title: SOTR12_TCR

first: Johannes

last: Wedel

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

description:
T cell receptor sequences (TCR)
TCR: contig annotations and cell barcode information

data_processing:
Raw reads were aligned to the human GRCh38 genome using Cell Ranger pipeline (version 7.0.1) and cell barcodes were used as whitelist to quantify ADT/HTO counts and TCR/BCR sequences. Both independent libraries were imported into a Seurat project (R version 4.3.2, Seurat version 5.0.1). Low quality reads (nFeature_RNA < 400, nCount_RNA < 1250, percent.mt > 10, nCount_HTO < 4000) were excluded prior to demultiplexing using the HTODemux function (positive.quantile = 0.99).
Assembly: GRCh38
Supplementary files format and content: Subject-level demultiplexed matrixes were exported from R in the 10x format.
Library strategy: CITE-seq

molecule: other

extract_protocol:
PBMC were isolated by high density centrifugation.
Multiomic scRNAseq was performed in two independent library preparations. PBMC were stained with hashtag and CITE-antibodies, pooled and loaded onto Chromium Next GEM Single Cell 5' Kit v2 channels. Libraries for gene expression (GEX), hashtags (HTO), CITE-antibodies (ADT) and immune cell repertoire (TCR and BCR) were constructed and pooled prior to sequencing.

value: Blood

value: PBMC


title: KLF4_G7883_resistant_H226_cells_rep1

status: Public on Dec 18 2025

type: SRA

city: South San Francisco

first: Bence

last: Daniel

state: CA

address: 1 DNA Way

department: Department Proteomic and Genomic Technologies

country: USA

institute: Genentech Inc.

description: Library name: KLF4_H226_Resistant_G7883_rep1

library_source: genomic

data_processing:
ChIP-seq results were analyzed using the ENCODE ChIP-seq pipeline (v2.2.1)61. ChIP-seq reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.4.3)63. Aligned reads were then filtered for quality and duplicates using samtools (v1.9)74 and Picard (Broad Institute - v2.20.7).
Assembly: hg38
Supplementary files format and content: Normalized bigwigs.

molecule: genomic DNA

organism: Homo sapiens

source_name: Lung

growth_protocol:
Two established preclinical models of malignant mesothelioma were used in this study: NCI-H226 (hereafter H226), which is NF2-null, and MSTO-211H (hereafter MSTO), which carries a PSEN1-LATS1 fusion leading to loss of LATS1 kinase activity and impaired phosphorylation of YAP. MSTO also harbors a 42-bp deletion in exon 5 of LATS2, resulting in its inactivation33,53,54. Cell lines were obtained from the American Type Culture Collection (ATCC) and maintained in RPMI-1640 medium supplemented with 10% FBS (Sigma-Aldrich), 2 mM L-glutamine (Gibco Life Sciences), and Penicillin?Streptomycin, in a humidified incubator at 37 °C with 5% CO?. GNE-7883?resistant NF2-null H226 and MSTO-211H cells were generated by long-term, stepwise dose adaptation to the pan-TEAD inhibitor GNE-7883. H226 cells were gradually exposed from 0.25 µM to 2.5 µM over ~55 days, and MSTO-211H cells from 0.25 µM to 3.0 µM, with incremental increases every 1?2 weeks while maintaining at least 25% cell confluence. During escalation, transient cytostasis was followed by the emergence of proliferating persister populations under sustained drug pressure. Resistant pools were expanded from these outgrowths and maintained in medium containing 5 µM GNE-7883. Characterization of these resistant models followed previously described procedures37. For acute treatment conditions, H226 and MSTO cells were treated with 2.5 µM GNE-7883 for 48-hours before collection.
Two established preclinical models of malignant mesothelioma were used in this study: NCI-H226 (hereafter H226), which is NF2-null, and MSTO-211H (hereafter MSTO), which carries a PSEN1-LATS1 fusion leading to loss of LATS1 kinase activity and impaired phosphorylation of YAP. MSTO also harbors a 42-bp deletion in exon 5 of LATS2, resulting in its inactivation33,53,54. Cell lines were obtained from the American Type Culture Collection (ATCC) and maintained in RPMI-1640 medium supplemented with 10% FBS (Sigma-Aldrich), 2 mM L-glutamine (Gibco Life Sciences), and Penicillin–Streptomycin, in a humidified incubator at 37 °C with 5% CO₂. GNE-7883–resistant NF2-null H226 and MSTO-211H cells were generated by long-term, stepwise dose adaptation to the pan-TEAD inhibitor GNE-7883. H226 cells were gradually exposed from 0.25 µM to 2.5 µM over ~55 days, and MSTO-211H cells from 0.25 µM to 3.0 µM, with incremental increases every 1–2 weeks while maintaining at least 25% cell confluence. During escalation, transient cytostasis was followed by the emergence of proliferating persister populations under sustained drug pressure. Resistant pools were expanded from these outgrowths and maintained in medium containing 5 µM GNE-7883. Characterization of these resistant models followed previously described procedures37. For acute treatment conditions, H226 and MSTO cells were treated with 2.5 µM GNE-7883 for 48-hours before collection.

extract_protocol:
NCI-H226 and MSTO-211 mesothelioma cells (10 x 106) were double crosslinked with 50mM DSG (disuccinimidyl glutarate, #C1104 - ProteoChem) for 30-minutes followed by 10-minutes of 1% formaldehyde. Formaldehyde was quenched by the addition of glycine. Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0). Nuclei were sheared with Covaris sonicator using the following setup: Fill level ? 10, Duty Cycle ? 15, PIP ? 350, Cycles/Burst ? 200, Time ? 8-minutes). Sheared chromatin was immunoprecipitated overnight with the following antibodies: FOSL1 (PA5-66880 ? Invitrogen), YAP (14074S ? Cell Signaling), KLF4 (AF3158 ? R&D Systems). Antibody chromatin complexes were pulled down with Protein A magnetic beads and washed twice in IP wash buffer I. (1% Triton, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer II. (1% Triton, 0.1% SDS, 500 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer III. (0.25 M LiCl, 0.5% NP-40, 1mM EDTA, 20 mM Tris, pH 8.0, 0.5% NaDOC) and once in TE buffer (10 mM EDTA and 200 mM Tris, pH 8.0). DNA was eluted from the beads by vigorous shaking for 20-minutes in elution buffer (100mM NaHCO3, 1% SDS). DNA was de-crosslinked overnight at 65C and purified with the MinElute PCR purification kit (Qiagen).
DNA was quantified by Qubit and equal amounts (2ng) of DNA was used for sequencing library construction with the Ovation Ultralow Library System V2 (Tecan) using 15 PCR cycles according to the manufacturer?s recommendations. Libraries were sequenced with Illumina Nextseq 2000, using paired-end 50bp read configuration.

