresh vial to provide the females ample space for egg-laying, preventing egg accumulation in the ovaries.

extract_protocol:
Bulk ovary RNA and small-RNA: 6-8 Ovary pairs from 3-4 days old females were dissected into ice-cold Phosphate-buffered saline (PBS) for bam mutant flies. Bam mutant and heat-shock bam ovarian cysts: 30 ovarian cysts were collected for each sample to compensate for their significantly smaller size.  RNA isolation for RNAseq and small-RNAseq: Samples were subjected to homogenization in TRIzolTM using handheld elecrtric pestle. After 5 minutes incubation Chloroform was added and samples were shaken vigorously and incubated for 3 minutes at RT, then centrifuged at 12,000g and 4°C for 15 minutes. The aqueous phase was transferred to a clean tube and the RNA was subsequently purified first using isopropanol and pelleting the RNA then 75% ethanol. The RNA was resuspended in Rnase-free water and concentrations were measured by spectrophotometry. The samples were stored at -70°C if not immediately used for RNA or small-RNA sequencing library preparation.  Cut&tag: approximately 150 whole ovaries were dissected into Drosophila Ringers buffer for 512C nurse cell nuclei FACS sorting. the ovaries were digested in 5mg/mL collagenase for 15 minutes at RT with continous shaking and intermittent pipetting. Cell suspension was collected by centrifugation 3min at 500rcf and rinced buffort adding nuclear isolation buffer. We disrupted cells with 10 strokes in a Dounce homogenizer with the B pestle and the homogenate was filtered twice through 100µM Nitex mesh. The filtered homogenate was placed on a sucrose step gradient of 2.2 M, 1.6 M, and 0.8 M sucrose and centrifuged for 20 min at 20,000 x g. After centrifugation the sucrose gradient was removed and the pellet was resuspended in nuclear isolation buffer. Hoechst was added to the homogenate at a concentration of 0.5 mg/ml. Nuclei were stored on ice until FACS. Approximately 400 ovaries from Vasa-GFP, bam-/- ovarian cysts, were dissected into Schneider’s insect medium supplemented with 10% fetal bovine serum. GSC-like cells were collected based GFP positive staining. Vasa-GFP, bam –/– ovaries were dissociated in 0,5% trypsin–0,05% EDTA and 5 mg/mL collagenase for 15 min at room temperature, with continuous shaking and intermittent pipetting. Ovarian cell suspension is then filtered through a 70µM Nitex mesh to remove aggregates or debris. The filter was rinsed with S-FBS and cells were collected by centrifugation 5min at 400g, 4ºC. Cells were stored on ice and GFP-positive germline cells were elected from the suspension via fluorescence-activated cell sorting (FACS).
RNAseq: RNA Sample of 2 µg were DNaseI treated and purified using the RNA clean & ConcentratorTM-5 kit (ZYMO #R1013). mRNA were isolated by polyA-RNA enrichment using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S). For total RNAseq, Ribosomal RNA was removed by hybridisation to standard 50nt DNA oligos covering relevant regions in the rRNA precursor and mitochrondrial genome in ratio 1µg RNA : 4µg oligomix and subsequent digestion using thermostable RNAse H (NEB #M0523S). Libraries were cloned using the NEBNextTM Ultra II directional RNA library prep kit for illumina (NEB # E7760) following the instructions. libraries were amplified by PCR using Q5 high-fidelity DNA polymerase with unique dual barcoded primers. Amplified libraries were purified using homemade SPRI (“Ampure”)-beads. Samples were multiplexed in equal amounts and sequenced by VBCF NGS facility on an illumina NovaSeq X flowcell single- or paried-end or an illumina HiSeq 4000 flowcell paired-end or at the CRUK facility in cambridge on an illumina NovaSeq 6000 flowcell singleRead.  Small-RNA: Argonaute bound small RNAs were isolated using the Trans-kingdom, rapid, affordable Purification of RISCs (TRAPR) isolation technique specified in the punlication: Grentzinger et al. 2020. “A Universal Method for the Rapid Isolation of All Known Classes of Functional Silencing Small RNAs.” Nucleic Acids Research 48 (14): e79. sRNA libraries were generated based on protocol from:  Jayaprakash et al. 2011. “Identification and Remediation of Biases in the Activity of RNA Ligases in Small-RNA Deep Sequencing.” Nucleic Acids Research 39 (21): e141. In brief, 3’ linker ligation was performed by adding uniquely barcoded 3’RNA linkers to the samples. Ligation was performed O/N using T4 RNA ligase 2, truncated K227Q (NEB #M0242). The samples were then multiplexed into sub-multiplexes of individually barcoded samples (biological replicates together), and purified using ZYMO RNA clean and concentrator-5 kit (ZYMO #R1013).  Then the samples were recovered and size selected for 52-63 nt reads (18-29nt RNAs + 3’linker) using PAGE purification. To follow exact size selection on the gel, fluorescently labeled oligos migrating similar to 40 and 60-nucleotide single-stranded RNA was added to samples prior to gel electrophoresis. PAGE purification was performed using ZYMO small-RNATM PAGE Recovery Kit (ZYMO #R1070). 5’ RNA linkers were added to samples, and ligation was performed O/N using T4 RNA ligase (NEB #M0204). The samples were subjected to SPRI purification. The sRNA libraries were then reverse transcribed using Superscript II (InvitrogenTM #18064014) following the manufacturer's instructions using the illumina_RvnTxn primer. Libraries were amplified by PCR using Q5 High-Fidelity DNA Polymerases (NEB #M0491) and unique dual-barcoded primers. Samples were then inspected and purified from a 2% low-melt agarose gel using the Zymoclean gel DNA recovery kit (ZYMO #D4001). Concentrations were measured using QubitTM DNA HS kit (InvitrogenTM Q32851) and sub-multiplexes were multiplexed in equal amounts and sequenced by VBCF NGS facility on a NovaSeqX XP flowcell singleRead.  Cut&tag: Library preparation were conduced on freshly FACS-isolated cells or nuclei in duplicates following the published protocol with minor modifications Kaya-Okur et al. 2019. “CUT&Tag for Efficient Epigenomic Profiling of Small Samples and Single Cells.” Nature Communications 10 (1): 1930. Around 40,000 GSCs sorted-cells (40,000 2C cells) and 500-800 512C sorted-nuclei  (128,000-200,000 2c nuclei) were used for each CUT&Tag reaction. The cells or nuclei were bound to 10µL of concanavalin A-coated beads (Polysciences,  86057-10) by incubation 15min at room temperature . The unbound supernatant was removed and bead-bound cells/nuclei were resuspended in Wash Buffer (WB150 : 20 mM HEPES pH 7.9; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin) containing 2 mM EDTA and 0,1% BSA with the appropriate primary antibody (listed in the Reagent Table). Primary antibody incubation was performed on a rotating platform overnight at 4 °C. Secondary antibodies were then added (1:100 dilution in WB150) and incubate for 1h at room temperature. Protein A–Tn5 transposase (gift from the Joan Barau laboratory), pre-loaded with MEDS adaptors (see Oligonucleotide Table), was added at a 1:200 dilution in WB150 with adapted 0,01% Digitonin (WB300). Following an incubation of 1h at room temperature, cells/nuclei and beads were washed with WB300 and mixed in a tagmentation buffer (10 mM MgCl2 in WB300). The tagmentation was performed 1h at 37ºC and stoped by adding 10µL a Digest solution ( 90mM EDTA, 1,2% SDS, 3mg/mL Proteinase K) and incubate 1h at 55ºC. DNA was extracted using the DNA Clean & Concentrator kit and libraries were amplified by Q5 high-fidelity DNA polymerase with unique dual barcoded primers for 10-15 amplification cycles. Amplified libraries were purified using homemade SPRI (“Ampure”)-beads and DNA quality was assessed using the 5200 Fragment Analyzer system. Pooled  libraries  were  sequenced by the VBCF NGS facility on an Illumina NextSeq 2000 sequencing device.

