title: Human CRC blood eosinophils, replicate 2, scRNAseq

status: Public on Aug 29 2025

city: Zürich

first: Kristina

last: Handler

address: Winterthurerstrasse

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zürich

description: Library name: Blood_patient_2_hs

data_processing:
Demultiplexing of BCL files with Bcl2fastq (v2.20.0433, Illumina)
Count matrix generation using the BD Rhapsody™ WTA analysis pipeline (v1.12.1) on the SevenBridges Genomics platform
Assembly: STAR index generation using STAR (v2.5.2b) with gene code GRCm38 v25 for mouse and GRCh38 v43 for human data
Supplementary files format and content: Text file showing the input data for the WTA Analysis pipeline at the beginning of the file. Followed by a matrix (first column: “Cell_index”, cell IDs; second column: “Bioproduct”, Gene Symbols; third column: “RSEC_Reads”, Number of UMI reads per cell ID and bioproduct; forth column: “Raw_Molecules”, Reads with the same cell ID, same UMI sequence and same bioproduct collapsed into single molecules; fifth column: “RSEC_Adjusted_Molecules”, Number of molecules detected after RSEC molecular identifier adjustment algorithm, this is the counts used for downstream analysis;

source_name: Blood

extract_protocol:
BD Rhapsody Express Single-Cell Analysis System (BD Bioscience)
mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol (BD Biosciences)

treatment_protocol: Cell hasing unsing BD Rhapsody Mouse and Human Single-Cell Multiplexing kit

value: Blood

tag: cellular enrighment

value: Eosinophils

tag: bd rhapsody_capture_bead_version

value: enhanced beads

tag: sample tag_(cell_hashing)_version

value: Single-Cell Multiplex Kit - Human

tag: sample tag_(cell_hashing)


title: Human CRC blood eosinophils, replicate 1, scRNAseq

type: SRA

description: Library name: Blood_patient_1_hs

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Homo sapiens

tag: tissue


title: C_1012

status: Public on Aug 31 2025

city: jerusalem

first: hermona

last: soreq

state: -- Select --

address: The Edmond J. Safra Campus, Givat Ram

department: Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

library_source: transcriptomic

data_processing:
Base calling, QC and fastq file generation by the illumina Basespace platform
counts were normalized using RLE
Alignment to mirBase v.21 using miRExpress 2
Normalization and Differential expression using Deseq2
Genome_build: mirBase v.21
Supplementary_files_format_and_content: One .txt file per sample with aligned miR counts

molecule: total RNA

source_name: Human blood leukocytes

extract_protocol:
[sample collection and cell extraction] Blood was withdrawn between 8 and 9 AM after over-night fasting after excluding current infection and heavy physical activity, heavy meal, and alcohol consumption on the previous day. 3 x 9.5 ml blood was collected in EDTA monovettes (not containing heparin) for white blood cell isolation. Tubes were gently mixed by manually inverting ten times each. For plasma collection 2 x 8 ml were used; for white blood cell isolation 3 x 1.5 ml were further processed. Buffer EL (7.5 ml, Qiagen, cat#: 79217) was added and samples were incubated on ice for 25 min. At 7 and 15 min the samples were mixed and then centrifuged (400 g, 10 min, 4°C). The supernatant was discarded and the cell pellet was re-suspended in 3 ml of Buffer EL before centrifuged again (400 g, 10 min, 4°C). The supernatant was again discarded and the cell pellet re-suspended in 1.5 ml of RNA protect cell reagent (Qiagen, cat#: 76526). Samples were then stored at -80°C before further processing.
Total RNA was extracted using the MiRNeasy miRNA isolation kit (Quiagen). All samples were kept on ice, tubes were centrifuged at 5000rcf to precipitate the cells, and overlaying RNA later solution was removed. Cells were disrupted with a plastic pestle and homogenized in 500µl (700µl for mouse tissues) Trizol lysis buffer. Following incubation for 5 min in room temperature 100 µl (accounting for 1:5 of the total volume) of chloroform was added to each sample. Samples were shortly vortexed and incubated for 2-3 min at room temperature, and were centrifuged at 4°C for 15 min at 12000rcf. The supernatant was mixed with absolute ethanol (1.25 times the supernatant volume) and the mixture was washed using the provided washing solutions and filter sets. Samples were eluted in 15µl (14µl for mouse tissues) RNAse free DDW. RNA quality and quantity was measured using a Nanodrop 2000 (PeqLab/Thermo Scientific). A total of 100µg per sample was run on an agarose gel for quality control. And RNA integrity was further tested using the 2100 Bioanalyzer (Agilent Technologies) using RNA 6000 Nano LabChip Kits (Agilent Technologies) and achieved an average RIN value of 7.5.
An even amount of 150ng RNA per sample was used for small-RNA library construction using the New England BioLabs NEB-next multiplex small-RNA library construction kit. The library was size selected based on DNA 1000 LabChip kits by 2100 Bioanalyzer (Agilent Technologies) results to 146bp long transcripts which include the barcodes, adaptors and ca. 20bp long miRNAs. This ensures that sequenced transcripts are in the maximum length of 30 bp only. Libraries were quantified using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Invitrogen)
Sequencing was run in the The NextSeq Series desktop sequencing system of the Illumina platform. The number of Pass Filter reads per sample was at the range of (13-14*10^6 reads). Read counts and quality for each sample were evaluated with the BaseSpace Sequencing QC report tool.

tag: individual

value: patient no. 1012

tag: developmental stage

value: Adult greater than or equal to 18 years old

tag: gender

value: pooled male and female

tag: disease state

value: Healthy controls

tag: cell type

value: leukocytes


title: NL1_1006

value: patient no. 1006

value: nerve lesion with pain


title: medullary thymic epithelial cell, Aebp2-flox, replicate 1, cut-tag_H3K27me3

status: Public on Aug 30 2025

city: Hangzhou

first: Yiyan

last: Zheng

address: Zhiqiang Road 428

country: China

institute: Westlake Laboratory of Life Sciences and Biomedicine

description: Library name: WT1 mTEC_cuttag_H3K27me3

library_source: other

data_processing:
For bulkRNAseq, raw reads were mapped to the Mus musculus (mm10) reference genome using HISAT2. HISAT was run in a 2-pass approach with options “--score-min L,0.0,-0.2” and known splice sites for the first pass, and novel splice sites detected across all samples for the second pass. Gene-level count data was obtained using featureCounts program (http://bioinf.wehi.edu.au/featureCounts/). For scRNAseq and scATACseq, barcode processing and mapping to the mouse genome was performed with Cell Ranger v3.0. For Cut&tag, all peak calling was performed with MACS2 (v 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets.
Assembly: Mouse mm10
Supplementary files format and content: Excel file, matrix files and bigwig files
Library strategy: CUT&Tag

molecule: other

organism: Mus musculus

source_name: thymus

extract_protocol:
Thymi were isolated and cleaned to get rid of the residual fat and connective tissue, followed by a serial steps of enzymatic digestion with 0.15% mg/ml Liberase TM in RPMI 1640 at 37 °C. For adult thymi, CD45- cells were enriched with anti-CD45 beads and MACS LS columns (Miltenyi) followed by FACS sorting to harvest living CD45-Ter119-EpCAM+ thymic epithelial cells. The enriched total TECs or mTEChi (UEA1+MHCIIhi) were subjected to scRNA-seq, scATAC-seq, Cut&Tag, bulk RNA-seq.
Liraries for scRNAseq, scATACseq, Cut&tag, and bulkRNAseq were prepared following the manufactures' instructions described in the paper's method section.

value: thymus

tag: cell line

value: thymic epithelial cell

value: medullary thymic epithelial cell

tag: genotype

tag: treatment

value: wild type


title: Human healthy blood eosinophils, replicate 7, scRNAseq

description: Library name: Blood_healthy_7_hs


title: Human healthy blood eosinophils, replicate 8, scRNAseq

description: Library name: Blood_healthy_8_hs


title: Human CRC blood eosinophils, replicate 7, scRNAseq

description: Library name: Blood_patient_7_hs


title: CRPS_1003

value: patient no. 1003

value: CRPS patient


title: Human CRC blood eosinophils, replicate 4, scRNAseq

description: Library name: Blood_patient_4_hs

value: Blood


title: Human CRC blood eosinophils, replicate 5, scRNAseq

description: Library name: Blood_patient_5_hs

value: Eosinophils


title: Human CRC blood eosinophils, replicate 6, scRNAseq

description: Library name: Blood_patient_6_hs

value: enhanced beads


title: Human CRC blood eosinophils, replicate 3, scRNAseq

description: Library name: Blood_patient_3_hs

value: Single-Cell Multiplex Kit - Human


title: Human healthy blood eosinophils, replicate 10, scRNAseq

description: Library name: Blood_healthy_10_hs


title: Human healthy blood eosinophils, replicate 9, scRNAseq

description: Library name: Blood_healthy_9_hs


title: CT_cont_ES_H3K27me3

status: Public on Aug 25 2025

city: Yokohama

first: Shinsuke

last: Ito

state: Kanagawa

address: 1-7-22 Suehirocho

department: IMS

country: Japan

institute: RIKEN

description: Library name: Sample 103

library_source: genomic

data_processing:
Reads were aligned to UCSC mm9 or UCSC hg38 using bowtie2. The SAM files were converted to the BAM format using Samtools. The PCR duplicates were removed by Picardtools. The BAM files were converted to bigwig files by deepTools2 for visualization. The bigwig files were normalized to reads per million mapped sequence reads (RPKM), and also normalized by the factor (Count of antibody mapped to mm9) / (Count of antibody mapped to hg38) * (Count of corresponding input mapped to hg38) / (Count of corresponding input mapped to mm9).
Assembly: mm9
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol: Embryos were disected out at day 9 pregnancy. Embryos with 15 to 20 somites were classified as 9.0 dpc and more than 20 somites were classified as 9.5 dpc. Embryonic stem cells were cultured in DMEM supplemented with 20% fetal bovine serum, GlutaMax, MEM nonessential amino acids, 2-mercaptoethanol, GlutaMax and LIF on MEF feeder layers at 37°C in a 5% CO2 incubator.

extract_protocol:
Cells were washed with DIG wash buffer (wash buffer with 0.05 % digitonin) and treat with secondary antibody for 1 hour at room temperature, then wash with Dig-300 buffer (20 mM HEPES pH7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01 % digitonin). Samples were incubated with pA-Tn5 (Diagenode: C01070001) for one hour at room temperature and wash with Dig-300 wash buffer. Samples were suspended with 100 ul of tagmentation buffer (Dig-300 buffer with 10mM MgCl2) and Incubate at 37°C for 30 minutes. Then, stop the reaction with 3.3 ul of 500 mM EDTA, 1 ul of 10% SDS, and 1 ul of 20 mg/ml Proteinase K, and then incubate at 65°C for 6 hours and 55°C overnight. DNA from these samples was purified using SPRI beads, and eluted DNA samples were used as 3D samples. Eluted samples were used for the CUT&Tag library.
CUT&Tag libraries were prepared by PCR with Nextera primers as described in Kaya-Okur and Henikoff (dx.doi.org/10.17504/protocols.io.wnufdew).