tag: tissue

value: Lung

tag: cell line

tag: cell type

value: Mesothelioma

tag: genotype

value: wild type


title: KLF4_G7883_treated_parental_H226_cells_rep2

description: Library name: KLF4_H226_Parental_G7883_rep2


title: KLF4_G7883_treated_parental_H226_cells_rep1

description: Library name: KLF4_H226_Parental_G7883_rep1


title: Liver, FL, TERM, Mouse 1

city: Saarbrücken

first: Friederike

last: Grandke

address: Saarbrücken Campus

country: Germany

institute: Saarland University

description: Library name: 376_Liver_FL-_ISS_Term-_1_L1_1

library_source: transcriptomic

data_processing:
Fastq files containing raw sequencing reads were mapped against GRCm39 and miRBase (version 22.1) 65 in order to profile miRNA counts using miRmaster (version 2.0). Information about miRNA family was obtained from mirgenedb 3.0. Detection filtering was performed by keeping only miRNAs with at least 5 raw reads in at least 10% of samples in each condition-tissue group. Expression data was normalized using rpmm normalization (reads per mapped million).
Assembly: GRCm39
Supplementary files format and content: miRNA_complete_quantification_raw.tsv: Tab-separated file of raw miRNA counts per sample.
Supplementary files format and content: lncRNA_complete_quantification_raw.tsv: Tab-separated file of raw lncRNA counts per sample.
Supplementary files format and content: piRNA_complete_quantification_raw.tsv: Tab-separated file of raw piRNA counts per sample.
Supplementary files format and content: rRNA_complete_quantification_raw.tsv: Tab-separated file of raw rRNA counts per sample.
Supplementary files format and content: scaRNA_complete_quantification_raw.tsv: Tab-separated file of raw scaRNA counts per sample.
Supplementary files format and content: snoRNA_complete_quantification_raw.tsv: Tab-separated file of raw snoRNA counts per sample.
Supplementary files format and content: snRNA_complete_quantification_raw.tsv: Tab-separated file of raw snRNA counts per sample.
Supplementary files format and content: tRNA_complete_quantification_raw.tsv: Tab-separated file of raw tRNA counts per sample.

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: For the Rodent Research Reference Mission 1 (RRR-1) / Rodent Research-8 (RR-8) 40 BALB/cAnNTac female mice were sent to the International Space Station (ISS) on 12/5/2018 (Flight mice).VGC mice were housed at NASA Kennedy Space Center in standard vivarium conditions at 4 mice per cage, 20-22.2 °C, 12hr light 12hr dark. HGC mice housing was matched to the conditions experienced by Flight mice (as closely as possible) by using double density housing (same Habitat Units and Transporters as Flight mice at launch), matched temperature, humidity, and carbon dioxide levels based on actual flight environmental monitoring. To dissect all mice together in matching conditions, VGC and HGC mice were transported to Scripps Institute just before the return of the Flight mice and were dissected in matching conditions (+/- 1 day).From each of the main experimental groups, half of the mice were assigned to the ISS Terminal (ISS Term) subgroup, which were sacrificed onboard the ISS (Flight) or on Earth (VGC, HGC) 22-24 days after launch. The other half were assigned to the Live Animal Return (LAR) group, which were returned alive to Earth on 1/14/2019 after 39.5 days on the ISS, and collected 2-4 days after splashdown following functional assays at Scripps Research Institute.

extract_protocol:
LAR mice were anesthetized with gas anesthesia and euthanized by means of cardiac puncture blood draw (exsanguination) and double thoracotomy. The liver was removed, weighed, dissected into individual lobes (1- left/right medial, 2- left lateral and 3- remaining lobes) and snap frozen on liquid nitrogen. All tissues were collected and frozen within 10-16 minutes of thoracotomy procedure. All groups were treated identically. Organ samples were maintained at -80C or lower temperatures throughout the storage, and during transportation and shipment. TERM mice were anesthetized with ketamine/xylazine/acepromazine at a dose of 120/15/3 mg/kg and euthanized by means of cardiac puncture blood draw (exsanguination) and double thoracotomy. The spleen was dissected fresh from each carcass and placed in a tube containing RNA Later. The carcass was then wrapped in foil and frozen in MELFI on board the ISS or in ground -80C freezers. Carcasses were maintained at -80C or lower temperatures throughout the storage on board the ISS, in ground freezers and during transportation and shipment. The mice were brought back to earth where dissection was held. It should be noted that carcasses frozen whole onboard the ISS were free-floating and thus in direct contact with air. This prevented them from snap freezing like samples collected on Earth which were placeddirectly in liquid nitrogen. Carcasses were thawed at room temperature one at a time (staggered)until the tissues were sufficiently pliable for dissection (approximately 60-90 minutes). Once thawed, multiple tissues were collected from each carcass within 30min of the first tissue collected. The liver was removed from each carcass, weighed, dissected into individual lobes (1-left/right medial, 2- left lateral and 3- remaining lobes) and snap frozen on liquid nitrogen.  The miRNeasy-96 protocol was followed for all samples with some modifications, as follows. Tissue Preparation: To avoid overloading the miRNeasy-96 columns, some frozen samples were trimmed to smaller sizes. All kidney, liver, and spleen samples were all trimmed to ~25mgs due to their high RNA content. Pancreas samples were trimmed to ~25mgs if they exceeded 45mgs. GAT, MAT, and SCAT samples >200mgs were trimmed to ~100mgs as samples of large size homogenize poorly in 96-well format, even though adipose tissues have relatively low RNA content. BAT and lung samples >100mgs were trimmed to ~50mgs, and thymi >50mgs were trimmed to ~25mgs. The diaphragm did not require trimming, and whole hemi-brains and whole hearts were homogenized by hand with the TissueRuptor in 1ml QIAzol per 50mgs tissue, since trimming samples in a reproducible way to capture the same organ subregion for each would be difficult. Bead homogenization: All samples, including those previously homogenized with the TissueRuptor, were randomized in 96-well format. Two 96-well plates were run simultaneously as follows. 96-well collection microtube plates were chilled on dry ice, and trimmed tissue samples were placed at the bottom of each well. One pre-chilled 5mm stainless steel bead was then placed on top of the tissue samples with bead dispenser. 700ul pre-chilled (4C) QIAzol was then added to each well, or 700ul QIAzol homogenate from the pre-homogenized heart and brain samples. Plates were immediately homogenized on the TissueLyser II for a total of four 5min runs at 25Hz, and plates were rotated and switched between the two arms of the TissueLyser II between each run. Plates were then left at room temperature for 5min before pelleting debris at 6000 x g for 1min at 4C. Phase Separation & RNA collection: Debris- and bead-free homogenate was then transferred to a new plate, to which 140ul chloroform was added to each well, and plates were shaken vigorously for 3min at room temperature before being spun at 6000 x g for 4min at 4C. 300ul aqueous phase was then transferred to a new S-Block, to which 525ul 100% EtOH was added and mixed by pipetting, followed by a room temperature spin at 6000 x g for 30s. The entire volume was then transferred to a miRNeasy-96 plate on top of an S-plate, sealed with AirPore tape sheet, and spun at 5600 x g for 4min at room temperature. Flow through was discarded, and columns washed with 800ul RWT and spun as above. This was repeated with 800ul RPE, and a final 800ul RPE wash was followed by a 10min spin. Finally, 50ul RNase-free water was added to each column and incubated at room temperature for 1min, then spun at 5600 x g for 4min at room temperature. The elution was repeated with a second volume of 50ul RNase-free water. RNA samples were stored at -80C.
All samples were processed using the MGIEasy Small RNA Library Prep Kit with the high-throughput MGI SP-960 sample prep system according to the manufacturer's protocol to generate sequencing libraries.

