title: input 35C imbibition rep2

description: Library name: inp_t35_2


title: input 35C imbibition rep1

status: Public on Jul 24 2026

type: SRA

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: Library name: inp_t35_1

library_source: transcriptomic

data_processing:
In our sequencing strategy, the R1 reads of pooled libraries contain two parts of UMI split by the barcode. We rearrange UMI sequences to position them next to each other and remove additional low-quality nucleotides, including  the oligo(dT) fragment and those that follow it. For this, we utilise the awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 of pooled libraries were demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex and R1 with parameters -p UB -UMI 14 -n 1. The resulting reads were trimmed to eliminate potential contamination with the poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then, they were mapped using STAR (v 2.7.8a) to a custom genome containing both Arabidopsis chromosomes and ERCC spike-in sequences with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes.
Assembly: TAIR10
Supplementary files format and content: gene count text files

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seed

growth_protocol: Plants were grown in a greenhouse under a long day-night cycle at 22°C. Seeds from 8 to 12 plants were combined to create a single biological replicate.

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211). For 4-SU labelled RNAs enrichment, biotinylation was performed for 12.5 μg of freshly isolated RNA in a 200 μl reaction mixture (10 mM Tris pH 7.5; 1 mM EDTA; 0.2 mg/ml EZ-Link Biotin-HPDP (ThermoFisher)) for 1.5 h at 22°C. 1 µl of tenfold diluted ERCC RNA Spike-In Mix (ThermoFisher) was added to the RNA before the biotinylation reactions, and a portion of the RNA after the addition of ERCC (500 ng) was retained as an input. Unbound Biotin-HPDP was removed by chloroform/isoamyl alcohol (24:1) extraction. Subsequently, a 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added, and RNA was precipitated by centrifugation at 20,000g for 20 minutes. The pellet was washed with 1 ml of 80% ethanol, and after drying, it was resuspended in 25 μl of RNase-free water. Biotinylated RNA was purified using 50 μl of streptavidin C1 Dynabeads (ThermoFisher). The beads were washed in binding buffer (0.2 M NaCl; 0.1 M sodium phosphate pH 6.8; 25 mM MgCl2; 0.4% Tween), blocked in the binding buffer with 1 μg/μl glycogen for 10 minutes, and washed again in binding buffer. RNA samples were denatured at 65°C for 5 minutes, followed by 5 minutes on ice. Then, 25 μl of 2x binding buffer and 50 μl of washed streptavidin beads were added, mixed, and incubated at 22°C with gentle shaking for 20 minutes. The beads were washed three times with 0.5 ml of washing buffer (100 mM Tris-HCl pH 7.5; 10 mM EDTA; 1 M NaCl; 0.1% Tween20) at 65°C, followed by three washes at room temperature. Biotinylated RNA was eluted from the beads by two incubations with 50 μl of 200 mM DTT. RNA from the combined eluates was purified using RNA Clean & Concentrator-5 columns (Zymo), following the protocol for long RNA purification with DNase treatment. The entire volume of the sample was used for reverse transcription.
Input and enriched RNA samples were used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.25 of each input and whole enriched RNA RT reaction were pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed at 4C, 22C and 35C for 3h in the presence of 2 mM 4-thiouridine (Merck; from a 50 mM stock solution in 6% methanol).

tag: tissue

value: seed

tag: ecotype

tag: treatment

value: 35C during imbibition

tag: treatment enrichment

value: input

tag: batch


title: input 22C imbibition rep2

description: Library name: inp_t22_2

value: 22C during imbibition


title: input 22C imbibition rep4

description: Library name: inp_t22_4


title: input 22C imbibition rep3

description: Library name: inp_t22_3


title: input 4C imbibition rep4

description: Library name: inp_t04_4

value: 4C during imbibition


title: input 22C imbibition rep1

description: Library name: inp_t22_1


title: input 4C imbibition rep2

description: Library name: inp_t04_2


title: input 4C imbibition rep3

description: Library name: inp_t04_3


title: input 4C imbibition rep1

description: Library name: inp_t04_1


title: imbibed input rep1

description: Library name: imb_in_1

library_source: genomic

data_processing:
Adapter sequences were trimmed from reads using cutadapt (v 1.18) with the parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -e 0.2 --minimum-length=30. Next, reads were mapped using bowtie2 (v 2.3.5.1) with parameters: --no-unal --local. The mapped reads were then converted to BAM files and sorted using samtools (v 1.13). Mapped reads were initially filtered with sambamba (v 0.8.0) using the parameter -F "[XS] == null and mapping_quality >= 10", followed by the removal of duplicated reads with gatk MarkDuplicates (v 4.2.6.1). Normalised bigwig tracks for each library and merged biological replicates were prepared using bedtools genomecov (v 2.30.0) and bedGraphToBigWig (v 4). Bigwig tracks normalised for the input were generated using bigwigCompare (v 3.5.1) with parameters --binSize 1 --outFileFormat bigwig --skipZeroOverZero --operation subtract. Peaks were called using macs2 callpeak (v 2.2.7.1) with the broad option.
Assembly: TAIR
Supplementary files format and content: bigwigs of deduplicated reads, normalised to sequencing depth
Supplementary files format and content: identified peaks in txt format

molecule: genomic DNA

extract_protocol:
250 mg of dry and 6-hour-imbibed seeds were ground in liquid nitrogen. The resulting powder was combined with 20 ml of crosslinking buffer (0.1 M sucrose; 0.1 M NaCl; 20 mM HEPES pH 7.0; 1% formaldehyde) in 50 ml tubes and gently mixed in the cold room for 10 minutes. Subsequently, 1.25 ml of 2 M glycine was added to each sample and mixed gently in the cold room for 5 minutes. The samples were then centrifuged at 1800 g for 15 minutes at 4°C, after which the supernatant was removed, and 20 ml of Honda buffer (0.44 M sucrose; 1.25% Ficoll; 2.5% Dextran 40; 25 mM HEPES pH 7.0; 10 mM MgCl2; 0.5% Triton X-100; 0.5 mM PMSF; 10 mM DTT; 1x cOmplete EDTA-free Protease Inhibitor Cocktail (Roche)) was added to the pellet, which was then resuspended by mixing with a spatula. The samples were mixed gently in the cold room for 10 minutes and filtered through two Miracloth layers. They were then centrifuged at 1800 g for 15 minutes at 4°C; the supernatant was removed, and the pellet was resuspended in 500 µl of fresh NLB buffer (50 mM Tris-HCl pH 8.0; 10 mM EDTA; 1% SDS; 1x cOmplete EDTA-free Protease Inhibitor Cocktail (Roche)), after which the samples were incubated on ice for 30 minutes. Next, 500 µl of ChIP dilution buffer I (16.7 mM Tris-HCl pH 8.0; 167 mM NaCl; 1.2 mM EDTA) was added to the samples. The samples were sonicated using a Bioruptor (Diagenode) with internal cooling, employing 30 seconds ON/30 seconds OFF (High) settings for 20 cycles with 5-minute breaks for cooling on ice after every 5 cycles.
The samples were centrifuged for 5 minutes at 20,000 g and 4°C, with the supernatants being carefully transferred to new tubes to avoid contamination from the upper layer. 60 μl of each sample were retained as input controls. Immunoprecipitation was conducted in high-recovery tubes using 400 µl of chromatin, to which 1600 µl of ChIP dilution buffer II (16.7 mM Tris-HCl pH 8.0; 167 mM NaCl; 1.2 mM EDTA; 1.1% Triton X-100; 0.6 mM PMSF; 1.2x cOmplete EDTA-free Protease Inhibitor Cocktail (Roche)) was added. The IP was performed with 2.5 µg of anti-RPB1 antibody (Agrisera AS11 1804), and the samples were incubated in the cold room with gentle rotation. The next day, 15 µl of ChIP dilution buffer II-washed Dynabeads Protein G (ThermoFisher) were added to the samples and incubated in the cold room with gentle rotation for 3 hours. The supernatant was discarded, and the beads were washed twice with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 2 mM EDTA; 20 mM Tris-HCl pH 8.0), once with high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 2 mM EDTA; 20 mM Tris-HCl pH 8.0), and twice with TE buffer. For ChIP-seq, antibody complexes were eluted by adding 100 µl of elution buffer (1% SDS; 0.1 M NaHCO3) to the beads and incubating at 65°C for 15 minutes. The supernatant was collected, and the elution was repeated with a fresh 100 µl of elution buffer. The supernatants were combined, mixed with 8 µl of 5M NaCl, and incubated overnight at 65°C. Input samples were processed similarly. To the input samples, 100 µl of TE buffer, 7.1 µl of 5 M NaCl, and 17.4 µl of 10% SDS were added, followed by an overnight incubation at 65°C. The following day, 5 µl of 0.5 M EDTA, 8 µl of 1 M Tris-HCl pH 6.5, and 2 µl of 20 mg/ml proteinase K were added to all samples, which were then incubated for 3 h at 55°C. DNA was recovered using ChIP DNA Clean & Concentrator columns (Zymo).
Libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina.

treatment_protocol: Seeds were imbibed for 6h.