treatment_protocol: For production of mutant embryos, pregnant mothers were injected tamoxifen peritonealy at 8.5 dpc. For PI treatment, pregnant mothers were injected Bortezomib 8.25 and 8.75 dpc twice.

value: mouse embryonic stem cells

tag: strain

value: Tamoxifen-

value: WT

tag: chip antibody


title: CTinput_9.5dpcPI_mb_H3K27ac_lot2

description: Library name: Sample 102

source_name: 9.5 dpc mouse embryonic midbrain

value: 9.5 dpc mouse embryonic midbrain

value: Tamoxifen- :Bortezomib+

value: no


title: medullary thymic epithelial cell, Aebp2-ko, replicate 1, cut-tag_H3K27me3

description: Library name: KO1 mTEC_cuttag_H3K27me3

value: knockout


title: CTinput_9.0dpc_mb_H3K27ac_lot2

description: Library name: Sample 98

source_name: 9.0 dpc mouse embryonic midbrain

value: 9.0 dpc mouse embryonic midbrain


title: CTinput_deltaRBS_ES_both_antibody

description: Library name: Sample 108

value: Tamoxifen+


title: CTinput_9.5dpc_mb_H3K27ac_lot2

description: Library name: Sample 100


title: CT_9.5dpcPI_mb_H3K27ac_lot2

description: Library name: Sample 101

value: anti-H3K27ac (CST, 8173)


title: CTinput_cont_ES_both_antibody

description: Library name: Sample 105


title: CT_cont_ES_RING1B

description: Library name: Sample 104

value: anti-RING1B (CST, 5694)


title: CT_9.5dpc_mb_H3K27ac_lot2

description: Library name: Sample 99


title: CTinput_9.5dpcPI_mb_H3K27ac_lot1

description: Library name: Sample 96


title: CT_9.0dpc_mb_H3K27ac_lot2

description: Library name: Sample 97


title: CT_deltaRBS_ES_RING1B

description: Library name: Sample 107


title: CTinput_9.5dpc_mb_H3K27ac_lot1

description: Library name: Sample 94


title: CT_9.5dpc_mb_H3K27ac_lot1

description: Library name: Sample 93


title: CTinput_9.0dpc_mb_H3K27ac_lot1

description: Library name: Sample 92


title: CT_9.0dpc_mb_H3K27ac_lot1

description: Library name: Sample 91


title: CTinput_9.5dpc_mb_FK1_lot2

description: Library name: Sample 88


title: CTinput_9.5dpcPI_mb_FK1_lot1

description: Library name: Sample 86


title: CT_9.5dpc_mb_FK1_lot2

description: Library name: Sample 87

value: anti-FK1 (MBL, D071-3)


title: CT_9.5dpcPI_mb_H3K27ac_lot1

description: Library name: Sample 95


title: CTinput_9.5dpcPI_mb_FK1_lot2

description: Library name: Sample 90


title: CTinput_9.5dpcPI_mb_RING1B_lot2

description: Library name: Sample 82


title: CT_9.5dpc_mb_FK1_lot1

description: Library name: Sample 83


title: CTinput_9.5dpc_mb_FK1_lot1

description: Library name: Sample 84


title: CT_9.5dpcPI_mb_FK1_lot1

description: Library name: Sample 85


title: CT_deltaRBS_ES_H3K27me3

description: Library name: Sample 106


title: CT_9.5dpcPI_mb_RING1B_lot2

description: Library name: Sample 81


title: CTinput_9.5dpc_mb_RING1B_lot2

description: Library name: Sample 80


title: CTinput_9.0dpc_mb_RING1B_lot2

description: Library name: Sample 78


title: CTinput_9.5dpcPI_mb_RING1B_lot1

description: Library name: Sample 76


title: CT_9.0dpc_mb_RING1B_lot2

description: Library name: Sample 77


title: CT_9.5dpc_mb_RING1B_lot1

description: Library name: Sample 73


title: CTinput_9.5dpc_mb_RING1B_lot1

description: Library name: Sample 74


title: CT_9.0dpc_mb_RING1B_lot1

description: Library name: Sample 71


title: CTinput_9.0dpc_mb_RING1B_lot1

description: Library name: Sample 72


title: CT_9.5dpc_mb_RING1B_lot2

description: Library name: Sample 79


title: CTinput_9.0dpc_mb_EED_lot2

description: Library name: Sample 66


title: CT_9.5dpc_mb_EED_lot2

description: Library name: Sample 67

value: anti-EED (CST, 85322)


title: CT_9.5dpcPI_mb_EED_lot2

description: Library name: Sample 69


title: CTinput_9.5dpcPI_mb_EED_lot1

description: Library name: Sample 64


title: CT_9.5dpcPI_mb_FK1_lot2

description: Library name: Sample 89


title: CT_9.0dpc_mb_EED_lot2

description: Library name: Sample 65


title: CTinput_9.5dpcPI_mb_EED_lot2

description: Library name: Sample 70


title: CTinput_9.5dpc_mb_EED_lot2

description: Library name: Sample 68


title: CT_9.5dpcPI_mb_EED_lot1

description: Library name: Sample 63


title: CT_9.5dpc_mb_EED_lot1

description: Library name: Sample 61


title: CTinput_9.0dpc_mb_EED_lot1

description: Library name: Sample 60


title: CTinput_Skp1aKO_mb_H3K27ac_lot2

description: Library name: Sample 58

value: Skp1a KO


title: CT_9.0dpc_mb_EED_lot1

description: Library name: Sample 59


title: CTinput_Skp1a9.5cont_mb_H3K27ac_lot2

description: Library name: Sample 56


title: CT_Skp1aKO_mb_H3K27ac_lot2

description: Library name: Sample 57


title: CT_Skp1a9.5cont_mb_H3K27ac_lot2

description: Library name: Sample 55


title: CT_Skp1aKO_mb_H3K27ac_lot1

description: Library name: Sample 53


title: CTinput_9.5dpc_mb_EED_lot1

description: Library name: Sample 62


title: CT_Skp1a9.5cont_mb_H3K27ac_lot1

description: Library name: Sample 51


title: CTinput_Skp1a9.5cont_mb_H3K27ac_lot1

description: Library name: Sample 52


title: CT_9.5dpcPI_mb_RING1B_lot1

description: Library name: Sample 75


title: CTinput_Skp1aKO_mb_H3K27ac_lot1

description: Library name: Sample 54


title: CTinput_Skp1a9.0cont_mb_H3K27ac_lot1

description: Library name: Sample 50


title: CTinput_Pcgf1KOPI_mb_RING1B_lot2

description: Library name: Sample 48

value: Tamoxifen+ :Bortezomib+

value: Pcgf1 KO


title: CT_Skp1a9.0cont_mb_H3K27ac_lot1

description: Library name: Sample 49


title: CTinput_Pcgf1KO_mb_RING1B_lot2

description: Library name: Sample 47


title: CTinput_Pcgf1cont_mb_RING1B_lot2

description: Library name: Sample 45


title: CTinput_Pcgf1KOPI_mb_RING1B_lot1

description: Library name: Sample 44


title: CTinput_Pcgf1contPI_mb_RING1B_lot1

description: Library name: Sample 42


title: CTinput_Pcgf1cont_mb_RING1B_lot1

description: Library name: Sample 41


title: CT_Skp1aPcgf1cont_mb_EED_lot2

description: Library name: Sample 35


title: CTinput_Skp1aPcgf1KO_mb_EED_lot2

description: Library name: Sample 40

value: Skp1aPcgf1 KO


title: CTinput_Skp1aPcgf1KO_mb_EED_lot1

description: Library name: Sample 34


title: CT_Skp1aPcgf1KO_mb_EED_lot2

description: Library name: Sample 39


title: CTinput_Skp1aPcgf1contPI_mb_EED_lot2

description: Library name: Sample 38


title: CT_Skp1aPcgf1KO_mb_EED_lot1

description: Library name: Sample 33


title: CTinput_Skp1aPcgf1contPI_mb_EED_lot1

description: Library name: Sample 32


title: CT_Skp1aPcgf1contPI_mb_EED_lot1

description: Library name: Sample 31


title: CT_Skp1aKO_mb_EED_lot2

description: Library name: Sample 27


title: CT_Skp1aPcgf1cont_mb_EED_lot1

description: Library name: Sample 29


title: CTinput_Skp1acontPI_mb_EED_lot2

description: Library name: Sample 26


title: CT_Skp1acontPI_mb_EED_lot2

description: Library name: Sample 25


title: CTinput_Skp1acont_mb_EED_lot2

description: Library name: Sample 24


title: CT_Skp1acont_mb_EED_lot2

description: Library name: Sample 23


title: CTinput_Skp1aKO_mb_EED_lot1

description: Library name: Sample 22


title: CTinput_Skp1aKO_mb_EED_lot2

description: Library name: Sample 28


title: CTinput_Pcgf1contPI_mb_RING1B_lot2

description: Library name: Sample 46


title: CTinput_Skp1acontPI_mb_EED_lot1

description: Library name: Sample 20


title: CT_Skp1aKO_mb_EED_lot1

description: Library name: Sample 21


title: CTinput_Skp1acont_mb_EED_lot1

description: Library name: Sample 18


title: CTinput_Pcgf1KO_mb_RING1B_lot1

description: Library name: Sample 43


title: CT_Skp1acontPI_mb_EED_lot1

description: Library name: Sample 19


title: CT_Skp1acont_mb_EED_lot1

description: Library name: Sample 17


title: CT_Skp1aPcgf1contPI_mb_EED_lot2

description: Library name: Sample 37


title: CTinput_Skp1aPcgf1cont_mb_EED_lot2

description: Library name: Sample 36


title: CT_Pcgf1KO_mb_EED_lot2

description: Library name: Sample 13


title: CTinput_Pcgf1KOPI_mb_EED_lot2

description: Library name: Sample 16


title: CTinput_Pcgf1KO_mb_EED_lot2

description: Library name: Sample 14


title: CT_Pcgf1KOPI_mb_EED_lot2

description: Library name: Sample 15


title: CTinput_Pcgf1cont_mb_EED_lot2

description: Library name: Sample 10


title: CT_Pcgf1KOPI_mb_EED_lot1

description: Library name: Sample 7


title: CT_Pcgf1contPI_mb_EED_lot2

description: Library name: Sample 11


title: CTinput_Pcgf1KO_mb_EED_lot1

description: Library name: Sample 6


title: CTinput_Skp1aPcgf1cont_mb_EED_lot1

description: Library name: Sample 30


title: CTinput_Pcgf1contPI_mb_EED_lot1

description: Library name: Sample 4


title: CT_Pcgf1contPI_mb_EED_lot1

description: Library name: Sample 3


title: CTinput_Pcgf1cont_mb_EED_lot1

description: Library name: Sample 2


title: CT_Pcgf1cont_mb_EED_lot2

description: Library name: Sample 9


title: Small RNAs from PacmFs2Ket-SV40 ovaries - replicate 1

status: Public on Aug 21 2025

city: Vienna

first: Dominik

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description: Library name: PacmFs(2)Ket-SV40 rep1