value: Liver

tag: experiment group

value: FL-TERM

tag: Sex

value: female

tag: strain

value: BALB/cAnNTac

tag: mouse id

tag: age

value: 3 months


title: KLF4_DMSO_treated_parental_H226_cells_rep2

description: Library name: KLF4_H226_Parental_DMSO_rep2


title: SOTR12_HTO

city: Boston

description:
Hashtag-derived oligonucleotide (HTO)
HTO: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

library_source: other

molecule: protein

source_name: Blood

tag: hto

value: TotalSeq-C0255 anti-human Hashtag 5 Antibody in run 1, TotalSeq-C0262 anti-human Hashtag 12 Antibody in run 2


title: SOTR12_ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

tag: adt

value: TotalSeq-C0045 anti-human CD4 Antibody, TotalSeq-C0080 anti-human CD8a Antibody, TotalSeq-C0063 anti-human CD45RA Antibody, TotalSeq-C0087 anti-human CD45RO Antibody, TotalSeq-C0148 anti-human CD197 (CCR7) Antibody


title: SOTR12_GEX

description:
mRNA
GEX ('5 mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

molecule: polyA RNA


title: SCAT, HGC, TERM, Mouse 4

description: Library name: 375_SCAT_HGC-_ISS_Term-_4_L1_1

source_name: SCAT

value: SCAT

value: HGC-TERM


title: KLF4_DMSO_treated_parental_H226_cells_rep1

description: Library name: KLF4_H226_Parental_DMSO_rep1


title: SOTR11_BCR

description:
B cell receptor sequences (BCR)
BCR: contig annotations and cell barcode information


title: GAT, HGC, TERM, Mouse 3

description: Library name: 374_GAT_HGC-_ISS_Term-_3_L1_1

source_name: GAT

value: GAT


title: p300_G7883_resistant_H226_cells_rep1

description: Library name: p300_H226_Resistant_G7883_rep1


title: SOTR12_BCR


title: p300_G7883_resistant_H226_cells_rep2

description: Library name: p300_H226_Resistant_G7883_rep2


title: SOTR11_TCR


title: p300_DMSO_treated_parental_H226_cells_rep2

description: Library name: p300_H226_Parental_DMSO_rep2


title: Pancreas, FL, VGC, LAR, Mouse 12

description: Library name: 373_Pancreas_FL-LAR-12_L1_1

source_name: Pancreas

value: Pancreas

value: VGC-LAR

value: 8 months


title: p300_G7883_treated_parental_H226_cells_rep2

description: Library name: p300_H226_Parental_G7883_rep2


title: CTCF_DMSO_treated_parental_H226_cells_rep2

description: Library name: CTCF_H226_Parental_DMSO_rep2


title: CTCF_DMSO_treated_parental_H226_cells_rep1

description: Library name: CTCF_H226_Parental_DMSO_rep1


title: SOTR11_HTO

value: Blood

value: PBMC

value: TotalSeq-C0254 anti-human Hashtag 4 Antibody


title: SCAT, VGC, TERM, Mouse 4

description: Library name: 371_SCAT_VGC-_ISS_Term-_4_L1_1

value: VGC-TERM


title: p300_DMSO_treated_parental_H226_cells_rep1

description: Library name: p300_H226_Parental_DMSO_rep1

value: Lung

value: Mesothelioma

value: wild type


title: GAT, VGC, LAR, Mouse 2

description: Library name: 377_GAT_VC-LAR-2_L1_1

value: female

value: BALB/cAnNTac


title: p300_G7883_treated_parental_H226_cells_rep1

description: Library name: p300_H226_Parental_G7883_rep1


title: CUTRUN_H3K4me3_G7883_resistant_H226_cells

description: Library name: CUTRUN_H3K4me3_H226_Resistant_G7883

data_processing:
For each sequence library, raw reads were aligned on the hg38 human genome reference using Bowtie2 (v2.4.1) followed by alignments sorting (samtools v1.9) of resulting bam files with filtering out of unmapped reads and keeping reads with mapping quality higher than 30. Duplicates were removed with Picard’s (v2.23.9) MarkDuplicates function followed by indexation of resulting bam files with samtools. For each bam file, genome coverage was computed with bedtools (v2.29.2) followed by generation of bigwig (wigToBigWig v357) files.
Assembly: hg38
Supplementary files format and content: Normalized bigwigs.
Library strategy: CUT&Run

growth_protocol: Two established preclinical models of malignant mesothelioma were used in this study: NCI-H226 (hereafter H226), which is NF2-null, and MSTO-211H (hereafter MSTO), which carries a PSEN1-LATS1 fusion leading to loss of LATS1 kinase activity and impaired phosphorylation of YAP. MSTO also harbors a 42-bp deletion in exon 5 of LATS2, resulting in its inactivation33,53,54. Cell lines were obtained from the American Type Culture Collection (ATCC) and maintained in RPMI-1640 medium supplemented with 10% FBS (Sigma-Aldrich), 2 mM L-glutamine (Gibco Life Sciences), and Penicillin–Streptomycin, in a humidified incubator at 37 °C with 5% CO₂. GNE-7883–resistant NF2-null H226 and MSTO-211H cells were generated by long-term, stepwise dose adaptation to the pan-TEAD inhibitor GNE-7883. H226 cells were gradually exposed from 0.25 µM to 2.5 µM over ~55 days, and MSTO-211H cells from 0.25 µM to 3.0 µM, with incremental increases every 1–2 weeks while maintaining at least 25% cell confluence. During escalation, transient cytostasis was followed by the emergence of proliferating persister populations under sustained drug pressure. Resistant pools were expanded from these outgrowths and maintained in medium containing 5 µM GNE-7883. Characterization of these resistant models followed previously described procedures37. For acute treatment conditions, H226 and MSTO cells were treated with 2.5 µM GNE-7883 for 48-hours before collection.

extract_protocol:
CUT&RUN profiling of H226 and H226-7883R cells was performed using the CUTANA ChIC/CUT&RUN Kit (Epicypher, #14-1048) following the manufacturer’s instructions. Briefly, cells were prepared as single-cell suspensions, immobilized on activated ConA beads, and incubated with SNAP-Certified™ histone modification antibodies: H3K27ac (EpiCypher 13-0059, clone 2114-3E4) and H3K4me3 (EpiCypher 13-0060) at ~0.5 µg per reaction. After primary antibody binding, pAG-MNase was added and chromatin digestion activated with CaCl₂. Released DNA fragments were purified and quantified. Sequencing libraries were constructed using the CUTANA CUT&RUN Library Prep Kit (Epicypher, #14-1001/14-1002), with end repair, adapter ligation, and SPRIselect bead cleanups according to the manufacturer’s protocol. Libraries were assessed on a TapeStation and sequenced as paired-end reads (~10 million PE reads per sample).
Library preparation was conducted according to manufacturer's recommendations.