value: 6h imbibed


title: imbibed input rep3

description: Library name: imb_in_3


title: imbibed input rep2

description: Library name: imb_in_2


title: new PUR imbibition rep1

description: Library name: new_PUR_1

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211). For 4-SU labelled RNAs enrichment, biotinylation was performed for 22.5 μg of freshly isolated RNA in a 200 μl reaction mixture (10 mM Tris pH 7.5; 1 mM EDTA; 0.2 mg/ml EZ-Link Biotin-HPDP (ThermoFisher)) for 1.5 h at 22°C. 1 µl of tenfold diluted ERCC RNA Spike-In Mix (ThermoFisher) was added to the RNA before the biotinylation reactions, and a portion of the RNA after the addition of ERCC (500 ng) was retained as an input. Unbound Biotin-HPDP was removed by chloroform/isoamyl alcohol (24:1) extraction. Subsequently, a 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added, and RNA was precipitated by centrifugation at 20,000g for 20 minutes. The pellet was washed with 1 ml of 80% ethanol, and after drying, it was resuspended in 25 μl of RNase-free water. Biotinylated RNA was purified using 50 μl of streptavidin C1 Dynabeads (ThermoFisher). The beads were washed in binding buffer (0.2 M NaCl; 0.1 M sodium phosphate pH 6.8; 25 mM MgCl2; 0.4% Tween), blocked in the binding buffer with 1 μg/μl glycogen for 10 minutes, and washed again in binding buffer. RNA samples were denatured at 65°C for 5 minutes, followed by 5 minutes on ice. Then, 25 μl of 2x binding buffer and 50 μl of washed streptavidin beads were added, mixed, and incubated at 22°C with gentle shaking for 20 minutes. The beads were washed three times with 0.5 ml of washing buffer (100 mM Tris-HCl pH 7.5; 10 mM EDTA; 1 M NaCl; 0.1% Tween20) at 65°C, followed by three washes at room temperature. Biotinylated RNA was eluted from the beads by two incubations with 50 μl of 200 mM DTT. RNA from the combined eluates was purified using RNA Clean & Concentrator-5 columns (Zymo), following the protocol for long RNA purification with DNase treatment. The entire volume of the sample was used for reverse transcription.
Input and enriched RNA samples were used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.25 of each input and whole enriched RNA RT reaction were pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed for 6h in the presence of 2 mM 4-thiouridine (Merck; from a 50 mM stock solution in 6% methanol) in the presence of 500 μM cycloheximide (Merck; from a 100 mg/ml stock solution in ethanol); 4 mM puromycin (BioShop) or mock.

tag: genotype

value: PUR

value: enriched


title: imbibed IP rep2

description: Library name: imb_2

value: IP


title: imbibed IP rep1

description: Library name: imb_1


title: new CHX imbibition rep2

description: Library name: new_CHX_2

value: CHX


title: imbibed IP rep3

description: Library name: imb_3


title: dry input rep1

description: Library name: dry_in_1

value: dry


title: dry input rep3

description: Library name: dry_in_3


title: dry input rep2

description: Library name: dry_in_2


title: dry IP rep2

description: Library name: dry_2


title: dry IP rep3

description: Library name: dry_3


title: dry IP rep1

description: Library name: dry_1


title: input mock imbibition rep3

description: Library name: inp_mock_3

value: mock


title: alpha-amanitin 6h ABA rep4

description:
Library name: A_A_06h_4
OK

data_processing:
In our sequencing strategy, the R1 reads of pooled libraries contain two parts of UMI split by the barcode. We rearrange UMI sequences to position them next to each other and remove additional low-quality nucleotides, including  the oligo(dT) fragment and those that follow it. For this, we utilise the awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 of pooled libraries were demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex and R1 with parameters -p UB -UMI 14 -n 1. The resulting reads were trimmed to eliminate potential contamination with the poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then, they were mapped using STAR (v 2.7.8a) to a custom genome containing both Arabidopsis and Saccharomyces cerevisiae chromosomes with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes.
Assembly: TAIR10
Supplementary files format and content: Arabidopsis genes count text files

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211).
500 ng of seed RNA was used in reverse transcription (25 ng total S. cerevisiae RNA spiked into each sample) with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.25 of each reaction was pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed for indicated times in the presence of mock and 250 μM α-amanitin (Merck; prepared from a 1 mM stock solution in water). For 6h time point, we also applied 3 μM ABA (Merck; from a 1 mM stock solution in ethanol).

tag: treatment inhibitor

value: alpha-amanitin

tag: treatment aba

value: ABA


title: alpha-amanitin 6h ABA rep2

description:
Library name: A_A_06h_2
OK


title: alpha-amanitin 6h ABA rep1

description:
Library name: A_A_06h_1
OK


title: alpha-amanitin 12h rep4

description:
Library name: A_X_12h_4
OK

value: 12h imbibed


title: alpha-amanitin 6h ABA rep3

description:
Library name: A_A_06h_3
OK


title: alpha-amanitin 12h rep3

description:
Library name: A_X_12h_3
OK


title: alpha-amanitin 12h rep1

description:
Library name: A_X_12h_1
OK


title: alpha-amanitin 6h rep3

description:
Library name: A_X_06h_3
OK


title: alpha-amanitin 6h rep4

description:
Library name: A_X_06h_4
OK


title: alpha-amanitin 12h rep2

description:
Library name: A_X_12h_2
OK


title: alpha-amanitin 6h rep2

description:
Library name: A_X_06h_2
OK


title: alpha-amanitin 3h rep3

description:
Library name: A_X_03h_3
OK

value: 3h imbibed


title: alpha-amanitin 3h rep4

description:
Library name: A_X_03h_4
OK


title: alpha-amanitin 3h rep2

description:
Library name: A_X_03h_2
OK


title: alpha-amanitin 6h rep1

description:
Library name: A_X_06h_1
OK


title: alpha-amanitin 3h rep1

description:
Library name: A_X_03h_1
OK


title: alpha-amanitin 1h rep4

description:
Library name: A_X_01h_4
OK

value: 1h imbibed


title: alpha-amanitin 1h rep2

description:
Library name: A_X_01h_2
OK

value: seed


title: alpha-amanitin 1h rep3

description:
Library name: A_X_01h_3
OK


title: alpha-amanitin 1h rep1

description:
Library name: A_X_01h_1
OK


title: mock 6h ABA rep4

description:
Library name: M_A_06h_4
OK


title: mock 12 rep4

description:
Library name: M_X_12h_4
OK


title: mock 6h ABA rep3

description:
Library name: M_A_06h_3
OK


title: mock 6h ABA rep1

description:
Library name: M_A_06h_1
OK


title: mock 6h ABA rep2

description:
Library name: M_A_06h_2
OK


title: mock 12 rep1

description:
Library name: M_X_12h_1
OK


title: mock 12 rep2

description:
Library name: M_X_12h_2
OK


title: mock 6h rep3

description:
Library name: M_X_06h_3
OK


title: mock 6h rep4

description:
Library name: M_X_06h_4
OK


title: mock 6h rep1

description:
Library name: M_X_06h_1
OK


title: mock 3h rep2

description:
Library name: M_X_03h_2
FAILED


title: mock 3h rep4

description:
Library name: M_X_03h_4
OK


title: mock 3h rep3

description:
Library name: M_X_03h_3
OK


title: mock 3h rep1

description:
Library name: M_X_03h_1
OK


title: mock 1h rep3

description:
Library name: M_X_01h_3
OK


title: mock 1h rep1

description:
Library name: M_X_01h_1
OK


title: new 6h mock imbibition rep3

description: Library name: new_mock_6h_3

treatment_protocol: Seeds were imbibed for 3h and 6h in the presence of 2 mM 4-thiouridine (Merck; from a 50 mM stock solution in 6% methanol) in the presence of 500 μM cycloheximide (Merck; from a 100 mg/ml stock solution in ethanol) or mock.


title: new 6h mock imbibition rep2

description: Library name: new_mock_6h_2


title: new 6h mock imbibition rep1

description: Library name: new_mock_6h_1


title: new 3h mock imbibition rep2

description: Library name: new_mock_3h_2


title: new 6h CHX imbibition rep3

description: Library name: new_CHX_6h_3


title: new 6h CHX imbibition rep1

description: Library name: new_CHX_6h_1


title: new 3h CHX imbibition rep3

description: Library name: new_CHX_3h_3


title: new 3h CHX imbibition rep2

description: Library name: new_CHX_3h_2


title: new 3h CHX imbibition rep1

description: Library name: new_CHX_3h_1


title: input 6h mock imbibition rep3

description: Library name: inp_mock_6h_3


title: input 6h mock imbibition rep2

description: Library name: inp_mock_6h_2


title: input 3h mock imbibition rep2

description: Library name: inp_mock_3h_2


title: input 6h CHX imbibition rep3

description: Library name: inp_CHX_6h_3


title: input 6h CHX imbibition rep1

description: Library name: inp_CHX_6h_1


title: input 3h mock imbibition rep1

description: Library name: inp_mock_3h_1


title: input 3h CHX imbibition rep3

description: Library name: inp_CHX_3h_3


title: input 3h CHX imbibition rep2

description: Library name: inp_CHX_3h_2


title: new 3h imbibed rep4

description: Library name: new3h_4

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211). For 4-SU labelled RNAs enrichment, biotinylation was performed for 12 μg of freshly isolated RNA in a 200 μl reaction mixture (10 mM Tris pH 7.5; 1 mM EDTA; 0.2 mg/ml EZ-Link Biotin-HPDP (ThermoFisher)) for 1.5 h at 22°C. 1 µl of tenfold diluted ERCC RNA Spike-In Mix (ThermoFisher) was added to the RNA before the biotinylation reactions, and a portion of the RNA after the addition of ERCC (250 ng) was retained as an input. Unbound Biotin-HPDP was removed by chloroform/isoamyl alcohol (24:1) extraction. Subsequently, a 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added, and RNA was precipitated by centrifugation at 20,000g for 20 minutes. The pellet was washed with 1 ml of 80% ethanol, and after drying, it was resuspended in 25 μl of RNase-free water. Biotinylated RNA was purified using 50 μl of streptavidin C1 Dynabeads (ThermoFisher). The beads were washed in binding buffer (0.2 M NaCl; 0.1 M sodium phosphate pH 6.8; 25 mM MgCl2; 0.4% Tween), blocked in the binding buffer with 1 μg/μl glycogen for 10 minutes, and washed again in binding buffer. RNA samples were denatured at 65°C for 5 minutes, followed by 5 minutes on ice. Then, 25 μl of 2x binding buffer and 50 μl of washed streptavidin beads were added, mixed, and incubated at 22°C with gentle shaking for 20 minutes. The beads were washed three times with 0.5 ml of washing buffer (100 mM Tris-HCl pH 7.5; 10 mM EDTA; 1 M NaCl; 0.1% Tween20) at 65°C, followed by three washes at room temperature. Biotinylated RNA was eluted from the beads by two incubations with 50 μl of 200 mM DTT. RNA from the combined eluates was purified using RNA Clean & Concentrator-5 columns (Zymo), following the protocol for long RNA purification with DNase treatment. The entire volume of the sample was used for reverse transcription.
Input and enriched RNA samples were used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.4 of each input and whole enriched RNA RT reaction were pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed for indicated times in the presence of 2 mM 4-thiouridine (Merck; from a 50 mM stock solution in 6% methanol).