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (CAGTG AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: 25˚C, 12h dark/light, ovaries dissected into PBS on ice, snap frozen

extract_protocol:
Argonaute-bound sRNAs were isolated using TraPR columns according to Grentzinger et al. (2020)
Libraries were prepared by ligation of 3' barcoded adaptors containing 6 random nucleotides and a 5 nt in-line barcode and 5' adaptors containing 4 random nucleotides at the ends to reduce ligation biases followed by reverse transcription and amplification by PCR.

value: Ovary

value: white; PacmFs(2)Ket-SV40 in attP2


title: CT_Pcgf1cont_mb_EED_lot1

description: Library name: Sample 1

value: Tamoxifen-

value: WT


title: Small RNAs from B3 embryos

description: Library name: B3_emb

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (ATGGA AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis

source_name: 0-30mins old Embryos

value: 0-30mins old Embryos


title: Small RNAs from PacmFs2Ket-SV40 ovaries - replicate 2

description: Library name: PacmFs(2)Ket-SV40 rep2

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (AGCAA AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis


title: Small RNAs from A2 embryos

description: Library name: A2_emb

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (CGTTC AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis


title: Small RNAs from Ber2 ovaries - replicate 2

description: Library name: BER2_rep2

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (TGACT AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis


title: Small RNAs from PacmFs2Ket heterozygous ovaries

description: Library name: PacmFs2Ket_Heterozygous

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (GTCAG AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis

value: white; PacmFs(2)Ket in attP2/Tm3,Sb


title: Small RNAs from Sam ovaries - replicate 1

description: Library name: SAM_rep1

value: Sam


title: Small RNAs from PacmFs2Ket homogygous ovaries

description: Library name: PacmFs2Ket_Homozygous

value: white; PacmFs(2)Ket in attP2/PacmFs(2)Ket in attP2


title: Small RNAs from Sam ovaries - replicate 2

description: Library name: SAM_rep2


title: Small RNAs from Iso1 ovaries - replicate 2

description: Library name: Iso1_rep2


title: Small RNAs from Iso1 ovaries with second chromosome replaced by IF/CyO

description: Library name: Iso1_MinusIIChr

value: Iso1(X)/Iso1(X); IF/CyO; +/Iso1(III)


title: Small RNAs from MTD driving white-sh expression in Iso1 genetic background - replicate 2

description: Library name: Iso_MTDwsh_rep2


title: Small RNAs from MTD driving aub-ago3-double sh expression in Iso1 genetic background - replicate 2

description: Library name: Iso_MTDaubago3_rep2

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (TACCA AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis


title: Small RNAs from Iso1 embryos

description: Library name: Iso1_emb

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (CTGAT AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis


title: Small RNAs from MTD driving aub-ago3-double sh expression in Iso1 genetic background - replicate 1

description: Library name: Iso_MTDaubago3_rep1

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (GGTAT AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis


title: Small RNAs from Ber2 ovaries - replicate 1

description: Library name: BER2_rep1


title: Small RNAs from Ber2 embryos

description: Library name: BER2_emb

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (TCCAT AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis


title: Small RNAs from MTD driving white-sh expression in Iso1 genetic background - replicate 1

description: Library name: Iso_MTDwsh_rep1


title: CTinput_Pcgf1contPI_mb_EED_lot2

description: Library name: Sample 12

value: 9.5 dpc mouse embryonic midbrain

value: Tamoxifen- :Bortezomib+

value: no


title: Small RNAs from B7 ovaries - replicate 2

description: Library name: B7_rep2


title: CT_Pcgf1KO_mb_EED_lot1

description: Library name: Sample 5

value: Tamoxifen+

value: anti-EED (CST, 85322)


title: Small RNAs from B2 ovaries - replicate 2

description: Library name: B2_rep2


title: Small RNAs from B4 ovaries - replicate 2

description: Library name: B4_rep2


title: Small RNAs from B3 ovaries - replicate 2

description: Library name: B3_rep2


title: Small RNAs from B6 embryos

description: Library name: B6_emb

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (GAACG AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis


title: Small RNAs from A7 ovaries - replicate 2

description: Library name: A7_rep2


title: Small RNAs from A6 ovaries - replicate 2

description: Library name: A6_rep2


title: Small RNAs from A6 embryos

description: Library name: A6_emb


title: Small RNAs from A5 ovaries - replicate 2

description: Library name: A5_rep2


title: Small RNAs from A4 ovaries - replicate 2

description: Library name: A4_rep2


title: Small RNAs from A4 embryos

description: Library name: A4_emb


title: Small RNAs from A5 embryos

description: Library name: A5_emb


title: Small RNAs from A3 embryos

description: Library name: A3_emb


title: Small RNAs from A3 ovaries - replicate 1

description: Library name: A3_rep1


title: Small RNAs from A2 ovaries - replicate 2

description: Library name: A2_rep2


title: Small RNAs from A1 embryos

description: Library name: A1_emb


title: Small RNAs from B7 embryos

description: Library name: B7_emb

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (ACGAG AGATCGGAAGAGCACACGTCT)
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis


title: Small RNAs from white-sh ovaries

description: Library name: wsh

value: white; white-sh


title: Small RNAs from A1 ovaries - replicate 2

description: Library name: A1_rep2


title: Small RNAs from tj-Gal4 ovaries

description: Library name: tj_gal4

value: white; tj-Gal4/CyO


title: Small RNAs from B4 embryos

description: Library name: B4_emb


title: Small RNAs from MTD ovaries

description: Library name: MTD

value: white P{otu-GAL4::VP16.R}1; P{GAL4-nanos.NGT}40; P{nos-GAL4-VP16} (MTD)


title: Small RNAs from B6 ovaries - replicate 2

description: Library name: B6_rep2

value: Ovary


title: Small RNAs from B2 embryos

description: Library name: B2_emb


title: Small RNAs from double balancers ovaries - w;IF/CyO;Sb/Tm3,Ser

description: Library name: DB

value: white; IF/CyO; Sb/Tm3,Ser


title: Small RNAs from A7 embryos

description: Library name: A7_emb


title: Small RNAs from B7 ovaries - replicate 1

description: Library name: B7_rep1


title: Small RNAs from B2 ovaries - replicate 1

description: Library name: B2_rep1


title: Small RNAs from aub-ago3-double sh ovaries

description: Library name: aubago3sh

value: white; aub-ago3-double sh


title: Small RNAs from B4 ovaries - replicate 1

description: Library name: B4_rep1


title: Small RNAs from B3 ovaries - replicate 1

description: Library name: B3_rep1


title: Small RNAs from attP40 ovaries

description: Library name: attP40

value: white; attP40


title: Small RNAs from B6 ovaries - replicate 1

description: Library name: B6_rep1


title: Small RNAs from attP2 ovaries

description: Library name: attP2

value: white ; attP2


title: Small RNAs from A7 ovaries - replicate 1

description: Library name: A7_rep1


title: Small RNAs from arrestin2/GD ovaries

description: Library name: arr2

value: white; arrestin2/GD


title: Small RNAs from A6 ovaries - replicate 1

description: Library name: A6_rep1


title: Small RNAs from A5 ovaries - replicate 1

description: Library name: A5_rep1


title: Small RNAs from A4 ovaries - replicate 1

description: Library name: A4_rep1


title: Small RNAs from A3 ovaries - replicate 2

description: Library name: A3_rep2


title: Small RNAs from vreteno2/GD ovaries

description: Library name: vret

value: white; vreteno2/GD


title: Small RNAs from A2 ovaries - replicate 1

description: Library name: A2_rep1


title: Small RNAs from Iso1 ovaries - replicate 1

description: Library name: Iso1_rep1


title: Small RNAs from A1 ovaries - replicate 1

description: Library name: A1_rep1


title: R6010_IT1

status: Public on Aug 20 2025

type: RNA

city: Kansas City

first: Irina

last: Tikhanovich

state: Kansas

address: 3901 Rainbow blvd

country: USA

institute: University of Kansas Medical Center

description:
The assay contains only one sample, i.e. one slide. There were 4 tissues on it defined by FOV numbers.
[FOV_tissue ID]  WDA_mouse_1: FOV 1-10 and 41 (low fibrosis); WDA_mouse_2: FOV 11-20 and 42-43 (high fibrosis);  Resolution_mouse_1: FOV  21-30 and 44 (low fibrosis);  Resolution_mouse_2: FOV 31-40 and 45 (high fibrosis);

hyb_protocol: Probe hybridization of ISH probes and antibodies and imaging on the SMI instrument for analyte readout and morphological imaging as well as initial bioinformatic analysis was performed by Nanostring (NanoString Technologies, Inc.) as a part of Technology Access Program

data_processing:
Data on image processing and cell segmentation can be found at He S, Bhatt R, Brown C, Brown EA, Buhr DL, Chantranuvatana K, Danaher P, et al. High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. Nat Biotechnol 2022;40:1794-1806.
data is available as individual transcript XY postions as well as transcripts assigned to individual cells
R6010_IT1_tx_file.csv (Transcript matrix)
R6010_IT1-polygons.csv (Cell boundaries)
R6010_IT1_fov_positions_file.csv (FOV positions)
R6010_IT1_exprMat_file.csv (Expression matrix)

source_name: liver

extract_protocol:
Assay was performed in CosMx® Spatial Molecular Imager (SMI) using Mouse Universal Cell Characterization Panel, 1000-plex, RNA with Cell Segmentation Kit (DAPI Nuclear Stain, CD298/B2M, PanCK/CD45, CD68).  Five-micron tissue sections were cut from FFPE tissue blocks using a microtome, placed in a heated water bath and adhered to Leica Bond Plus Microscope slides (Leica Biosystems). Slides were then dried at 37 °C overnight and stored at 4 °C.
The Spatial Molecular Imager utilizes standard sample preparation methods typical for FISH or IHC on FFPE tissue sections, followed by cyclic image acquisition and registration.

treatment_protocol: Mice were fed high fat Western diet and 20% alcohol in the drinking water (WDA ALD model) for 20 weeks, mice were then placed on chow diet with plain water to assess disease resolution for 4 weeks. 2 mice with high and low fibrosis were selected for each condition and analyzed on the same slide. FOV for WDA: 1-20 and 41-43 ; FOV for Resolution 21-40 and 44-45.