title: GAT, HGC, LAR, Mouse 5

description: Library name: 370_GAT_HC-LAR-5_L1_1

value: HGC-LAR

value: 3 months


title: CUTRUN_H3K4me3_G7883_treated_parental_H226_cells

description: Library name: CUTRUN_H3K4me3_H226_Parental_G7883


title: SOTR11_GEX

description:
mRNA
GEX ('5 mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Spleen, VGC, TERM, Mouse 3

description: Library name: 372_Spleen_VGC-_ISS_Term-_3_L1_1

source_name: Spleen

value: Spleen


title: SOTR11_ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: TotalSeq-C0045 anti-human CD4 Antibody, TotalSeq-C0080 anti-human CD8a Antibody, TotalSeq-C0063 anti-human CD45RA Antibody, TotalSeq-C0087 anti-human CD45RO Antibody, TotalSeq-C0148 anti-human CD197 (CCR7) Antibody


title: Liver, HGC, LAR, Mouse 14

description: Library name: 369_Liver_HC-LAR-14_L1_1

value: Liver


title: SOTR10_BCR

description:
B cell receptor sequences (BCR)
BCR: contig annotations and cell barcode information


title: CUTRUN_H3K27ac_G7883_resistant_H226_cells

description: Library name: CUTRUN_H3K27ac_H226_Resistant_G7883


title: CUTRUN_H3K4me3_DMSO_treated_parental_H226_cells

description: Library name: CUTRUN_H3K4me3_H226_Parental_DMSO


title: BAT, FL, TERM, Mouse 4

description: Library name: 368_BAT_FL-_ISS_Term-_4_L1_1

source_name: BAT

value: BAT

value: FL-TERM


title: SOTR10_TCR

description:
T cell receptor sequences (TCR)
TCR: contig annotations and cell barcode information


title: Heart, VGC, LAR, Mouse 12

description: Library name: 367_Heart_VC-LAR-12_L1_1

source_name: Heart

value: Heart

value: VGC-LAR

value: 8 months


title: ATAC_G7883_resistant_MSTO_cells_rep1

description: Library name: ATAC_MSTO_Resistant_G7883_rep1

data_processing:
hg38
Normalized bigwig files.
Supplementary files format and content: Normalized bigwigs.

source_name: Ascites

growth_protocol:
For each sample, ~100k viable cells were processed with the Active Motif ATAC-seq kit according to the manufacturer’s instructions. Nuclei were isolated, tagmentation was performed with Tn5 transposase for 30-minutes at 37C, and libraries were PCR-amplified (12 cycles) using indexing primers. Libraries were size-selected, quality-checked by Tapestation, quantified by Qubit, and sequenced as paired-end (2 × 50 bp).
Two established preclinical models of malignant mesothelioma were used in this study: NCI-H226 (hereafter H226), which is NF2-null, and MSTO-211H (hereafter MSTO), which carries a PSEN1-LATS1 fusion leading to loss of LATS1 kinase activity and impaired phosphorylation of YAP. MSTO also harbors a 42-bp deletion in exon 5 of LATS2, resulting in its inactivation33,53,54. Cell lines were obtained from the American Type Culture Collection (ATCC) and maintained in RPMI-1640 medium supplemented with 10% FBS (Sigma-Aldrich), 2 mM L-glutamine (Gibco Life Sciences), and Penicillin–Streptomycin, in a humidified incubator at 37 °C with 5% CO₂. GNE-7883–resistant NF2-null H226 and MSTO-211H cells were generated by long-term, stepwise dose adaptation to the pan-TEAD inhibitor GNE-7883. H226 cells were gradually exposed from 0.25 µM to 2.5 µM over ~55 days, and MSTO-211H cells from 0.25 µM to 3.0 µM, with incremental increases every 1–2 weeks while maintaining at least 25% cell confluence. During escalation, transient cytostasis was followed by the emergence of proliferating persister populations under sustained drug pressure. Resistant pools were expanded from these outgrowths and maintained in medium containing 5 µM GNE-7883. Characterization of these resistant models followed previously described procedures37. For acute treatment conditions, H226 and MSTO cells were treated with 2.5 µM GNE-7883 for 48-hours before collection.

extract_protocol: Raw data were processed with the ENCODE ATAC-seq pipeline (v2.2.2) under default settings61. Adapters were trimmed with cutadapt (v2.5)62 , reads were aligned to hg38 with Bowtie2 (v2.3.4.3)63, and alignments were filtered for mapping quality and duplicates using samtools (v1.9)64 and Picard (v2.20.7) (Broad Institute). Peaks were called with MACS2 (v2.2.4) using Tn5 offset correction and smoothing65, and hg38 ENCODE blacklist regions were removed66 . Reproducibility was assessed with IDR (v2.0.4.2)67, and standard QC included mapping statistics, library complexity, replicate concordance, and TSS enrichment.

treatment_protocol: Libraries were prepared accoring to the Active Motif ATAC-seq kit.

value: Ascites


title: CUTRUN_H3K27ac_DMSO_treated_parental_H226_cells

description: Library name: CUTRUN_H3K27ac_H226_Parental_DMSO


title: ATAC_G7883_resistant_MSTO_cells_rep2

description: Library name: ATAC_MSTO_Resistant_G7883_rep2


title: CUTRUN_H3K27ac_G7883_treated_parental_H226_cells

description: Library name: CUTRUN_H3K27ac_H226_Parental_G7883


title: ATAC_G7883_treated_parental_MSTO_cells_rep2

description: Library name: ATAC_MSTO_Parental_G7883_rep2


title: SOTR10_HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: Blood

value: PBMC

value: TotalSeq-C0253 anti-human Hashtag 3 Antibody


title: ATAC_G7883_treated_parental_MSTO_cells_rep1

description: Library name: ATAC_MSTO_Parental_G7883_rep1

value: Mesothelioma

value: wild type


title: SCAT, VGC, TERM, Mouse 11

description: Library name: 366_SCAT_VGC-_ISS_Term-_11_L1_1

value: SCAT

value: VGC-TERM

value: female

value: BALB/cAnNTac


title: SOTR10_ADT

value: TotalSeq-C0045 anti-human CD4 Antibody, TotalSeq-C0080 anti-human CD8a Antibody, TotalSeq-C0063 anti-human CD45RA Antibody, TotalSeq-C0087 anti-human CD45RO Antibody, TotalSeq-C0148 anti-human CD197 (CCR7) Antibody


title: Lung, HGC, LAR, Mouse 5

description: Library name: 365_Lung_HC-LAR-5_L1_1

value: Lung

value: HGC-LAR

value: 3 months


title: ATAC_DMSO_treated_parental_MSTO_cells_rep2

description: Library name: ATAC_MSTO_Parental_DMSO_rep2


title: SOTR10_GEX

description:
mRNA
GEX ('5 mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: ATAC_G7883_resistant_H226_cells_rep2

