title: siControl, DMSO control, 3

status: Public on Jul 23 2026

city: Vienna

first: Aleksandra

middle: S

last: Anisimova

address: Dr. Bohr Gasse 9

country: Austria

institute: Max Perutz Labs, Vienna BioCenter, University of Vienna, Medical University of Vienna

description: Library name: DMSO_siControl_3

data_processing:
The quality- and adapter-trimmed reads were aligned to human genome hg38 using GENCODE annotation (release 36) with STAR v2.7.5c allowing up to one or two mismatches. Gene read counts were obtained with featureCounts v2.0.1.
Assembly: hg38
Supplementary files format and content: csv, gene read count table

growth_protocol: HCT116 WT cells were a kind gift from Prof. Manuela Baccarini (MPL, University of Vienna). HCT116 cells were cultured in McCoy’s 5A (modified) medium (Sigma, M9309) supplemented with 10% fetal bovine serum (Gibco, 10437028), 2 mM L-Glutamine (Sigmam, G7513), 1% Pen/Step (Sigma, P0781) in a humidified incubator at 37°C and 5% CO2. For siRNA knockdown, cells were transfected with ON-TARGETplus Human IGF2BP2 (Dharmacon, L-017705-00-0005) or IGF2BP3 (Dharmacon, L-003976-00-0005) SMARTpool siRNAs  at 75 nM for 48 hours using DharmaFECT 2 (Dharmacon, T-2002-01). ON-TARGETplus nontargeting siRNA #1 (Dharmacon, D-001810-01-05) was used as a control.

extract_protocol:
One ~80% confluent well of a 6-well plate per condition (three biological replicates per condition) was washed with ice-cold PBS (Sigma) supplemented with 100 mg/mL cycloheximide, lysed on a plate on ice with 350 μL of ice-cold lysis buffer (20 mM HEPES pH 7.3, 150 mM KCl, 5 mM MgCl2, 1% Triton X-100, 100 mg/mL cycloheximide, 1 mM DTT, 1x EDTA-free protease inhibitor cocktail), scraped, and transferred to 1.5 mL RNase-free tube. Cell lysates were passed three times through the 27G needle, incubated on ice for 10 min with intermittent vortexing, and clarified on a table-top centrifuge at maximum speed (20,000 g) for 20 min at 4°C. Total RNA concentration in the lysate was estimated using OD A260 measurement on Nanodrop. The lysate concentrations were brought to 240 ng/μL, 15 μL aliquots were taken for matching RNA-Seq.
RNA-Seq libraries were prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7765L) and sequenced on a NovaSeq SP on SR100 (Illumina) aiming for 30 million reads per sample on average.

treatment_protocol: Endoplasmic reticulum (ER) stress was induced with 5 µg/mL tunicamycin (TM) for 4 hours (1:1000 DMSO was used as a control).

value: human colorectal carcinoma

value: DMSO control


title: Brain single cell 237

status: Public on Jul 22 2026

type: SRA

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Library name: Sample 237

library_source: transcriptomic

data_processing:
The sequencing reads were first aligned to the Ensembl mouse reference genome GRCm39 with STRA (version 2.7.3a). The duplicated reads were removed using samtools software (version 1.16.1). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
Brain tissue from adult mice was mechanically and enzymatically dissociated, and vascular fragments were isolated, followed by further digestion to obtain a single-cell suspension.
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: tissue

value: brain

tag: cell type

value: microglia


title: Brain single cell 236

description: Library name: Sample 236


title: OS71701

city: 北京市

first: Zhaochen

last: Wang

address: 2 Yuanmingyuan West Road, Haidian District, Beijing

country: China

institute: China Agricultural University

description: Library name: B9O

data_processing:
Clean paired-end RNA-seq reads were aligned to the Bos taurus reference genome (ARS-UCD1.2) using HISAT2 (v2.2.1) with default settings except that only uniquely mapping reads were retained.
Gene-level read quantification was performed with featureCounts (Subread) using parameters -t exon -g gene_id against the corresponding GTF annotation.
Assembly: ARS-UCD1.2
Supplementary files format and content: counts_hisat2_all.txt

molecule: polyA RNA

organism: Bos taurus

source_name: ovary

extract_protocol:
For single oocytes and cumulus cells (CCs), cells were lysed directly using the Single Cell Full-Length mRNA Amplification Kit (Vazyme). For mural granulosa cells (MGCs), total RNA was extracted using standard protocols.
For oocytes and CCs, cDNA was amplified using the SMART-seq2 protocol and libraries were constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme). For MGCs, standard bulk RNA-seq libraries were constructed. All libraries were sequenced on an Illumina NovaSeq 6000 platform.

value: ovary

value: Oocyte

tag: treatment

value: oocyte from small follicle (3.8mm)


title: OS50502

description: Library name: B8O


title: Brain single cell 235

description: Library name: Sample 235


title: OS70702

description: Library name: B7O

value: oocyte from small follicle (3.7mm)


title: Brain single cell 234

description: Library name: Sample 234


title: OM62201

description: Library name: D1O

value: oocyte from medium follicle (6.2mm)


title: OS70701

description: Library name: B6O


title: Brain single cell 233

description: Library name: Sample 233


title: OS62003

description: Library name: B5O


title: Control, parental, sample 1, 2

description: Library name: Control_parental_1_rep2

data_processing:
The quality- and adapter-trimmed reads were aligned to human genome hg38 using GENCODE annotation (release 36) with STAR v2.7.5c allowing up to two mismatches per read.
Assembly: hg38
Supplementary files format and content: csv, gene read count table

organism: Homo sapiens

growth_protocol: HCT116 conditionally expressing doxycycline-inducible (tetON) OsTIR1 were obtained from the Masato Kanemaki lab (Natsume et al. 2016).  HCT116 cells were cultured in McCoy’s 5A (modified) medium (Sigma, M9309) supplemented with 10% fetal bovine serum (Gibco, 10437028), 2 mM L-Glutamine (Sigmam, G7513), 1% Pen/Step (Sigma, P0781) in a humidified incubator at 37°C and 5% CO2. For knockout cell line generation, gRNA sequences (IGF2BP3 KO clones E4 and A3: 5′TGGCACCGACTGATAGAGCT 3′; clone D12: 5′ACGCGTAGCCAGTCTTCACC 3′; IGF2BP2 KO clones F6 and B7: 5′GAGCTGCCGGAGGTCGTCGG 3′; clone G6: 5′AGGCGTAGCCGGACTTCAGC 3') were cloned into the pSpCas9 (BB)-2A-GFP (PX458) (plasmid #48138; Addgene) (Ran et al. 2013 ). HCT116 tetON OsTIR1 cells were transiently transfected using jetOPTIMUS reagent (Tamar, 101000051), and GFP-positive single-cell clones were FACS sorted at BD FACSAria IIIu at Max Perutz Labs BioOptics FACS Facility.

extract_protocol:
Total RNA was isolated using peqGOLD TriFast (Peqlab, VWR), treated with RNase-free DNase I (NEB), and re-purified with peqGOLD TriFast (Peqlab, VWR). RNA precipitation was done using isopropanol method.
Total RNA sequencing libraries were prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7765L) by Vienna BioCenter NGS facility sequenced on a NovaSeq S4 on PE100 (Illumina) with 55 million reads per sample on average.

treatment_protocol: HCT116 tetON OsTIR1 IGF2BP3 KO clones E4, A3, and D12 (in duplicates) and parental cells (four replicates) were treated with 5 µg/mL tunicamycin (TM) for 4 hours (1:1000 DMSO was used as a control).

tag: cell line

tag: genotype


title: Brain single cell 232

description: Library name: Sample 232


title: OS62004

description: Library name: B4O

value: oocyte from small follicle (3.6mm)


title: OS62005

description: Library name: B3O

value: oocyte from small follicle (3.5mm)


title: Brain single cell 231

description: Library name: Sample 231


title: OS50506

description: Library name: W6O

value: oocyte from small follicle (3.3mm)


title: Brain single cell 230

description: Library name: Sample 230


title: OS70501

description: Library name: B2O

value: oocyte from small follicle (3.2mm)


title: OS50501

description: Library name: B1O

value: oocyte from small follicle (3.1mm)


title: Brain single cell 229

description: Library name: Sample 229


title: Brain single cell 227

description: Library name: Sample 227


title: CL71801

description: Library name: E8C

value: cumulus cells

value: CCs from large follicle (11.5mm)


title: CL70504

description: Library name: E9C

value: CCs from large follicle (11.6mm)


title: Brain single cell 226

description: Library name: Sample 226


title: Brain single cell 225

description: Library name: Sample 225


title: Brain single cell 228

description: Library name: Sample 228


title: CL72101

description: Library name: E7C

value: CCs from large follicle (11.3mmmm)


title: Brain single cell 224

description: Library name: Sample 224


title: CL62803

description: Library name: E6C

value: CCs from large follicle (11.2mm)


title: Control, parental, sample 1, 1

description: Library name: Control_parental_1_rep1

value: human colorectal carcinoma

value: DMSO control


title: Brain single cell 223

description: Library name: Sample 223

value: brain

value: microglia


title: CL70703

description: Library name: E5C

value: ovary

value: CCs from large follicle (10.2mm)


title: Brain single cell 222

description: Library name: Sample 222


title: CL50505

description: Library name: W5C


title: Brain single cell 221

description: Library name: Sample 221


title: CL62802

description: Library name: E4C


title: Control, parental, sample 2, 2

description: Library name: Control_parental_2_rep2


title: Control, IGF2BP2 KO, clone G6, 2

description: Library name: Control_IGF2BP2KO_G6_rep2

value: IGF2BP2 KO, clone G6, Tet-OsTIR1-PURO

value: Tunicamycin (TM)


title: Brain single cell 220

description: Library name: Sample 220


title: CL72102

description: Library name: E3C

value: CCs from large follicle (10.0mm)


title: IM12_Nonsymptomatic

city: Nijmegen

first: Niels

last: Velthuijs

address: Houtlaan 4

department: Cell Biology

country: Netherlands

institute: Radboud University

description: Library name: IM12_Nonsymptomatic

library_source: genomic

data_processing:
Preprocessing and quality control were performed using the ATAC-seq pipeline from seq2science (v1.2.5) for adapter trimming (fastp), alignment (bwa-mem2, hg38), filtering of valid reads, applying a Tn5 shift, and creating a trackhub using default settings. Based on read numbers, duplicate read ratios, TSSE enrichment, and FriP, low-quality and outlying samples were removed.
We removed all paired-end information from the BAM files and called peaks using macs3 (v3.0.4) on the pooled BAM files per group. Using the combine_peaks and coverage_table scripts from GimmeMotifs (v0.18.0), we merged the three sets of peaks into a consensus set of 200bp-wide peaks and counted reads per sample in these peaks. Peaks were filtered for having at least 0.3 CPM in more than 15 samples of a single patient group.
Assembly: Hg38
Supplementary files format and content: Counts.tsv contains all called peaks (rows, first column describes peak locations) and all samples (columns, as described in samples.txt)

molecule: genomic DNA

source_name: Blood

extract_protocol:
Ficoll PBMC isolation followed by MACS pan-monocyte isolation kit on fresh blood
https://doi.org/10.1002/0471142727.mb2129s109