tag: Sex

value: male


title: Campylobacter hepaticus isolated from infected Liver 2

status: Public on Aug 18 2025

city: Gainesville

first: Subhashinie

last: Kariyawasam

state: Florida

address: 1945 SW 16th Ave

department: Comparative, Diagnostic, and Population Medicine

institute: University of Florida

description:
Library name: Sample11
raw data processed with Campylobacter hepaticus  UF2019SK1 as reference

data_processing:
CLC Genomics workbench v.25.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC-genomics bench work
Read count extraction and normalization were performed using CLC genomics workbench
Assembly: NZ_CP065357.1 or NZ_CP031611.1
Supplementary files format and content: fataq.gz file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

organism: Campylobacter hepaticus

source_name: Liver

growth_protocol: C. hepaticus NCTC13823 was cultured on Columbia  agar with  5% Sheep blood agar under microaerophilic conditions (5% CO₂) at 37°C for 48–72 hours and Colonies were harvested, resuspended in Brucella broth, and centrifuged to collect bacterial pellets for RNA extraction

extract_protocol:
Total RNA was extracted using RiboPure™ RNA Purification Kit (Invitrogen™). The samples further processed for rRNA depletion to enrich bacterial mRNA using using MICROBExpress™ Bacterial mRNA Enrichment Kit (Invitrogen™). All steps were carried out according to the manufacturer’s instructions. Quality and concentration of RNA samples in each step was measured using NanoDrop™ 2000/2000c Spectrophotometer (Thermo Scientific™).
Library preparation was done using TruSeq® Stranded mRNA library kit (Illumina Inc., San Diego, CA, USA) as per manufacturer’s recommendations

treatment_protocol: For bile exposure, bacterial pellets were resuspended in chicken bile and incubated at 37°C with 5% CO₂ for 72 hours,LMH cells were cultured in Waymouth’s medium with 10% FBS Cells were then infected with C. hepaticus and incubated for 12 h

value: Liver

value: WT

value: Infected liver sample from field


title: Campylobacter hepaticus isolated from infected Liver 3

description:
Library name: Sample12
raw data processed with Campylobacter hepaticus  UF2019SK1 as reference


title: Campylobacter hepaticus isolated from infected Liver 1

description:
Library name: Sample10
raw data processed with Campylobacter hepaticus  UF2019SK1 as reference


title: LMH 1 infected with Campylobacter hepaticus

description:
Library name: Sample7
raw data processed with Campylobacter hepaticus  UF2019SK1 as reference

value: LMH CRL-2117

value: Chicken hepatocellular carcinoma cell line )

value: Infected in LMH cells


title: LMH 3 infected with Campylobacter hepaticus

description:
Library name: Sample9
raw data processed with Campylobacter hepaticus  UF2019SK1 as reference


title: LMH 2 infected with Campylobacter hepaticus

description:
Library name: Sample8
raw data processed with Campylobacter hepaticus  UF2019SK1 as reference


title: Campylobacter hepaticus in bile 3

description:
Library name: Sample6
raw data processed with Campylobacter hepaticus  UF2019SK1 as reference

value: Incubated in Bile


title: Campylobacter hepaticus in bile 2

description:
Library name: Sample5
raw data processed with Campylobacter hepaticus  UF2019SK1 as reference


title: Campylobacter hepaticus in brucella broth 3

description:
Library name: Sample3
raw data processed with Campylobacter hepaticus  UF2019SK1 as reference

value: Incubated in Luria Bertini broth


title: Campylobacter hepaticus in bile 1

description:
Library name: Sample4
raw data processed with Campylobacter hepaticus  UF2019SK1 as reference


title: Unmodified tRNA-recipient THP1-derived macrophages, rep 2

status: Public on Aug 11 2025

city: Avon

first: Beiyan

last: Zhou

state: Connecticut

address: 263 Farmington Ave, Immunology

department: Immunology

institute: UCONN Health

description:
Library name: UnmodtRNA_2
matrix column 8

data_processing:
Reads in Fastq files were aligned using HISAT2 v2.2.1 on the GRCh38 index, with SAMtools v1.9 for BAM conversion.
A matrix of fragments per kilobase of transcript per million fragments mapped (FPKM) was calculated using Stringtie v2.1.3 with Ballgown on the GRCm38 index.
FPKM data was converted to gene count data matrix using tximport v1.32.0 R package
Assembly: GRCh38
Supplementary files format and content: comma separated file including unfiltered gene FPKM

growth_protocol: in vitro

extract_protocol:
RNA was purified using Zymo Directzol RNA kit
RNA libraries were prepared using the Illumina TruSeq Stranded mRNA library prep kit following manufacter's protocols.

treatment_protocol:
THP1-derived macrophages were differentiated via phorbol 12-myristate-13-acetate (PMA) for 24 hours then transfected with either of the following:
1. small RNA harvested from HeLa cells (UntxtRNA)
2. PNGase F-treated small RNA harvested from HeLa cells (PNGaseRNA)
3. Unmodified synthetic 18-mer tRNA fragment (Unmod-tRNA)
4. Acp3U-8C modified synthetic 18-mer tRNA fragment (Acp3U8C-tRNA)
Cells were incubated for 6 hours post-transfection.

value: THP1-derived macrophage

value: control synthetic 18-mer tRNA


title: Campylobacter hepaticus in brucella broth 2

description:
Library name: Sample2
raw data processed with Campylobacter hepaticus  UF2019SK1 as reference


title: CxSea66_Sanford_S4

status: Public on Aug 13 2025

city: La Jolla

first: K. Garrett

last: Evensen

state: CA

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

hyb_protocol: Spatial transcriptomics experiments were performed with the CosMx Spatial Molecular Imager (NanoString, Seattle, WA), using the 1,000-gene Mouse Neuroscience Panel. Floating sections were placed on a microscope slide, processed, and imaged following manufacturer’s instructions.

scan_protocol: Initial image processing, including cell segmentation and read counting, were performed with AtoMx (NanoString).

data_processing:
Flat files for each CosMx slide were processed using Seurat (v4.9.9.9050). The individual tissue samples from each slide were split and to be treated as individual samples. The FOVs for each tissue (nine/tissue) were combined to form one large FOV/tissue. See metadata_full.csv for treatment-level assignments for each FOV. Cells in the top and bottom 15th percentile for number of features and with counts less than 20 were removed. The samples were then re-merged, normalized using SCTransform (v0.3.5) with a clip range of -10 to 10, and integrated using Harmony (v1.2.3). Each cluster, as determined by Seurat, was further subclustered (resolution 0.1 to 0.3). Cell type annotation was first checked using CellKB (https://www.cellkb.com) after filtering for only “liver” studies. The top five markers, sorted by log2 fold change were used as input genes for CellKB. Cell type annotation was further confirmed using known markers for liver cell types (Immune Cells: Ptprc; B Cells: Cd79a; Cholangiocytes: Spp1, Krt19, Epcam, Sox9; Hepatocytes: Apoa1, Glul, Serpina1a, Apoe; HSC: Dcn, Bmp5, Col1a1, Col1a2; Kupffer Cells: Cd5l, Cd74, C1qa, C1qb; LSEC: Lyve1; NK Cells: Stat4, Nkg7; T Cells: Cd2, Cd3d, Cd3g). Hepatocytes were considered Ccnd1+ if their normalized expression of Ccnd1 was greater than 0.
Unormalized raw counts/cell

extract_protocol: The M lobe (Median lobe) of each mouse liver (n = 12) was excised immediately after euthanasia; one mouse (ID 1177) was first cardiac‑perfused with ice‑cold PBS and zinc‑based fixative (Z‑fix). All excised lobes were incubated in fresh Z‑fix for 48 h at room temperature, then transferred to 70 % ethanol and stored at 4 °C. Livers were processed and embedded in paraffin according to CosMx recommended guidelines. The blocks were sectioned on a microtome to obtain 5 µm scrolls, which were floated on an RNase‑free, molecular‑grade water bath and collected onto slides.


title: CxSea66_Sanford_S1


title: CxSea66_Sanford_S3


title: Acp3U-8C-modified tRNA-recipient THP1-derived macrophages, rep 2

description:
Library name: Acp3U8CtRNA_2
matrix column 10

value: acpu3U-8C-modified synthetic 18-mer tRNA


title: CxSea66_Sanford_S2


title: PNGase treated RNA-recipient THP1-derived macrophages, rep 2

description:
Library name: PNGaseRNA_2
matrix column 6

value: PNGase F-treated small RNA


title: Campylobacter hepaticus in brucella broth 1

description:
Library name: Sample1
raw data processed with Campylobacter hepaticus  UF2019SK1 as reference


title: PNGase treated RNA-recipient THP1-derived macrophages, rep 1

description:
Library name: PNGaseRNA_1
matrix column 5


title: Unmodified tRNA-recipient THP1-derived macrophages, rep 1

description:
Library name: UnmodtRNA_1
matrix column 7


title: Acp3U-8C-modified tRNA-recipient THP1-derived macrophages, rep 1

description:
Library name: Acp3U8CtRNA_1
matrix column 9


title: Untreated RNA-recipient THP1-derived macrophages, rep 2

description:
Library name: UntxtRNA_2
matrix column 4

value: small RNA


title: Untreated RNA-recipient THP1-derived macrophages, rep 1

description:
Library name: UntxtRNA_1
matrix column 3


title: muscle, trained, 72h post exercise, rep_3

status: Public on Aug 05 2025

city: Basel

first: Laura

middle: Maria

last: de Smalen

state: Basel-Stadt

address: Spitalstrasse 41

department: Biozentrum

institute: University of Basel

description:
Library name: Trained_72h_3
ATAC-seq

data_processing:
Reads were trimmed with Trimmomatic v0.39.
Reads were mapped to mouse genome assembly GRCm39 and directly sorted by Bowtie v2.4.4 and Samtools v1.15.
Peak calling was performed using Genrich v.0.6.1
Differential peak analysis was performed using DiffBind v3.4.11 and peaks were annotated using ChIPseeker v1.30.3.
Assembly: GRCm39
Supplementary files format and content: 'ATAC-seq_Differential_Peaks_allconditions-vs-sedentary_normalized_theshold FDR 0.05.xlsx

source_name: quadriceps muscle

extract_protocol:
M. quadriceps muscles were crushed and homogenized in Fastprep tubes (MP Biomedicals) with a metal bead. Nuclei were separated in cell strainers, and myonuclei were isolated through magnetic microbead separation with a PCM1 antibody.
ATAC-seq libraries from PCM1+ myonuclei were prepared as reported in Corces, M.R., et al. (2017).

treatment_protocol: Mice underwent endurance training for 12 weeks by voluntary wheel running (Trained), or no training (Untrained). Untrained and Trained mice underwent one exhaustive bout of exercise and were sacrificed at 0h, 6h or 72h post-exercise. Sedentary mice performed no exercise.