treatment_protocol: For heat-shock bam experiments: Heat-shock treatment was performed on 3-4 day old females as described in (Samuels et al. 2024). The treatment involved 1 hour at 37°C followed by 2 hours at 34°C. The 'hours after HS' is defined as starting immediately after this 3-hour treatment.

value: bam mutant ovarian cysts

value: Bulk ovarian cysts

tag: batch


title: cDNA replicate 1

value: neuroblastoma


title: H1299, control, 3

description:
Library name: H1299 control 3
H1299_TWI-HI_11
H1299 normalised counts.xlsx

value: Cells grown as tumour xenografts in NOD-SCID-IL2Rgamma mice


title: AS081_I

value: Non-progressor

value: Ascendens


title: Kidney 8

description:
Library name: Sample 8
Kidney nuclei pooled from three Doxorubicin-treated mice, 2 days after treatment – replicate 2

value: Doxo


title: AS027_IV

value: Sigmoideum


title: Blastocyst (mouse), miR-21-5p agomir 50 nM, rep2 (pool of 5 embryos)

city: Wuhan

first: Yuehan

last: Li

address: No. 1095, Jiefang Ave.

institute: Huazhong University of Scicence and Technology

description:
Library name: Blastocyst_miR21_agomir_rep2
RNA-seq of 5 pooled IVF-derived mouse blastocysts; replicate 2; miR-21-5p agomir 50 nM treatment

data_processing:
Adapters and low-quality bases were removed with fastp (v0.18.0); QC by FastQC/MultiQC.
Clean reads were aligned to the mouse reference genome GRCm39 (mm39) using HISAT2 (v2.1.0).
Gene expression quantification was performed using StringTie (v1.3.1) and RSEM to calculate FPKM values.
Differential expression between miR-21-5p agomir and blank control groups was assessed with DESeq2 (v1.36.0) using the raw count matrix; p-values were adjusted by the Benjamini–Hochberg method, and genes with FDR < 0.05 and |log2FC| > 1 were considered differentially expressed.
Assembly: Mus musculus GRCm39 (mm39); annotation Gencode M28.
Supplementary files format and content: "genes_expression.xls" is the  gene-level matrix combining normalized expression, raw counts, and annotations.  id: Ensembl gene ID (mm39 / Gencode M28).  FPKM columns: Control_1_fpkm, Control_2_fpkm, Control_3_fpkm, Control_4_fpkm, miR-21-5p_1_fpkm, miR-21-5p_2_fpkm, miR-21-5p_3_fpkm, miR-21-5p_4_fpkm  Raw count columns: Control_1_count, Control_2_count, Control_3_count, Control_4_count, miR-21-5p_1_count, miR-21-5p_2_count, miR-21-5p_3_count, miR-21-5p_4_count  Annotation columns: Symbol, Description, KEGG_A_class, KEGG_B_class, Pathway, K_ID, GO Component, GO Function, GO Process, TF_family.  Rows correspond to genes; columns correspond to samples listed in the Series.

source_name: embryo, blastocyst

growth_protocol: Female ICR mice (6–8 wk) were superovulated with 5 IU PMSG followed 48 h later by 5 IU hCG. At 16–18 h post-hCG, cumulus–oocyte complexes were collected from the oviductal ampullae. Sperm from 8–10 wk ICR males were capacitated in HTF for 1 h at 37 °C. IVF was performed by co-incubating COCs with capacitated sperm for 6 h. Zygotes were washed and cultured in KSOM micro-drops at 37 °C under 5% CO₂, 5% O₂, 90% N₂ until the blastocyst stage.

extract_protocol:
At the blastocyst stage, pools of 5 embryos were lysed in TRIzol (Invitrogen) and total RNA extracted per manufacturer’s instructions, using glycogen as carrier.
mRNA libraries were prepared with Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit (Yeasen) following the poly(A)-selection workflow: RNA fragmentation, first/second-strand cDNA synthesis, end-repair/A-tailing, adaptor ligation, PCR amplification, and bead-based size selection. Libraries were sequenced PE150 on Illumina NovaSeq X Plus.

treatment_protocol: Embryos in the treatment group were cultured in KSOM containing miR-21-5p agomir (50 nM) from post-fertilization to blastocyst (~75 h). Blank control embryos received vehicle only (no oligo). For RNA-seq, each biological replicate comprised 5 pooled blastocysts; n = 4 replicates per condition.

value: embryo, blastocyst

value: blastocyst

value: wild-type, ICR

value: miR-21-5p agomir 50 nM


title: H1299, control, 1

description:
Library name: H1299 control 1
H1299_TWI-HI_6
H1299 normalised counts.xlsx

value: Human lung cancer cell line

value: control (Twl-PGKgfp-H1 )


title: MG RNA replicate 5

description: MG_RNA_rep5_REF, MG_RNA_rep5_ALT

data_processing:
Reads were demultiplexed using cutadapt (v2.7)
UMIs were appended to each read name with umi_tools (v1.0.0)
Primer sequences were trimmed using cutadapt
Resulting reads were mapped to the MPRA oligo library using bowtie2
Reads containing mismatches were filtered out using samtools (v1.10)
The number of unique reads for each oligo sequence were counted using umi_tools count.
Assembly: hg38
Supplementary files format and content: unique_counts.txt contains tab-delimited unique reads for the REF and ALT oligo of each variant evaluated by MPRA