value: Blood

tag: donor group

value: Nonsymptomatic

value: Monocyte


title: CL70503

description: Library name: E2C

value: cumulus cells


title: Brain single cell 219

description: Library name: Sample 219


title: Brain single cell 218

description: Library name: Sample 218


title: ER stress (TM), IGF2BP3 KO, clone E4, 1

description: Library name: TM_IGF2BP3KO_E4_rep1

value: IGF2BP3 KO, clone E4, Tet-OsTIR1-PURO


title: CL71802

description: Library name: E1C

value: CCs from large follicle (9.6mm)


title: CM71001

description: Library name: C10C

value: CCs from medium follicle (7.1mm)


title: Brain single cell 216

description: Library name: Sample 216


title: Brain single cell 217

description: Library name: Sample 217


title: Brain single cell 306

description: Library name: Sample 306

value: endothelial


title: CM72404

description: Library name: C9C

value: CCs from medium follicle (7.0mm)


title: Brain single cell 214

description: Library name: Sample 214


title: CM71804

description: Library name: C7C


title: Brain single cell 215

description: Library name: Sample 215


title: IM06_Mild

description: Library name: IM06_Mild

value: Mild


title: CM71002

description: Library name: C6C


title: CM71805

description: Library name: C8C


title: Brain single cell 213

description: Library name: Sample 213

value: brain


title: CM72403

description: Library name: C5C

value: CCs from medium follicle (6.7mm)


title: Brain single cell 212

description: Library name: Sample 212

value: microglia


title: T47Dbs1 PBS biorep 3

city: Richardson

first: Nikki

last: Delk

address: 800 West Campbell Road

department: Biological Sciences

country: USA

institute: University of Texas at Dallas

description: Library name: 341-15

data_processing:
Fastq files were checked for quality using fastqc and fastq_screen and were quality trimmed using fastq-mcf
Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using TopHat
duplicates were marked using picard-tools, read counts were generated using featureCounts and differential expression analysis was performed using edgeR
Assembly: hg19
Supplementary files format and content: The Excel files contain RNA-seq differential expression analysis results, gene overlap analyses identifying shared and unique differentially expressed genes, genes of interest (GOI), and Gene Ontology (GO) over-representation analysis (ORA) results with associated enrichment statistics.

growth_protocol: To establish stable chronic IL-1-exposed sublines, MCF7 cells were cultured in DMEM/10% FB Essence (FBE) containing 0.5ng/mL IL-1α or 0.5ng/mL IL-1β for 6 months and T47D cells were cultured in RPMI 1640/10% FBE containing 0.5 ng/mL IL-1α or IL-1β for 6 months (7 months for the T47Dbs1 subline due to slowed prolifer-ation and expansion). Following chronic IL-1 exposure, cells were moved out of IL-1-containing medium and maintained in normal growth medium without IL-1 for phenotype characterization. Parental cell lines (MCF71, T47D1) were cultured in vehicle control (1× phosphate buffer saline, PBS) alongside the sublines. Sublines: MCF7 chronic IL-1α subline termed MCas1, MCF7 chronic IL-1β sublines termed MCbs1, T47D chronic IL-1α subline termed T47Das1, and termed T47D chronic IL-1β subline T47Dbs1.

extract_protocol:
RNA was extracted from cells treated with cytokines using GeneJET RNA Purification kit (Thermo Fisher Scientific, Waltham, MA; K0732) as per manufacturer’s instructions. Genomic DNA contamination was removed by treating 1 ug of RNA with 1 U of DNase-I (Thermo scientific, Waltham, MA; EN0521) following manufacturer’s instructions.
RNA-seq was performed by the Genome Center at tThe University of Texas at Dallas (Richardson, TX). Total RNA library was prepared using Illumina Truseq Stranded Total RNA prep Gold kit (Illumina). The prepared libraries were sequenced on an Illumina NextSeq 500 platform (San Diego, CA) with 100bp single-end reads.

treatment_protocol: We performed RNA sequencing (RNA-seq) and differential gene expression analysis for the parental (MCF71, T47D1) cells treated acutely with vehicle control, 25ng/mL IL-1α or 25ng/mL IL-1β for 4 days and for the chronic IL-1 sublines (MCas1, MCbs1, T47Das1, T47Dbs1) grown in vehicle control only.

value: breast cancer


title: ER stress (TM), IGF2BP2 KO, clone G6, 1

description: Library name: TM_IGF2BP2KO_G6_rep1

value: human colorectal carcinoma

value: IGF2BP2 KO, clone G6, Tet-OsTIR1-PURO


title: CM71704

description: Library name: C4C

value: ovary

value: CCs from medium follicle (6.4mm)


title: Brain single cell 211

description: Library name: Sample 211


title: Brain single cell 210

description: Library name: Sample 210


title: CM70502

description: Library name: C3C


title: Brain single cell 208

description: Library name: Sample 208


title: Brain single cell 207

description: Library name: Sample 207


title: Brain single cell 209

description: Library name: Sample 209


title: CM72104

description: Library name: C2C

value: CCs from medium follicle (6.2mm)


title: Brain single cell 206

description: Library name: Sample 206


title: CM62201

description: Library name: C1C


title: T47Das1 PBS biorep 1

description: Library name: 341-10


title: CS71701

description: Library name: A9C

value: CCs from small follicle (3.8mm)


title: CS50502

description: Library name: A8C

value: cumulus cells


title: CS70702

description: Library name: A7C

value: CCs from small follicle (3.7mm)


title: Brain single cell 204

description: Library name: Sample 204


title: Brain single cell 205

description: Library name: Sample 205


title: CS70701

description: Library name: A6C


title: Brain single cell 294

description: Library name: Sample 294


title: IGF2BP3 PAR-CLIP, DMSO control for TM samples, 2

description:
Library name: S142_DMSO_2
PAR-CLIP

library_source: other

data_processing:
Basecalling was performed using Real-Time Analysis (RTA) v1.18.54.4. BCL files were converted to demultiplexed fastq files with bcl2fastq v2.20.0.422. Tiles within the rages 1150-1223, 2101-2125, 2254-2278 and 1242 were excluded due to low quality of produced reads.
For the demultiplexed data sets unique molecular identifiers were extracted and adapter sequences were trimmed using UMI-tools v1.1.1. The reads were size and quality trimmed using trimmomatic v0.30 to have the length between 18 and 45 nt.
The reads then were mapped to the GENCODE human genome assembly GRCh38.p13 with bowtie v0.12.7 allowing up to 3 mismatches and deduplicated using UMI-tools v1.1.1. Gene counts were obtained using :featureCounts v2.0.1. IGF2BP3-binding clusters were called with PARalyzer v1.5 (.ini file parameters: BANDWIDTH=3, CONVERSION=T>C, MINIMUM_READ_COUNT_PER_GROUP=5, MINIMUM_READ_COUNT_PER_CLUSTER=2, MINIMUM_READ_COUNT_FOR_KDE=3, MINIMUM_CLUSTER_SIZE=11, MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=2, MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=2,  MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=1, MINIMUM_READ_LENGTH=18, MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=1)
Assembly: hg38
Supplementary files format and content: csv, PARalyzer output (clusters)
Supplementary files format and content: csv, gene counts

molecule: other

growth_protocol: HCT116 conditionally expressing Tet-OsTIR1 were obtained from Masato Kanemaki Lab and cultured in McCoy's 5A (Modified) Medium (Sigma) with 10% Fetal Bovine Serum (Gibco), 2 mM Glutamine (Sigma), 1% Pen/Step (Sigma).