title: new 3h imbibed rep3

description: Library name: new3h_3


title: new 3h imbibed rep2

description: Library name: new3h_2


title: new 3h imbibed rep1

description: Library name: new3h_1


title: new 1h imbibed rep4

description: Library name: new1h_4


title: new 1h imbibed rep3

description: Library name: new1h_3


title: new 1h imbibed rep2

description: Library name: new1h_2


title: new 1h imbibed rep1

description: Library name: new1h_1


title: input 3h imbibed rep4

description: Library name: inp3h_4


title: mock 12 rep3

description:
Library name: M_X_12h_3
OK


title: mock 6h rep2

description:
Library name: M_X_06h_2
OK


title: input 3h imbibed rep3

description: Library name: inp3h_3


title: input 3h imbibed rep2

description: Library name: inp3h_2


title: input 3h imbibed rep1

description: Library name: inp3h_1


title: mock 1h rep2

description:
Library name: M_X_01h_2
OK


title: mock 1h rep4

description:
Library name: M_X_01h_4
OK


title: dry rep1

description:
Library name: D_X_00h_1
OK


title: dry rep3

description:
Library name: D_X_00h_3
OK


title: dry rep2

description:
Library name: D_X_00h_2
OK


title: dry rep4

description:
Library name: D_X_00h_4
OK


title: input 1h imbibed rep3

description: Library name: inp1h_3


title: input 1h imbibed rep2

description: Library name: inp1h_2


title: input 1h imbibed rep4

description: Library name: inp1h_4


title: input 1h imbibed rep1

description: Library name: inp1h_1


title: new mock_ANT imbibed rep4

description:
Library name: new_mock_ant_4
OK

data_processing:
In our sequencing strategy, the R1 reads of pooled libraries contain two parts of UMI split by the barcode. We rearrange UMI sequences to position them next to each other and remove additional low-quality nucleotides, including  the oligo(dT) fragment and those that follow it. For this, we utilise the awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 of pooled libraries were demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex and R1 with parameters -p UB -UMI 14 -n 1. The resulting reads were trimmed to eliminate potential contamination with the poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then, they were mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes.
Assembly: TAIR10
Supplementary files format and content: gene count text files

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211). For 4-SU labelled RNAs enrichment, biotinylation was performed for 15 μg of freshly isolated RNA in a 200 μl reaction mixture (10 mM Tris pH 7.5; 1 mM EDTA; 0.2 mg/ml EZ-Link Biotin-HPDP (ThermoFisher)) for 1.5 h at 22°C. A portion of the RNA (250 ng) was retained as an input. Unbound Biotin-HPDP was removed by chloroform/isoamyl alcohol (24:1) extraction. Subsequently, a 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added, and RNA was precipitated by centrifugation at 20,000g for 20 minutes. The pellet was washed with 1 ml of 80% ethanol, and after drying, it was resuspended in 25 μl of RNase-free water. Biotinylated RNA was purified using 50 μl of streptavidin C1 Dynabeads (ThermoFisher). The beads were washed in binding buffer (0.2 M NaCl; 0.1 M sodium phosphate pH 6.8; 25 mM MgCl2; 0.4% Tween), blocked in the binding buffer with 1 μg/μl glycogen for 10 minutes, and washed again in binding buffer. RNA samples were denatured at 65°C for 5 minutes, followed by 5 minutes on ice. Then, 25 μl of 2x binding buffer and 50 μl of washed streptavidin beads were added, mixed, and incubated at 22°C with gentle shaking for 20 minutes. The beads were washed three times with 0.5 ml of washing buffer (100 mM Tris-HCl pH 7.5; 10 mM EDTA; 1 M NaCl; 0.1% Tween20) at 65°C, followed by three washes at room temperature. Biotinylated RNA was eluted from the beads by two incubations with 50 μl of 200 mM DTT. RNA from the combined eluates was purified using RNA Clean & Concentrator-5 columns (Zymo), following the protocol for long RNA purification with DNase treatment. The entire volume of the sample was used for reverse transcription.
Input and enriched RNA samples were used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.4 of each input and whole enriched RNA RT reaction were pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed for 6h in the presence of 2 mM 4-thiouridine (Merck; from a 50 mM stock solution in 6% methanol), and 3 μM ABA (Merck; from a 1 mM stock solution in ethanol), 100 μM antabactin (Kerafst; from a 50 mM stock solution in DMSO), or the respective mock solution.

value: mock antabactin


title: new 3h mock imbibition rep3

description: Library name: new_mock_3h_3


title: new mock_ANT imbibed rep3

description:
Library name: new_mock_ant_3
OK


title: new 6h CHX imbibition rep2

description: Library name: new_CHX_6h_2


title: new 3h mock imbibition rep1

description: Library name: new_mock_3h_1


title: new mock_ANT imbibed rep1

description:
Library name: new_mock_ant_1
OK


title: new ANT imbibed rep4

description:
Library name: new_ANT_4
OK

value: antabactin


title: new mock_ABA imbibed rep1

description:
Library name: new_mock_aba_1
OK

value: mock ABA


title: new mock_ABA imbibed rep4

description:
Library name: new_mock_aba_4
OK


title: new mock_ANT imbibed rep2

description:
Library name: new_mock_ant_2
OK


title: new mock_ABA imbibed rep3

description:
Library name: new_mock_aba_3
OK


title: new ANT imbibed rep3

description:
Library name: new_ANT_3
OK


title: new ANT imbibed rep1

description:
Library name: new_ANT_1
OK


title: new ANT imbibed rep2

description:
Library name: new_ANT_2
OK


title: new mock_ABA imbibed rep2

description:
Library name: new_mock_aba_2
OK


title: new ABA imbibed rep3

description:
Library name: new_ABA_3
OK


title: new ABA imbibed rep4

description:
Library name: new_ABA_4
OK


title: input 6h mock imbibition rep1

description: Library name: inp_mock_6h_1

value: input


title: new ABA imbibed rep2

description:
Library name: new_ABA_2
OK


title: input 3h mock imbibition rep3

description: Library name: inp_mock_3h_3


title: new ABA imbibed rep1

description:
Library name: new_ABA_1
OK


title: input mock_ANT imbibed rep4

description:
Library name: inp_mock_ant_4
OK


title: input 6h CHX imbibition rep2

description: Library name: inp_CHX_6h_2

value: 6h imbibed


title: input mock_ANT imbibed rep3

description:
Library name: inp_mock_ant_3
OK


title: input mock_ANT imbibed rep2

description:
Library name: inp_mock_ant_2
OK


title: input mock_ANT imbibed rep1

description:
Library name: inp_mock_ant_1
FAILED


title: input mock_ABA imbibed rep3

description:
Library name: inp_mock_aba_3
OK


title: input mock_ABA imbibed rep2

description:
Library name: inp_mock_aba_2
OK


title: input mock_ABA imbibed rep1

description:
Library name: inp_mock_aba_1
OK


title: input ANT imbibed rep3

description:
Library name: inp_ANT_3
OK


title: input ANT imbibed rep4

description:
Library name: inp_ANT_4
OK


title: input ANT imbibed rep1

description:
Library name: inp_ANT_1
OK


title: input mock_ABA imbibed rep4

description:
Library name: inp_mock_aba_4
OK


title: input ANT imbibed rep2

description:
Library name: inp_ANT_2
OK


title: input ABA imbibed rep4

description:
Library name: inp_ABA_4
OK


title: input ABA imbibed rep3

description:
Library name: inp_ABA_3
OK


title: Keloid-WNH and Hispanic

type: RNA

city: Los Angeles

first: Min

last: Deng

state: CA

address: 650 Charles E. Young Dr. S., CHS-52-139

department: Medicine

country: USA

institute: University of California, Los Angeles

hyb_protocol: A total of 360 genes were included in the analysis. Gene panel probe hybridization occurred overnight for 18 hours at 50°C. Slides were washed the next day to remove unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37°C) followed by enzymatic rolling circle amplification (2 hours at 30°C). Slides were washed in TE buffer before background fluorescence was chemically quenched.