source_name: SV40-immortalized microglia

growth_protocol:
SH: 1:1 mixture of EMEM (American Type Culture Collection; ATCC) and F12K medium (10025-CV, Thermo Fisher Scientific) with 10% (vol/vol) fetal bovine serum (ATCC) and 1% penicillin and streptomycin
MG: Prigrow III medium with 10% (vol/vol) fetal bovine serum (16000-044, Thermo Fisher Scientific) and 1% penicillin-streptomycin in type I collagen-coated (1:30; Sigma-Aldrich, C3867) six 6-well plates

extract_protocol:
AllPrep DNA/RNA mini kit (Qiagen). Poly-A RNA was isolated using Dynabeads oligo(dT)25 (Thermo Fisher Scientific) and mRNA treated with gDNA wipeout buffer (Qiagen) before preparing sequencing libraries
Poly(A)RNA (500 ng) from each independent transfection was reverse transcribed to cDNA using QuantiTech Reverse Transcription kit (Qiagen) using a reporter-specific first strand primer that contains the R1 Illumina adapter sequence, a 9-12 nt barcode (with staggered starts) and a 10 nt unique molecular index (UMI). The resulting cDNA was then PCR-amplified with a primer containing the R2 Illumina adapter sequence and one of 6 barcodes, one for each independent transfection (HJ7214-HJ7219).
DNA was PCR-amplified with another first strand primer and one of 6 barcodes for replicate

treatment_protocol: Lipofectamine 3000 used for transfection

value: SV40-immortalized microglia

value: microglia


title: MG RNA replicate 6

description: MG_RNA_rep6_REF, MG_RNA_rep6_ALT


title: AS069_V

data_processing: Expression signals were normalized with the limma R package. Control probes were removed before processing. Background correction was done with the backgroundCorrect function, using the normexp method and offset 16. Hence the lowest possible normalized expression value is log2(16) = 4. Batch correction was done using the normalizeBetweenArrays function, using the quantile method.

extract_protocol: Total RNA was isolated using AllPrep kit (Qiagen, Hilden, Germany). The tissue biopsies were homogenized in Buffer RLT using a 5 mm steal bead in the FastPrep-24 Classic Instrument (MP Biomedicals, Irvine, CA, USA) at 6 m/s for 40 sec. The samples were centrifuged and the lysate transferred to new tubes. Further processing was according to the manufacture’s protocol. RNA concentration was measured using the QiaCubeNanoDrop ND-1000 spectrophotometer (Qiagen). The RNA quality, indicated by the RNA integrity number (RIN), was assessed with an Agilent 2100 Bioanalyser, Agilent 2100 Expert software and Agilent RNA 6000 Nano Kit (Agilent Technologies Inc., Santa Clara, CA, USA). RNA samples with RIN number below 7.0 were excluded.

value: gut epithelium

value: Rectum


title: MG RNA replicate 4

description: MG_RNA_rep4_REF, MG_RNA_rep4_ALT


title: Kidney 7

description:
Library name: Sample 7
Kidney nuclei pooled from three Doxorubicin-treated mice, 2 days after treatment – replicate 1

value: Kidney

value: male

value: Kidney cells

value: 3 months old


title: H1299, control, 2

description:
Library name: H1299 control 2
H1299_TWI-HI_7
H1299 normalised counts.xlsx

value: Cells grown as tumour xenografts in NOD-SCID-IL2Rgamma mice


title: AS038_I

value: Non-progressor

value: Ascendens


title: AS044_I


title: A549, miR-9-5p overexpression, 3

description:
Library name: A549 miR-9-5p 3
A549_MIR9_8
A549 normalised counts.xlsx


title: Kidney 6

description:
Library name: Sample 6
Kidney nuclei pooled from three Doxorubicin-treated mice, 1 day after treatment – replicate 3

value: Doxo


title: AS038_III

source_name: Gut epithelium, NP, Descendens

value: Descendens


title: A549, miR-9-5p overexpression, 4

description:
Library name: A549 miR-9-5p 4
A549_MIR9_9
A549 normalised counts.xlsx


title: MG RNA replicate 3

description: MG_RNA_rep3_REF, MG_RNA_rep3_ALT


title: Kidney 4

description:
Library name: Sample 4
Kidney nuclei pooled from three Doxorubicin-treated mice, 1 day after treatment – replicate 1


title: Blastocyst (mouse), miR-21-5p agomir 50 nM, rep1 (pool of 5 embryos)

description:
Library name: Blastocyst_miR21_agomir_rep1
RNA-seq of 5 pooled IVF-derived mouse blastocysts; replicate 1; miR-21-5p agomir 50 nM treatment

value: embryo, blastocyst

value: blastocyst

value: wild-type, ICR


title: Kidney 5

description:
Library name: Sample 5
Kidney nuclei pooled from three Doxorubicin-treated mice, 1 day after treatment – replicate 2


title: AS042_V

source_name: Gut epithelium, P, Rectum

value: Progressor


title: AS036_V


title: AS036_III


title: MG RNA replicate 2

description: MG_RNA_rep2_REF, MG_RNA_rep2_ALT

value: SV40-immortalized microglia


title: Kidney 3

description:
Library name: Sample 3
Kidney nuclei pooled from three untreated mice – replicate 3

value: untreated


title: A549, miR-9-5p overexpression, 1

description:
Library name: A549 miR-9-5p 1
A549_MIR9_2
A549 normalised counts.xlsx

value: Human lung cancer cell line


title: Kidney 2

description:
Library name: Sample 2
Kidney nuclei pooled from three untreated mice – replicate 2


title: AS036_I

source_name: Gut epithelium, NP, Ascendens

value: gut epithelium


title: AS027_V

source_name: Gut epithelium, NP, Rectum

value: Rectum


title: MG DNA replicate 6

description: MG_DNA_rep6_REF, MG_DNA_rep6_ALT

value: microglia


title: Kidney 1

description:
Library name: Sample 1
Kidney nuclei pooled from three untreated mice – replicate 1

value: Kidney

value: male

value: Kidney cells


title: MG DNA replicate 5

description: MG_DNA_rep5_REF, MG_DNA_rep5_ALT


title: A549, control, 3

description:
Library name: A549 control 3
A549_TWI-H1_8
A549 normalised counts.xlsx

value: control (Twl-PGKgfp-H1 )

value: Cells grown as tumour xenografts in NOD-SCID-IL2Rgamma mice


title: A549, control, 4

description:
Library name: A549 control 4
A549_TWI-H1_9
A549 normalised counts.xlsx


title: A.tauschii, PolyA RNA-seq, AL8-78,root, replicate2

description: Library name: PolyA_RNA-seq_dd_AL8-78_root_rep2

organism: Aegilops tauschii

source_name: root

value: root


title: A549, control, 2

description:
Library name: A549 control 2
A549_TWI-H1_4
A549 normalised counts.xlsx