extract_protocol:
Five 15 cm (diameter) dishes of 60 % confluent cells per condition were put on ice, washed with ice-cold PBS (Sigma) and crosslinked with the UV light at 365nm with 0.15 J/cm2 and pelleted. Cell pellets were lysed in 1250 μL of ice-cold lysis buffer (25 mM HEPES pH 7.3, 150 mM NaCl, 0.5% NP-40, 0.5 mM EDTA, 10% Glycerol, 0.1% SDS, 0.2% Sodium Deoxycholate, 1x protease inhibitors cocktail, 0.1mM DTT), by incubation on ice for 15 min with intermittent vortexing and passing three times through the 27G needle. The lysate was clarified by centrifugation for 20 min at 20,000g at +4ºC. 1100 μL of the supernatant was taken for the in-lysate RNase digestion on a rotator for 15 min at room temperature. The RNase I (Ambion) was used at 0.1 or 0.05 U/μL and RNase T1 (Thermo Scientific) at 1 or 0.25 U/μL. For IP 50 μg of Proteintech anti-IGF2BP3 antibody (14642-1-AP, lot 00088732) or Proteintech IgG control (30000-0-AP) were coupled to the 200 μL of protein G Dynabeads (Invitrogen) in 1 mL of lysis buffer for 20 min rotating at room temperature, washed three times with 1 mL of the lysis buffer, resuspended in the original bead volume (200 μL) and added to 1 mL of the RNase treated lysate. The IP was incubated on a rotator at +4ºC for 4 hours, washed twice and resuspended in 1 mL of the lysis buffer. For the on-beads RNase treatment RNase I (Ambion) was added at 0.05 or 0.025 U/μL and RNase T1 (Thermo Scientific) at 1 or 0.25 U/μL. For RNase treatment, the samples were incubated on the rotator for 15 min at room temperature and cooled on ice for 5 min. Then the beads were washed three times with 1 mL of ice-cold high salt wash buffer (25 mM HEPES pH 7.3, 400 mM NaCl, 0.5% NP-40, 0.5 mM EDTA, 10% Glycerol, 1x protease inhibitors cocktail, 0.1mM DTT), with 3 min incubations on ice after each wash step.
Library strategy: PAR-CLIP For dephosphorylation of the crosslinked RNA fragments, the beads were washed once with 1 mL of PNK wash buffer (20 mM Tris-HCl pH 6.5, 10 mM MgCl2, 0.2% Tween20, 0.1mM DTT), resuspended in 200 μL of dephosphorylation mix (1x PNK buffer pH 6.5 (70 mM Tris-HCl pH 6.5, 10 mM MgCl2, 1 mM DTT), 100 U T4 polynucleotide kinase (NEB), 20 U SUPERase·In (Invitrogen)) and incubated at 37 °C for 30 min with shaking at 1100 rpm. Afterwards, the beads were kept on ice and washed once with 1 mL of PNK wash buffer, incubated in 1 mL of high salt wash buffer for 5 min on ice and washed once more with 1 mL of PNK wash buffer. For 3’ adapter ligation (ordered as /5Phos/NNNNNATCGTAGATCGGAAGAGCACACGTCTGAA/3AzideN/, pre-adenylated using 5’ DNA Adenylation Kit (NEB) and conjugated to the IRdye-800CW-DBCO (LiCor) was via “click” chemistry at 37 °C for 2 hours as described in (Zarnegar et al. 2016), the beads were resuspended in 200 μL of the ligation reaction mix (20% PEG8000, 1x T4 RNA Ligase Reaction Buffer (NEB), 1000 U T4 RNA Ligase 2 truncated KQ (NEB), 50 pmol 5' pre-adenylated IR-dye conjugated DNA adapter and 20 U SUPERase·In) and incubated at 25°C for 3 hours with shaking at 1100rpm in the dark. Next, the beads were transferred on ice and washed once with 1 mL of PNK wash buffer, incubated in 1 mL of high salt wash buffer for 5 min on ice, resuspended in 1 mL of PNK wash buffer and transferred to the new low-bind RNase-free 1.5 mL tube. The PNK wash buffer was removed and the crosslinked protein-RNA complexes were eluted in 40 μL of 1x SDS sample buffer without DTT at +70ºC for 10 min. DTT at 20mM concentration was added to the collected eluates and the samples were heated at +70ºC for 10 min and stored at -80ºC. Next, the crosslinked protein-RNA complexes were resolved on a 10 well 4-12% NuPAGE Novex Bis-Tris gel (Invitrogen) in 1x MOPS-SDS running buffer (Invitrogen) at 200 V for 65 min. The gel was visualized at 800nm using LI-COR Odyssey CLx near infrared imager and RBP-RNA complexes were size selected using imager’s grid. The bands corresponding to IGF2BP3-RNA complexes were excised from the gel and transferred to a low-bind RNase-free tube. For the samples with the RNase treatment conditions in-lysate and on-beads: RNase I 0.05 U/µl, RNase T1 1 U/µl proteinase K digestion was performed as described in (Acosta-Alvear et al. 2018). The gel piece was transferred to nuclease free water preequilibrated Pur-A-Lyzer Midi Dialysis Tube (MWCO 3.5 kDa, Sigma) with 200 μL 1x MOPS-SDS running buffer (Invitrogen) and electroelution was performed at 100 V for 2 h. The polarity of the electric current was reversed for 120 seconds, sample was transferred to the new 2 mL low-bind RNase-free tube with an equal volume of 2x Proteinase K buffer (100 mM HEPES pH 7.3, 100 mM NaCl, 20 mM EDTA, 2% SDS) and proteinase K (Invitrogen) at the final concentration of 1.2 mg/ml and incubated for 30 min at +55 ºC. For the samples with RNase treatment conditions: RNase I 0.05 U/µl in-lysate and 0.025 U/µl on-beads, RNase I 0.01 U/µl in-lysate and 0.025 U/µl on-beads, and RNase T1 0.25 U/µl in-lysate and on-beads gel extraction and protein digestion were performed as described in (Anastasakis et al. 2021). Gel pieces were transferred to 1.5 mL low-bind RNase-free tube, frozen at -80ºC, thawed at +55ºC and crashed with a single use RNase-free pellet pestle. Gel slurry was boiled in 2x proteinase K buffer with 50 mM DTT at +95ºC for 2 min and was subsequently incubated three times with fresh addition of proteinase K at 2.4 mg/ml, 1.5 mg/ml, and 2.4 mg/ml in 2x proteinase K buffer at +50 ºC for 30 min with shaking at 1100rpm. Extracted 3’ adapter-ligated RNA fragments were separated from the gel by centrifugation at 10,000g for 10 min through Spin-X centrifuge filter (Costar). For all samples, RNA was extracted with 1 mL of acidic phenol – chloroform – IAA (25:24:1, pH 4.0), isopropanol precipitated, resuspended 1x TBE-Urea dye (Invitrogen), denatured by heating at +75ºC for 2 min and resolved on a 10 well 15% TBE-Urea gel (Invitrogen) in 1x TBE running buffer (Invitrogen) at 180 V for 70 min. The gel was visualized at 800 nm using LI-COR Odyssey CLx near infrared imager and the 3’ adapter-ligated RNA fragments were size selected using imager’s grid. Gel pieces were transferred to 1.5 mL low-bind RNase-free tube, frozen at -80º C, thawed at +55º C and crashed with a single use RNase-free pellet pestle. 3’ adapter-ligated RNA fragments were extracted from the gel during overnight incubation rotating in 300 μL of RNA elution buffer at +4ºC (10mM Tris-HCl pH 7.0, 0.3 M NaOAc pH 5.5, 2mM EDTA, 20 U SUPERase·In). Extracted complexes were separated from the gel fragments by centrifugation at 10,000 g for 10 min through Spin-X centrifuge filter, ethanol precipitated and resuspended in 11.5 μL of nuclease-free water. For reverse transcription, 1 μL of 1 μM reverse transcription primer (/5Phos/RNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG/iSp18/GTGACTGGAGTTCAGACGTGTGCTC) was added to the sample. The sample was incubated at +70 ºC for 10 min and transferred on ice. Then the components of the reverse transcription mix were added to the sample making final volume of 20 μL (1x Superscript IV buffer, dNTPs 0.2 mM each, 5 mM DTT, 10 U SUPERase·In, 200 U Superscript IV (Invitrogen)), the reaction was performed at +55 ºC for 20 min and inactivated at +80 ºC for 5 min. 2.2 µl of 1 M NaOH was added and RNA was hydrolyzed in 30 min incubation at 98 °C. The reaction was neutralized by addition of 2.2 µl of 1 M HCl. The reverse transcription reaction was purified on Oligo Clean & Concentrator columns (Zymo) according to the manufacturer’s instructions and eluted in 6 µl of nuclease-free water. cDNA was mixed with 6 µl of 2x TBE-Urea dye), denatured by heating at +75ºC for 2 min and resolved on a 10 well 10% TBE-Urea gel (Invitrogen) in 1x TBE running buffer at 180 V for 70 min. The gel was stained with SYBR gold (Invitrogen), visualized and the reverse transcription product was separated from the unreacted primer and no-insert products. Gel extraction was performed similarly as for the 3’ adapter-ligated RNA fragments using DNA elution buffer (10 mM Tris-HCl pH 8.0, 0.3 M NaOAc pH 5.5). After ethanol precipitation, the pellet was resuspended in 10 μL of circular ligation reaction mix (1x CircLigase II buffer, 2.5 mM MnCl2, 50 U CircLigase II (Lucigen)). Circular ligation was performed at +60°C for 2 hours and the enzyme was inactivated through heating at +80°C for 10 min. To amplify the libraries the PCR reactions were performed with NEB Phusion polymerase and index primers (NEB, E6609S). The reaction mix of 50 µl (1x High fidelity buffer, dNTPs 0.2 mM each, 500 nM NEB Universal primer, 500 nM NEB Index primer, 2 µl circularization reaction, 1 U Phusion polymerase) was run according to the following program: 98 °C, 30 sec; 20 cycles of 98 °C, 10 sec; 65 °C, 10 sec; 72 °C, 10 sec; 72 °C, 5 min. Typically, the number of cycles was 16-18 for IGF2BP3 IP and 22-23 for IgG control. Libraries were ethanol precipitated, resolved on 10 well of 6% TBE gel similarly to the cycle selection PCR, and separated from the no-insert library and unreacted primers. Gel extraction was performed similarly to the extraction after reverse transcription reaction, but the gel pieces were not heated higher than +30 °C. After ethanol precipitation, pellets were resuspended in 10 µl of nuclease-free water. Library size distribution and quantity were determined using Agilent Bioanalyzer 2100 with High Sensitivity DNA Kit (Agilent) and via qPCR with NEBNext Library Quant Kit for Illumina (NEB). Libraries were sequenced on a NovaSeq 6000 S1 at SR100 mode (Illumina) at the Vienna BioCenter NGS facility.

treatment_protocol: 4-thiouridine (4sU, Sigma) was added to the cell culture media 15 hours prior collection at 100 µM. ER stress was induced with 5 µg/mL tunicamycin (TM) for 4 hours prior to collection. DMSO in 1:1000 dilution was used a control. Oxidative stress was induced with 250 µM sodium arsenate (As) for 2 hours prior to collection. PBS in 1:1000 dilution was used a control (samples named "Control").

value: 4-thiouridine (4sU) 100 μM 15h, DMSO 1:1000 4h

tag: par-clip antibody


title: Brain single cell 203

description: Library name: Sample 203


title: IGF2BP3 PAR-CLIP, TM 1 hour, 2

description:
Library name: S142_TM_1h_2
PAR-CLIP

value: 4-thiouridine (4sU) 100 μM 15h, 5 μg/mL TM 1h


title: CS62003

description: Library name: A5C


title: Brain single cell 202

description: Library name: Sample 202


title: CS62004

description: Library name: A4C

value: CCs from small follicle (3.6mm)


title: Brain single cell 201

description: Library name: Sample 201


title: CS62005

description: Library name: A3C

value: CCs from small follicle (3.5mm)


title: Brain single cell 200

description: Library name: Sample 200


title: CS50506

description: Library name: W6C

value: CCs from small follicle (3.3mm)


title: CS70501

description: Library name: A2C

value: CCs from small follicle (3.2mm)


title: Brain single cell 198

description: Library name: Sample 198

value: brain


title: Brain single cell 199

description: Library name: Sample 199

value: microglia


title: Brain single cell 197

description: Library name: Sample 197


title: GL70504

description: Library name: M70504

value: mural granulosa cells

value: MGCs from large follicle (11.6mm)


title: Brain single cell 196

description: Library name: Sample 196


title: GL71801

description: Library name: M71801

value: MGCs from large follicle (11.5mm)


title: Brain single cell 195

description: Library name: Sample 195


title: CS50501

description: Library name: A1C

value: ovary

value: CCs from small follicle (3.1mm)


title: GL62803

description: Library name: M62803

value: MGCs from large follicle (11.2mm)


title: Brain single cell 194

description: Library name: Sample 194


title: GL72101

description: Library name: M72101

value: MGCs from large follicle (11.3mmmm)


title: Brain single cell 193

description: Library name: Sample 193


title: GL50505

description: Library name: W-5M


title: Brain single cell 192

description: Library name: Sample 192


title: GL70703

description: Library name: M70703

value: MGCs from large follicle (10.2mm)


title: Brain single cell 190

description: Library name: Sample 190


title: Brain single cell 289

description: Library name: Sample 289

value: endothelial


title: GL72102

description: Library name: M72102

value: MGCs from large follicle (10.0mm)


title: GL70503

description: Library name: M70503


title: Brain single cell 188

description: Library name: Sample 188


title: GL71802

description: Library name: M71802

value: MGCs from large follicle (9.6mm)


title: Brain single cell 189

description: Library name: Sample 189


title: Brain single cell 185

description: Library name: Sample 185


title: IgG PAR-CLIP, DMSO control for TM samples, 1

description:
Library name: S141_IgG_DMSO
PAR-CLIP

value: human colorectal carcinoma

value: 4-thiouridine (4sU) 100 μM 15h, DMSO 1:1000 4h

value: IgG control (Proteintech, #30000-0-AP)


title: GM71805

description: Library name: M71805

value: MGCs from medium follicle (7.0mm)


title: GM71804

description: Library name: M71804


title: Brain single cell 183

description: Library name: Sample 183

value: brain


title: Brain single cell 182

description: Library name: Sample 182

value: microglia


title: Brain single cell 184

description: Library name: Sample 184


title: GM72404

description: Library name: M72404

value: mural granulosa cells


title: Brain single cell 186

description: Library name: Sample 186


title: Brain single cell 180

description: Library name: Sample 180


title: GM71704

description: Library name: M71704

value: MGCs from medium follicle (6.4mm)


title: GM71002

description: Library name: M71002


title: GM72104

description: Library name: M72104

value: MGCs from medium follicle (6.2mm)


title: GM62201

description: Library name: M62201

value: ovary


title: GS71701

description: Library name: M71701

value: MGCs from small follicle (3.8mm)


title: Brain single cell 175

description: Library name: Sample 175


title: GS70702

description: Library name: M70702

value: MGCs from small follicle (3.7mm)


title: GS50502

description: Library name: M50502


title: Brain single cell 172

description: Library name: Sample 172


title: Brain single cell 171

description: Library name: Sample 171


title: Brain single cell 169

description: Library name: Sample 169


title: GS50501

description: Library name: M50501

value: MGCs from small follicle (3.1mm)