value: quadriceps muscle

value: PCM1+ myonuclei

value: wildtype

value: trained 72h post-exercise


title: muscle, trained, 6h post exercise, rep_3

description:
Library name: Trained_6h_3
ATAC-seq

value: trained 6h post-exercise


title: muscle, trained, 72h post exercise, rep_2

description:
Library name: Trained_72h_2
ATAC-seq


title: muscle, trained, 72h post exercise, rep_1

description:
Library name: Trained_72h_1
ATAC-seq


title: psoriasis vulgaris patient 2

status: Public on Aug 07 2025

city: Jakarta

first: Ariel

last: Pradipta

state: Jakarta

address: Jl. Salemba Raya No.6

department: Biochemistry and Molecular Biology

country: Indonesia

institute: Faculty of Medicine Universitas Indonesia

description:
Library name: PV005
RRMS Adaptive Sampling Strategy

data_processing:
Basecalling was performed using the Dorado model, version 7.8.3, which is embedded in MinKNOW, version 25.03.9. The high-accuracy model was used, and reads with a quality score lower than 9 were filtered, along with base modifications for the detection of 5mC and 5hmC methylation.
Minimap2 2.28-r1209 was used for genome mapping with the GRCh38 build and the genome version GCA_000001405.15.
ModKit 0.4.3 was used to tabulate the bedMethyl pileup file.
Assembly: GRCh38
Supplementary files format and content: The BAM file includes the MM and ML methylation tags, which indicate the methylation sites and confidence.
Supplementary files format and content: The BED file contains bedMethyl tables that tabulate the number of base modifications in each sequencing read at every aligned reference genomic position.

source_name: PBMC

growth_protocol: no growth protocol

extract_protocol:
Approximately 2–3 million PBMCs were centrifuged to obtain a cell pellet, which was then processed for DNA extraction using the Monarch Genomic DNA Purification Kit (T3010, New England Biolabs), following the protocol for Cells, Blood, and Tissues. The eluted DNA was quantified using a Qubit 4 Fluorometer (Invitrogen), and its purity was assessed with a Nanophotometer N50 (Implen). DNA fragment size was evaluated using the TapeStation (4150 Agilent), targeting a fragment length of approximately 10–12 kb.
After shearing, 2,000 ng of DNA was used as the input for preparing the library with the Ligation Sequencing Kit V14 (SQK-LSK114, Oxford Nanopore Technologies), according to the Reduced Representation Methylation Sequencing (RRMS) protocol.

treatment_protocol: no treatment protocol

value: PBMC


title: healthy control

description:
Library name: Healthy
RRMS Adaptive Sampling Strategy


title: psoriasis vulgaris patient 1

description:
Library name: PV001
RRMS Adaptive Sampling Strategy


title: muscle, trained, 6h post exercise, rep_2

description:
Library name: Trained_6h_2
ATAC-seq


title: muscle, trained, 6h post exercise, rep_1

description:
Library name: Trained_6h_1
ATAC-seq


title: muscle, trained, 0h post exercise, rep_2

description:
Library name: Trained_0h_2
ATAC-seq

value: trained 0h post-exercise


title: muscle, trained, 0h post exercise, rep_3

description:
Library name: Trained_0h_3
ATAC-seq


title: muscle, trained, 0h post exercise, rep_1

description:
Library name: Trained_0h_1
ATAC-seq


title: muscle, untrained, 72h post exercise, rep_3

description:
Library name: Untrained_72h_3
ATAC-seq

value: untrained 72h post-exercise


title: generalized pustular psoriasis patient

description:
Library name: PPG003
RRMS Adaptive Sampling Strategy


title: muscle, untrained, 72h post exercise, rep_2

description:
Library name: Untrained_72h_2
ATAC-seq


title: muscle, untrained, 72h post exercise, rep_1

description:
Library name: Untrained_72h_1
ATAC-seq


title: muscle, untrained, 6h post exercise, rep_2

description:
Library name: Untrained_6h_2
ATAC-seq

value: untrained 6h post-exercise


title: muscle, untrained, 6h post exercise, rep_1

description:
Library name: Untrained_6h_1
ATAC-seq


title: muscle, untrained, 0h post exercise, rep_3

description:
Library name: Untrained_0h_3
ATAC-seq

value: untrained 0h post-exercise


title: muscle, sedentary, rep_3

description:
Library name: Sedentary_3
ATAC-seq

value: sedentary


title: muscle, sedentary, rep_2

description:
Library name: Sedentary_2
ATAC-seq


title: muscle, untrained, 0h post exercise, rep_2

description:
Library name: Untrained_0h_2
ATAC-seq


title: Control, biol rep 3

status: Public on Aug 01 2025

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

description: Library name: Control_R3

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt (v4.8).
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.12.1)(www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were aligned to the Gencode GRCh38.p13 genome using STAR (v2.7.11a). Gencode v38 gene annotations were provided to STAR to improve the accuracy of mapping. featureCounts (v2.0.6) was used to count the number of mapped reads to each gene. Only protein coding genes were used in the down-stream analysis
Assembly: GRCh38.p13
Supplementary files format and content: Tab-separated file with raw counts

source_name: SC

growth_protocol: SC cells were seeded in 2 mg/mL type I collagen as single cells and grown for 12 days. Collagen was plated using a sandwich method where a middle  layer of cells in collagen was plated between two layer of collagen. Media containing treatment was then plated on top of the three collagen layers.

extract_protocol:
Middle layer of collagen containing cells was isolated and RNA extracted using the Qiagen RNeasy kit following the manufacturer's protocol.
Library was prepared using NEBNext® rRNA depletion kit according to the manufacurer's protocol.

treatment_protocol: Collagen cultures were treated with drugs at a final concentration of 10 µM for 12 days. Media with drugs was replaced every 2-3 days over the course of the culture.

value: SC

value: Colorectal Cancer

value: WT

value: No drug treatment, 12 days

tag: batch


title: Azithromycin, biol rep 3

description: Library name: Azithromycin_R3

value: 10 µM Azithromycin, 12 days


title: Clindamycin, biol rep 3

description: Library name: Clindamycin_R3

value: 10 µM Clindamycin, 12 days


title: Linezolid, biol rep 3

description: Library name: Linezolid_R3

value: 10 µM Linezolid, 12 days


title: Azithromycin, biol rep 2

description: Library name: Azithromycin_R2


title: Clindamycin, biol rep 2

description: Library name: Clindamycin_R2


title: Linezolid, biol rep 2

description: Library name: Linezolid_R2


title: Control, biol rep 1

description: Library name: Control_R1


title: Azithromycin, biol rep 1

description: Library name: Azithromycin_R1


title: muscle, untrained, 6h post exercise, rep_3

description:
Library name: Untrained_6h_3
ATAC-seq

value: quadriceps muscle

value: PCM1+ myonuclei


title: Linezolid, biol rep 1

description: Library name: Linezolid_R1


title: muscle, untrained, 0h post exercise, rep_1

description:
Library name: Untrained_0h_1
ATAC-seq

value: wildtype


title: muscle, sedentary, rep_1

description:
Library name: Sedentary_1
ATAC-seq


title: Control, biol rep 2

description: Library name: Control_R2


title: A4427_011625

status: Public on Jul 30 2025

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

description: Library name: A4427_011625

data_processing:
ChIP-seq paired-end reads were trimmed and mapped to a custom E. coli MG1655 reference genome (based on GenBank accession NC_000913.3) using fastp (Chen et al., 2018) and Bowtie2 (Langmead et al., 2012) with default parameters, respectively. The custom E. coli MG1655 strain has genomically encoded GFP and RFP genes, in between which custom TnpB target sites were inserted. A genomic lacZ/lacI region and flanking regions, which are partially identical to plasmid-encoded sequences, were masked in all alignments (genomic coordinates 366,386-367,588).
Mapped reads were sorted and indexed using the SAMtools software package (Li et al., 2009) (samtools sort and samtools index commands, respectively). For all data sets, the command samtools view was used to eliminate multi-mapping reads with a MAPQ-score <10 (-bq 10 option).
Alignments were normalised by CPM (Counts Per Million) and converted to 1 bp-bin bigwig files using the deepTools2 (Ramirez et al., 2016) command bamCoverage (--normalizeUsing CPM -bs 1 parameters).
After normalization, genome-mapping reads were visualised in IGV (Robinson et al., 2011). The Bedtools software package (bedtools makewindows -w 1000 and bedtools map -o max) (Quinlan et al., 2010) and IGV were used to generate all genome-wide views. Maximum read coverage values were plotted in 1-kb bins across the genome, as described previously (Cooper et al., 2018).
Peaks were called on pre-normalised alignments using MACS3 (Zhang et al., 2008), with the parameters -g 4500000 --nomodel --extsize 400 -q 0.05 -B, with respect to a non-immunoprecipitated control sample of Eco_dTnpB (-n option). The peak summit coordinates in the MACS3 output summits.bed file were extended to encompass a 200-bp window using the following Bedtools command: bedtools slop -l 100 -r 99. Sequence motifs were identified using MEME ChIP (Bailey et al., 2009) with default parameters.
Assembly: NC_000913.3
Supplementary files format and content: bigWig (.bw) files represent CPM-normalized files, generated using deepTools2 bamCoverage.
Supplementary files format and content: .xlsx file contains meta information on individual sequencing files.
RIP-seq data processing was performed as described in Tang et al. 2024. RIP-seq and corresponding input datasets were processed using cutadapt (v4.2) to remove Illumina adapter sequences, trim low-quality ends from reads, and filter out reads shorter than 15 bp.
Reads were mapped to combined reference files containing the MG1655 genome (NC_000913.3) and relevant plasmid sequences using bwa-mem2 (v2.2.1) with default parameters.
SAMtools (v1.17) was used to sort and index alignments.
Coverage tracks were generated using bamCoverage (v3.5.1) with a bin size of 1, with combined top and bottom strand alignments, or separation of top and bottom strand alignments, and scaling of coverage according to sequencing depth (based on the total number of reads passing initial trimming and length filtering).
Coverage tracks were visualized in IGV.
For transcriptome-wide analyses of RNAs enriched by RIP-seq, aligned reads were assigned to annotated transcriptome features using featureCounts (v2.0.2) with -s 1 for strandedness.
The resulting counts matrices were passed to DESeq2 to calculate fold-change and FDR (using the Benjamini-Hochberg procedure) between input and IP for each annotated transcript.
Comparisons were visualized using ggplot2, plotting the “baseMean” (mean normalized counts across all conditions) against log2(fold change).
Assembly: NC_000913.3
Supplementary files format and content: bigWig (.bw) files represent CPM-normalized files, generated using deepTools2 bamCoverage.
Supplementary files format and content: .xlsx file contains meta information on individual sequencing files.
RNA-seq datasets were processed as described in Tang et al. 2024, using cutadapt (v4.2) to remove Illumina adapter sequences, trim low-quality ends from reads, and filter out reads shorter than 15 bp.
Reads were mapped to combined reference files containing the MG1655 genome (NC_000913.3) and relevant plasmid sequence using bwa-mem2 (v2.2.1) with default parameters.
SAMtools (v1.17) was used to sort and index alignments.
Coverage tracks were generated using bamCoverage (v3.5.1) with a bin size of 1, separation of top and bottom strand alignments, and scaling of coverage according to sequencing depth (based on the total number of reads passing initial trimming and length filtering).
Coverage tracks were visualized in IGV.
For transcriptome-wide analyses of RNAs, aligned reads were assigned to annotated transcriptome features using featureCounts (v2.0.2) with -s 1 for strandedness.
The resulting counts matrices were passed to DESeq2 to calculate fold-change and FDR (using the Benjamini-Hochberg procedure) between input and IP for each annotated transcript.
Comparisons were visualized using ggplot2, plotting the “baseMean” (mean normalized counts across all conditions) against log2(fold change).
Assembly: CP001509.1 and native F. taeanensis genome (MCCC strain 1K06699)
Supplementary files format and content: bigWig (.bw) files represent CPM-normalized files, generated using deepTools2 bamCoverage.
Supplementary files format and content: .xlsx file contains meta information on individual sequencing files.