description: Library name: ATAC_H226_Resistant_G7883_rep2


title: ATAC_DMSO_treated_parental_MSTO_cells_rep1

description: Library name: ATAC_MSTO_Parental_DMSO_rep1


title: Liver, HGC, TERM, Mouse 16

description: Library name: 364_Liver_HGC-_ISS_Term-_16_L1_1

value: Liver

value: HGC-TERM


title: ATAC_G7883_treated_parental_H226_cells_rep2

description: Library name: ATAC_H226_Parental_G7883_rep2


title: SOTR9_BCR

description:
B cell receptor sequences (BCR)
BCR: contig annotations and cell barcode information


title: Heart, HGC, TERM, Mouse 16

description: Library name: 363_Heart_HGC-_ISS_Term-_16_L1_1

value: Heart

value: 8 months


title: ATAC_G7883_treated_parental_H226_cells_rep1

description: Library name: ATAC_H226_Parental_G7883_rep1


title: SOTR9_TCR

description:
T cell receptor sequences (TCR)
TCR: contig annotations and cell barcode information

value: Blood


title: ATAC_DMSO_treated_parental_H226_cells_rep2

description: Library name: ATAC_H226_Parental_DMSO_rep2


title: Liver, VGC, TERM, Mouse 11

description: Library name: 362_Liver_VGC-_ISS_Term-_11_L1_1


title: ATAC_DMSO_treated_parental_H226_cells_rep1

description: Library name: ATAC_H226_Parental_DMSO_rep1


title: Ribo-Seq, Human CD8+ T cells, chronic, donor 5

city: Berkeley

first: Jamie

last: Cate

address: 2151 Berkeley Way

institute: UC Berkeley

description: Library name: D5C

data_processing:
The adapters were trimmed, unique molecular identifiers (UMIs) were annotated, and reads shorter than 20 nucleotides or of poor quality were discarded using Cutadapt
Reads were sequentially mapped to rRNA, ncRNA, mtDNA, mRNA, gDNA, size-selection oligos, and OTTR adapter references using bowtie2.
PCR duplicates were collapsed using UMI-tools (Smith et al., 2017).
Reads mapping outside of the coding sequence (+15th to -10th codon) were removed using Bedtools intersect (Quinlan, 2014).
The remaining reads were counted using Salmon
Assembly: NCBI RefSeq MANE v0.95 transcript set and the 13 mitochondrial mRNA sequences from Ensembl (Ferguson et al., 2023)
Supplementary files format and content: CSV file contains TPM for each sample
Library strategy: Ribo-Seq

source_name: CD8+ T cells

extract_protocol:
Briefly, cells were lysed and triturated through a 26 G needle. Lysates were digested with P1 nuclease. Ribosomes were pelleted by sucrose cushion. Ribosome protected fragments were extracted using the mirRICH method (Choi et al., 2018).
Library generation was carried out using the OTTR cDNA library construction kit (Karnateq) following the manufacturer’s protocol. 40 ng of RNA per sample was used as input for the OTTR reaction.

value: CD8+ T cells

tag: treatment

value: Chronic


title: Ribo-Seq, Human CD8+ T cells, chronic, donor 4

description: Library name: D4C


title: Heart, VGC, TERM, Mouse 14

description: Library name: 361_Heart_VGC-_ISS_Term-_14_L1_1


title: Ribo-Seq, Human CD8+ T cells, chronic, donor 2

description: Library name: D2C


title: SOTR9_ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: PBMC


title: Ribo-Seq, Human CD8+ T cells, re-activated, donor 5

description: Library name: D5R

value: Re-activated


title: SOTR9_GEX


title: Ribo-Seq, Human CD8+ T cells, chronic, donor 1

description: Library name: D1C


title: Brain, HGC, TERM, Mouse 18

description: Library name: 360_Brain_HGC-_ISS_Term-_18_L1_1

source_name: Brain

value: Brain


title: Thymus, FL, VGC, LAR, Mouse 1

description: Library name: 359_Thymus_FL-LAR-1_L1_1

source_name: Thymus

value: Thymus

value: VGC-LAR


title: Ribo-Seq, Human CD8+ T cells, re-activated, donor 2

description: Library name: D2R


title: ATAC_G7883_resistant_H226_cells_rep1

description: Library name: ATAC_H226_Resistant_G7883_rep1

value: Mesothelioma

value: wild type


title: SOTR8_TCR


title: Ribo-Seq, Human CD8+ T cells, re-activated, donor 4

description: Library name: D4R


title: Pancreas, VGC, LAR, Mouse 11

description: Library name: 357_Pancreas_VC-LAR-11_L1_1

value: Pancreas

value: female

value: BALB/cAnNTac


title: Ribo-Seq, Human CD8+ T cells, acute, donor 5

description: Library name: D5A

value: Acute


title: SOTR8_HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: TotalSeq-C0264 anti-human Hashtag 14 Antibody in run 1, TotalSeq-C0263 anti-human Hashtag 13 Antibody in run 2


title: Ribo-Seq, Human CD8+ T cells, acute, donor 2

description: Library name: D2A


title: Ribo-Seq, Human CD8+ T cells, acute, donor 4

description: Library name: D4A


title: Ribo-Seq, Human CD8+ T cells, re-activated, donor 1

description: Library name: D1R


title: Liver, HGC, TERM, Mouse 14

description: Library name: 356_Liver_HGC-_ISS_Term-_14_L1_1

value: Liver

value: HGC-TERM


title: Human CD8+ T cells, chronic, donor 5

description: Library name: D5C

data_processing:
Reads were aligned to a custom transcriptome that includes both the NCBI RefSeq MANE v0.95 transcript set and the 13 mitochondrial mRNA sequences from Ensembl (Ferguson et al., 2023).
We used Salmon to quantify transcript-level abundances (Patro et al., 2017).
Assembly: NCBI RefSeq MANE v0.95 transcript set and the 13 mitochondrial mRNA sequences from Ensembl (Ferguson et al., 2023)
Supplementary files format and content: CSV file contains TPM for each sample

extract_protocol:
Total RNA was extracted using the Direct-zol RNA miniprep kit (Zymo Research).
Library preparation was carried out by Novogene using polyA enrichment.