title: Brain single cell 167

description: Library name: Sample 167


title: E13.5 PGC WT-8

type: genomic

city: Philadelphia

first: Rexxi

middle: Diptya

last: Prasasya

state: PA

address: 3400 Civic Center Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

description: Bisulfite treated

hyb_protocol: Klenow amplified bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Mouse285 Methylation BeadChip 12v1-0 using standard Illumina Protocol

scan_protocol: Illumina iScan System

data_processing:
Raw IDAT files were processed using SeSAMe R package and the MM285 array manifest file to obtain methylation beta values with ELBAR prep (I). Between-run batch correction (batches are identified by the array numbers in the first 12digits of the file name) was done using the R Package limma removeBatchEffect().
Beta values of individual probe for each individual sample. Probes that did not pass SeSAMe quality control ELBAR approach is masked with NA

label: Cy3 and Cy5

source_name: E13.5 male primordial germ cells

label_protocol: Standard Illumina Protocol

extract_protocol: Snap forzen cell pellets were directly lysed and bisulfite converted using Zymo Research EZ DNA methylation-Direct Kit

value: E13.5 male primordial germ cells

value: WT


title: Brain single cell 166

description: Library name: Sample 166


title: E13.5 PGC WT-7

description: Bisulfite treated


title: E13.5 PGC WT-6

description: Bisulfite treated


title: Brain single cell 164

description: Library name: Sample 164


title: E13.5 PGC WT-5

description: Bisulfite treated


title: E13.5 PGC WT-4

description: Bisulfite treated


title: Brain single cell 162

description: Library name: Sample 162


title: GM72403

description: Library name: M72403

value: MGCs from medium follicle (6.7mm)


title: Brain single cell 181

description: Library name: Sample 181


title: Brain single cell 179

description: Library name: Sample 179


title: Brain single cell 178

description: Library name: Sample 178


title: Brain single cell 177

description: Library name: Sample 177


title: Brain single cell 176

description: Library name: Sample 176


title: E13.5 PGC WT-3

description: Bisulfite treated


title: Brain single cell 173

description: Library name: Sample 173


title: GS62003

description: Library name: M62003


title: E13.5 PGC WT-2

description: Bisulfite treated


title: GS62005

description: Library name: M62005

value: MGCs from small follicle (3.5mm)


title: E13.5 PGC WT-1

description: Bisulfite treated


title: E13.5 PGC KO-8

description: Bisulfite treated

value: KO


title: GS70501

description: Library name: M70501

value: MGCs from small follicle (3.2mm)


title: E13.5 PGC KO-7

description: Bisulfite treated


title: Brain single cell 159

description: Library name: Sample 159


title: E13.5 PGC KO-6

description: Bisulfite treated


title: Brain single cell 157

description: Library name: Sample 157


title: Peripheral_Monocytes_UC03

city: London

first: Eve

last: Hornsby

address: 4 Newark St

department: Blizard Institue/CIB

country: United Kingdom

institute: QMUL

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultplexing, barcoded processing,  gene counting and aggregation were performed using 10x Genomics Cell Ranger pipeline (version 6.0.2).
Assembly: GRCh38 GENCODE v2/ Ensembl 98
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral Blood

extract_protocol:
Peripheral Blood Mononuclear Cells (PBMC) were obtained by centrifugation in Ficoll®Paque PLUS (GE Healthcare). Total monocytes were enriched from PBMC using negative magnetic selection (Pan-monocyte isolation kit, Miltenyi Biotech). Cells were then washed twice in Phosphate Buffered Saline(Ca2+ and Mg2+ -free) containing 0.04% Bovine Serum Albumin.
Samples were loaded to the Chromium Chip B Single Cell Kit (PN-1000074) using the Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (PN-1000092) as described in the manufacturer’s user guide (10X Genomics, California, USA), aiming to capture 1000 cells per sample. 11 cycles of cDNA amplification were performed on the purified GEM-RT product, and cDNA was examined for quality using the Agilent 2200 Tapestation with the High-sensitivity D5000 screentape and reagents (Agilent Technologies, Waldbronn, Germany), and the Qubit® 2.0 Fluorometer and Qubit dsDNA HS Assay Kit (Life Technologies, California, USA). 10µL of cDNA was used to prepare the 10X 3’RNA library and 13 cycles were used for sample index PCR. Final cleaned libraries were quantified using the Qubit® 2.0 Fluorometer and Qubit dsDNA HS Assay Kit and average fragment size checked using the Agilent D1000 screentape and reagents.  An equimolar amount of each sample library was pooled for sequencing on one lane of an Illumina NovaSeq S4 flow cell at 150bp paired-end.

value: Peripheral Blood

tag: diagnosis

value: Ulcerative Colitis

value: Total monocytes


title: Brain single cell 156

description: Library name: Sample 156

value: brain

value: microglia


title: E13.5 PGC KO-5

description: Bisulfite treated


title: Brain single cell 155

description: Library name: Sample 155


title: E13.5 PGC KO-4

description: Bisulfite treated


title: Brain single cell 154

description: Library name: Sample 154


title: E13.5 PGC KO-3

description: Bisulfite treated


title: E13.5 PGC KO-2

description: Bisulfite treated


title: Brain single cell 152

description: Library name: Sample 152


title: E13.5 PGC KO-1

description: Bisulfite treated


title: Brain single cell 151

description: Library name: Sample 151


title: Brain single cell 165

description: Library name: Sample 165


title: input-spg_5hmC

description: Library name: input-spg_5hmC

data_processing:
5hmC-Seal reads were trimmed using TrimGalore with default parameters
5hmC-Seal reads were aligned to mm10 using Bowtie2 version 2.5.0 with parameters: --N, 1 -sensitive -local
Low quality read (QMAP <= 10) and non-primary alignments were removed using SAMtools version 1.16.1 with parameters: view -q 10 -F 256
Duplicated reads were removed using SAMtool rmdup and mitochondrial reads were removed using grep function. Blacklisted regions were removed usign BEDtools version 2.27.1
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: mm10
Supplementary files format and content: bigWig files were prepared using deepTools version 3.5.1 with function bamCoverage and parameters -bs 1 --normalizeUsing CPM
Supplementary files format and content: bigWig (normalized to counts per million), broadPeak (for 5hmC-Seal, peaks called with input as background)

source_name: Prospermatogonia

growth_protocol: All animals were housed in polysulfone cages containing drinking water and chow (Laboratory Irradiated Rodent Diet 5LG4, LabDiet) ad libitum.

extract_protocol:
Phenol:Chloroform:Isoamyl Alcohol (25:24:1; Sigma-Aldrich) and ethanol precipitated
5hmC-Seal was done using 5hmC profiling kit by Active Motif followed by library preparation using NEBNext UltraII DNA Library Prep Kit for Illumina

value: Prospermatogonia

value: Input genomic DNA of Biotin labeled glucose-protected  5hmC before  streptavidin capture

tag: batch


title: Brain single cell 150

description: Library name: Sample 150


title: spg_5hmC

description: Library name: spg_5hmC

value: Biotin labeled glucose-protected  5hmC followed by streptavidin capture


title: Brain single cell 149

description: Library name: Sample 149


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB354FIW)

status: Public on Jul 24 2026

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR723XYM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR723XYM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB354FIW

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens male adult (42 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

tag: encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 42 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

tag: link

value: ENCBS587ZEO at ENCODE; https://www.encodeproject.org/ENCBS587ZEO/


title: E17.5 Prospermatogonia WT 4

description: Library name: WT3042-1

data_processing:
Unique molecular index sequences were located within adaptor positions from raw reads using UMI tools. UMI sequences were added to read names and reads were quality trimmed using Trim Galore (--phred 33 -clip_R2 6)
Reads were aligned to mouse mm10 reference genome using STAR with default parameters and a maximum fragment size of 2000bp. Reads with the same mapping coordinates and idential UMIs were collaped into a single read.
FeatureCounts (version 1.5.0) was used to generate a matrix of mapped fragments against GENCODE annotation release M25.
To remove lowly expressed genes prior to differential expression analysis, we applied library-size aware filtering using edgeR filterByExpr() function to retain genes with at least ~10 raw quants, scaled to each library's sequencing depth, in a sufficient number of replicates with at least one experimental group
Filtered count matrix were fed into DESeq2 to perform normalization and differential expression analysis with FDR cut off of < 0.05 and minimum fold change of 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

extract_protocol:
RNA was extracted from snap frozen cell pellets using TRIzol reagent followed by chloform phase separation and isopropanol percipitation. To eliminate carry-over genomic DNA, total RNA was treated with Qiagen DNaseI followed by clean up using RNAClean XP beads.
Ribosomal RNA-depleted total RNA libraries were generated using the SMART-seq Total RNA Pico Input Kit with UMIs and ZapR Mammalian from Takara Bio. 5ng of total RNA was used as input.

tag: tissue


title: Brain single cell 148

description: Library name: Sample 148

tag: cell type


title: E17.5 Prospermatogonia WT 3

description: Library name: WT977-6


title: Brain single cell 147

description: Library name: Sample 147


title: E17.5 Prospermatogonia WT 2

description: Library name: WT922-3


title: Brain single cell 146

description: Library name: Sample 146


title: E17.5 Prospermatogonia WT 1

description: Library name: WT591-8


title: Brain single cell 145

description: Library name: Sample 145


title: E17.5 Prospermatogonia KO 4

description: Library name: KO2696-6


title: Brain single cell 144

description: Library name: Sample 144


title: E17.5 Prospermatogonia KO 3

description: Library name: KO1982-1


title: Brain single cell 143

description: Library name: Sample 143


title: Brain single cell 142

description: Library name: Sample 142


title: E17.5 Prospermatogonia KO 2

description: Library name: KO1701-5


title: Brain single cell 141

description: Library name: Sample 141


title: Brain single cell 140

description: Library name: Sample 140


title: E17_IGG_WT2

description: Library name: IGG_WT2

data_processing:
CUT&RUN reads were trimmed using TrimGalore with default parameters
CUT&RUN reads were aligned to mm10 using Bowtie2 version 2.5.0 with parameters: --N, 1 -sensitive -local
Low quality read (QMAP <= 10) and non-primary alignments were removed using SAMtools version 1.16.1 with parameters: view -q 10 -F 256
Duplicated reads were removed using SAMtool rmdup and mitochondrial reads were removed using grep function. Blacklisted regions were removed usign BEDtools version 2.27.1
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were prepared using deepTools version 3.5.1 with function bamCoverage and parameters -bs 1 --normalizeUsing CPM
Supplementary files format and content: bigWig (normalized to counts per million), narrowPeak (for H3K4me3, peaks called with IgG as background)
Library strategy: CUT&Run

extract_protocol:
Extracted nuclei (nuclei extraction buffer: 20 mM HEPES-KOH pH 7.9, 10mM KCl, 0.5 mM fresh spermidine, 0.1% Triton X-100, 20% glycerol plus protease inhibitors) were bound to concanavalin A-coated magenetic beads and wash and permeabilize using C&R Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, with 1x Roche complete protease inhibitor EDTA Free) with 0.05% Digitonin and 2 mM EDTA
CUT&RUN was done using CUTANA ChIC/CUT&RUN kit from EpiCypher. CUT&RUN libraries were prepared NEBNext Ultra II DNA Library Prep Kit for Illuminal. All of DNA that was recovered following Phenol:Chloroform extraction was used as input.