title: A.tauschii, PolyA RNA-seq, AL8-78,root, replicate1

description: Library name: PolyA_RNA-seq_dd_AL8-78_root_rep1


title: MG DNA replicate 4

description: MG_DNA_rep4_REF, MG_DNA_rep4_ALT


title: AS027_III

value: Non-progressor

value: Descendens


title: A549, control, 1

description:
Library name: A549 control 1
A549_TWI-H1_2
A549 normalised counts.xlsx


title: MG DNA replicate 3

description: MG_DNA_rep3_REF, MG_DNA_rep3_ALT


title: A.tauschii, PolyA RNA-seq, AL8-78,leaf, replicate2

description: Library name: PolyA_RNA-seq_dd_AL8-78_leaf_rep2

source_name: leaf

value: leaf


title: AS027_I

value: Ascendens


title: AS050_III

value: Chronic active


title: MG DNA replicate 2

description: MG_DNA_rep2_REF, MG_DNA_rep2_ALT

value: SV40-immortalized microglia


title: Pkd1RC/RC_3

city: Oklahoma City

first: Kurt

last: Zimmerman

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Internal Medicine

institute: University of Oklahoma Health Sciences Center

description:
Library name: 4772
10X genomics

data_processing:
Processed data files were generated using CellRanger7.1.0
Assembly: Mouse mm10
Supplementary files format and content: Tab seperated values and matrix files

extract_protocol:
Kidneys were minced and digested in 1ml of 2.5 mg/ml type II collagenase (Worthington, cat No; LS004176), 7.5 mg/ml B. licheniformis cold activated protease (Creative enzymes, Cat no: NATE-0633), and 125 U/ml DNase (Sigma-Aldrich, Cat no: D5025) in D-PBS for ~45 minutes at 12C as previously described1. After digestion, kidney tissue was passed through individual 70-µm cell-strainers yielding single-cell suspensions. Cells were centrifuged at 300 X g for 5 minutes at 4ºC, resuspended in ACK red blood cell lysis buffer, and incubated at 37ºC for 5 minutes.  After 5 minutes, 10 ml RPMI was added to each tube, cells were spun for 5 minutes at 4C, and cells were resuspended in 0.04% BSA with FC blocking solution (1:200, BioXcell; catalog #: BE0307) for 30 minutes on ice. After blocking, cells were spun and incubated with the following antibodies in 0.04% BSA for 30 minutes: PE rat anti-mouse CD45 (catalog no. 12–0451, 30-F11; eBioscience), and Fixable Aqua Dead Cell Stain (catalog no. L34957; Invitrogen). Stained cells were then washed with 0.04% BSA and resuspended in 0.04% BSA for sorting. We sorted ~25,000 live, CD45+ or CD45- cells into individual BSA coated tubes. Cells were counted and approximately 5,000 cells from each group were combined into a single tube followed by performing bead emulsion and 10X genomics as described below.
10x Chromium single cell libraries were prepared according to the standard protocol outlined in the manual. Briefly, sorted single cell suspension, 10x barcoded gel beads, and oil were loaded into Chromium™ Single Cell Chip G to capture single cells in nanoliter-scale oil droplets by Chromium™ Controller and to generate Gel Bead-In-EMulsions (GEMs). We used “Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3.1” and chip G for these experiments.  Full length cDNA libraries were prepared by incubation of GEMs in a thermocycler machine. GEMs containing cDNAs were broken and all single cell cDNA libraries were pooled together, cleaned using DynaBeads MyOne™ Silane beads (Fisher PN 37002D), and pre-amplified by PCR to generate sufficient mass for sequencing library construction. Sequencing libraries were constructed by following the steps: cDNA fragmentation, end repair & A-tailing, size selection by SPRIselect beads (Beckman Coulter, PN B23318), adaptor ligation, sample index PCR amplification, and a repeat of SPRIselect beads size selection. The final constructed single cell libraries were sequenced by Illumina Nextseq2000 machine with total reads per cell targeted for a minimum of 25,000.

treatment_protocol: Control (Pkd1RC/WT) and cystic (Pkd1RC/RC) kidneys were harvested at one year of age and processed for scRNAseq as described below. scRNAseq experiments were done on at least N=2 mice per group (2 control, 3 cystic; 1M control, 1 F control; 1M cystic, 2F cystic).

value: Male

value: March, 2024


title: A.tauschii, PolyA RNA-seq, AL8-78,leaf, replicate1

description: Library name: PolyA_RNA-seq_dd_AL8-78_leaf_rep1

data_processing:
PolyA RNA-seq data were cleaned using fastp (version 0.20.1).
SortMeRNA (version 2.1b) was used to remove reads originating from chloroplasts, mitochondria and rRNA.
The remaining clean reads were mapped to the corresponding genome sequences using hisat2 (v2.1.0)
Reads with a mapping quality score < 20 or mapping to multiple positions were eliminated using SAMtools (v1.16.1).
StringTie (v2.1.7) were used for transcript assembly and gene abundance estimation.
Assembly: Triticum urartu (AA, IGDB version 1.0), Aegilops tauschii (DD, Aet_v4.0), Triticum aestivum (AABBDD, IWGSC version 1.0), Hordeum vulgare (HH, IBSC_v2), Secale cereale (Weining.v1.0) , Zea mays (B73_RefGen_v4) and Oryza sativa (MSU7.0)
Supplementary files format and content: tab-delimited text files include locus, FPKM and TPM for transcripts in each sample

extract_protocol:
Nuclei were isolated from 1 mL tissue powder solubilized in 20 mL ice-cold Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextron T40, 20 mM HEPES, pH7.4, 10 mM MgCl2, 0.75% Triton X-100, 0.5 mM EDTA, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF). The mixture was incubated on ice for 5 min, then filtered through 110 µm nylon mesh and a 40 µm cell strainer. The crude nuclei were spun down at 3,500 g for 5 min at 4°C, followed by washes with 150 µL of resuspension buffer (50% Glycerol, 0.5 mM EDTA, 25 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor) and 300 µL of wash buffer (25 mM Tris-HCl, pH 7.5, 300 mM NaCl, 1 M urea, 0.5 mM EDTA, 1% Tween 20, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor). Again, the obtained nuclei were washed with another 150 µL of resuspension buffer and 150 µL of wash buffer. CB RNA was extracted from washed nuclei using TRIzol reagent and subjected to genomic DNA removal by TURBOTM DNase (Life Technologies). After purification with RNA Clean & ConcentratorTM-5 kit (Zymo Research, R1013), ~1 µg CB RNA was subjected to rRNA depletion by a riboPOOL kit (siTOOLs Biotech, PanPlant-10 nmol) and polyA RNA removal by oligo (dT) beads (NEB, S1419). PolyA RNA was enriched from total RNA by oligo(dT) beads. Purified CB RNA and PolyA RNA were transformed into cDNA libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765) and sequenced on an Illumina NovaSeq platform.
RNA-seq