organism: Escherichia coli

growth_protocol:
For ChIP-seq, E. coli transformations were performed using a single plasmid encoding dCas12f, σE and HTH proteins as well as two non-coding regions downstream of the native dCas12f-encoding gene and in between the σE and HTH-encoding genes. Either dCas12f, σE or HTH were 3xFLAG-tagged. Protein and gRNA components were expressed using separate constitutive promoters. The E. coli growth protocol generally followed the ChIP-seq protocols that were previously described (Hoffmann, Kim, Beh et al. 2022; Meers et al. 2023; Wiegand et al. 2024) with exception for cells grown in liquid media instead of solid media. In brief, colonies were inoculated into 25 ml liquid LB media. After 16 h incubation at 37 °C in liquid LB media with antibiotics, cells were harvested.
For RIP-seq, E. coli cells were grown as for ChIP-sample generation.
For RNA-seq, E. coli transformations were performed using two plasmids encoding a) dCas12f, σE and HTH proteins as well as two non-coding regions encoding a gRNA and a potential ncRNA (protein and gRNA components were expressed using separate constitutive promoters) and b) a plasmid encoding the native F. taeanesis RNA polymerase subunit genes rpoA, rpoB, rpoC and rpoZ driven by two T7 promoters and required induction by 0.01 mM IPTG. Colonies were inoculated into liquid LB media. After around 24 h incubation at 28 °C in liquid LB media with antibiotics, cells were harvested. Native F. taeanensis (MCCC strain 1K06699) cells were grown in Marine Broth 2216 (Difco) for 3 days at 28°C before harvesting.

extract_protocol:
For ChIP-seq, liquid LB overnight E. coli cultures were made up to 40 ml of volume using LB media. Crosslinking and immunoprecipitation generally followed our previous ChIP-seq protocols (Hoffmann, Kim, Beh et al., 2022; Meers et al., 2023), based on previously established protocols (Bonocora and Wade, 2015; Davis et al. 2011). 1 ml of 37% formaldehyde (Fisher Scientific) was added to the tubes containing 40 ml of overnight culture (~1% final concentration), and the solution was mixed immediately by inverting and vortexing. Crosslinking was performed by gently shaking at room temperature for 20 min. To stop crosslinking, 4.6 ml of 2.5 M glycine (~0.25 M final concentration) were added, followed by 10 min incubation with gentle shaking. Cells were pelleted at 4 °C by spinning at 4,000 x g for 8 min. The following steps were performed on ice, using buffers that had been sterile-filtered through a 0.22 µm filter. The supernatant was discarded and pellets were fully resuspended in 40 ml TBS buffer (20 mM Tris-HCl pH 7.5, 0.15 M NaCl) by vortexing. After another spin at 4,000 x g for 8 min at 4°C, the supernatant was removed and the pellet again resuspended in 40 ml TBS buffer. Next, the OD at 600 nm was measured for a 1:1 mixture of the cell suspension and fresh TBS buffer, and a standardised volume equivalent to 40 ml of OD600 = 0.6 was aliquoted into new 50 ml conical tubes. A final 8 min spin at 4,000 x g and 4 °C was performed, cells were pelleted, and the supernatant was discarded. Residual liquid was removed by briefly inverting the tube, and cell pellets were flash frozen using liquid nitrogen and stored at -80 °C or kept on ice for the subsequent steps. Bovine serum albumin (GoldBio) was dissolved in 1X PBS buffer (Gibco) and sterile-filtered to generate a 5 mg/ml BSA solution. For each sample, 25 µl of Dynabeads Protein G (Thermo Fisher) slurry (hereafter referred to as ‘beads’ or ‘magnetic beads’) were prepared for immunoprecipitation. Beads from up to 250 µl of the initial slurry were processed together in a single tube, and washes were performed at room temperature, as follows: The slurry was transferred to a 1.5 ml tube and placed onto a magnetic rack until the beads had fully settled. The supernatant was removed carefully, 1 ml BSA solution was added, and beads were fully resuspended by vortexing, followed by rotating for 30 seconds. This was repeated for three more washes. Finally, beads were resuspended in 25 µl (× n samples) of BSA solution, followed by addition of 4 µl (× n samples) of monoclonal ANTI-FLAG M2 antibody produced in mouse (Sigma-Aldrich). The suspension was moved to 4 °C and rotated for >3 h to conjugate antibodies to magnetic beads. While conjugation was proceeding, crosslinked cell pellets were thawed on ice, resuspended in FA Lysis Buffer 150 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 150 mM NaCl) with protease inhibitor cocktail (Sigma-Aldrich) and transferred to a 1 ml milliTUBE AFA Fiber (Covaris). Samples were sonicated on a M220 Focused-ultrasonicator (Covaris) with the following SonoLab 7.2 settings: min. temp. 4°C, set point 6 °C, max. temp. 8°C, peak power 75.0, duty factor 10, cycles/bursts 200, 17.5 min sonication time. After sonication, samples were cleared of cell debris by centrifugation at 20,000 x g and 4 °C for 20 min. The pellet was discarded, and the supernatant (~1 ml) was transferred into a fresh tube and kept on ice for immunoprecipitation. For non-inmunoprecipitated input control samples, 10 µl (~1%) of the sheared cleared lysate were transferred into a separate 1.5 ml tube, flash-frozen in liquid nitrogen, and stored at -80 °C. After >3 h, the conjugation mixture of magnetic beads and antibody was washed four times as described above, but at 4 °C. Next, the beads were resuspended in 30 µl (× n samples) FA Lysis Buffer 150 with protease inhibitor, and 31 µl of resuspended antibody-conjugated beads were mixed with each sample of sheared cell lysate. Samples were rotated overnight for 12–16 h at 4 °C for immunoprecipitation of FLAG-tagged proteins. The next day, tubes containing beads were placed on a magnetic rack and the supernatant was discarded. Then, six bead washes were performed at room temperature as follows, using 1 ml of each buffer followed by sample rotation for 1.5 min: (1) Two washes with FA Lysis Buffer 150 (without protease inhibitor); (2) one wash with FA Lysis Buffer 500 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); (3) one wash with ChIP Wash Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); and (4) two washes with TE Buffer 10/1 (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were then placed on a magnetic rack, the supernatant was removed, and beads were resuspended in 200 µl of ChIP Elution Buffer (1% (w/v) SDS, 0.1 M NaHCO3), freshly made on the day of the washes. To release protein-DNA complexes from beads, the suspensions were incubated at 65 °C for 1.25 h with gentle vortexing every 15 min to resuspend settled beads. During this incubation, the non-immunoprecipitated input samples were thawed, and 190 µl of ChIP Elution Buffer was added, followed by the addition of 10 µl of 5 M NaCl. After the 1.25 h incubation of the immunoprecipitated samples was complete, tubes were placed back onto a magnetic rack, and the supernatant containing eluted protein-DNA complexes was transferred to a new tube. 9.75 µl of 5 M NaCl were added to ~195 µl of eluate, and samples (both immunoprecipitated and non-immunoprecipitated controls) were incubated at 65°C overnight (without shaking) to reverse-crosslink proteins and DNA. The next day, samples were mixed with 1 µl of 10 mg/ml RNase A (Thermo Fisher) and incubated for 1 h at 37 °C, followed by addition of 2.8 µl of 20 mg/ml Proteinase K (Fisher Scientific) and 1 h incubation at 55 °C. After the addition of 1 ml of buffer PB (QIAGEN recipe), samples were purified using QIAquick spin columns (QIAGEN) and eluted in 40 ul TE Buffer 10/0.1 (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA).
For ChIP-seq, Illumina libraries were generated for immunoprecipitated and input samples using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Sample concentrations for ChIP-seq were determined using the DeNovix dsDNA Ultra High Sensitivity Kit. Starting DNA amounts were standardised such that an approximately equal mass of all input and immunoprecipitated DNA was used for library preparation. After adapter ligation, a single PCR amplification was performed to add Illumina barcodes, and ~450 bp-sized DNA fragments were selected using a two-sided AMPure XP bead (Beckman Coulter) size selection, as follows: The volume of barcoded immunoprecipitated and input DNA was brought up to 50 µl with TE Buffer 10/0.1; in the first size selection step, 0.55X AMPure beads (27.5 µl) were added to the DNA, the sample was placed on a magnetic rack, and the supernatant was discarded and the AMPure beads were kept; in the second size selection step, 0.35X AMPure beads (17.5 µl) were added to the DNA, the sample was placed on a magnetic rack, and the AMPure beads were discarded and the supernatant was kept. The concentration of DNA was determined for pooling using the DeNovix dsDNA High Sensitivity Kit. Illumina libraries were sequenced in paired-end mode on the Illumina NextSeq 500 and Element Biosciences Aviti Cloudbreak Freestyle platform.
The extraction protocol was performed as described in Tang et al. 2024. After overnight growth, cells equivalent to 20 ml of OD600=0.5 were aliquoted. Cells were harvested by centrifugation at 4000 × g for 10 min at 4°C, and the supernatant was removed. The pellet was washed with cold TBS (20 mM Tris-HCl, pH 7.5 at 25°C, 150 mM NaCl) and spun down again as before. The supernatant was removed, and the pellet was flash-frozen in liquid nitrogen and stored at -80°C. Antibodies for immunoprecipitation were conjugated to magnetic beads as follows: for each sample, 60 μl Dynabeads Protein G (Thermo Fisher Scientific) were washed 3× in 1 ml IP lysis buffer (20 mM Tris-HCl, pH 7.5 at 25°C, 150 mM KCl, 1 mM MgCl2, 0.2% Triton X-100), resuspended in 1 ml IP lysis buffer, combined with 20 μl anti-FLAG M2 antibody (Sigma-Aldrich, F1804), and rotated for >3 hours at 4°C. Antibody-bead complexes were washed 2× to remove unconjugated antibodies and resuspended in 60 μl of IP lysis buffer per sample. Flash-frozen pellets were thawed on ice and resuspended in 1.2 ml IP lysis buffer supplemented with 1× cOmplete Protease Inhibitor Cocktail (Roche) and 0.1 U μl−1 SUPERase•In RNase Inhibitor (Thermo Fisher Scientific). To lyse cells, samples were sonicated using a 1/8″ sonicator probe for 1.5 min total (2 s ON, 5 s OFF) at 20% amplitude. To clear cell debris and insoluble material, lysates were centrifuged at 21,000 × g for 15 min at 4 °C, and 1 ml supernatant was transferred to a new tube. At this point, two small volumes of each sample (10 μl for RIP-seq and 10 μl for cDIP-seq) were set aside as “input” starting material and stored at -80°C. For immunoprecipitation, each sample was combined with 60 μl antibody-bead complex and rotated overnight at 4°C. The next day, each sample was washed 3× with 1 ml ice-cold IP wash buffer (20 mM Tris-HCl, pH 7.5 at 25°C, 150 mM KCl, 1 mM MgCl2), using a magnetic rack to immobilize the beads in between each wash. During the final wash, each sample was separated into two separate 500 μl volumes for downstream RIP or cDIP processing. For RIP elution, the supernatant was removed, and beads were resuspended in 1000 μl TRIzol (Thermo Fisher Scientific). After 5 min incubation at RT, the supernatant containing eluted RNA was transferred to a new tube and combined with 200 μl chloroform. Samples were mixed vigorously by inversion, incubated at RT for 3 min, and centrifuged at 12,000 × g for 15 min at 4°C. RNA was isolated from the upper aqueous phase using the RNA Clean & Concentrator-5 kit (Zymo Research) and eluted in 15 μl RNase-free water. RNA from input samples was isolated in the same manner using TRIzol and column purification. Purified RNA was stored at -80°C before proceeding to library preparation.
For RIP-seq library preparation (input and RIP eluates), RNA was fragmented by random hydrolysis by combining 7 μl RNA, 6 μl water, and 2 μl NEBuffer 2, and heating to 92°C for 2 min. To remove DNA and prepare RNA ends for adapter ligation, samples were treated with 2 μl TURBO DNase (Thermo Fisher Scientific) and 2 μl RppH (NEB) in the presence of 1 μl SUPERase•In RNase Inhibitor for 30 min at 37°C. This was followed by treatment with 1 μl T4 PNK (NEB) in 1× T4 DNA ligase buffer (NEB) for 30 min at 37°C. Reactions were column-purified using the Zymo RNA Clean and Concentrator-5 kit and eluted in 10.5 μl RNase-free water. RNA concentrations were quantified using the DeNovix RNA Assay. Illumina sequencing libraries were prepared using the NEBNext Small RNA Library Prep kit. Illumna ibraries were sequenced in paired-end mode on the Illumina NextSeq 500 and Element Biosciences Aviti Cloudbreak Freestyle platform.
For RNA-seq, overnight cultures were generally processed as described in Tang et al. 2024. Cells equivalent to 20 ml of OD600 = 0.5 were aliquoted and harvested by centrifugation at 4000 × g for 10 min at 4°C, and the supernatant was removed. The pellet was washed with cold TBS (20 mM Tris-HCl, pH 7.5 at 25°C, 150 mM NaCl) and spun down again as before. The supernatant was removed, and the pellet was flash-frozen in liquid nitrogen and stored at -80°C. Cell pellets were resuspended in 1,000 μl TRIzol (Thermo Fisher Scientific). After 5 min incubation at RT, the supernatant containing eluted RNA was transferred to a new tube and combined with 200 μl chloroform. Samples were mixed vigorously by inversion, incubated at RT for 3 min, and centrifuged at 12,000 × g for 15 min at 4°C. RNA was isolated from the upper aqueous phase using the RNA Clean & Concentrator kit (Zymo Research) and eluted in 15 μl RNase-free water. Purified RNA was stored at -80°C before proceeding to library preparation.
For RNA-seq library preparation, RNA was fragmented by random hydrolysis by combining 7 μl RNA, 6 μl water, and 2 μl NEBuffer 2, and heating to 92°C for 2 min. To remove DNA and prepare RNA ends for adapter ligation, samples were treated with 2 μl TURBO DNase (Thermo Fisher Scientific) and 2 μl RppH (NEB) in the presence of 1 μl SUPERase•In RNase Inhibitor for 30 min at 37°C. This was followed by treatment with 1 μl T4 PNK (NEB) in 1× T4 DNA ligase buffer (NEB) for 30 min at 37°C. Reactions were column-purified using the Zymo RNA Clean and Concentrator-5 kit and eluted in 10.5 μl RNase-free water. RNA concentrations were quantified using the DeNovix RNA Assay. Illumina sequencing libraries were prepared using the NEBNext Small RNA Library Prep kit, and libraries were sequenced on an Illumina NextSeq 500 or Element Biosciences Aviti instrument in paired-end mode with 75 or 150 cycles per end.