scan_protocol: Imaging processing, decoding, quality score generation, and DAPI-based cell segmentation was automatically performed by the Xenium Analyzer system. Data was analyzed on version xenium-4.1.1

data_processing: Xenium Onboard Analysis: 4.4.0. R using Seurat v5.3.0 packages.

label: Xenium probe set

organism: Homo sapiens

source_name: One keloid-WNH and Hispanic

label_protocol: Xenium probe set

growth_protocol: Not applicable; primary human tissue.

extract_protocol: tissue preparation protocol: Tissue sections were cut at a thickness of 10µM and placed onto a Xenium slide followed by fixation and permeabilization.

treatment_protocol: Human skin tissue was formalin-fixed and paraffin-embedded. Tissue sections were prepared according to the 10x Genomics Xenium In Situ tissue-preparation protocol and placed on Xenium slides.

value: Skin

tag: tissue preservation method

value: FFPE

value: Keloid


title: input ABA imbibed rep1

description:
Library name: inp_ABA_1
OK


title: zuo1 S288C, MG132 + AZC 45min, biol rep 2, flowcell 1

city: Baltimore

first: Jeff

last: Coller

state: MD

address: 725 N Wolfe St

institute: Johns Hopkins University

description:
Library name: zuo1-MGAZC-2
flowcell 1

data_processing:
FASTQs were passed through FASTQC  to identify possible adapter contamination or sequencing biases prior to processing. Read ends below quality cutoffs of 30 were removed with cutadapt v4.9 with the following parameters: -q 30,30 -m 1. FASTQs were mapped to a noncoding gene reference pulled from the Saccharomyces Genome Database ‘rna_coding’, including rRNA, tRNA, snRNA, snoRNA, and other ncRNA sequences, using Bowtie2 v2.4.4  with the following parameters: -q -p 8 --local --quiet. Reads unmapped by Bowtie2 were subsequently mapped to the pre-compiled Hisat2 R64-1-1 genome reference using Hisat2 v2.2.1  with the following parameters: -q -p 8 --quiet --rna-strandedness F. Footprint length distributions were obtained from samtools v1.21, and mapped reads were subsetted to RPFs of 20-29 nucleotides for downstream analysis.
Assembly: NCBI Saccharomyces cerevisiae S288C Genome Assembly R64 (GCF_000146045.2)
Supplementary files format and content: The processed data is a data frame in tab-delimited format with reads as rows. Columns represent characteristics of the reads, with A,P, and E-site amino acids and codons annotated. Samples are indicated in the ‘sampleType’ column.
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were seeded at an OD600 of 0.1 in YPD media and grown at room temperature to an OD600 of 0.4, at which time treatment was performed.

extract_protocol:
Cell pellets were resuspended in 200 µL Phenol/LET (100 mM LiCl, 20 mM EDTA, 25 mM Tris-HCl pH 8) and approximately 200 µL of glass microbeads were added to lyse the cells. After vortexing for 5 minutes at room temperature, 300 µL of Phenol/Chloroform/LET and 300 µL DEPC-treated water was added. After 5 minutes of additional vortexing, and spinning down for 5 minutes at 16,000 x g at room temperature, aqueous phase was collected and added to 500 µL Phenol/Chloroform/LET, vortexed for 5 minutes and spun down. Aqueous phase was collected and added to 500 µL Chloroform, vortexed for 5 minutes, and spun down. Aqueous phase was collected, 40 µL of 3 M Sodium Acetate (final concentration 0.3 M), 1 mL 100% ethanol was added to precipitate RNA at -20°C for approximately 1 hour. RNA was pelleted by spinning at 16,000 x g for 20 minutes at room temperature, washed with 75% ethanol, air dried, and resuspended in DEPC-treated water.
or MG132 and AZC treatment, both wild-type and zuo1Δ strains carried a PDR5 deletion to enable MG132 treatment. Cells were grown to an OD600 of 0.5 to 0.7 in 100 mL YPD media, and two 50 mL aliquots of culture were each treated with 100 µM MG132 with or without 2 mg/mL AZC at 24°C for 45 minutes. Upon collection, cultures were filtered using a 0.45 µm Whatman membrane (GE Life Sciences, USA) using a vacuum filter apparatus. After filtration, Cells were immediately scraped from the filter with a straight-edge metal spatula and plunged into 50 mL liquid nitrogen. Next, samples were ground using a Spex 6775 freezing grinding mill (Spex sample prep, USA) in the presence of 10 mL lysis buffer (20 mM Tris (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide, 1% Triton X-100, 25 U/mL DNase I). The RNA concentration of each cell lysate was determined using Qubit RNA HS Assay Kit (ThermoFisher Q32852) with the Qubit Fluorometer 2.0 (Invitrogen, USA). For the ribosome profiling experiments under heat and oxidative stress, 30 µg total RNA was diluted to 200 µL with polysome buffer (20 mM Tris (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide) and digested using 15 U RNase I (EpiCentre, USA N6901K) for 45 minutes at room temperature. Then, 200 U SUPERase*In RNase inhibitor (Invitrogen, USA AM2694) was added to quench the digestion reaction. To pellet the ribosomes, samples were transferred to a 13 mm × 51 mm polycarbonate ultracentrifuge tube containing 0.9 mL sucrose cushion (1 M sucrose in polysome buffer) and centrifuged at 70,000 rpm for 2 hours. For the ribosome profiling experiments under AZC treatment, 73.2 µg total RNA was diluted to 300 µL with polysome buffer and digested using 2.93 U RNase I (EpiCentre, USA N6901K) for 10 minutes at room temperature. Then, 39.2 U SUPERase*In RNase inhibitor (Invitrogen, USA AM2694) was added to quench the digestion reaction. To pellet the ribosomes, samples were transferred to a 13 mm × 51 mm polycarbonate ultracentrifuge tube containing 0.7 mL sucrose cushion (1 M sucrose in polysome buffer) and centrifuged in Beckman TLA-120.2 rotor at 55,000 rpm for 1.5 hours. Translucent ribosome pellets were resuspended in 300 µL polysome buffer followed by RNA purification using TRIzol reagent (Invitrogen, USA 15596026), according to the manufacturer's instructions. Samples were size-separated by running on 15% polyacrylamide TBE-Urea gels for 60 minutes at 200 V followed by gel-purification of the approximately 20 - 40 nucleotide (nt) length ribosome protected fragments (RPFs) using 17 - 34 nt length oligonucleotides as size markers. RPFs were treated with T4 PNK (NEB M0201S) to heal the 2′-3′ cyclic phosphate that results from RNase I cleavage. After end-healing reaction, pre-adenylated adapter oligonucleotides (35 nt length) were ligated to RPFs using T4 Rnl2(tr) K227Q ligase (NEB M0351S). Excess adapter oligos in the reaction were depleted by adding yeast 5′-deadenylase (EpiCentre, USA DA11101K) and RecJ exonuclease (EpiCentre, USA RJ411250) enzymes directly to the ligase reaction and incubated at 30°C for 45 minutes. Samples were purified using Oligo Clean & Concentrator kit (Zymo Research D4060) followed by ribosomal RNA (rRNA) depletion using either yeast Ribo-Zero Gold rRNA removal kit (Illumina, MRZG12324) for heat and oxidative stress samples or QIAseq FastSelect rRNA Yeast kit (Qiagen 334215) for AZC treated samples according to the manufacturer's instructions. Ligated RNA samples were reverse transcribed using Protoscript II RT (NEB M0368). Reverse transcription products were separated from the unextended primer products by polyacrylamide TBE-Urea gel electrophoresis followed by gel purification of the full-length cDNAs (80-120 nt length). Size-selected cDNAs were circularized using CircLigase II (EpiCentre, USA CL9021K). 10-15 rounds of PCR enrichment of the libraries were performed with the proper forward and reverse primers. Enriched libraries were used for cluster generation and sequencing. Single-end (50 bp) sequencing was carried out for two cDNA libraries (two biological replicates of each sample) using the Illumina HiSeq 4000 sequencing platform (Illumina, USA).

treatment_protocol: Once samples reached an OD600 of 0.4, AZC (final 2mg/mL) and/or MG132 (final 100uM) was added, and cells were grown at room temperature for 45 minutes before pelleting via centrifugation, freezing, and RNA extraction.

tag: cell line

value: MG132 + AZC


title: zuo1 S288C, MG132 + AZC 45min, biol rep 1, flowcell 1

description:
Library name: zuo1-MGAZC-1
flowcell 1


title: zuo1 S288C, MG132 45min, biol rep 1, flowcell 1

description:
Library name: zuo1-MG-1
flowcell 1


title: WT S288C, MG132 + AZC 45min, biol rep 2, flowcell 1

description:
Library name: wt-MGAZC-2
flowcell 1

value: WT


title: WT S288C, MG132 45min, biol rep 1, flowcell 1

description:
Library name: wt-MG-1
flowcell 1


title: WT S288C, MG132 + AZC 45min, biol rep 1, flowcell 1

description:
Library name: wt-MGAZC-1
flowcell 1


title: B. napus 8h new mRNAs rep2

description: Library name: napus_new_8h_2

data_processing:
In our sequencing strategy, the R1 reads of pooled libraries contain two parts of UMI split by the barcode. We rearrange UMI sequences to position them next to each other and remove additional low-quality nucleotides, including  the oligo(dT) fragment and those that follow it. For this, we utilise the awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 of pooled libraries were demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex and R1 with parameters -p UB -UMI 14 -n 1. The resulting reads were trimmed to eliminate potential contamination with the poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then, they were mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes.
Assembly: AST_PRJEB5043_v1
Supplementary files format and content: gene count text files

organism: Brassica napus

growth_protocol: Plants were grown in a greenhouse under a long day-night cycle at 22°C. Seeds from 2 plants were combined to create a single biological replicate.