title: AS050_I

value: gut epithelium


title: Control Pkd1RC/WT_2

description:
Library name: 4790
10X genomics

value: Female


title: A.tauschii, PolyA RNA-seq, AL8-78,embryo,replicate2

description: Library name: PolyA_RNA-seq_dd_AL8-78_embryo_rep2

source_name: embryo

value: embryo


title: MG DNA replicate 1

description: MG_DNA_rep1_REF, MG_DNA_rep1_ALT

value: microglia


title: SH RNA replicate 6

description: SH_RNA_rep6_REF, SH_RNA_rep6_ALT

value: neuroblastoma


title: Control Pkd1RC/WT_1

description:
Library name: 4793
10X genomics

value: Kidney


title: SH RNA replicate 5

description: SH_RNA_rep5_REF, SH_RNA_rep5_ALT


title: AS048_IV

source_name: Gut epithelium, P, Sigmoideum

value: Progressor

value: Sigmoideum

value: Chronic

value: LGD


title: AS048_V

value: Rectum


title: A.tauschii, Chromatin_Bound(CB) RNA-seq, AL8-78,root, replicate2

description: Library name: CB_RNA-seq_dd_AL8-78_root_rep2

value: root


title: A.tauschii, Chromatin_Bound(CB) RNA-seq, AL8-78,root, replicate1

description: Library name: CB_RNA-seq_dd_AL8-78_root_rep1


title: AS048_I

source_name: Gut epithelium, P, Ascendens

value: Ascendens


title: AS044_V

value: Non-progressor


title: IP3_MLTC-1_6, IgG

city: Chapel Hill

first: Silvia

middle: B

last: Ramos

state: NC

address: 133 Medical Drive

department: Biochemistry and Biophysics

institute: UNC-Chapel Hill

description:
Library name: IP3_MLTC-1_6
IP library contains the RBP-bound sequences immuoprecipitated with the antibody of interest

data_processing:
The eCLIP cDNA adapter contains a sequence of 10 random nucleotides at the 5' end. This random sequence serves as a unique molecular identifier (UMI) [Ref: PMID: 22101854] after sequencing primers are ligated to the 3' end of cDNA molecules. Therefore, eCLIP reads begin with the UMI and, in the first step of analysis, UMIs were pruned from read sequences using umi_tools (v1.1.1) [Ref: PMID: 28100584]. UMI sequences were saved by incorporating them into the read names in the FASTQ files to be utilized in subsequent analysis steps. .
3' adapters were trimmed from reads using cutadapt (v3.2) [Ref: http://journal.embnet.org/index.php/embnetjournal/article/view/200], and reads shorter than 18 bp in length were removed. Reads were then mapped to a database of mouse repetitive elements and rRNA sequences compiled from Dfam [Ref: PMID: 26612867] and Genbank [Ref: PMID: 23193287]. All non-repeat mapped reads were mapped to the mouse genome (mm10) using STAR (v2.7.7a) [Ref: PMID: 23104886]
PCR duplicates were removed using umi_tools (v1.1.1) by utilizing UMI sequences from the read names and mapping positions. Peaks were identified within eCLIP samples using the peak caller CLIPper (https://github.com/YeoLab/clipper) [Ref: PMID: 24213538]. For each peak, IP versus input fold enrichment values were calculated as a ratio of counts of reads overlapping the peak region in the IP and the input samples (read counts in each sample were normalized against the total number of reads in the sample after PCR duplicate removal)
A p-value was calculated for each peak by the Yates’ Chi-Square test, or Fisher Exact Test if the observed or expected read number was below 5. Comparisons of different sample conditions were performed using DESeq2 (v1.34.0).
Peaks were annotated using transcript information from GENCODE vM25 [Ref: PMID: 30357393] with the following priority hierarchy to define the final annotation of overlapping features: protein coding transcript (CDS, UTRs, intron), followed by non-coding transcripts (exon, intron).
Assembly: GENCODE vM25
Supplementary files format and content: bigWig
Library strategy: eCLIP-seq

extract_protocol:
Twenty ug of RNA with a RIN of 8.35 was used for immunoprecipitation using the validated Abcam ab70775 antibody. As a negative control, in parallel, we used a rabbit IgG antibody (ab313801 from Abcam)
Following the immunoprecipitation, the samples were treated with proteinase K. The IP-RNA was first fragmented and used to create a library using an RNA adapter on the 3' end of the target RNA.

treatment_protocol: A total of 80 x 106 cells were resuspended in 4 mL of PBS and placed in a clean 100 mm petri dish, on top of an ice plate, inside the UV cross-linker (Hoefer UVC 500 crosslinker) with 254-nm UV bulbs. The distance from the UV light source to the cells was 11 cm. Then, the cells were exposed to UV cross-link at 254-nm with an energy setting of 400 mJoules/cm2. After the UV crosslink, cells were washed in PBS, counted again and 20 x 106 cells were pelleted in an Eppendorf tube and snap frozen. Enhanced Cross-Linking&ImmunoPreciptation (eCLIP) was performed by EclipseBio BioInnovations Inc (San Diego; https://www.eclipsebio.com/) according to (25) protocol.

value: Mouse Testicular Cell Line

tag: eclip antibody

value: UV Crosslink


title: A.tauschii, Chromatin_Bound(CB) RNA-seq, AL8-78,leaf, replicate2

description: Library name: CB_RNA-seq_dd_AL8-78_leaf_rep2

data_processing:
CB RNA-seq data were cleaned using fastp (version 0.20.1).
SortMeRNA (version 2.1b) was used to remove reads originating from chloroplasts, mitochondria and rRNA.
The remaining clean reads were mapped to the corresponding genome sequences using hisat2 (v2.1.0)
Reads with a mapping quality score < 20 or mapping to multiple positions were eliminated using SAMtools (v1.16.1).
For each species, all CB RNA samples were subsampled to match the read count of each sample with the lowest number of reads. The subsampled data were then merged in each species for further analysis. Peak calling were conducted using MACS2 as described for ChIP-seq data processing.
Assembly: Triticum urartu (AA, IGDB version 1.0), Aegilops tauschii (DD, Aet_v4.0), Triticum aestivum (AABBDD, IWGSC version 1.0), Hordeum vulgare (HH, IBSC_v2), Secale cereale (Weining.v1.0) , Zea mays (B73_RefGen_v4) and Oryza sativa (MSU7.0)
Supplementary files format and content: bw files