treatment_protocol:
For ChIP-seq, dCas12f systems were heterologously expressed in E. coli MG1655 using constitutive promoters.
For RIP-seq, dCas12f systems were heterologously expressed in E. coli MG1655 using constitutive promoters.
For RNA-seq, dCas12f systems were heterologously expressed in E. coli BL21(DE3) using constitutive promoters and the native F. taeanensis RNA polymerase was induced from T7 promoters with 0.01 mM IPTG.

tag: culture type

value: Liquid cell culture

tag: induction parameters

value: constitutive expression, 0.01 mM IPTG for F. taeanensis RNAP, 24 h, 28°C


title: A4490_112224

description: Library name: A4490_112224


title: A4422_011625

description: Library name: A4422_011625


title: A4500_112224

description: Library name: A4500_112224


title: A4481_011625

description: Library name: A4481_011625


title: A4455_011625

description: Library name: A4455_011625


title: A4464_112224

description: Library name: A4464_112224


title: A4488_112224

description: Library name: A4488_112224


title: A4473_092424

description: Library name: A4473_092424

organism: Flagellimonas taeanensis

source_name: MCCC strain 1K06699

value: MCCC strain 1K06699

value: native expression in F. taeanensis


title: A4425_011625

description: Library name: A4425_011625


title: A4420_011625

description: Library name: A4420_011625


title: A4442_011625

description: Library name: A4442_011625


title: A4476_011625

description: Library name: A4476_011625


title: A4467_011625

description: Library name: A4467_011625


title: Clindamycin, biol rep 1

description: Library name: Clindamycin_R1


title: A4470_112224

description: Library name: A4470_112224


title: A4457_112224

description: Library name: A4457_112224


title: A4459_112224

description: Library name: A4459_112224


title: A4446_112224

description: Library name: A4446_112224


title: A4444_112224

description: Library name: A4444_112224


title: CTinput_Pcgf1KOPI_mb_EED_lot1

description: Library name: Sample 8

data_processing:
Reads were aligned to UCSC mm9 or UCSC hg38 using bowtie2. The SAM files were converted to the BAM format using Samtools. The PCR duplicates were removed by Picardtools. The BAM files were converted to bigwig files by deepTools2 for visualization. The bigwig files were normalized to reads per million mapped sequence reads (RPKM), and also normalized by the factor (Count of antibody mapped to mm9) / (Count of antibody mapped to hg38) * (Count of corresponding input mapped to hg38) / (Count of corresponding input mapped to mm9).
Assembly: mm9
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

value: 9.5 dpc mouse embryonic midbrain

value: Tamoxifen+ :Bortezomib+

value: Pcgf1 KO

value: no


title: A4461_112224

description: Library name: A4461_112224


title: A4473_111324

description: Library name: A4473_111324


title: A4440_112224

description: Library name: A4440_112224


title: A4414_011625

description: Library name: A4414_011625


title: A4449_112224

description: Library name: A4449_112224


title: A4485_112224

description: Library name: A4485_112224


title: A4443_112224

description: Library name: A4443_112224


title: A4439_112224

description: Library name: A4439_112224


title: A4438_112224

description: Library name: A4438_112224


title: A4407_112224

description: Library name: A4407_112224


title: A4409_112224

description: Library name: A4409_112224


title: A4434_112224

description: Library name: A4434_112224


title: A4400_112224

description: Library name: A4400_112224


title: A4412_112224

description: Library name: A4412_112224


title: A4431_112224

description: Library name: A4431_112224


title: A4501_092424

description: Library name: A4501_092424


title: A4411_112224

description: Library name: A4411_112224


title: A4413_112224

description: Library name: A4413_112224


title: A4408_112224

description: Library name: A4408_112224


title: A4415_092424

description: Library name: A4415_092424


title: A4492_011625

description: Library name: A4492_011625

value: Monoclonal ANTI-FLAG M2 antibody, produced in mouse (Sigma-Aldrich, cat. number:F1804)

tag: epitop tag_on_sample_protein

value: constitutive expression, 16 h, 37°C

tag: flag-tagged protein

value: σE


title: A4503_011625

description: Library name: A4503_011625


title: A4463_011625

description: Library name: A4463_011625


title: A4433_092424

description: Library name: A4433_092424


title: A4456_011625

description: Library name: A4456_011625

value: constitutive expression, 0.01 mM IPTG for F. taeanensis RNAP, 16 h, 37°C


title: A4491_092424

description: Library name: A4491_092424


title: A4465_092424

description: Library name: A4465_092424


title: A4478_011625

description: Library name: A4478_011625

value: HTH


title: A4475_011625

description: Library name: A4475_011625


title: A4452_011625

description: Library name: A4452_011625


title: A4480_011625

description: Library name: A4480_011625


title: A4450_011625

description: Library name: A4450_011625


title: A4435_011625

description: Library name: A4435_011625


title: A4441_011625

description: Library name: A4441_011625


title: K562, TT-seq, dTAG7, rep2, 1h

city: Göttingen

last: Žumer

address: Am Faßberg 11

department: Department of Molecular Biology

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciences

data_processing:
TT-seq reads were aligned to the human reference genome (GRCh38) that had been augmented with synthetic RNA spike-in sequences. We utilized STAR version 2.6.0 (Dobinet al., 2013) for alignment with the following parameters: --runThreadN24 --readFilesCommandzcat--outFilterTypeBySJout--outFilterMultimapNmax1 --alignSJoverhangMin8 --alignSJDBoverhangMin1 --outFilterMismatchNmax999 --outFilterMismatchNoverLmax0.02 --alignIntronMin20 --alignIntronMax1000000 --alignMatesGapMax1000000. For TT-seq and mNET-seq, the quantifications of reads aligning to the spike-in sequences were used to calculate normalization factors, ensuring accurate comparison of expression levels across samples as in Zumer et al., 2024. Spike-in read counts were assessed by summarizeOverlaps function (Bioconductor package “IRanges”) and normalization factors were calculated with DESeq2 (Love et al., 2014).
Differential gene expression analysis using spike-in-normalized counts was performed with DESeq2.
Assembly: GRCh38
Supplementary files format and content: bigwig
Supplementary files format and content: results table generated with DESeq2 contains the differential gene expression analysis output including a column with the gene names.