extract_protocol:
RNA was isolated according to a standard seed protocol (https://doi.org/10.1002/biot.200900211). For 4-SU labelled RNAs enrichment, biotinylation was performed for 25 μg of freshly isolated RNA in a 200 μl reaction mixture (10 mM Tris pH 7.5; 1 mM EDTA; 0.2 mg/ml EZ-Link Biotin-HPDP (ThermoFisher)) for 1.5 h at 22°C. A portion of the RNA (500 ng) was retained as an input. Unbound Biotin-HPDP was removed by chloroform/isoamyl alcohol (24:1) extraction. Subsequently, a 1/10 volume of 5 M NaCl and an equal volume of isopropanol were added, and RNA was precipitated by centrifugation at 20,000g for 20 minutes. The pellet was washed with 1 ml of 80% ethanol, and after drying, it was resuspended in 25 μl of RNase-free water. Biotinylated RNA was purified using 50 μl of streptavidin C1 Dynabeads (ThermoFisher). The beads were washed in binding buffer (0.2 M NaCl; 0.1 M sodium phosphate pH 6.8; 25 mM MgCl2; 0.4% Tween), blocked in the binding buffer with 1 μg/μl glycogen for 10 minutes, and washed again in binding buffer. RNA samples were denatured at 65°C for 5 minutes, followed by 5 minutes on ice. Then, 25 μl of 2x binding buffer and 50 μl of washed streptavidin beads were added, mixed, and incubated at 22°C with gentle shaking for 20 minutes. The beads were washed three times with 0.5 ml of washing buffer (100 mM Tris-HCl pH 7.5; 10 mM EDTA; 1 M NaCl; 0.1% Tween20) at 65°C, followed by three washes at room temperature. Biotinylated RNA was eluted from the beads by two incubations with 50 μl of 200 mM DTT. RNA from the combined eluates was purified using RNA Clean & Concentrator-5 columns (Zymo), following the protocol for long RNA purification with DNase treatment. The entire volume of the sample was used for reverse transcription.
Dry seed, input and enriched RNA samples were used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.25 of each input/dry and whole enriched RNA RT reaction were pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (0.85x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: Seeds were imbibed for 4h and 8h in the presence of 2 mM 4-thiouridine (Merck; from a 50 mM stock solution in 6% methanol).

tag: cultivar

value: Bazyl

value: 8h imbibed

value: enriched


title: B. napus 8h new mRNAs rep4

description: Library name: napus_new_8h_4


title: B. napus 4h new mRNAs rep2

description: Library name: napus_new_4h_2

value: 4h imbibed


title: B. napus 8h new mRNAs rep1

description: Library name: napus_new_8h_1


title: B. napus 4h new mRNAs rep3

description: Library name: napus_new_4h_3


title: WT S288C, MG132 45min, biol rep 2, flowcell 1

description:
Library name: wt-MG-2
flowcell 1


title: B. napus 8h new mRNAs rep3

description: Library name: napus_new_8h_3


title: B. napus 4h new mRNAs rep1

description: Library name: napus_new_4h_1


title: B. napus 8h imbibed seeds rep4

description: Library name: napus_imb_8h_4


title: B. napus 8h imbibed seeds rep3

description: Library name: napus_imb_8h_3


title: B. napus 8h imbibed seeds rep2

description: Library name: napus_imb_8h_2


title: B. napus 4h imbibed seeds rep4

description: Library name: napus_imb_4h_4


title: B. napus 8h imbibed seeds rep1

description: Library name: napus_imb_8h_1


title: HEK293T transfected 250ng HSP90AA1 bicistronic reporter, 4h with 100nM PladB biol rep 2

city: Kansas City

first: Ariel

middle: Alejandro

last: Bazzini

state: Missouri

institute: Stowers Institute for Medical Research

description:
Library name: Sample 38
Row name in splice_junctions_All_Samples.csv: HSP90AA1_4h_PladB2

data_processing:
Paired-end RNA-seq reads (75 bp) were aligned to a custom reference genome consisting of the human genome assembly (hg38) supplemented with a gene-specific reporter construct sequence (bicistronic minigene) for each target gene (BCAP, CANX, HOXB7, CTDSP2, PHIP, HSP90AA1). Separate STAR indices were built for each gene using STAR v2.7.11b with --sjdbOverhang 74. Reads were aligned in two-pass mode (--twopassMode Basic) with the following parameters: end-to-end alignment (--alignEndsType EndToEnd), only uniquely mapping reads retained (-- outFilterMultimapNmax 1), zero mismatches permitted (--outFilterMismatchNmax 0), minimum splice junction overhang of 6 nt for both novel and annotated junctions (--alignSJoverhangMin 6, --alignSJDBoverhangMin 6), and non-canonical intron motifs removed (--outFilterIntronMotifs RemoveNoncanonical). The strand of each alignment was inferred from the intron motif (-- outSAMstrandField intronMotif). Output BAM files were coordinate-sorted and indexed with SAMtools.
Splice junction quantification was performed using a custom Python script (pysam v0.23.3). Only primary, uniquely mapped, non-supplementary alignments were considered. A read was classified as supporting a specific splice junction if its CIGAR string contained an N operation flanked by at least 6 matched bases (M/=/X) on each side. The donor coordinate was defined as the last exonic base before the intron (1-based), and the acceptor coordinate as the first exonic base after the intron. The number of reads supporting an exact donor–acceptor pair is reported as exact junction reads. For each splice site, unspliced reads were counted within a 12-nt window centred on the splice site boundary (half-window = 6 nt): for a donor site at position d, the window spans [d − 5, d + 6]; for an acceptor site at position a, the window spans [a − 6, a + 5]. A read was counted as unspliced if: (i) its CIGAR string contained no N operations (indicating no spliced alignment across an intron) and no D operations (indicating no deletion relative to the reference genome); and (ii) it continuously covered the entire 12-nt window without interruption. Duplicate alignments sharing the same read name, FLAG, reference start, and CIGAR string were counted only once.
Assembly: hg38
Supplementary files format and content: .csv file contains the splice junctions identified for each transfected construct in the corresponding sample

growth_protocol: HEK293T cells were grown in DMEM media supplemented with 10% FBS, 2mM L-Glutamine and Penstrep in humidified atmosphere at % CO2 at 37C

extract_protocol:
RNA was isolated by mixing cells with Trizol Reagent, adding choloroform, and isolating the aqueous layer after centrifugation and purified using the Zymo Direct-zol RNA MicroPrep kit. 100ng of total RNA was used as input for library prep.
RNA libraries for RNA-seq were prepared using the Watchmaker mRNA Library Prep Kit at 1/5 reaction volume.

treatment_protocol: When cells were treated with DMSO or PladB, the treatment was added at the indicated concentration just prior to transfetion

tag: cell type

value: human embryonic kidney

value: 100nM PladB

tag: time

value: 4 hours


title: HEK293T transfected 250ng HSP90AA1 bicistronic reporter, 4h with 20nM PladB biol rep 2

description:
Library name: Sample 36
Row name in splice_junctions_All_Samples.csv: HSP90AA1_4h_PladB1

value: 20nM PladB


title: HEK293T transfected 250ng HSP90AA1 bicistronic reporter, 4h with 100nM PladB biol rep 1

description:
Library name: Sample 37
Row name in splice_junctions_All_Samples.csv: HSP90AA1_4h_PladB2


title: B. napus 4h imbibed seeds rep3

description: Library name: napus_imb_4h_3

value: seed


title: B. napus 4h imbibed seeds rep2

description: Library name: napus_imb_4h_2


title: HEK293T transfected 250ng HSP90AA1 bicistronic reporter, 4h with 20nM PladB biol rep 1

description:
Library name: Sample 35
Row name in splice_junctions_All_Samples.csv: HSP90AA1_4h_PladB1


title: B. napus 4h imbibed seeds rep1

description: Library name: napus_imb_4h_1


title: B. napus dry seeds rep4

description: Library name: napus_dry_4

value: dry


title: B. napus dry seeds rep3

description: Library name: napus_dry_3


title: HEK293T transfected 250ng PHIP bicistronic reporter, 4h with 100nM PladB biol rep 1

description:
Library name: Sample 31
Row name in splice_junctions_All_Samples.csv: PHIP_4h_PladB2


title: B. napus dry seeds rep2

description: Library name: napus_dry_2


title: HEK293T transfected 250ng PHIP bicistronic reporter, 4h with 20nM PladB biol rep 2

description:
Library name: Sample 30
Row name in splice_junctions_All_Samples.csv: PHIP_4h_PladB1


title: B. napus dry seeds rep1

description: Library name: napus_dry_1


title: HEK293T transfected 250ng PHIP bicistronic reporter, 4h with 20nM PladB biol rep 1

description:
Library name: Sample 29
Row name in splice_junctions_All_Samples.csv: PHIP_4h_PladB1


title: HEK293T transfected 250ng PHIP bicistronic reporter, 4h with DMSO biol rep 2

description:
Library name: Sample 28
Row name in splice_junctions_All_Samples.csv: PHIP_4h_DMSO

value: DMSO


title: total RNA-seq from technical sample (ENCLB594AST)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR154RVC/
***************
biological replicate number: 1
technical replicate number: 1
description: LRGASP_mix
experiment encode accession: ENCSR154RVC
assay title: total RNA-seq
encode release date: 2021-05-06
lab: Barbara Wold, Caltech
library encode accession: ENCLB594AST
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).
nucleic acid starting quantity: 400
nucleic acid starting quantity units: ng