extract_protocol:
Nuclei were isolated from 1 mL tissue powder solubilized in 20 mL ice-cold Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextron T40, 20 mM HEPES, pH7.4, 10 mM MgCl2, 0.75% Triton X-100, 0.5 mM EDTA, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF). The mixture was incubated on ice for 5 min, then filtered through 110 µm nylon mesh and a 40 µm cell strainer. The crude nuclei were spun down at 3,500 g for 5 min at 4°C, followed by washes with 150 µL of resuspension buffer (50% Glycerol, 0.5 mM EDTA, 25 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor) and 300 µL of wash buffer (25 mM Tris-HCl, pH 7.5, 300 mM NaCl, 1 M urea, 0.5 mM EDTA, 1% Tween 20, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor). Again, the obtained nuclei were washed with another 150 µL of resuspension buffer and 150 µL of wash buffer. CB RNA was extracted from washed nuclei using TRIzol reagent and subjected to genomic DNA removal by TURBOTM DNase (Life Technologies). After purification with RNA Clean & ConcentratorTM-5 kit (Zymo Research, R1013), ~1 µg CB RNA was subjected to rRNA depletion by a riboPOOL kit (siTOOLs Biotech, PanPlant-10 nmol) and polyA RNA removal by oligo (dT) beads (NEB, S1419). PolyA RNA was enriched from total RNA by oligo(dT) beads. Purified CB RNA and PolyA RNA were transformed into cDNA libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765) and sequenced on an Illumina NovaSeq platform.
Chromatin-bound(CB) RNA-seq

value: leaf


title: IP2_MLTC-1_5, ZFP36L2

description:
Library name: IP2_MLTC-1_5
IP library contains the RBP-bound sequences immuoprecipitated with the antibody of interest

value: Abcam (ab70775)


title: SH RNA replicate 2

description: SH_RNA_rep2_REF, SH_RNA_rep2_ALT


title: A.tauschii, Chromatin_Bound(CB) RNA-seq, AL8-78,leaf, replicate1

description: Library name: CB_RNA-seq_dd_AL8-78_leaf_rep1


title: A.tauschii, Chromatin_Bound(CB) RNA-seq, AL8-78,embryo,replicate2

description: Library name: CB_RNA-seq_dd_AL8-78_embryo_rep2


title: SH RNA replicate 1

description: SH_RNA_rep1_REF, SH_RNA_rep1_ALT


title: SH DNA replicate 6

description: SH_DNA_rep6_REF, SH_DNA_rep6_ALT


title: Input3_MLTC-1_6, IgG

description:
Library name: Input3_MLTC-1_6
The input library is an all protein backround control.


title: A.tauschii, Chromatin_Bound(CB) RNA-seq, AL8-78,embryo,replicate1

description: Library name: CB_RNA-seq_dd_AL8-78_embryo_rep1


title: A.tauschii, ChIP-seq, H3K27me3, AL8-78, seedling

description: Library name: DD_AL8-78_Seedling_ChIP-seq_H3K27me3

source_name: 9-day-old seedling

value: 9-day-old seedling

value: H3 trimethyl-Lys 27 (ABclonal, A2363)


title: Input2_MLTC-1_5, ZFP36L2

description:
Library name: Input2_MLTC-1_5
The input library is an all protein backround control.


title: Input1_MLTC-1_4, ZFP36L2

description:
Library name: Input1_MLTC-1_4
The input library is an all protein backround control.


title: SH DNA replicate 4

description: SH_DNA_rep4_REF, SH_DNA_rep4_ALT


title: SH DNA replicate 3

description: SH_DNA_rep3_REF, SH_DNA_rep3_ALT


title: plexiform neurofibroma DRGs, scRNAseq

city: DALLAS

first: CHUNHUI

last: JIANG

address: 6000 HARRY HINES BLVD

department: DERMATOLOGY

institute: UT SOUTHWESTERN

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The gene expression matrix from Cell Ranger was used as input to the Seurat R package (v4.0.2) for downstream analysis
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PNF tumor tissue

extract_protocol:
Paraspinal pNF DRGs were excised immediately following euthanasia and minced into pieces, followed by digestion with a cocktail of type I collagenase (2.5 mg/ml) and dispase B (2.5 mg/ml) for 20 mins. Debris was removed using a 40 μm cell strainer and the cell suspension was centrifuged at 200 g.  Cell pellets were resuspended in 100 μL of 1× PBS/0.04% BSA.
Cells were processed in the Chromium Single Cell Gene Expression (10X Genomics) to build the 3’ transcriptome libraries

value: PNF tumor tissue


title: SH DNA replicate 2

description: SH_DNA_rep2_REF, SH_DNA_rep2_ALT

value: neuroblastoma


title: AS053_IV

value: gut epithelium

value: Chronic active

value: HGD


title: S.cereale, PolyA RNA-seq, Weining, replicate2

description: Library name: PolyA_RNA-seq_rye_Weining_rep2

organism: Secale cereale


title: T.urartu, PolyA RNA-seq, G1812,embryo, replicate2

description: Library name: PolyA_RNA-seq_aa_G1812_embryo_rep2

organism: Triticum urartu

value: embryo


title: T.urartu, PolyA RNA-seq, G1812,embryo, replicate1

description: Library name: PolyA_RNA-seq_aa_G1812_embryo_rep1


title: S.cereale, PolyA RNA-seq, Weining, replicate1

description: Library name: PolyA_RNA-seq_rye_Weining_rep1


title: WTRv_HdB_SO4_3.fastq

city: seattle

first: Ashutosh

middle: P

last: Tripathi

state: Washington

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

institute: Seattle Children's Research Institute

description: Library name: WTRv_HdB_SO4_3.fastq

data_processing:
Read alignment was performed using the Bowtie 2 custom processing pipeline (https://github.com/robertdouglasmorrison/DuffyNGS, https://github.com/robertdouglasmorrison/DuffyTools), as previously described (PMID: 25784701)
The pipeline consists of 2 stages: 1) a pre-alignment filtering step to remove unwanted transcripts such as rRNA, and 2) a genomic alignment step using Bowtie2 with the command line option 'very-sensitive.'
BAM files from step 2 are combined into read depth wiggle tracks that record both uniquely mapped and multiply mapped reads from each of the forward and reverse strangs of the genome. Multiply mapped reads are prorated over all highest-quality aligned locations. Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.
Assembly: MT_H37Rv_V3
Supplementary files format and content: Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis culture

growth_protocol: Wild-type (WT) Mycobacterium tuberculosis H37Rv was cultured in Middlebrook 7H9 medium supplemented with 10% OADC, 0.5% glycerol, 0.05% tyloxapol, and 100 µM sodium propionate until an OD₆₀₀ of 0.8 was reached. Cells were then harvested by centrifugation, washed three times with phosphate-buffered saline (PBS), and resuspended in sulfate-free HdB medium. Cultures were incubated for an additional 48 h in the presence or absence of 100 µM sodium sulfate