tag: treatment

value: CUTANA Rabbit IgG negative control antibody


title: E17_IGG_WT1

description: Library name: IGG_WT1


title: E17_IGG_HxD3

description: Library name: IGG_HxD3


title: Brain single cell 137

description: Library name: Sample 137


title: E17_IGG_HxD2

description: Library name: IGG_HxD2


title: Brain single cell 136

description: Library name: Sample 136


title: Brain single cell 158

description: Library name: Sample 158


title: E17_IGG_HxD1

description: Library name: IGG_HxD1


title: Brain single cell 135

description: Library name: Sample 135


title: E17_IGG_KO3

description: Library name: IGG_KO3


title: E17_IGG_KO2

description: Library name: IGG_KO2


title: Brain single cell 134

description: Library name: Sample 134


title: Brain single cell 133

description: Library name: Sample 133


title: E17_IGG_KO1

description: Library name: IGG_KO1


title: E17_H3K4me3_WT3

description: Library name: H3K4me3_WT3

value: Cell Signaling Technology 2729


title: Brain single cell 132

description: Library name: Sample 132


title: Brain single cell 131

description: Library name: Sample 131


title: Brain single cell 130

description: Library name: Sample 130


title: Brain single cell 129

description: Library name: Sample 129


title: Brain single cell 128

description: Library name: Sample 128


title: Brain single cell 127

description: Library name: Sample 127


title: E17_H3K4me3_HxD2

description: Library name: H3K4me3_HxD2


title: E17_H3K4me3_HxD1

description: Library name: H3K4me3_HxD1


title: Brain single cell 125

description: Library name: Sample 125


title: Brain single cell 124

description: Library name: Sample 124


title: E17_H3K4me3_KO1

description: Library name: H3K4me3_KO1


title: Brain single cell 123

description: Library name: Sample 123


title: Brain single cell 122

description: Library name: Sample 122


title: Leaf tissue, FR light treatment, Time 96 h, replica 3

city: Wageningen

first: Elena

last: Vincenzi

address: Droevendaalsesteeg 1

department: Horticulture and Product Physiology

institute: Wageningen University and Research (Netherlands)

description:
Library name: T96_Leaf_FR49
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Leaf_FR_rep3

data_processing:
Raw reads were filtered using SOAPnuke (software version 1.5.6), removing low-quality reads, reads containing adapters, and reads with unknown base content greater than 0.1%.
Clean reads were aligned to the reference tomato genome ITAG4. 0 using Bowtie2 (software version 2.5.0).
Gene expression quantification was carried out using RSEM (software version 1.3.1).
Read counts normalisation was carried out using DESeq2 (software version 1.40.2)
Assembly: Tomato Genome ITAG 4.0 (Solanum Lycopersicum)
Supplementary files format and content: Raw read count can be found in file ReadCountsRaw_allSamples.txt, a tab delimited file.
Supplementary files format and content: Normalized read count can be found in file  ReadCountsNormalised_allSamples.txt, a tab delimited file.

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: All treatments received a PPFD of 258 ± 5 µmol m-2 s-1 supplied from transplant into the climate chamber to the end of the experiment.

extract_protocol:
RNA was extract by BGI Genomics from 100 mg of frozen powdered fresh material. All RNA samples had RNA integrity (RIN) values ≥ 6.0, a total RNA ≥ 400 ng and 28S/18S ≥ 1.0.
RNA libraries for RNA sequencing were prepared by BGI Genomics using the DNA Nanoball Sequencing (DNBSEQ) with PE150 (paired-end, read length).

treatment_protocol: For plants under Leaf FR treatment, 77 ± 1 µmol m-2 s-1 of additional Far-red (700-800 nm) were supplied from overhead modules. The FR treatment started 10 days after anthesis of the first flower of the second truss (63 days after sowing). Leaf and fruit samples were collected at six time points, 0 (pre FR-exposure), 6, 12, 24, 48 and 96 hours after the start of the FR treatment. Fruit samples consisted of the first fruit from the second truss at “immature green” stage (10 ± 1 days after anthesis). Leaf samples consisted of the right leaflet from the most distal pair on the leaf above the second truss (leaf 13, when leaf 0 is the first true leaf). Four plants per treatment were sampled per time point, with no plant harvested twice or from the same unit at the same time point. Samples were immediately labelled and frozen in liquid nitrogen, with all samples for each time point harvested within 10 minutes. Frozen samples were ground into fine powder with mortar and pestle.

value: Leaf

value: cultivar Foundation

value: FR

tag: time

tag: biological replicates


title: Brain single cell 121

description: Library name: Sample 121

value: brain

value: microglia


title: E17_IGG_WT3

description: Library name: IGG_WT3

value: Prospermatogonia

tag: genotype


title: E17.5 Prospermatogonia KO 1

description: Library name: KO591-4


title: Brain single cell 139

description: Library name: Sample 139


title: Leaf tissue, FR light treatment, Time 96 h, replica 2

description:
Library name: T96_Leaf_FR23
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Leaf_FR_rep2


title: Brain single cell 138

description: Library name: Sample 138


title: Brain single cell 120

description: Library name: Sample 120


title: Leaf tissue, FR light treatment, Time 96 h, replica 1

description:
Library name: T96_Leaf_FR13
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Leaf_FR_rep1


title: Brain single cell 119

description: Library name: Sample 119


title: Brain single cell 118

description: Library name: Sample 118


title: Leaf tissue, NFR light treatment, Time 96 h, replica 4

description:
Library name: T96_Leaf_NFR103
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Leaf_NFR_rep4

value: NFR


title: Leaf tissue, NFR light treatment, Time 96 h, replica 3

description:
Library name: T96_Leaf_NFR93
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Leaf_NFR_rep3


title: Brain single cell 117

description: Library name: Sample 117


title: Leaf tissue, NFR light treatment, Time 96 h, replica 2

description:
Library name: T96_Leaf_NFR67
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Leaf_NFR_rep2


title: E17_H3K4me3_WT2

description: Library name: H3K4me3_WT2


title: Leaf tissue, NFR light treatment, Time 96 h, replica 1

description:
Library name: T96_Leaf_NFR7
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Leaf_NFR_rep1


title: Brain single cell 116

description: Library name: Sample 116


title: Brain single cell 115

description: Library name: Sample 115


title: E17_H3K4me3_WT1

description: Library name: H3K4me3_WT1


title: Fruit tissue, FR light treatment, Time 96 h, replica 4

description:
Library name: T96_Fruit_FR84
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Fruit_FR_rep4

source_name: Fruit

value: Fruit


title: E17_H3K4me3_HxD3

description: Library name: H3K4me3_HxD3


title: Brain single cell 114

description: Library name: Sample 114


title: Fruit tissue, FR light treatment, Time 96 h, replica 3

description:
Library name: T96_Fruit_FR50
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Fruit_FR_rep3


title: Fruit tissue, FR light treatment, Time 96 h, replica 2

description:
Library name: T96_Fruit_FR24
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Fruit_FR_rep2


title: Brain single cell 113

description: Library name: Sample 113


title: Brain single cell 112

description: Library name: Sample 112


title: Brain single cell 126

description: Library name: Sample 126


title: Fruit tissue, FR light treatment, Time 96 h, replica 1

description:
Library name: T96_Fruit_FR14
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Fruit_FR_rep1


title: Brain single cell 111

description: Library name: Sample 111


title: Fruit tissue, NFR light treatment, Time 96 h, replica 4

description:
Library name: T96_Fruit_NFR104
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Fruit_NFR_rep4


title: Brain single cell 110

description: Library name: Sample 110


title: E17_H3K4me3_KO3

description: Library name: H3K4me3_KO3


title: Fruit tissue, NFR light treatment, Time 96 h, replica 3

description:
Library name: T96_Fruit_NFR94
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Fruit_NFR_rep3


title: Brain single cell 109

description: Library name: Sample 109


title: Fruit tissue, NFR light treatment, Time 96 h, replica 2

description:
Library name: T96_Fruit_NFR68
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Fruit_NFR_rep2


title: E17_H3K4me3_KO2

description: Library name: H3K4me3_KO2


title: Brain single cell 108

description: Library name: Sample 108


title: Fruit tissue, NFR light treatment, Time 96 h, replica 1

description:
Library name: T96_Fruit_NFR8
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Fruit_NFR_rep1


title: Brain single cell 107

description: Library name: Sample 107


title: Leaf tissue, FR light treatment, Time 48 h, replica 4

description:
Library name: T48_Leaf_FR85
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Leaf_FR_rep4


title: Brain single cell 106

description: Library name: Sample 106


title: Leaf tissue, FR light treatment, Time 48 h, replica 3

description:
Library name: T48_Leaf_FR75
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Leaf_FR_rep3


title: Brain single cell 105

description: Library name: Sample 105


title: Brain single cell 104

description: Library name: Sample 104


title: Leaf tissue, FR light treatment, Time 48 h, replica 2

description:
Library name: T48_Leaf_FR55
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Leaf_FR_rep2


title: Leaf tissue, FR light treatment, Time 48 h, replica 1

description:
Library name: T48_Leaf_FR25
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Leaf_FR_rep1


title: Brain single cell 103

description: Library name: Sample 103


title: Leaf tissue, NFR light treatment, Time 48 h, replica 4

description:
Library name: T48_Leaf_NFR69
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Leaf_NFR_rep4


title: Brain single cell 102

description: Library name: Sample 102


title: Leaf tissue, NFR light treatment, Time 48 h, replica 3

description:
Library name: T48_Leaf_NFR59
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Leaf_NFR_rep3


title: Leaf tissue, NFR light treatment, Time 48 h, replica 2

description:
Library name: T48_Leaf_NFR33
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Leaf_NFR_rep2


title: Brain single cell 101

description: Library name: Sample 101


title: Leaf tissue, NFR light treatment, Time 48 h, replica 1

description:
Library name: T48_Leaf_NFR9
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Leaf_NFR_rep1


title: Brain single cell 100

description: Library name: Sample 100


title: Leaf tissue, FR light treatment, Time 96 h, replica 4

description:
Library name: T96_Leaf_FR83
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T96_Leaf_FR_rep4


title: Brain single cell 99

description: Library name: Sample 99


title: Fruit tissue, FR light treatment, Time 48 h, replica 4

description:
Library name: T48_Fruit_FR86
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Fruit_FR_rep4


title: Brain single cell 98

description: Library name: Sample 98


title: Fruit tissue, FR light treatment, Time 48 h, replica 3

description:
Library name: T48_Fruit_FR76
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Fruit_FR_rep3


title: Brain single cell 97

description: Library name: Sample 97


title: Fruit tissue, FR light treatment, Time 48 h, replica 2

description:
Library name: T48_Fruit_FR56
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Fruit_FR_rep2


title: Brain single cell 96

description: Library name: Sample 96


title: Fruit tissue, FR light treatment, Time 48 h, replica 1

description:
Library name: T48_Fruit_FR26
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Fruit_FR_rep1


title: Brain single cell 95

description: Library name: Sample 95


title: Brain single cell 94

description: Library name: Sample 94


title: Fruit tissue, NFR light treatment, Time 48 h, replica 4

description:
Library name: T48_Fruit_NFR70
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Fruit_NFR_rep4


title: Fruit tissue, NFR light treatment, Time 48 h, replica 3

description:
Library name: T48_Fruit_NFR60
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Fruit_NFR_rep3