title: SOTR9_HTO

value: Blood

value: TotalSeq-C0276 anti-human Hashtag 16 Antibody


title: Liver, VGC, LAR, Mouse 3

description: Library name: 358_Liver_VC-LAR-3_L1_1

value: 8 months


title: Human CD8+ T cells, chronic, donor 4

description: Library name: D4C

value: CD8+ T cells

value: Chronic


title: SOTR8_ADT

value: PBMC

value: TotalSeq-C0045 anti-human CD4 Antibody, TotalSeq-C0080 anti-human CD8a Antibody, TotalSeq-C0063 anti-human CD45RA Antibody, TotalSeq-C0087 anti-human CD45RO Antibody, TotalSeq-C0148 anti-human CD197 (CCR7) Antibody


title: Human CD8+ T cells, chronic, donor 2

description: Library name: D2C


title: Thymus, VGC, TERM, Mouse 14

description: Library name: 355_Thymus_VGC-_ISS_Term-_14_L1_1

value: Thymus

value: VGC-TERM


title: SOTR8_GEX

description:
mRNA
GEX ('5 mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Human CD8+ T cells, chronic, donor 1

description: Library name: D1C


title: Kidney, FL, TERM, Mouse 4

description: Library name: 354_Kidney_FL-_ISS_Term-_4_L1_1

source_name: Kidney

value: Kidney

value: FL-TERM

value: 3 months


title: SOTR7_BCR

description:
B cell receptor sequences (BCR)
BCR: contig annotations and cell barcode information


title: Human CD8+ T cells, re-activated, donor 5

description: Library name: D5R

value: Re-activated


title: SOTR8_BCR


title: Human CD8+ T cells, re-activated, donor 4

description: Library name: D4R


title: Lung, VGC, LAR, Mouse 11

description: Library name: 353_Lung_VC-LAR-11_L1_1

value: Lung

value: VGC-LAR

value: female

value: BALB/cAnNTac


title: SOTR7_TCR

value: Blood


title: Human CD8+ T cells, re-activated, donor 1

description: Library name: D1R


title: Brain, FL, TERM, Mouse 17

description: Library name: 352_Brain_FL-_ISS_Term-_17_L1_1

value: Brain


title: Human CD8+ T cells, acute, donor 5

description: Library name: D5A

value: Acute


title: SOTR7_HTO

value: TotalSeq-C0257 anti-human Hashtag 7 Antibody


title: Pancreas, FL, VGC, LAR, Mouse 3

description: Library name: 351_Pancreas_FL-LAR-3_L1_1

value: Pancreas

value: 8 months


title: Human CD8+ T cells, acute, donor 1

description: Library name: D1A

value: CD8+ T cells


title: Human CD8+ T cells, acute, donor 2

description: Library name: D2A


title: Human CD8+ T cells, acute, donor 4

description: Library name: D4A


title: BAT, HGC, TERM, Mouse 13

description: Library name: 350_BAT_HGC-_ISS_Term-_13_L1_1

value: BAT

value: HGC-TERM


title: SOTR7_ADT

value: PBMC

value: TotalSeq-C0045 anti-human CD4 Antibody, TotalSeq-C0080 anti-human CD8a Antibody, TotalSeq-C0063 anti-human CD45RA Antibody, TotalSeq-C0087 anti-human CD45RO Antibody, TotalSeq-C0148 anti-human CD197 (CCR7) Antibody


title: SCAT, VGC, TERM, Mouse 14

description: Library name: 349_SCAT_VGC-_ISS_Term-_14_L1_1

value: SCAT

value: VGC-TERM


title: Ribo-Seq, Human CD8+ T cells, acute, donor 1

description: Library name: D1A


title: SOTR6_BCR


title: SOTR7_GEX


title: L1037_1, D7V, caudal; L1037_2, D7V, proximal; L1041_1, R0G, caudal; L1041, R0G, proximal; all T1-Diff media

city: Durham

first: Laila

last: Roudsari

state: NC

address: 2 Maughan Drive

institute: United Therapeutics

description: Library name: L1037_1, L1037_2, L1041_1, L1041_2

library_source: transcriptomic single cell

data_processing:
The sequencing reads were analyzed using Cell Ranger v9.0. Introns were included in the analysis.
Assembly: GRCh38-2024-A
Supplementary files format and content: h5 file containing 18129 rows and 108142 columns

molecule: nuclear RNA

source_name: Human lung

extract_protocol:
Recellularized lung FFPE tissues were sectioned and dissociated into single-cell suspensions using the gentleMACS Octo Dissociator, followed by single-cell capture with the 10x Genomics Chromium X system.
Single Cell Fixed RNA libraries were constructed using the Chromium Single Cell Gene Expression Flex kit for multiplex samples. The libraries were sequenced with ~200 million PE150 reads per sample on Illumina NovaSeq X Plus.

value: Human lung

value: Alveolar epithelial type 2


title: Biological replicate 3, passage 2

description: Library name: Donor3_P2

data_processing:
The sequencing reads were analyzed using Cell Ranger v9.0. Introns were included in the analysis.
Assembly: GRCh38-2024-A
Supplementary files format and content: h5 file containing 38606 rows, 53193 columns

extract_protocol:
Following isolation or harvest from culture, cells were cryopreserved. Upon thawing, cells were prepared for sequencing.
Single cells were captured and 3' single cell gene expression libraries were constructed (GEM-X v4 version) using the 10x Genomics Chromium-X system. The libraries were sequenced with ~500 million PE150 reads per sample on Illumina NovaSeq X Plus.

tag: individual

tag: group


title: L1042_1, R0G, caudal; L1042_2, R0G, proximal; L1043_1, D7V, caudal; L1043, D7V, proximal; all T2-Max media

description: Library name: L1042_1, L1042_2, L1043_1, L1043_2


title: Biological replicate 3, passage 0

description: Library name: Donor3_P0


title: SOTR6_TCR

description:
T cell receptor sequences (TCR)
TCR: contig annotations and cell barcode information


title: Biological replicate 3, isoAT2 (UC, uncultured)

description: Library name: Donor3_UC

value: UC


title: BAT, VGC, LAR, Mouse 5

description: Library name: 347_BAT_VC-LAR-5_L1_1

value: VGC-LAR

value: female

value: BALB/cAnNTac

value: 3 months


title: Biological replicate 2, passage 2

description: Library name: Donor2_P2


title: SOTR6_HTO

value: Blood

value: TotalSeq-C0259 anti-human Hashtag 9 Antibody


title: Biological replicate 2, passage 0

description: Library name: Donor2_P0


title: MAT, FL, VGC, LAR, Mouse 13

description: Library name: 346_MAT_FL-LAR-13_L1_1

source_name: MAT

value: MAT


title: Human CD8+ T cells, re-activated, donor 2

description: Library name: D2R

value: CD8+ T cells

value: Re-activated


title: SOTR6_ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads


title: Biological replicate 2, isoAT2 (UC, uncultured)

description: Library name: Donor2_UC


title: Biological replicate 1, passage 2

description: Library name: Donor1_P2


title: SCAT, FL, VGC, LAR, Mouse 5

description: Library name: 345_SCAT_FL-LAR-5_L1_1


title: SOTR6_GEX


title: SOTR5_BCR


title: Biological replicate 1, passage 0

description: Library name: Donor1_P0


title: Biological replicate 1, isoAT2 (UC, uncultured)

description: Library name: Donor1_UC


title: BAT, HGC, LAR, Mouse 12

description: Library name: 344_BAT_HC-LAR-12_L1_1

value: BAT

value: HGC-LAR

value: 8 months


title: L1035_1, D7V, caudal; L1035_2, D7V, proximal; L1036_1, R0G, caudal; L1036_2, R0G, proximal; all T1-Base media