extract_protocol:
The bacteria were harvested at the indicated timepoint and resuspended in Trizol, and lysed by bead beating for 30 seconds at 6 m/s for 3 cycles, with intermittent cooling on ice. Cell debris was pelleted at 20,000 g for 1 minute, and the supernatant was transferred to a heavy phase-lock gel tube containing 300 μL of chloroform. The tubes were inverted for 2 minutes and centrifuged at 20,000 g for 5 minutes. RNA in the aqueous phase was precipitated with 300 μL of isopropanol and 300 μL of high-salt solution (0.8 M sodium citrate, 1.2 M sodium chloride). RNA was purified using the QIAGEN RNeasy kit, and ribosomal RNA was depleted using a previously published protocol [Culviner, P. H. et al doi:10.1128/mBio.00010-20 (2020)]. Briefly, a biotinylated oligo mixture of 23S, 16S, and 5S was incubated with RNA to anneal to rRNA, followed by incubation with streptavidin beads. mRNA was purified from the supernatant using Ampure XP beads.
The cDNA library was generated using the NEBNext Ultra II RNA Library Prep Kit and each replicate was barcoded in the DNA library using the NEBNext Multiplex Oligos for Illumina. Libraries were quantified using the KAPA qPCR quantification kit, pooled, and the WT H37RV with and without 100 µM SO4 samples were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit while the WT H37RV and pe22/ppe36 KO in sulphate deplete and 10 mM replete condition samples were sequenced at Fred Hutch with Illumina NovoSeqX+.

treatment_protocol: With and without 100 µM SO4 in HdB media. In SO4 repletion experiment with and without 10 mM SO4 after 48 h of starvation in sulphate free modified Sauton's media.

value: M. tuberculosis culture

value: HdB media with 100 uM Sulfate


title: AS066_V

value: Rectum


title: IP1_MLTC-1_4, ZFP36L2

description:
Library name: IP1_MLTC-1_4
IP library contains the RBP-bound sequences immuoprecipitated with the antibody of interest


title: AS058_V


title: SH DNA replicate 5

description: SH_DNA_rep5_REF, SH_DNA_rep5_ALT


title: AS058_III

value: Descendens


title: S.cereale, Chromatin_Bound(CB) RNA-seq, Weining, replicate2

description: Library name: CB_RNA-seq_rye_Weining_rep2


title: AS066_III

value: Non-progressor


title: S.cereale, Chromatin_Bound(CB) RNA-seq, Weining, replicate1

description: Library name: CB_RNA-seq_rye_Weining_rep1


title: AS066_I

value: Ascendens


title: WTRv_HdB_SO4_1.fastq

description: Library name: WTRv_HdB_SO4_1.fastq


title: T.urartu, Chromatin_Bound(CB) RNA-seq, G1812,leaf, replicate2

description: Library name: CB_RNA-seq_aa_G1812_leaf_rep2


title: S.cereale, ChIP-seq, H3K27me3, Weining, seedling

description: Library name: Rye_Weining_Seedling_ChIP-seq_H3K27me3

data_processing:
The sequencing reads were trimmed with fastp (0.22.0).
The clean reads were aligned with bwa program (version 0.7.17-r1188).
Peaks were called using MACS (v2.1.0.20150731).
Assembly: Aegilops tauschii (DD, Aet_v4.0), Secale cereale (Weining.v1.0)
Supplementary files format and content: peak files

extract_protocol:
The 9-day-old seedlings (above-ground parts) were harvested and directly vacuum-infiltrated with a formaldehyde cross-linking solution for ChIP-seq. More than 10 ng of ChIP DNA extracted from each sample was used to prepare the sequencing samples.
ChIP-seq


title: AS062_V


title: WTRv_HdB_3.fastq

description: Library name: WTRv_HdB_3.fastq

value: HdB media without Sulfate grown for 48 h


title: T.urartu, Chromatin_Bound(CB) RNA-seq, G1812,leaf, replicate1

description: Library name: CB_RNA-seq_aa_G1812_leaf_rep1

value: leaf


title: S.cereale, ChIP-seq, H3K9me2, Weining, seedling

description: Library name: Rye_Weining_Seedling_ChIP-seq_H3K9me2

value: H3 dimethyl-Lys 9 (Abcam)


title: AS062_III


title: WTRv_HdB_2.fastq

description: Library name: WTRv_HdB_2.fastq


title: T.urartu, Chromatin_Bound(CB) RNA-seq, G1812,embryo, replicate2

description: Library name: CB_RNA-seq_aa_G1812_embryo_rep2


title: T.urartu, Chromatin_Bound(CB) RNA-seq, G1812,root, replicate2

description: Library name: CB_RNA-seq_aa_G1812_root_rep2

value: root


title: WTRv_HdB_SO4_2.fastq

description: Library name: WTRv_HdB_SO4_2.fastq


title: S.cereale, ChIP-seq, H3K9ac, Weining, seedling

description: Library name: Rye_Weining_Seedling_ChIP-seq_H3K9ac

value: 9-day-old seedling

value: H3 acetyl-Lys 9 (Upstate)


title: AS062_I


title: T.urartu, Chromatin_Bound(CB) RNA-seq, G1812,root, replicate1

description: Library name: CB_RNA-seq_aa_G1812_root_rep1


title: WTRv_HdB_1.fastq

description: Library name: WTRv_HdB_1.fastq


title: T.urartu, Chromatin_Bound(CB) RNA-seq, G1812,embryo, replicate1

description: Library name: CB_RNA-seq_aa_G1812_embryo_rep1


title: MG RNA replicate 1

description: MG_RNA_rep1_REF, MG_RNA_rep1_ALT

value: SV40-immortalized microglia

value: microglia


title: A549, miR-9-5p overexpression, 2

description:
Library name: A549 miR-9-5p 2
A549_MIR9_4
A549 normalised counts.xlsx

value: Human lung cancer cell line

value: Cells grown as tumour xenografts in NOD-SCID-IL2Rgamma mice


title: S.cereale, ChIP-seq, H3K4me3, Weining, seedling

description: Library name: Rye_Weining_Seedling_ChIP-seq_H3K4me3

value: H3 trimethyl-Lys 4 (Abcam)


title: AS061_V

value: gut epithelium

value: Chronic active


title: Arabidopsis root tip, 31°C (control), 2 day after transfer, replicate 5

status: Public on Jun 14 2026

city: Tainan

first: Joon-Keat

last: Lai

address: No. 100, Sec. 1, Guiren 13th Rd., Guiren Dist.