source_name: genome edited K562

growth_protocol: K562 human cells were sourced from the DSMZ-German Collection of Microorganisms and Cell Cultures GmbH. K562 cells and genome edited cell lines were cultured in RPMI medium (Thermo Fisher Scientific), enriched with 10% fetal bovine serum and 1x GlutaMax, within a humidified incubator at 37°C and 5% CO2. These cells underwent subculturing every 2-3 days, maintaining a density of 150,000 to 700,000 cells/mL. To deplete IWS1-dTAG, the culture medium was supplemented with 500 nM of dTAG7 ligand, previously dissolved in dimethyl sulfoxide (DMSO) at a 10 mM concentration. Control cells were treated with solvent only with the same treatment time.

extract_protocol:
Subsequent to labeling, cells were lysed using Qiazol (QIAGEN), and the lysates were spiked with three 4sU-labeled and three unlabeled synthetic spike-in RNAs. The extraction of total RNA was then carried out using the standard Qiazol-chloroform extraction method. Post-extraction, the RNA was fragmented for 10 seconds using an S220 Focused-ultrasonicator (Covaris). This was followed by the biotinylation of 4sU-incorporated RNA fragments. For each sample, biotinylation was executed in two separate reactions, each containing 150 µg of fragmented RNA, 10 mM Tris (pH 7.5), 1 mM EDTA (pH 8.0), 200 µg/mL HPDP-biotin, and 40% DMSO. The reactions were then combined post-purification using the µMACS Streptavidin Kit (Miltenyi). The 4sU-labeled RNA was eluted using 100 mM DTT and further purified with the miRNeasy Micro kit (Qiagen).
100 ng of the purified, 4sU-labeled RNA was used for NGS library preparation using the Stranded Total RNA Prep with Ribo-Zero Plus kit (Illumina), according to the manufacturer’s instructions with a 5-minute RNA fragmentation step and seven cycles of PCR amplification . Finally, the quality of the libraries was assessed using a Fragment Analyzer. The libraries were then pooled and sequenced paired-end with a 75-cycle sequencing run on a Nextseq550 (Illumina) platform.
Total stranded RNA-seq

treatment_protocol: TT-seq was performed as previously described bySchwalbet al., 2016 andZumeret al., 2021, utilizing two biological replicates. For each replicate, 30 million cells were treated with dTAG7 or DMSO solvent only for 1 hour, followed by a5 minuteincubation with 500 µM 4-thiouridine (4sU) to label the RNA.

value: genome edited K562

value: chronic myelogenous leukemia

value: IWS1 N-terminal dTAG

value: dTAG7 1h


title: A4416_112224

description: Library name: A4416_112224

value: Liquid cell culture


title: K562, TT-seq, dTAG7, rep1, 1h


title: K562, TT-seq, DMSO, rep1, 1h

value: DMSO 1h


title: A4482_031224

description: Library name: A4482_031224

value: constitutive expression, 0.01 mM IPTG for F. taeanensis RNAP, 24 h, 28°C


title: A4471_031224

description: Library name: A4471_031224


title: A4486_031224

description: Library name: A4486_031224


title: A4477_031224

description: Library name: A4477_031224


title: A4464_032724

description: Library name: A4464_032724


title: A4485_032724

description: Library name: A4485_032724


title: A4416_032724

description: Library name: A4416_032724


title: A4408_032724

description: Library name: A4408_032724


title: A4413_032724

description: Library name: A4413_032724


title: A4479_031224

description: Library name: A4479_031224


title: A4446_032724

description: Library name: A4446_032724


title: A4497_021424

description: Library name: A4497_021424


title: A4498_021424

description: Library name: A4498_021424


title: A4493_021424

description: Library name: A4493_021424


title: A4431_032724

description: Library name: A4431_032724


title: K562, TT-seq, DMSO, rep2, 1h


title: A4496_021424

description: Library name: A4496_021424


title: A4491_021424

description: Library name: A4491_021424


title: A4503_021424

description: Library name: A4503_021424


title: A4487_021424

description: Library name: A4487_021424


title: A4472_021424

description: Library name: A4472_021424


title: A4466_021424

description: Library name: A4466_021424


title: A4465_021424

description: Library name: A4465_021424


title: A4437_021424

description: Library name: A4437_021424


title: A4447_021424

description: Library name: A4447_021424


title: A4433_021424

description: Library name: A4433_021424


title: A4500_032724

description: Library name: A4500_032724


title: A4430_021424

description: Library name: A4430_021424


title: A4484_031224

description: Library name: A4484_031224


title: A4425_021424

description: Library name: A4425_021424


title: A4417_021424

description: Library name: A4417_021424


title: A4420_021424

description: Library name: A4420_021424


title: A4483_061224

description: Library name: A4483_061224


title: A4457_061224

description: Library name: A4457_061224


title: A4441_061224

description: Library name: A4441_061224


title: A4443_061224

description: Library name: A4443_061224


title: A4412_061224

description: Library name: A4412_061224


title: A4481_021424

description: Library name: A4481_021424


title: A4478_031224

description: Library name: A4478_031224


title: A4489_031224

description: Library name: A4489_031224


title: A4475_031224

description: Library name: A4475_031224


title: A4474_031224

description: Library name: A4474_031224


title: A4476_031224

description: Library name: A4476_031224


title: A4481_031224

description: Library name: A4481_031224


title: A4400_061224

description: Library name: A4400_061224


title: A4472_031224

description: Library name: A4472_031224


title: A4455_031224

description: Library name: A4455_031224


title: A4492_031224

description: Library name: A4492_031224


title: A4458_031224

description: Library name: A4458_031224


title: A4467_031224

description: Library name: A4467_031224


title: A4445_031224

description: Library name: A4445_031224


title: A4442_031224

description: Library name: A4442_031224


title: A4427_031224

description: Library name: A4427_031224


title: A4425_031224

description: Library name: A4425_031224


title: A4422_031224

description: Library name: A4422_031224


title: A4417_031224

description: Library name: A4417_031224


title: A4420_031224

description: Library name: A4420_031224


title: A4461_061224

description: Library name: A4461_061224


title: A4414_031224

description: Library name: A4414_031224


title: A4459_021424

description: Library name: A4459_021424


title: A4464_021424

description: Library name: A4464_021424


title: A4485_021424

description: Library name: A4485_021424


title: A4461_021424

description: Library name: A4461_021424


title: A4457_021424

description: Library name: A4457_021424


title: A4446_021424

description: Library name: A4446_021424


title: A4436_021424

description: Library name: A4436_021424


title: A4443_021424

description: Library name: A4443_021424


title: A4413_021424

description: Library name: A4413_021424


title: A4416_021424

description: Library name: A4416_021424


title: A4412_021424

description: Library name: A4412_021424


title: A4408_021424

description: Library name: A4408_021424


title: A4400_021424

description: Library name: A4400_021424


title: drought treated plant time 0 (30% SWC)

status: Public on Jul 29 2025

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Tissue sections were imaged at single-molecule resolution to capture transcript localization. For this experiment we used MERFISH 2.0 Chemistry, and the experiment was done on the Merscope Ultra Platform.
The .vzg file is the standard output format from Vizgen's MERSCOPE platform for viewing and interacting with complex spatial transcriptomics data.

organism: Arabidopsis thaliana

source_name: Leaves, drought treated at time 0

growth_protocol: Spatial transcriptomics was performed using the MERSCOPE platform (Vizgen) to visualize gene expression across Arabidopsis leaf tissue under four water conditions: well-watered (time 0 and 15 minutes), drought, and 15 minutes post-rehydration.

extract_protocol: Leaf samples were collected (leaf number 7/20 from top-youngest), fixed, and processed according to the Vizgen protocol. Tissue sections were imaged at single-molecule resolution to capture transcript localization. For this experiment we used MERFISH 2.0 Chemistry, and the experiment was done on the Merscope Ultra Platform. Tissue sections were imaged at single-molecule resolution to capture transcript localization. For this experiment we used MERFISH 2.0 Chemistry, and the experiment was done on the Merscope Ultra Platform.

treatment_protocol: W0 = well-watered time 0 (1 hour after light turns on); D0 = drought time 0 (30% SWC);W15 = well-watered time 15 minutes;R15 = drought treated plants that were rehydrated for 15 minutes.

tag: tissue

value: Leaves

value: drought treated at time 0


title: A4431_021424

description: Library name: A4431_021424


title: well-watered plants time 0 (1 hour after light turns on)

source_name: Leaves, well-watered at time 0

value: well-watered at time 0


title: A4407_021424

description: Library name: A4407_021424


title: well-watered plants time 15 minutes

source_name: Leaves, well-watered for 15 ins

value: well-watered for 15 ins


title: A4411_021424

description: Library name: A4411_021424


title: drought treated plants that were rehydrated for 15 minutes

source_name: Leaves, rehydrated for 15 mins

value: rehydrated for 15 mins


title: camta1 stress recovery 15 minutes replicate 1

status: Public on Jul 23 2025

description: Library name: camta1_R15_1

data_processing:
Raw data were first checked with Fastqc and then mapped to TARI10 with STAR. The gene expression profiles were quantified with HOMER.
Assembly: TAIR10
Supplementary files format and content: Tab-separated values file

source_name: Leaves

extract_protocol:
Col-0 and camta1 mutants (SALK_008187.38.30.x) were grown on plates for 14 days. Seedlings of the same developmental stage were then trasfered to control plates and moderate low water plates (50% water content). after 14 days on stress plates, plants were transfered to control plates with increased water availability, and whole rosettes (n= 3 – 4) were sampled and frozen. Treatments: Well-watered, moderate stress, recovery 15 mins, well-watered (controlled for plant transfer and watering and collected after 15 mins).
The library was prepared using illumina mRNA prep kit following manufacturer's protocols.

value: bulk

value: Recovery from moderate osmotic stress (collected 15 minutes after trasfer to control plates)


title: camta1 stress recovery 15 minutes replicate 3

description: Library name: camta1_R15_3


title: camta1 well-watered 15 minutes replicate 3

description: Library name: camta1_W15_3

value: Well-watered (Control plates, with 100% water content, collected 15 minutes after transfer to new control plates with additional water)


title: camta1 well-watered 15 minutes replicate 1

description: Library name: camta1_W15_1


title: camta1 moderate stress replicate 2

description: Library name: camta1_D_2

value: Moderate osmotic stress (low-water plates, with 50% water content based on method describes in Gonzalez et al., 2023)


title: camta1 stress recovery 15 minutes replicate 2

description: Library name: camta1_R15_2


title: camta1 moderate stress replicate 3

description: Library name: camta1_D_3


title: camta1 well-watered 15 minutes replicate 2

description: Library name: camta1_W15_2


title: camta1 moderate stress replicate 4

description: Library name: camta1_D_4