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

organism: synthetic construct

source_name: control

value: technical sample

tag: biosample encode accession

tag: biosample term name

value: synthetic construct

tag: age

value: 60 days

tag: lab

value: Ryan Tewhey, JAX

tag: Sex

value: not applicable


title: HEK293T transfected 250ng HOXB7 bicistronic reporter, 4h with 100nM PladB biol rep 2

description:
Library name: Sample 26
Row name in splice_junctions_All_Samples.csv: HOXB7_4h_PladB2

value: WT


title: total RNA-seq from HG03129 (ENCLB395EVR)

description:
https://www.encodeproject.org/experiments/ENCSR998MYO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR998MYO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB395EVR
nucleic acid starting quantity: 39
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03129 cell line

extract_protocol: not provided

tag: line

value: cell line

tag: encode accession

tag: note

value: HG03129 LCLs; Donor from the Esan in Nigeria (ESN)

value: female

tag: dev stage

value: adult

value: Stephen Montgomery, Stanford

tag: source

value: Coriell

tag: link

value: ENCBS603YDJ at ENCODE; https://www.encodeproject.org/ENCBS603YDJ/


title: HEK293T transfected 250ng HOXB7 bicistronic reporter, 4h with 100nM PladB biol rep 1

description:
Library name: Sample 25
Row name in splice_junctions_All_Samples.csv: HOXB7_4h_PladB2

value: human embryonic kidney

tag: genotype

tag: treatment

value: 100nM PladB

value: 4 hours


title: total RNA-seq from GM19449 (ENCLB725VUZ)

description:
https://www.encodeproject.org/experiments/ENCSR997LSS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR997LSS
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB725VUZ
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19449 cell line

value: GM19449 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: ENCBS260NXZ at ENCODE; https://www.encodeproject.org/ENCBS260NXZ/


title: HEK293T transfected 250ng HOXB7 bicistronic reporter, 4h with 20nM PladB biol rep 2

description:
Library name: Sample 24
Row name in splice_junctions_All_Samples.csv: HOXB7_4h_PladB1

tag: cell line

value: 20nM PladB


title: HEK293T transfected 250ng HOXB7 bicistronic reporter, 4h with DMSO biol rep 2

description:
Library name: Sample 22
Row name in splice_junctions_All_Samples.csv: HOXB7_4h_DMSO

value: DMSO


title: HEK293T transfected 250ng HOXB7 bicistronic reporter, 4h with DMSO biol rep 1

description:
Library name: Sample 21
Row name in splice_junctions_All_Samples.csv: HOXB7_4h_DMSO


title: total RNA-seq from GM19437 (ENCLB182RTU)

description:
https://www.encodeproject.org/experiments/ENCSR982AOX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR982AOX
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB182RTU
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19437 cell line

value: GM19437 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: ENCBS714VVI at ENCODE; https://www.encodeproject.org/ENCBS714VVI/


title: HEK293T transfected 250ng CANX bicistronic reporter, 4h with 100nM PladB biol rep 1

description:
Library name: Sample 19
Row name in splice_junctions_All_Samples.csv: CANX_4h_PladB2

value: WT


title: total RNA-seq from GM19321 (ENCLB084GXM)

description:
https://www.encodeproject.org/experiments/ENCSR978HDN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR978HDN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB084GXM
nucleic acid starting quantity: 23
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19321 cell line

value: cell line

value: GM19321 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: ENCBS879JGK at ENCODE; https://www.encodeproject.org/ENCBS879JGK/


title: HEK293T transfected 250ng HSP90AA1 bicistronic reporter, 4h with DMSO biol rep 1

description:
Library name: Sample 33
Row name in splice_junctions_All_Samples.csv: HSP90AA1_4h_DMSO


title: HEK293T transfected 250ng PHIP bicistronic reporter, 4h with 100nM PladB biol rep 2

description:
Library name: Sample 32
Row name in splice_junctions_All_Samples.csv: PHIP_4h_PladB2


title: HEK293T transfected 250ng CANX bicistronic reporter, 4h with 20nM PladB biol rep 1

description:
Library name: Sample 17
Row name in splice_junctions_All_Samples.csv: CANX_4h_PladB1


title: HEK293T transfected 250ng PHIP bicistronic reporter, 4h with DMSO biol rep 1

description:
Library name: Sample 27
Row name in splice_junctions_All_Samples.csv: PHIP_4h_DMSO


title: total RNA-seq from technical sample (ENCLB277JVI)

description:
https://www.encodeproject.org/experiments/ENCSR154RVC/
***************
biological replicate number: 2
technical replicate number: 1
description: LRGASP_mix
experiment encode accession: ENCSR154RVC
assay title: total RNA-seq
encode release date: 2021-05-06
lab: Barbara Wold, Caltech
library encode accession: ENCLB277JVI
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).
nucleic acid starting quantity: 400
nucleic acid starting quantity units: ng

value: technical sample

value: synthetic construct

value: 60 days

value: Ryan Tewhey, JAX

value: not applicable


title: HEK293T transfected 250ng CANX bicistronic reporter, 4h with DMSO biol rep 2

description:
Library name: Sample 16
Row name in splice_junctions_All_Samples.csv: CANX_4h_DMSO

value: human embryonic kidney


title: total RNA-seq from HG03378 (ENCLB163NHV)

description:
https://www.encodeproject.org/experiments/ENCSR974SWF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR974SWF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB163NHV
nucleic acid starting quantity: 39
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03378 cell line

tag: description

value: HG03378 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: female

value: adult

value: unknown

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS351XYO at ENCODE; https://www.encodeproject.org/ENCBS351XYO/

value: Derived from ENCODE donor ENCDO965KAC; https://www.encodeproject.org/ENCDO965KAC/


title: total RNA-seq from HG03069 (ENCLB492TYE)

description:
https://www.encodeproject.org/experiments/ENCSR976HAT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR976HAT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB492TYE
nucleic acid starting quantity: 39
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03069 cell line

value: cell line

value: HG03069 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: male

value: ENCBS742ANB at ENCODE; https://www.encodeproject.org/ENCBS742ANB/


title: HEK293T transfected 250ng HOXB7 bicistronic reporter, 4h with 20nM PladB biol rep 1

description:
Library name: Sample 23
Row name in splice_junctions_All_Samples.csv: HOXB7_4h_PladB1

tag: cell type

value: WT

value: 20nM PladB

value: 4 hours


title: total RNA-seq from GM21775 (ENCLB520FSI)

description:
https://www.encodeproject.org/experiments/ENCSR989SXC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR989SXC
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB520FSI
nucleic acid starting quantity: 16
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21775 cell line

value: GM21775 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS436WYF at ENCODE; https://www.encodeproject.org/ENCBS436WYF/


title: total RNA-seq from GM21600 (ENCLB106AQL)

description:
https://www.encodeproject.org/experiments/ENCSR973GTG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR973GTG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB106AQL
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21600 cell line

value: GM21600 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS120NIZ at ENCODE; https://www.encodeproject.org/ENCBS120NIZ/


title: HEK293T transfected 250ng CANX bicistronic reporter, 4h with DMSO biol rep 1

description:
Library name: Sample 15
Row name in splice_junctions_All_Samples.csv: CANX_4h_DMSO

value: human embryonic kidney

value: DMSO

tag: time


title: total RNA-seq from GM19020 (ENCLB625EKB)

description:
https://www.encodeproject.org/experiments/ENCSR984PRR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR984PRR
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB625EKB
nucleic acid starting quantity: 17
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19020 cell line

tag: biosample encode accession

value: GM19020 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: adult

value: Stephen Montgomery, Stanford

value: ENCBS653MGK at ENCODE; https://www.encodeproject.org/ENCBS653MGK/


title: HEK293T transfected 250ng HSP90AA1 bicistronic reporter, 24h biol rep 2

description:
Library name: Sample 14
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_HSP90AA1_24hr

value: 24 hours


title: total RNA-seq from GM19037 (ENCLB600POO)

description:
https://www.encodeproject.org/experiments/ENCSR983OGO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR983OGO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB600POO
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19037 cell line

value: cell line

value: GM19037 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: female

value: Coriell

value: ENCBS178RHU at ENCODE; https://www.encodeproject.org/ENCBS178RHU/


title: HEK293T transfected 250ng HSP90AA1 bicistronic reporter, 24h biol rep 1

description:
Library name: Sample 13
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_HSP90AA1_24hr

value: WT


title: total RNA-seq from HG03169 (ENCLB420GPL)

description:
https://www.encodeproject.org/experiments/ENCSR971RIR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR971RIR
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB420GPL
nucleic acid starting quantity: 23
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03169 cell line

value: HG03169 LCLs; Donor from the Esan in Nigeria (ESN)

value: male

value: ENCBS451RSV at ENCODE; https://www.encodeproject.org/ENCBS451RSV/


title: total RNA-seq from HG03369 (ENCLB365ING)

description:
https://www.encodeproject.org/experiments/ENCSR981CYF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR981CYF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB365ING
nucleic acid starting quantity: 38
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03369 cell line

value: HG03369 LCLs; Donor from the Esan in Nigeria (ESN)

value: ENCBS791UWG at ENCODE; https://www.encodeproject.org/ENCBS791UWG/


title: HEK293T transfected 250ng PHIP bicistronic reporter, 24h biol rep 2

description:
Library name: Sample 12
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_PHIP_24hr

value: human embryonic kidney


title: total RNA-seq from GM21417 (ENCLB067EUW)

description:
https://www.encodeproject.org/experiments/ENCSR967LOO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR967LOO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB067EUW
nucleic acid starting quantity: 60
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21417 cell line