title: Brain single cell 93

description: Library name: Sample 93


title: Brain single cell 92

description: Library name: Sample 92


title: Fruit tissue, NFR light treatment, Time 48 h, replica 2

description:
Library name: T48_Fruit_NFR34
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Fruit_NFR_rep2


title: Fruit tissue, NFR light treatment, Time 48 h, replica 1

description:
Library name: T48_Fruit_NFR10
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T48_Fruit_NFR_rep1


title: Brain single cell 91

description: Library name: Sample 91


title: Leaf tissue, FR light treatment, Time 24 h, replica 4

description:
Library name: T24_Leaf_FR87
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Leaf_FR_rep4


title: Brain single cell 90

description: Library name: Sample 90


title: Leaf tissue, FR light treatment, Time 24 h, replica 3

description:
Library name: T24_Leaf_FR77
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Leaf_FR_rep3


title: Brain single cell 89

description: Library name: Sample 89


title: Leaf tissue, FR light treatment, Time 24 h, replica 2

description:
Library name: T24_Leaf_FR51
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Leaf_FR_rep2


title: Brain single cell 88

description: Library name: Sample 88


title: Leaf tissue, FR light treatment, Time 24 h, replica 1

description:
Library name: T24_Leaf_FR17
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Leaf_FR_rep1


title: Leaf tissue, NFR light treatment, Time 24 h, replica 4

description:
Library name: T24_Leaf_NFR97
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Leaf_NFR_rep4


title: Brain single cell 87

description: Library name: Sample 87


title: Brain single cell 86

description: Library name: Sample 86


title: Leaf tissue, NFR light treatment, Time 24 h, replica 3

description:
Library name: T24_Leaf_NFR61
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Leaf_NFR_rep3


title: Leaf tissue, NFR light treatment, Time 24 h, replica 2

description:
Library name: T24_Leaf_NFR35
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Leaf_NFR_rep2


title: Brain single cell 84

description: Library name: Sample 84


title: Brain single cell 85

description: Library name: Sample 85


title: Brain single cell 83

description: Library name: Sample 83


title: Leaf tissue, NFR light treatment, Time 24 h, replica 1

description:
Library name: T24_Leaf_NFR3
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Leaf_NFR_rep1


title: Fruit tissue, FR light treatment, Time 24 h, replica 4

description:
Library name: T24_Fruit_FR88
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Fruit_FR_rep4


title: Brain single cell 82

description: Library name: Sample 82


title: Fruit tissue, FR light treatment, Time 24 h, replica 3

description:
Library name: T24_Fruit_FR78
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Fruit_FR_rep3


title: Brain single cell 80

description: Library name: Sample 80


title: Brain single cell 81

description: Library name: Sample 81


title: Fruit tissue, FR light treatment, Time 24 h, replica 2

description:
Library name: T24_Fruit_FR52
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Fruit_FR_rep2


title: Fruit tissue, FR light treatment, Time 24 h, replica 1

description:
Library name: T24_Fruit_FR18
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Fruit_FR_rep1


title: Brain single cell 79

description: Library name: Sample 79


title: Brain single cell 78

description: Library name: Sample 78


title: Fruit tissue, NFR light treatment, Time 24 h, replica 4

description:
Library name: T24_Fruit_NFR98
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Fruit_NFR_rep4


title: Brain single cell 77

description: Library name: Sample 77


title: Fruit tissue, NFR light treatment, Time 24 h, replica 2

description:
Library name: T24_Fruit_NFR36
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Fruit_NFR_rep2


title: Fruit tissue, NFR light treatment, Time 24 h, replica 3

description:
Library name: T24_Fruit_NFR62
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Fruit_NFR_rep3


title: GS70701

description: Library name: M70701

value: ovary

value: mural granulosa cells

value: MGCs from small follicle (3.7mm)


title: Brain single cell 76

description: Library name: Sample 76


title: Fruit tissue, NFR light treatment, Time 24 h, replica 1

description:
Library name: T24_Fruit_NFR4
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T24_Fruit_NFR_rep1


title: Brain single cell 75

description: Library name: Sample 75


title: Brain single cell 74

description: Library name: Sample 74


title: Leaf tissue, FR light treatment, Time 12 h, replica 2

description:
Library name: T12_Leaf_FR57
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Leaf_FR_rep2


title: Leaf tissue, FR light treatment, Time 12 h, replica 3

description:
Library name: T12_Leaf_FR79
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Leaf_FR_rep3


title: Brain single cell 73

description: Library name: Sample 73


title: Leaf tissue, FR light treatment, Time 12 h, replica 1

description:
Library name: T12_Leaf_FR21
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Leaf_FR_rep1


title: Brain single cell 72

description: Library name: Sample 72


title: Brain single cell 71

description: Library name: Sample 71


title: Leaf tissue, NFR light treatment, Time 12 h, replica 4

description:
Library name: T12_Leaf_NFR63
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Leaf_NFR_rep4


title: Leaf tissue, NFR light treatment, Time 12 h, replica 3

description:
Library name: T12_Leaf_NFR41
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Leaf_NFR_rep3


title: Brain single cell 70

description: Library name: Sample 70


title: Leaf tissue, NFR light treatment, Time 12 h, replica 2

description:
Library name: T12_Leaf_NFR27
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Leaf_NFR_rep2


title: Brain single cell 69

description: Library name: Sample 69


title: Leaf tissue, NFR light treatment, Time 12 h, replica 1

description:
Library name: T12_Leaf_NFR5
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Leaf_NFR_rep1


title: Brain single cell 68

description: Library name: Sample 68


title: Fruit tissue, FR light treatment, Time 12 h, replica 4

description:
Library name: T12_Fruit_FR80
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Fruit_FR_rep4


title: Brain single cell 67

description: Library name: Sample 67


title: Fruit tissue, FR light treatment, Time 12 h, replica 3

description:
Library name: T12_Fruit_FR58
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Fruit_FR_rep3


title: Fruit tissue, FR light treatment, Time 12 h, replica 2

description:
Library name: T12_Fruit_FR44
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Fruit_FR_rep2


title: Brain single cell 65

description: Library name: Sample 65


title: Fruit tissue, FR light treatment, Time 12 h, replica 1

description:
Library name: T12_Fruit_FR22
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Fruit_FR_rep1


title: Fruit tissue, NFR light treatment, Time 12 h, replica 4

description:
Library name: T12_Fruit_NFR64
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Fruit_NFR_rep4


title: Brain single cell 63

description: Library name: Sample 63


title: Brain single cell 66

description: Library name: Sample 66


title: Brain single cell 64

description: Library name: Sample 64


title: Fruit tissue, NFR light treatment, Time 12 h, replica 3

description:
Library name: T12_Fruit_NFR42
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Fruit_NFR_rep3


title: Brain single cell 62

description: Library name: Sample 62


title: Fruit tissue, NFR light treatment, Time 12 h, replica 2

description:
Library name: T12_Fruit_NFR28
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Fruit_NFR_rep2


title: Brain single cell 61

description: Library name: Sample 61


title: Fruit tissue, NFR light treatment, Time 12 h, replica 1

description:
Library name: T12_Fruit_NFR6
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T12_Fruit_NFR_rep1


title: Brain single cell 60

description: Library name: Sample 60


title: Leaf tissue, FR light treatment, Time 6 h, replica 4

description:
Library name: T6_Leaf_FR81
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Leaf_FR_rep4


title: Brain single cell 59

description: Library name: Sample 59


title: Brain single cell 58

description: Library name: Sample 58


title: Leaf tissue, FR light treatment, Time 6 h, replica 2

description:
Library name: T6_Leaf_FR19
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Leaf_FR_rep2


title: Leaf tissue, FR light treatment, Time 6 h, replica 3

description:
Library name: T6_Leaf_FR45
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Leaf_FR_rep3


title: Brain single cell 57

description: Library name: Sample 57


title: Leaf tissue, FR light treatment, Time 6 h, replica 1

description:
Library name: T6_Leaf_FR15
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Leaf_FR_rep1


title: Brain single cell 56

description: Library name: Sample 56


title: Brain single cell 163

description: Library name: Sample 163


title: Leaf tissue, NFR light treatment, Time 6 h, replica 4

description:
Library name: T6_Leaf_NFR95
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Leaf_NFR_rep4


title: Brain single cell 55

description: Library name: Sample 55


title: Leaf tissue, NFR light treatment, Time 6 h, replica 3

description:
Library name: T6_Leaf_NFR65
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Leaf_NFR_rep3


title: Brain single cell 54

description: Library name: Sample 54


title: Leaf tissue, NFR light treatment, Time 6 h, replica 2

description:
Library name: T6_Leaf_NFR29
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Leaf_NFR_rep2


title: Brain single cell 53

description: Library name: Sample 53


title: Leaf tissue, NFR light treatment, Time 6 h, replica 1

description:
Library name: T6_Leaf_NFR1
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Leaf_NFR_rep1


title: Brain single cell 52

description: Library name: Sample 52


title: Fruit tissue, FR light treatment, Time 6 h, replica 4

description:
Library name: T6_Fruit_FR82
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Fruit_FR_rep4


title: Brain single cell 51

description: Library name: Sample 51


title: Brain single cell 50

description: Library name: Sample 50


title: Fruit tissue, FR light treatment, Time 6 h, replica 3

description:
Library name: T6_Fruit_FR46
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Fruit_FR_rep3


title: Brain single cell 49

description: Library name: Sample 49


title: Fruit tissue, FR light treatment, Time 6 h, replica 2

description:
Library name: T6_Fruit_FR20
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Fruit_FR_rep2


title: Fruit tissue, FR light treatment, Time 6 h, replica 1

description:
Library name: T6_Fruit_FR16
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Fruit_FR_rep1


title: Brain single cell 48

description: Library name: Sample 48


title: Fruit tissue, NFR light treatment, Time 6 h, replica 4

description:
Library name: T6_Fruit_NFR96
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Fruit_NFR_rep4


title: Brain single cell 47

description: Library name: Sample 47


title: Fruit tissue, NFR light treatment, Time 6 h, replica 3

description:
Library name: T6_Fruit_NFR66
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Fruit_NFR_rep3


title: Brain single cell 161

description: Library name: Sample 161


title: Brain single cell 46

description: Library name: Sample 46


title: Brain single cell 45

description: Library name: Sample 45


title: Fruit tissue, NFR light treatment, Time 6 h, replica 2

description:
Library name: T6_Fruit_NFR30
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Fruit_NFR_rep2


title: Brain single cell 44

description: Library name: Sample 44


title: Fruit tissue, NFR light treatment, Time 6 h, replica 1

description:
Library name: T6_Fruit_NFR2
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T6_Fruit_NFR_rep1


title: Brain single cell 42

description: Library name: Sample 42


title: Leaf tissue, FR light treatment, Time 0 h, replica 2

description:
Library name: T0_Leaf_FR47
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Leaf_FR_rep2


title: Leaf tissue, FR light treatment, Time 0 h, replica 3

description:
Library name: T0_Leaf_FR53
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Leaf_FR_rep3


title: Leaf tissue, FR light treatment, Time 0 h, replica 4

description:
Library name: T0_Leaf_FR89
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Leaf_FR_rep4


title: Brain single cell 41

description: Library name: Sample 41


title: Brain single cell 43

description: Library name: Sample 43


title: Leaf tissue, FR light treatment, Time 0 h, replica 1

description:
Library name: T0_Leaf_FR11
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Leaf_FR_rep1