description: Library name: L1035_1, L1035_2, L1036_1, L1036_2


title: PW7_94J_168_experimental

city: West Lafayette

first: Nathan

last: Backenstose

state: Indiana

address: 915 Mitch Daniels Blvd

institute: Purdue University

description: Library name: PW7_94J_168

data_processing:
Paired-end RNA sequencing reads were mapped to the indexed D. pulex reference (NCBI Accession: GCF_021134715) using HISAT2 v2.2.1 (Kim et al. 2019).
Alignment files for each sample were used to reconstruct transcripts, assign them to known genes and estimate their abundances with Stringtie v2.2.1 (Kovaka et al. 2019).
The assembled transcripts from all samples were then merged into a comprehensive annotation file using StringTie --merge (Kovaka et al. 2019).
The FeatureCounts subcommand of the Subread package v1.6.4 (Liao et al. 2013) was used to count the features of the annotation files, quantifying the number of reads overlapping with specified genomic features such as exons and genes. Feature count data, sample information, and the merged annotated transcripts were imported into the statistical software R v4.0.4 (Team 2020) and analyzed with DESeq2 package (Love et al. 2014).
Assembly: NCBI Accession: GCF_021134715)
Supplementary files format and content: Count matrix with read counts for genomic features for each sample.

organism: Daphnia pulex

source_name: whole body

growth_protocol: D. pulex individuals were identified to species via morphological features, isolated into individual 50mL beakers of well water, and fed 5 x 105 cells of Ankistrodesmus falcatus algae daily. After the first clutch was produced by a field-collected individual, all offspring were transferred to a 400 mL beaker of well water and fed 4.0 x 106 cells of A. falcatus algae daily. These lines were reared for several generations, such that clones were established for a single individual from each site. To standardize possible maternal and grandmaternal effects , we created maternal lines by selecting a juvenile individual from the community beaker and rearing it alone in a 50mL beaker, with the first two clutches of offspring discarded. An individual from the third clutch was then removed and reared alone, and this process was repeated to establish a controlled environment and density for maternal lines. Throughout the rearing process, excess offspring were removed to maintain densities of one individual per 50 mL well water. Ultimately, all experimental clones were derived from at least second-clutch offspring of third-generation maternal lines, as is standard practice to standardize environmental, maternal, and grandmaternal effects on gene expression (Searle et al. 2015; Strauss et al. 2019). Individuals in the experiment were isolated in 50 mL conical tubes and kept at ambient room temperature (20°C) for 12 days prior to being exposed to different temperature regimes in the experiment.

extract_protocol:
D. pulex samples were individually homogenized and bulk RNA was extracted with Qiagen RNeasy Micro Kits (Germantown, MD, USA) adhering to manufacturer protocol.
RNA libraries were prepped and sequenced by Novogene (Sacramento, CA, USA) on a single lane on the Illumina NovaSeq 6000 platform.

treatment_protocol: Ambient temperatures were kept at a target of 20°C (the room’s temperature) under a 16:8 light and dark cycle. Experimental water baths were heated above ambient temperature by Hygger HG-802 aquarium heaters and circulated with Marineland Maxi-Jet ® 400

value: whole body


title: PW7_97J_96_control

description: Library name: PW7_97J_96


title: BAT, HGC, TERM, Mouse 11

description: Library name: 343_BAT_HGC-_ISS_Term-_11_L1_1

value: HGC-TERM


title: Diaphragm, VGC, LAR, Mouse 16

description: Library name: 348_Diaphragm_VC-LAR-16_L1_1

source_name: Diaphragm

value: Diaphragm


title: PW7_83I_96_control

description: Library name: PW7_83I_96


title: PW7_82I_168_experimental

description: Library name: PW7_82I_168


title: PW7_89I_96_control

description: Library name: PW7_89I_96


title: PW7_76H_96_control

description: Library name: PW7_76H_96


title: PW7_72H_168_experimental

description: Library name: PW7_72H_168


title: SOTR5_ADT

value: PBMC

value: TotalSeq-C0045 anti-human CD4 Antibody, TotalSeq-C0080 anti-human CD8a Antibody, TotalSeq-C0063 anti-human CD45RA Antibody, TotalSeq-C0087 anti-human CD45RO Antibody, TotalSeq-C0148 anti-human CD197 (CCR7) Antibody


title: SOTR5_TCR


title: PW7_64G_96_control

description: Library name: PW7_64G_96


title: Heart, FL, TERM, Mouse 5

description: Library name: 342_Heart_FL-_ISS_Term-_5_L1_1

value: Heart

value: FL-TERM


title: SOTR5_GEX


title: Pancreas, FL, VGC, LAR, Mouse 16

description: Library name: 340_Pancreas_FL-LAR-16_L1_1

value: Pancreas

value: VGC-LAR

value: female

value: BALB/cAnNTac


title: SOTR5_HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: Blood

value: TotalSeq-C0255 anti-human Hashtag 5 Antibody


title: PW7_62G_168_experimental

description: Library name: PW7_62G_168


title: Kidney, FL, TERM, Mouse 16

description: Library name: 339_Kidney_FL-_ISS_Term-_16_L1_1

value: Kidney


title: PW7_54F_96_control

description: Library name: PW7_54F_96


title: PW7_5A_96_control

description: Library name: PW7_5A_96


title: SOTR4_BCR


title: GAT, HGC, LAR, Mouse 14

description: Library name: 338_GAT_HC-LAR-14_L1_1

value: GAT

value: 3 months


title: PW7_51F_168_experimental

description: Library name: PW7_51F_168


title: PW7_43E_168_experimental

description: Library name: PW7_43E_168


title: SOTR4_TCR


title: Lung, VGC, LAR, Mouse 14

description: Library name: 337_Lung_VC-LAR-14_L1_1

source_name: Lung

value: Lung


title: SOTR4_HTO

source_name: Blood

value: TotalSeq-C0265 anti-human Hashtag 15 Antibody


title: PW7_33D_168_experimental

description: Library name: PW7_33D_168

value: whole body


title: BAT, VGC, TERM, Mouse 1

description: Library name: 341_BAT_VGC-_ISS_Term-_1_L1_1

value: BAT

value: VGC-TERM


title: SOTR4_ADT

value: PBMC

value: TotalSeq-C0045 anti-human CD4 Antibody, TotalSeq-C0080 anti-human CD8a Antibody, TotalSeq-C0063 anti-human CD45RA Antibody, TotalSeq-C0087 anti-human CD45RO Antibody, TotalSeq-C0148 anti-human CD197 (CCR7) Antibody


title: PW7_6A_96_control

description: Library name: PW7_6A_96


title: PW7_25C_96_control

description: Library name: PW7_25C_96


title: SOTR4_GEX

description:
mRNA
GEX ('5 mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Heart, FL, TERM, Mouse 4

description: Library name: 335_Heart_FL-_ISS_Term-_4_L1_1

value: Heart

value: FL-TERM


title: PW7_15B_96_control

description: Library name: PW7_15B_96


title: PW7_1A_168_experimental

description: Library name: PW7_1A_168


title: SOTR3_BCR

description:
B cell receptor sequences (BCR)
BCR: contig annotations and cell barcode information