value: GM21417 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS434KGI at ENCODE; https://www.encodeproject.org/ENCBS434KGI/


title: HEK293T transfected 250ng CANX bicistronic reporter, 4h with 100nM PladB biol rep 2

description:
Library name: Sample 20
Row name in splice_junctions_All_Samples.csv: CANX_4h_PladB2

value: 100nM PladB

value: 4 hours


title: total RNA-seq from HG02464 (ENCLB353AKV)

description:
https://www.encodeproject.org/experiments/ENCSR966FVT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR966FVT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB353AKV
nucleic acid starting quantity: 25
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02464 cell line

value: HG02464 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: adult

value: Stephen Montgomery, Stanford

value: ENCBS726GNZ at ENCODE; https://www.encodeproject.org/ENCBS726GNZ/


title: HEK293T transfected 250ng PHIP bicistronic reporter, 24h biol rep 1

description:
Library name: Sample 11
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_PHIP_24hr

value: 24 hours


title: total RNA-seq from GM21441 (ENCLB280FZX)

description:
https://www.encodeproject.org/experiments/ENCSR965QXB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR965QXB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB280FZX
nucleic acid starting quantity: 22
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21441 cell line

value: cell line

value: GM21441 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: Coriell

value: ENCBS288HHL at ENCODE; https://www.encodeproject.org/ENCBS288HHL/


title: HEK293T transfected 250ng HOXB7 bicistronic reporter, 24h biol rep 3

description:
Library name: Sample 10
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_HOXB7_24hr

value: WT


title: total RNA-seq from HG03268 (ENCLB483UBF)

description:
https://www.encodeproject.org/experiments/ENCSR979JWV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR979JWV
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB483UBF
nucleic acid starting quantity: 23
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03268 cell line

value: HG03268 LCLs; Donor from the Esan in Nigeria (ESN)

value: male

value: ENCBS987ILK at ENCODE; https://www.encodeproject.org/ENCBS987ILK/


title: input 3h CHX imbibition rep1

description: Library name: inp_CHX_3h_1

source_name: seed

tag: tissue

value: seed

tag: ecotype

value: CHX

value: 3h imbibed

tag: treatment enrichment

value: input

tag: batch


title: HEK293T transfected 250ng HOXB7 bicistronic reporter, 24h biol rep 2

description:
Library name: Sample 9
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_HOXB7_24hr

value: human embryonic kidney


title: total RNA-seq from HG03086 (ENCLB420JXW)

description:
https://www.encodeproject.org/experiments/ENCSR963SQT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR963SQT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB420JXW
nucleic acid starting quantity: 36
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03086 cell line

tag: line

value: HG03086 LCLs; Donor from the Mende in Sierra Leone (MSL)

tag: Sex

value: adult

tag: lab

value: Stephen Montgomery, Stanford

value: ENCBS128FKW at ENCODE; https://www.encodeproject.org/ENCBS128FKW/


title: total RNA-seq from GM21478 (ENCLB355OEI)

description:
https://www.encodeproject.org/experiments/ENCSR964NYB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR964NYB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB355OEI
nucleic acid starting quantity: 38
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21478 cell line

value: cell line

tag: encode accession

tag: note

value: GM21478 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

tag: dev stage

value: ENCBS450GQI at ENCODE; https://www.encodeproject.org/ENCBS450GQI/


title: total RNA-seq from GM19431 (ENCLB468JDQ)

description:
https://www.encodeproject.org/experiments/ENCSR963NSP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR963NSP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB468JDQ
nucleic acid starting quantity: 20
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19431 cell line

value: GM19431 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: female

tag: source

value: Coriell

tag: link

value: ENCBS861OVL at ENCODE; https://www.encodeproject.org/ENCBS861OVL/


title: HEK293T transfected 250ng CANX bicistronic reporter, 4h with 20nM PladB biol rep 2

description:
Library name: Sample 18
Row name in splice_junctions_All_Samples.csv: CANX_4h_PladB1

tag: cell line

tag: genotype

value: WT

tag: treatment

value: 20nM PladB

value: 4 hours


title: total RNA-seq from GM21739 (ENCLB763ZTK)

description:
https://www.encodeproject.org/experiments/ENCSR962PNR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR962PNR
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB763ZTK
nucleic acid starting quantity: 24
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21739 cell line

value: GM21739 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: ENCBS814WIA at ENCODE; https://www.encodeproject.org/ENCBS814WIA/


title: HEK293T transfected 250ng HOXB7 bicistronic reporter, 24h biol rep 1

description:
Library name: Sample 8
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_HOXB7_24hr

tag: cell type

value: human embryonic kidney

tag: time

value: 24 hours


title: HEK293T transfected 250ng CANX bicistronic reporter, 24h biol rep 1

description:
Library name: Sample 6
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_CANX_24hr


title: total RNA-seq from GM21529 (ENCLB877NZJ)

description:
https://www.encodeproject.org/experiments/ENCSR961HMI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR961HMI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB877NZJ
nucleic acid starting quantity: 36
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21529 cell line

tag: description

value: GM21529 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

tag: biosample encode accession

value: adult

tag: age

value: unknown

value: Stephen Montgomery, Stanford

value: ENCBS994HTW at ENCODE; https://www.encodeproject.org/ENCBS994HTW/

value: Derived from ENCODE donor ENCDO127JBU; https://www.encodeproject.org/ENCDO127JBU/


title: HEK293T transfected 250ng BCAP29 bicistronic reporter, 24h biol rep 2

description:
Library name: Sample 5
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_BCAP29_24hr


title: HEK293T transfected 250ng CANX bicistronic reporter, 24h biol rep 2

description:
Library name: Sample 7
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_CANX_24hr


title: total RNA-seq from GM21390 (ENCLB082JUJ)

description:
https://www.encodeproject.org/experiments/ENCSR959ULL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR959ULL
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB082JUJ
nucleic acid starting quantity: 40
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21390 cell line

value: cell line

value: GM21390 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS686KHA at ENCODE; https://www.encodeproject.org/ENCBS686KHA/

value: Derived from ENCODE donor ENCDO317SJE; https://www.encodeproject.org/ENCDO317SJE/


title: HEK293T transfected 250ng BCAP29 bicistronic reporter, 24h biol rep 1

description:
Library name: Sample 4
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_BCAP29_24hr

value: WT


title: total RNA-seq from GM18522 (ENCLB654RGH)

description:
https://www.encodeproject.org/experiments/ENCSR959BHR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR959BHR
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB654RGH
nucleic acid starting quantity: 28
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18522 cell line

value: GM18522 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: Coriell

value: ENCBS215JXD at ENCODE; https://www.encodeproject.org/ENCBS215JXD/


title: HEK293T transfected 250ng CTDSP2 bicistronic reporter, 24h biol rep 3

description:
Library name: Sample 3
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_CTDSP2_24hr


title: total RNA-seq from GM21336 (ENCLB795DRW)

description:
https://www.encodeproject.org/experiments/ENCSR954KWV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR954KWV
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB795DRW
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21336 cell line

value: GM21336 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: ENCBS552ZUB at ENCODE; https://www.encodeproject.org/ENCBS552ZUB/


title: HEK293T transfected 250ng CTDSP2 bicistronic reporter, 24h biol rep 2

description:
Library name: Sample 2
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_CTDSP2_24hr

value: human embryonic kidney

value: 24 hours


title: total RNA-seq from HG02840 (ENCLB737XRV)

description:
https://www.encodeproject.org/experiments/ENCSR952TUJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR952TUJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB737XRV
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02840 cell line

value: HG02840 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: adult

value: unknown

value: ENCBS575UUQ at ENCODE; https://www.encodeproject.org/ENCBS575UUQ/

value: Derived from ENCODE donor ENCDO021AFR; https://www.encodeproject.org/ENCDO021AFR/


title: total RNA-seq from HG03052 (ENCLB915KUK)

description:
https://www.encodeproject.org/experiments/ENCSR952FHK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR952FHK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB915KUK
nucleic acid starting quantity: 44
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03052 cell line

value: cell line

value: HG03052 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: Stephen Montgomery, Stanford

value: ENCBS191QFX at ENCODE; https://www.encodeproject.org/ENCBS191QFX/


title: total RNA-seq from HG03027 (ENCLB140TWX)

description:
https://www.encodeproject.org/experiments/ENCSR950VCC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR950VCC
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB140TWX
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03027 cell line

value: HG03027 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: male

value: ENCBS036KPW at ENCODE; https://www.encodeproject.org/ENCBS036KPW/


title: HEK293T transfected 250ng CTDSP2 bicistronic reporter, 24h biol rep 1

description:
Library name: Sample 1
Row name in splice_junctions_All_Samples.csv: 293T_RNAtransfect_CTDSP2_24hr

value: WT


title: ME-1_SPNS2_2

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

description: Library name: ME-1_SPNS2_2

data_processing:
Sequencing reads were pseudo aligned to genome and genes quantified using Salmon, raw counts extracted using tximport
Assembly: GRCh38v96
Supplementary files format and content: Tab delimited table containing gene symbol and sample normalized counts

molecule: polyA RNA

source_name: Hematopietic cells

extract_protocol:
Total RNA was extracted using QIAGEN RNAeasy plus mini kit following manufacturer's instructions
Sequencing libraries were prepared using TruSeq Stranded mRNA LT Sample Prep Kit

tag: tissue

value: Hematopietic cells


title: total RNA-seq from GM21519 (ENCLB222KGI)

description:
https://www.encodeproject.org/experiments/ENCSR947TOB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR947TOB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB222KGI
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21519 cell line