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

description:
Library name: Sample_LGL25-CJ20
Column name in raw_counts.txt: Sample_LGL25-CJ20

data_processing:
fastp + subread + featureCounts + DESeq2
Sequence reads were trimmed for adaptor sequence/low-quality using fastp program (version 1.0.1) (parameters: --trim_poly_g --trim_poly_x --detect_adapter_for_pe)
Trimmed sequence reads were mapped to TAIR10 using subread program (version 2.1.1) (parameters: default). Read count extraction was subsequently performed using featureCounts function included in the subread program (version 2.1.1) (parameters: -p --countReadPairs -M -O --fraction --largestOverlap -B -C -J -g gene_id -t exon,miRNA_primary_transcript).
Normalization and differentially expressed genes analysis were performed using an R package ‒ DESeq2 (version 1.48.1) (parameters: default).
Assembly: Arabidopsis thaliana (TAIR10)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Arabidopsis thaliana

source_name: root tip

growth_protocol: Seedlings were grown vertically in a growth chamber at 22°C under long-day conditions (16 h light/8 h dark) for 7 days.

extract_protocol:
The similarly sized root tip tissues, including three developmental zones, were precisely cut, then homogenized in RNA extraction buffer, and processed as described in the manufacturer’s recommended protocol. Each RNA sample was extracted from 50 root tissues. Total RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration was quantified using a Qubit fluorometer (Invitrogen). RNA quality was assessed using a 2100 Bioanalyzer (Agilent), and all samples exhibited RNA integrity numbers above 8.0
RNA-seq libraries were prepared from 300 ng of total RNA using the Universal Plus Total RNA-Seq with NuQuant Library Preparation Kit (Tecan Trading AG), following the manufacturer’s instructions. Libraries from 5 biological replicates of root samples under the control temperature (22°C) and the non-lethal high temperature (31°C) at 1 and 2 DAT were sequenced on an Illumina NextSeq 3300 platform, generating 150-base paired-end reads.

treatment_protocol: Seven-day-old Arabidopsis seedlings were transferred to growth chambers set at different temperatures (27-32°C) for 3 days.

value: root tip

value: 31°C, 2 day


title: Arabidopsis root tip, 31°C (control), 2 day after transfer, replicate 4

description:
Library name: Sample_LGL25-CJ19
Column name in raw_counts.txt: Sample_LGL25-CJ19


title: Arabidopsis root tip, 31°C (control), 2 day after transfer, replicate 3

description:
Library name: Sample_LGL25-CJ18
Column name in raw_counts.txt: Sample_LGL25-CJ18


title: Arabidopsis root tip, 31°C (control), 2 day after transfer, replicate 2

description:
Library name: Sample_LGL25-CJ17
Column name in raw_counts.txt: Sample_LGL25-CJ17


title: Arabidopsis root tip, 22°C (control), 2 day after transfer, replicate 5

description:
Library name: Sample_LGL25-CJ15
Column name in raw_counts.txt: Sample_LGL25-CJ15

value: 22°C, 2 day


title: Arabidopsis root tip, 31°C (control), 2 day after transfer, replicate 1

description:
Library name: Sample_LGL25-CJ16
Column name in raw_counts.txt: Sample_LGL25-CJ16


title: Arabidopsis root tip, 22°C (control), 2 day after transfer, replicate 3

description:
Library name: Sample_LGL25-CJ13
Column name in raw_counts.txt: Sample_LGL25-CJ13


title: Arabidopsis root tip, 22°C (control), 2 day after transfer, replicate 4

description:
Library name: Sample_LGL25-CJ14
Column name in raw_counts.txt: Sample_LGL25-CJ14


title: Arabidopsis root tip, 22°C (control), 2 day after transfer, replicate 2

description:
Library name: Sample_LGL25-CJ12
Column name in raw_counts.txt: Sample_LGL25-CJ12


title: Arabidopsis root tip, 22°C (control), 2 day after transfer, replicate 1

description:
Library name: Sample_LGL25-CJ11
Column name in raw_counts.txt: Sample_LGL25-CJ11


title: Arabidopsis root tip, 31°C (control), 1 day after transfer, replicate 5

description:
Library name: Sample_LGL25-CJ10
Column name in raw_counts.txt: Sample_LGL25-CJ10

value: 31°C, 1 day


title: A.tauschii, PolyA RNA-seq, AL8-78,embryo,replicate1

description: Library name: PolyA_RNA-seq_dd_AL8-78_embryo_rep1

value: embryo


title: AS048_II

first: Hilde

last: Nilsen

address: Sykehusveien 25

institute: Akershus University Hospital

source_name: Gut epithelium, P, Transversum

value: Progressor

value: Transversum

value: Chronic


title: SH RNA replicate 4

description: SH_RNA_rep4_REF, SH_RNA_rep4_ALT

value: neuroblastoma


title: Arabidopsis root tip, 31°C (control), 1 day after transfer, replicate 4

description:
Library name: Sample_LGL25-CJ09
Column name in raw_counts.txt: Sample_LGL25-CJ09


title: Pkd1RC/RC_2

description:
Library name: 4841
10X genomics

source_name: Kidney

value: Kidney

value: Female

value: March, 2024


title: Arabidopsis root tip, 31°C (control), 1 day after transfer, replicate 3

description:
Library name: Sample_LGL25-CJ08
Column name in raw_counts.txt: Sample_LGL25-CJ08


title: Arabidopsis root tip, 31°C (control), 1 day after transfer, replicate 2

description:
Library name: Sample_LGL25-CJ07
Column name in raw_counts.txt: Sample_LGL25-CJ07


title: Pkd1RC/RC_1

description:
Library name: 4842
10X genomics

value: Male


title: Arabidopsis root tip, 31°C (control), 1 day after transfer, replicate 1

description:
Library name: Sample_LGL25-CJ06
Column name in raw_counts.txt: Sample_LGL25-CJ06


title: SH RNA replicate 3

description: SH_RNA_rep3_REF, SH_RNA_rep3_ALT


title: Arabidopsis root tip, 22°C (control), 1 day after transfer, replicate 4

description:
Library name: Sample_LGL25-CJ04
Column name in raw_counts.txt: Sample_LGL25-CJ04

value: 22°C, 1 day


title: Arabidopsis root tip, 22°C (control), 1 day after transfer, replicate 3

description:
Library name: Sample_LGL25-CJ03
Column name in raw_counts.txt: Sample_LGL25-CJ03


title: Arabidopsis root tip, 22°C (control), 1 day after transfer, replicate 5

description:
Library name: Sample_LGL25-CJ05
Column name in raw_counts.txt: Sample_LGL25-CJ05


title: Arabidopsis root tip, 22°C (control), 1 day after transfer, replicate 1

description:
Library name: Sample_LGL25-CJ01
Column name in raw_counts.txt: Sample_LGL25-CJ01


title: Arabidopsis root tip, 22°C (control), 1 day after transfer, replicate 2

description:
Library name: Sample_LGL25-CJ02
Column name in raw_counts.txt: Sample_LGL25-CJ02


title: AS061_III

value: Non-progressor

value: Descendens