title: Brain single cell 40

description: Library name: Sample 40


title: Brain single cell 39

description: Library name: Sample 39


title: Leaf tissue, NFR light treatment, Time 0 h, replica 4

description:
Library name: T0_Leaf_NFR91
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Leaf_NFR_rep4


title: Leaf tissue, NFR light treatment, Time 0 h, replica 3

description:
Library name: T0_Leaf_NFR73
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Leaf_NFR_rep3


title: Brain single cell 38

description: Library name: Sample 38


title: Leaf tissue, NFR light treatment, Time 0 h, replica 2

description:
Library name: T0_Leaf_NFR37
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Leaf_NFR_rep2


title: Leaf tissue, NFR light treatment, Time 0 h, replica 1

description:
Library name: T0_Leaf_NFR31
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Leaf_NFR_rep1


title: Brain single cell 37

description: Library name: Sample 37


title: Brain single cell 36

description: Library name: Sample 36


title: Fruit tissue, FR light treatment, Time 0 h, replica 4

description:
Library name: T0_Fruit_FR90
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Fruit_FR_rep4


title: Brain single cell 35

description: Library name: Sample 35


title: Fruit tissue, FR light treatment, Time 0 h, replica 3

description:
Library name: T0_Fruit_FR54
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Fruit_FR_rep3


title: Brain single cell 34

description: Library name: Sample 34


title: Fruit tissue, FR light treatment, Time 0 h, replica 2

description:
Library name: T0_Fruit_FR48
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Fruit_FR_rep2


title: Brain single cell 33

description: Library name: Sample 33


title: Fruit tissue, FR light treatment, Time 0 h, replica 1

description:
Library name: T0_Fruit_FR12
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Fruit_FR_rep1


title: Fruit tissue, NFR light treatment, Time 0 h, replica 4

description:
Library name: T0_Fruit_NFR92
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Fruit_NFR_rep4


title: Brain single cell 32

description: Library name: Sample 32


title: Brain single cell 31

description: Library name: Sample 31


title: Brain single cell 30

description: Library name: Sample 30


title: Fruit tissue, NFR light treatment, Time 0 h, replica 2

description:
Library name: T0_Fruit_NFR38
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Fruit_NFR_rep2


title: Brain single cell 29

description: Library name: Sample 29


title: Fruit tissue, NFR light treatment, Time 0 h, replica 3

description:
Library name: T0_Fruit_NFR74
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Fruit_NFR_rep3


title: Brain single cell 28

description: Library name: Sample 28


title: Fruit tissue, NFR light treatment, Time 0 h, replica 1

description:
Library name: T0_Fruit_NFR32
Col name in ReadCountsRaw_allSamples.txt and ReadCountsNormalised_allSamples.txt: T0_Fruit_NFR_rep1


title: Brain single cell 27

description: Library name: Sample 27


title: NPS_8819_CD_1

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

institute: Amsterdam UMC - locatie AMC

description:
Library name: NPS_8819_CD_1
RNA-Seq of non-CHIM NPS

data_processing:
Paired-end reads that passed Illumina quality filters were further screened to remove sequences aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The remaining reads were aligned to the GRCh38 human reference genome with Gencode v27 annotations using STAR (v2.6.1) [PMID: 23104886]. Read complexity was assessed with PRINSEQ Lite (v0.20.3) [PMID: 21278185], and low-complexity reads (DUST score > 4) were excluded from the BAM files. The alignment results were parsed via the SAMtools [PMID: 19505943] to generate SAM files. Gene-level counts were then obtained using featureCounts (v1.6.5) [PMID: 24227677] using the default option along with a minimum quality cut-off (Phred > 10), and transcripts per million (TPM) reads values were calculated. T cell receptor (TCR) transcripts were aggregated into four groups: TCR-α, TCR-β, TCR-γ, and TCR-δ. B cell receptor (BCR) transcripts were aggregated into light chains (IGK and IGL) and heavy chains (IGH-), with isotype transcripts (IGHG1-4, IGHM, IGHD, IGHE, IGHA1-2) analyzed separately. Transcripts were filtered using EdgeR’s filterByExpr function (v4.2.2) [PMID: 39844453] with “participants + timepoint” as the design. For each participant, baseline TPMs were averaged and raw counts were summed. Differential expression was assessed using the DESeq2 package (v1.44.0) [PMID: 25516281] for NPS and EdgeR for PBMCs in an R (v4.4.0) environment, with gene expression called differential with an FDR<0.05. Gene set enrichment analysis (GSEA) was performed using Metascape [PMID: 30944313] and GSEA (v4.4.0) [PMID: 16199517], both with the Gene Ontology (GO) gene sets [PMID: 36866529].
Assembly: GRCh38
Supplementary files format and content: "PBMC_counts.tsv" contains raw count values per sample and gene of PBMC.
Supplementary files format and content: "PBMC_tpm.tsv" contains TPM values per sample and gene of PBMC.
Supplementary files format and content: "PBMC_tpm_baseline_means_BCR_TCR_aggr.csv" contains TPM values per sample and gene in which TCR and BCR genes were aggregated and baseline PBMC samples per participant were averaged.
Supplementary files format and content: "PBMC_counts_baseline_sums_BCR_TCR_aggr.csv" contains counts per sample and gene in which TCR and BCR genes were aggregated and baseline PBMC samples per participant were summed.
Supplementary files format and content: "NPS_counts.csv" contains raw count values per sample and gene of NPS.
Supplementary files format and content: "NPS_tpm.csv" contains TPM values per sample and gene of NPS.
Supplementary files format and content: "NPS_tpm_baseline_means_TCR_BCR_aggr.csv" contains TPM values per sample and gene in which TCR and BCR genes were aggregated and baseline NPS samples per participant were averaged.
Supplementary files format and content: NPS_counts_baseline_sums_BCR.TCR.aggr.csv" contains counts per sample and gene in which TCR and BCR genes were aggregated and baseline NPS samples per participant were summed.
Supplementary files format and content: "participant_metadata_filtered.csv" contains metadata per participant.

source_name: Nose

extract_protocol:
NPS: RNA was extracted with on-column DNase treatment using the miRNeasy Mini Kit (Qiagen) following the manufacturer's instructions. RNA was quantified by qPCR using the housekeeping gene B2M.
PBMC: 500K cells were stored in 750 μL TRIzol at -80°C. RNA until further processing. RNA was extracted with on-column DNase treatment using the miRNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
NPS: For cDNA synthesis, 10 ng of RNA was reverse-transcribed and pre-amplified (14 cycles) according to the Smart-Seq2 protocol. cDNA was purified with AMPure XP beads (Beckman Coulter), and 0.5 ng was used for Nextera XT sequencing library preparation with 8-bp Unique Dual Index (UDI) barcodes (IDT, Illumina) and the Nextera XT DNA Library Preparation Kit (Illumina). To minimize inter-assay variability, all purification steps were performed using an EpMotion 5075 (Eppendorf), and sequencing libraries were prepared in a 96-well format using a Mantis microfluidics liquid dispenser (Formulamatrix). Quality control included assessment of total RNA quality and quantity, optimization of pre-amplification cycle numbers, and fragment size analysis by capillary electrophoresis (5300 Fragment Analyzer, Agilent). cDNA and final libraries were quantified with the Quant-iT PicoGreen assay (Thermo Fisher Scientific). All samples passed quality thresholds, with >70% of fragments ranging from 300–700 bp and <5% primer dimers. Libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche), normalized to equimolar concentrations, and loaded onto a NovaSeq X Plus sequencing platform (Illumina) with a 25B flow cell. Paired-end sequencing (150 bp) yielded 4.2 billion total reads, corresponding to an average depth of ~15 million reads per sample.
PBMC: Quantabio Sparq mRNA-Seq kit was used to prepare stranded libraries using 8 ng of high-quality total RNA as input, except in 10 samples where the yield was below 8 ng. Libraries underwent 16-18 PCR amplification cycles and libraries were indexed with xGen 10 nt Unique Dual Indexes (UDIs). Paired-end (50x50) sequencing was performed on a NovaSeq 6000 targeting 40 million reads per library.