tag: line

value: GM21519 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: Coriell

value: ENCBS509NKS at ENCODE; https://www.encodeproject.org/ENCBS509NKS/


title: ME-1_SPNS2_1

description: Library name: ME-1_SPNS2_1


title: ME-1_SPNS2_3

description: Library name: ME-1_SPNS2_3


title: total RNA-seq from HG02760 (ENCLB831EAK)

description:
https://www.encodeproject.org/experiments/ENCSR940SIV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR940SIV
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB831EAK
nucleic acid starting quantity: 26
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02760 cell line

value: HG02760 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

tag: Sex

value: female

value: ENCBS883CQG at ENCODE; https://www.encodeproject.org/ENCBS883CQG/


title: ME-1_CTRL_2

description: Library name: ME-1_CTRL_2


title: total RNA-seq from GM21693 (ENCLB503KNV)

description:
https://www.encodeproject.org/experiments/ENCSR939PUS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR939PUS
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB503KNV
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21693 cell line

value: GM21693 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: adult

tag: lab

value: ENCBS631SZD at ENCODE; https://www.encodeproject.org/ENCBS631SZD/


title: ME-1_CTRL_3

description: Library name: ME-1_CTRL_3


title: total RNA-seq from GM21367 (ENCLB534CCI)

description:
https://www.encodeproject.org/experiments/ENCSR940RSZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR940RSZ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB534CCI
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21367 cell line

value: cell line

value: GM21367 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: unknown

value: ENCBS908YUU at ENCODE; https://www.encodeproject.org/ENCBS908YUU/

value: Derived from ENCODE donor ENCDO335VOB; https://www.encodeproject.org/ENCDO335VOB/


title: ME-1_CTRL_1

description: Library name: ME-1_CTRL_1


title: total RNA-seq from GM19401 (ENCLB787FXD)

description:
https://www.encodeproject.org/experiments/ENCSR939BEP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR939BEP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB787FXD
nucleic acid starting quantity: 27
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19401 cell line

tag: encode accession

value: GM19401 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: Stephen Montgomery, Stanford

value: ENCBS785YLP at ENCODE; https://www.encodeproject.org/ENCBS785YLP/


title: V379-U54-HRA-201-D

city: New York

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

description: Library name: V379-U54-HRA-201-D

data_processing:
Each sequenced 10X Visium library was aligned to a standard reference genome (hg38; GENCODE v32/Ensembl98) and counted with spaceranger
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.h5 file contains spaceranger counts in spaceranger h5 format
Supplementary files format and content: spatial.tar file contains slide images and spot & scaling metadata from spaceranger outs/spatial
Library strategy: Spatial Transcriptomics

extract_protocol:
Frozen tissue blocks, kept at -80°C prior to processing, were equilibrated to -16°C inside a Leica CM3050S cryostat, embedded in Tissue Plus OCT Compound (Fisher Healthcare, #4585), and sectioned in a perpendicular orientation with regard to the pial surface. Tissue sections (10 µm-thick) from quality controlled blocks (H&E staining and imaging) were collected onto prechilled Visium Spatial Gene Expression Slides (10X Genomics, #1000185) while briefly warming the back of the slide with a gloved finger to improve adherence and minimize artifacts.
Visium libraries were prepared using unique Illumina-compatible PCR primers with Dual Index Kit TT Set A (10X Genomics, #1000215). Size distribution profiles of the final libraries were assessed by running Agilent High Sensitivity DNA chips (#5067-4626) on a 2100 Bioanalyzer system (Agilent, #G2939BA). Libraries outside the expected range (450 ± 50 bp) or that contained adapter dimer contaminants were discarded and reprocessed. Total yields were initially measured on a Qubit 3.0 fluorometer before final qPCR quantification (KAPA Library Quantification Kit for Illumina Platforms, KAPA Biosystems, #KK4824).

tag: subject id

tag: diagnosis

value: Non-neurological control

tag: pmi

value: F


title: V379-U54-HRA-201-C

description: Library name: V379-U54-HRA-201-C


title: total RNA-seq from HG03557 (ENCLB005DKI)

description:
https://www.encodeproject.org/experiments/ENCSR938GML/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR938GML
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB005DKI
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03557 cell line

tag: note

value: HG03557 LCLs; Donor from the Mende in Sierra Leone (MSL)

tag: dev stage

tag: source

value: Coriell

tag: link

value: ENCBS076KQW at ENCODE; https://www.encodeproject.org/ENCBS076KQW/


title: V374-CGND-HRA-04087-B

description: Library name: V374-CGND-HRA-04087-B

tag: rin


title: total RNA-seq from GM21458 (ENCLB588CKX)

description:
https://www.encodeproject.org/experiments/ENCSR937CYO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR937CYO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB588CKX
nucleic acid starting quantity: 38
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21458 cell line

value: GM21458 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: ENCBS189BRP at ENCODE; https://www.encodeproject.org/ENCBS189BRP/


title: total RNA-seq from GM21493 (ENCLB487FYM)

description:
https://www.encodeproject.org/experiments/ENCSR931TXM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR931TXM
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB487FYM
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21493 cell line

value: GM21493 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: adult

value: ENCBS633JVD at ENCODE; https://www.encodeproject.org/ENCBS633JVD/


title: V374-CGND-HRA-04087-A

description: Library name: V374-CGND-HRA-04087-A


title: total RNA-seq from GM21300 (ENCLB081SUK)

description:
https://www.encodeproject.org/experiments/ENCSR929NBE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR929NBE
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB081SUK
nucleic acid starting quantity: 4
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21300 cell line

value: cell line

value: GM21300 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS805OCZ at ENCODE; https://www.encodeproject.org/ENCBS805OCZ/


title: V374-CGND-HRA-04082-D

description: Library name: V374-CGND-HRA-04082-D


title: total RNA-seq from HG02611 (ENCLB017LGB)

description:
https://www.encodeproject.org/experiments/ENCSR924QLE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR924QLE
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB017LGB
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02611 cell line

value: HG02611 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: Stephen Montgomery, Stanford

value: ENCBS904CAM at ENCODE; https://www.encodeproject.org/ENCBS904CAM/


title: V374-CGND-HRA-04082-C

description: Library name: V374-CGND-HRA-04082-C

value: Non-neurological control

value: F


title: V373-CGND-HRA-04087-B

description: Library name: V373-CGND-HRA-04087-B


title: total RNA-seq from GM21578 (ENCLB851FWF)

description:
https://www.encodeproject.org/experiments/ENCSR923SGT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR923SGT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB851FWF
nucleic acid starting quantity: 19
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21578 cell line

value: GM21578 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: Coriell

value: ENCBS126PYD at ENCODE; https://www.encodeproject.org/ENCBS126PYD/


title: total RNA-seq from HG03469 (ENCLB483LUS)

description:
https://www.encodeproject.org/experiments/ENCSR924HWA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR924HWA
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB483LUS
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03469 cell line

value: HG03469 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: male

value: unknown

value: ENCBS322ITX at ENCODE; https://www.encodeproject.org/ENCBS322ITX/

value: Derived from ENCODE donor ENCDO177NIC; https://www.encodeproject.org/ENCDO177NIC/


title: total RNA-seq from GM21580 (ENCLB084DWV)

description:
https://www.encodeproject.org/experiments/ENCSR922VBQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR922VBQ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB084DWV
nucleic acid starting quantity: 25
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21580 cell line

value: GM21580 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: adult

value: ENCBS784UAM at ENCODE; https://www.encodeproject.org/ENCBS784UAM/


title: V373-CGND-HRA-04082-D

description: Library name: V373-CGND-HRA-04082-D


title: V373-CGND-HRA-04082-C

description: Library name: V373-CGND-HRA-04082-C


title: total RNA-seq from HG02595 (ENCLB529DXE)

description:
https://www.encodeproject.org/experiments/ENCSR921UIK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR921UIK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB529DXE
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02595 cell line

value: cell line

value: HG02595 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: ENCBS286KKP at ENCODE; https://www.encodeproject.org/ENCBS286KKP/


title: total RNA-seq from CD14-positive monocyte (ENCLB511BAZ)

description:
https://www.encodeproject.org/experiments/ENCSR921XFY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR921XFY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB511BAZ

source_name: Homo sapiens male adult (21 years) CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: primary cell

value: 21 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS070INQ at ENCODE; https://www.encodeproject.org/ENCBS070INQ/


title: V373-CGND-HRA-04087-A

description: Library name: V373-CGND-HRA-04087-A

value: Non-neurological control

value: F


title: total RNA-seq from HG02837 (ENCLB004WZV)

description:
https://www.encodeproject.org/experiments/ENCSR917OYF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR917OYF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB004WZV
nucleic acid starting quantity: 46
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02837 cell line

value: HG02837 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS267ETZ at ENCODE; https://www.encodeproject.org/ENCBS267ETZ/


title: V371-U54-HRA-187-D

description: Library name: V371-U54-HRA-187-D

value: M


title: total RNA-seq from GM19030 (ENCLB211ONH)

description:
https://www.encodeproject.org/experiments/ENCSR916XPW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR916XPW
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB211ONH
nucleic acid starting quantity: 38
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19030 cell line

value: GM19030 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: female

value: adult

value: ENCBS397ZGD at ENCODE; https://www.encodeproject.org/ENCBS397ZGD/


title: V371-CGND-HRA-00235-B

description: Library name: V371-CGND-HRA-00235-B

value: ALS


title: V371-CGND-HRA-00235-A

description: Library name: V371-CGND-HRA-00235-A