value: Nose

value: NPS

value: female


title: Brain single cell 26

description: Library name: Sample 26


title: NPS_8812_CD_1

description:
Library name: NPS_8812_CD_1
RNA-Seq of non-CHIM NPS

value: male


title: NPS_8811_CD_1

description:
Library name: NPS_8811_CD_1
RNA-Seq of non-CHIM NPS


title: Brain single cell 25

description: Library name: Sample 25


title: Brain single cell 24

description: Library name: Sample 24


title: NPS_8587_CD_1

description:
Library name: NPS_8587_CD_1
RNA-Seq of non-CHIM NPS


title: NPS_8586_CD_1

description:
Library name: NPS_8586_CD_1
RNA-Seq of non-CHIM NPS


title: NPS_8585_CD_1

description:
Library name: NPS_8585_CD_1
RNA-Seq of non-CHIM NPS


title: Brain single cell 23

description: Library name: Sample 23


title: Brain single cell 22

description: Library name: Sample 22


title: NPS_7970_CD_1

description:
Library name: NPS_7970_CD_1
RNA-Seq of non-CHIM NPS


title: Brain single cell 19

description: Library name: Sample 19


title: NPS_7803_CD_1

description:
Library name: NPS_7803_CD_1
RNA-Seq of non-CHIM NPS


title: NPS_7666_CD_1

description:
Library name: NPS_7666_CD_1
RNA-Seq of non-CHIM NPS


title: NPS_7151_CD_1

description:
Library name: NPS_7151_CD_1
RNA-Seq of non-CHIM NPS


title: Brain single cell 18

description: Library name: Sample 18


title: Brain single cell 21

description: Library name: Sample 21


title: Brain single cell 20

description: Library name: Sample 20


title: NPS_5770_CD_1

description:
Library name: NPS_5770_CD_1
RNA-Seq of non-CHIM NPS


title: Brain single cell 17

description: Library name: Sample 17


title: NPS_5685_CD_1

description:
Library name: NPS_5685_CD_1
RNA-Seq of non-CHIM NPS


title: Brain single cell 16

description: Library name: Sample 16


title: NPS_5663_CD_1

description:
Library name: NPS_5663_CD_1
RNA-Seq of non-CHIM NPS


title: Brain single cell 15

description: Library name: Sample 15


title: Brain single cell 14

description: Library name: Sample 14


title: PBMC_8879_CD_7

description:
Library name: PBMC_8879_CD_7
RNA-Seq of CHIM PBMC

value: Blood

value: PBMC

tag: days post_challenge


title: Brain single cell 13

description: Library name: Sample 13


title: PBMC_8876_CD_8_reprep

description:
Library name: PBMC_8876_CD_8_reprep
RNA-Seq of CHIM PBMC

tag: reprep

value: Yes


title: PBMC_8878_CD_9

description:
Library name: PBMC_8878_CD_9
RNA-Seq of CHIM PBMC


title: PBMC_8877_CD_7

description:
Library name: PBMC_8877_CD_7
RNA-Seq of CHIM PBMC


title: Brain single cell 12

description: Library name: Sample 12


title: Brain single cell 11

description: Library name: Sample 11


title: PBMC_8876_CD_8

description:
Library name: PBMC_8876_CD_8
RNA-Seq of CHIM PBMC


title: Brain single cell 10

description: Library name: Sample 10


title: Brain single cell 9

description: Library name: Sample 9


title: PBMC_8803_CD_8

description:
Library name: PBMC_8803_CD_8
RNA-Seq of CHIM PBMC


title: PBMC_8801_CD_9_reprep

description:
Library name: PBMC_8801_CD_9_reprep
RNA-Seq of CHIM PBMC


title: Brain single cell 8

description: Library name: Sample 8


title: PBMC_8801_CD_9

description:
Library name: PBMC_8801_CD_9
RNA-Seq of CHIM PBMC


title: PBMC_8799_CD_9_reprep

description:
Library name: PBMC_8799_CD_9_reprep
RNA-Seq of CHIM PBMC


title: Brain single cell 7

description: Library name: Sample 7


title: Brain single cell 6

description: Library name: Sample 6


title: PBMC_8799_CD_9

description:
Library name: PBMC_8799_CD_9
RNA-Seq of CHIM PBMC


title: Brain single cell 5

description: Library name: Sample 5


title: Brain single cell 4

description: Library name: Sample 4


title: PBMC_8793_CD_9

description:
Library name: PBMC_8793_CD_9
RNA-Seq of CHIM PBMC


title: Brain single cell 3

description: Library name: Sample 3


title: PBMC_8797_CD_8

description:
Library name: PBMC_8797_CD_8
RNA-Seq of CHIM PBMC


title: PBMC_8790_CD_8

description:
Library name: PBMC_8790_CD_8
RNA-Seq of CHIM PBMC


title: Brain single cell 2

description: Library name: Sample 2


title: PBMC_8784_CD_8_reprep

description:
Library name: PBMC_8784_CD_8_reprep
RNA-Seq of CHIM PBMC


title: Brain single cell 1

description: Library name: Sample 1


title: PBMC_8784_CD_8

description:
Library name: PBMC_8784_CD_8
RNA-Seq of CHIM PBMC


title: PBMC_8783_CD_7

description:
Library name: PBMC_8783_CD_7
RNA-Seq of CHIM PBMC


title: AtY34 overexpressor, total RNA, rep3

city: Hong Kong

first: Hon-Ming

last: LAM

address: Room EG02, East Block, Science Centre,The Chinese University of Hong Kong,Shatin, N.T. Hong Kong.

department: School of Life Sciences

institute: The Chinese University of Hong Kong

description: Total RNA

data_processing:
nf-core/rnaseq bioinformatics pipeline version 3.5 (https://nf-co.re/rnaseq/3.5)
FastQC/MultiQC was used to perform quality checking and reporting of sequencing data
mapped to the Arabidopsis thaliana genome (TAIR10) using STAR mapper
read counts of transcripts were quantified using SALMON
Assembly: Mapped to Arabidopsis thaliana genome (TAIR10)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Arabidopsis

source_name: 11-days seedlings

extract_protocol:
RNA was isolated and purified with Direct-zol RNA Miniprep Kits (Cat.# R2052, Zymo Research).
Stranded rRNA depleted library construction

value: 11-days seedlings

tag: cell line

value: AtY34 overexpressor

value: Mock


title: AtY34 overexpressor, total RNA, rep2

description: Total RNA


title: PBMC_8782_CD_8

description:
Library name: PBMC_8782_CD_8
RNA-Seq of CHIM PBMC


title: AtY34 overexpressor, total RNA, rep1

description: Total RNA


title: PBMC_8781_CD_8

description:
Library name: PBMC_8781_CD_8
RNA-Seq of CHIM PBMC


title: AtY34 overexpressor, light polysome, rep2

description: Light polysome


title: PBMC_8780_CD_7

description:
Library name: PBMC_8780_CD_7
RNA-Seq of CHIM PBMC


title: PBMC_8780_CD_7_reprep

description:
Library name: PBMC_8780_CD_7_reprep
RNA-Seq of CHIM PBMC


title: AtY34 overexpressor, light polysome, rep3

description: Light polysome


title: PBMC_8779_CD_7_reprep

description:
Library name: PBMC_8779_CD_7_reprep
RNA-Seq of CHIM PBMC


title: AtY34 overexpressor, heavy polysome, rep2

description: Heavy polysome


title: PBMC_8778_CD_8

description:
Library name: PBMC_8778_CD_8
RNA-Seq of CHIM PBMC


title: PBMC_8775_CD_4

description:
Library name: PBMC_8775_CD_4
RNA-Seq of CHIM PBMC


title: PBMC_8590_CD_8

description:
Library name: PBMC_8590_CD_8
RNA-Seq of CHIM PBMC


title: PBMC_8662_CD_7

description:
Library name: PBMC_8662_CD_7
RNA-Seq of CHIM PBMC


title: AtYchF1 knockdown mutant, total RNA, rep2

description: Total RNA

value: AtYchF1 knockdown mutant


title: PBMC_8591_CD_6

description:
Library name: PBMC_8591_CD_6
RNA-Seq of CHIM PBMC


title: GRO WT 37

type: RNA

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: GRO labelling for wt 37ºC sample. Replicates 1-3

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them by pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a Fujifilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing: Raw image quantization with background subtracted and Median Absolute Desviation normalization of each triplicate. The average processed value for each gene was corrected by percentage of guanines (RA data) or uracils (TR data) present in each probe-coding strand as described in García-Martinez et al. 2004.

organism: Saccharomyces cerevisiae

source_name: wild type

label_protocol: Genomic Run On (GRO) protocol For GRO samples: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were frozen in liquid nitrogen. Samples were then permeabilized with 1 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix. For cDNA samples: cDNA was synthetized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labelling.

growth_protocol: Cells were grown in YPD at 25ºC for at least 15 hours to reach early exponential phase at 0.4-0.5 OD600. Then, an aliquot of these cells was spun-down and collected. Another aliquot was transferred to 37ºC and grown for 4 hours. Each sample was analyzed in biological triplicates.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

tag: strain


title: GRO WT 25

description: GRO labelling for wt 25ºC sample. Replicates 1-3


title: PBMC_8589_CD_7

description:
Library name: PBMC_8589_CD_7
RNA-Seq of CHIM PBMC


title: GRO eIF5A 37

description: GRO labelling for eIF5A 37ºC sample. Replicates 1-3

source_name: eIF5a thermo sensitive


title: AtYchF1 knockdown mutant, total RNA, rep1

description: Total RNA


title: PBMC_8334_CD_8

description:
Library name: PBMC_8334_CD_8
RNA-Seq of CHIM PBMC


title: AtYchF1 knockdown mutant, light polysome, rep3

description: Light polysome


title: PBMC_8336_CD_8

description:
Library name: PBMC_8336_CD_8
RNA-Seq of CHIM PBMC


title: PBMC_8325_CD_10

description:
Library name: PBMC_8325_CD_10
RNA-Seq of CHIM PBMC


title: GRO eIF5A 25

description: GRO labelling for eIF5A 25ºC sample. Replicates 1-3


title: AtYchF1 knockdown mutant, light polysome, rep2

description: Light polysome


title: PBMC_8878_CD_7

description:
Library name: PBMC_8878_CD_7
RNA-Seq of CHIM PBMC


title: PBMC_8877_CD_6

description:
Library name: PBMC_8877_CD_6
RNA-Seq of CHIM PBMC


title: AtYchF1 knockdown mutant, light polysome, rep1

description: Light polysome


title: cDNA WT 25

description: cDNA labelling for wt 25ºC sample. Replicates 1-3


title: PBMC_8876_CD_7

description:
Library name: PBMC_8876_CD_7
RNA-Seq of CHIM PBMC


title: cDNA eIF5A 37

description: cDNA labelling for eIF5A 37ºC sample. Replicates 1-3


title: AtYchF1 knockdown mutant, heavy polysome, rep3

description: Heavy polysome


title: PBMC_8803_CD_7

description:
Library name: PBMC_8803_CD_7
RNA-Seq of CHIM PBMC


title: cDNA eIF5A 25

description: cDNA labelling for eIF5A 25ºC sample. Replicates 1-3


title: PBMC_8801_CD_8

description:
Library name: PBMC_8801_CD_8
RNA-Seq of CHIM PBMC


title: AtYchF1 knockdown mutant, heavy polysome, rep2

description: Heavy polysome


title: P11 horiztonal cells

city: Los Angeles

first: Yi-Rong

last: Peng

address: 100 Stein Plaza Driveway, B-133

department: Department of Ophthalmology

institute: University of California, Los Angeles

description:
Library name: P11HC_7768
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retina

extract_protocol:
Tg(Cx57icre;Ai14) mice were used to label and isolate horizontal cells. Retinas were dissociated using papain, followed by FACS sorting to isolate horizontal cells, then dissociated into a single-cell suspension for single cell capture and scRNA-seq library preparation
Single cell libraries were generated using the Chromium 3’ V3 platform (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, single cells were partitioned into Gel-beads-in-EMulsion (GEMs) where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full-length cDNA; this was followed by amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment to yield the final libraries.

value: Retina

value: Horizontal cells


title: AtY34 overexpressor, heavy polysome, rep3

description: Heavy polysome


title: AtY34 overexpressor, light polysome, rep1

description: Light polysome


title: PBMC_8799_CD_8

description:
Library name: PBMC_8799_CD_8
RNA-Seq of CHIM PBMC


title: PBMC_8779_CD_7

description:
Library name: PBMC_8779_CD_7
RNA-Seq of CHIM PBMC


title: AtY34 overexpressor, heavy polysome, rep1

description: Heavy polysome


title: PBMC_8797_CD_7

description:
Library name: PBMC_8797_CD_7
RNA-Seq of CHIM PBMC


title: AtYchF1 knockdown mutant, heavy polysome, rep1

description: Heavy polysome


title: PBMC_8796_CD_9_reprep

description:
Library name: PBMC_8796_CD_9_reprep
RNA-Seq of CHIM PBMC


title: AtYchF1 knockdown mutant, total RNA, rep3

description: Total RNA


title: P8 horiztonal cells

description:
Library name: P8HC_7202
10X Genomics


title: PBMC_8796_CD_9

description:
Library name: PBMC_8796_CD_9
RNA-Seq of CHIM PBMC


title: P6 horiztonal cells

description:
Library name: P6HC_8052
10X Genomics


title: PBMC_8793_CD_8

description:
Library name: PBMC_8793_CD_8
RNA-Seq of CHIM PBMC


title: Col-2, total RNA, rep3

description: Total RNA

value: WT


title: Col-2, total RNA, rep2

description: Total RNA


title: PBMC_8790_CD_7

description:
Library name: PBMC_8790_CD_7
RNA-Seq of CHIM PBMC


title: WT-2

city: Bunkyo-Ku

first: Ge

state: Tokyo

address: 2-1-1 Hongo

country: Japan

institute: Juntendo University Graduate School of Medicine

description:
Library name: SAMPLE-10
Column name in Mus musculus_tpm_table.csv:cKO-2

data_processing:
The process includes poly(A) mRNA enrichment and fragmentation followed by cDNA synthesis, end repair, adaptor ligations, and PCR amplification.
Assembly: Homo sapiens: GRCh38；Mus musculus: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: mouse melanoma tissue

extract_protocol:
Total RNA was isolated from cultured keratinocytes using an Rneasy Plus Micro Kit according to the manufacturer's instructions
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit

value: mouse melanoma tissue

value: Campf/f

value: Topical Imiquimod cream