title: PW10_94J_96_control

description: Library name: PW10_94J_96


title: Heart, VGC, LAR, Mouse 13

description: Library name: 333_Heart_VC-LAR-13_L1_1

value: VGC-LAR


title: SOTR3_TCR


title: SOTR3_HTO

value: TotalSeq-C0264 anti-human Hashtag 14 Antibody


title: PW10_87I_96_control

description: Library name: PW10_87I_96


title: PW10_81I_168_experimental

description: Library name: PW10_81I_168


title: PW7_12B_168_experimental

description: Library name: PW7_12B_168


title: BAT, VGC, TERM, Mouse 3

description: Library name: 331_BAT_VGC-_ISS_Term-_3_L1_1

value: female

value: BALB/cAnNTac


title: PW10_79H_96_control

description: Library name: PW10_79H_96


title: PW10_71H_168_experimental

description: Library name: PW10_71H_168


title: SOTR3, ADT

value: Blood


title: Spleen, HGC, TERM, Mouse 4

description: Library name: 336_Spleen_HGC-_ISS_Term-_4_L1_1

value: Spleen

value: HGC-TERM


title: Thymus, VGC, LAR, Mouse 2

description: Library name: 332_Thymus_VC-LAR-2_L1_1

value: Thymus

value: 3 months


title: Thymus, FL, TERM, Mouse 1

description: Library name: 330_Thymus_FL-_ISS_Term-_1_L1_1


title: PW7_2A_168_experimental

description: Library name: PW7_2A_168


title: PW10_63G_96_control

description: Library name: PW10_63G_96


title: SOTR3, GEX


title: PW10_61G_168_experimental

description: Library name: PW10_61G_168


title: GAT, HGC, TERM, Mouse 4

description: Library name: 329_GAT_HGC-_ISS_Term-_4_L1_1

value: GAT


title: PW7_39D_96_control

description: Library name: PW7_39D_96

value: whole body


title: Kidney, HGC, TERM, Mouse 13

description: Library name: 328_Kidney_HGC-_ISS_Term-_13_L1_1

value: Kidney

value: 8 months


title: PW10_51F_168_experimental

description: Library name: PW10_51F_168


title: Pancreas, FL, VGC, LAR, Mouse 4

description: Library name: 334_Pancreas_FL-LAR-4_L1_1

value: Pancreas


title: PW10_54F_96_control

description: Library name: PW10_54F_96


title: SOTR2_TCR

description:
T cell receptor sequences (TCR)
TCR: contig annotations and cell barcode information

value: PBMC


title: PW10_42E_168_experimental

description: Library name: PW10_42E_168


title: PW10_95J_168_experimental

description: Library name: PW10_95J_168


title: PW10_8A_96_control

description: Library name: PW10_8A_96


title: SOTR2_HTO

value: TotalSeq-C0259 anti-human Hashtag 9 Antibody


title: Thymus, FL, TERM, Mouse 13

description: Library name: 327_Thymus_FL-_ISS_Term-_13_L1_1

value: FL-TERM


title: PW10_32D_168_experimental

description: Library name: PW10_32D_168


title: PW10_2A_168_experimental

description: Library name: PW10_2A_168


title: Spleen, VGC, LAR, Mouse 5

description: Library name: 326_Spleen_VC-LAR-5_L1_1

value: VGC-LAR


title: SOTR2_ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: TotalSeq-C0045 anti-human CD4 Antibody, TotalSeq-C0080 anti-human CD8a Antibody, TotalSeq-C0063 anti-human CD45RA Antibody, TotalSeq-C0087 anti-human CD45RO Antibody, TotalSeq-C0148 anti-human CD197 (CCR7) Antibody


title: PW10_21C_168_experimental

description: Library name: PW10_21C_168


title: Brain, VGC, LAR, Mouse 5

description: Library name: 325_Brain_VC-LAR-5_L1_1

value: Brain

value: female


title: SOTR2_GEX

value: Blood


title: PW10_18B_96_control

description: Library name: PW10_18B_96


title: Diaphragm, FL, TERM, Mouse 14

description: Library name: 324_Diaphragm_FL-_ISS_Term-_14_L1_1

value: Diaphragm

value: BALB/cAnNTac


title: SOTR1_BCR


title: PW10_12B_168_experimental

description: Library name: PW10_12B_168


title: LP_9A_96_control

description: Library name: LP_9A_96


title: SOTR2_BCR


title: Lung, VGC, LAR, Mouse 3

description: Library name: 323_Lung_VC-LAR-3_L1_1

value: Lung


title: SOTR1_TCR


title: LP_94J_96_control

description: Library name: LP_94J_96


title: SOTR1_ADT


title: BAT, FL, VGC, LAR, Mouse 11

description: Library name: 320_BAT_FL-LAR-11_L1_1

value: BAT


title: PW10_36D_96_control

description: Library name: PW10_36D_96


title: Kidney, HGC, TERM, Mouse 16

description: Library name: 321_Kidney_HGC-_ISS_Term-_16_L1_1

value: HGC-TERM


title: LP_83I_96_control

description: Library name: LP_83I_96

value: whole body


title: LP_71H_168_experimental

description: Library name: LP_71H_168


title: LP_89I_168_experimental

description: Library name: LP_89I_168


title: LP_78H_96_control

description: Library name: LP_78H_96


title: SOTR1_HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: TotalSeq-C0256 anti-human Hashtag 6 Antibody


title: SOTR1_GEX


title: LP_63G_168_experimental

description: Library name: LP_63G_168


title: LP_65G_96_control

description: Library name: LP_65G_96


title: PW10_24C_96_control

description: Library name: PW10_24C_96


title: Diaphragm, HGC, TERM, Mouse 1

description: Library name: 319_Diaphragm_HGC-_ISS_Term-_1_L1_1

value: 3 months


title: HC8_BCR


title: LP_54F_96_control

description: Library name: LP_54F_96


title: PW10_10A_96_control

description: Library name: PW10_10A_96


title: Diaphragm, HGC, TERM, Mouse 3

description: Library name: 317_Diaphragm_HGC-_ISS_Term-_3_L1_1


title: BAT, FL, TERM, Mouse 1

description: Library name: 316_BAT_FL-_ISS_Term-_1_L1_1


title: LP_3A_96_control

description: Library name: LP_3A_96


title: LP_36D_96_control

description: Library name: LP_36D_96


title: LP_32D_168_experimental

description: Library name: LP_32D_168


title: HC8_HTO

value: TotalSeq-C0284 anti-human Hashtag 24 Antibody


title: LP_2A_168_experimental

description: Library name: LP_2A_168


title: Pancreas, HGC, LAR, Mouse 14

description: Library name: 315_Pancreas_HC-LAR-14_L1_1

value: Pancreas

value: HGC-LAR


title: LP_28C_96_control

description: Library name: LP_28C_96


title: HC8_ADT

value: PBMC


title: Diaphragm, VGC, TERM, Mouse 12

description: Library name: 314_Diaphragm_VGC-_ISS_Term-_12_L1_1

value: VGC-TERM

value: 8 months


title: LP_22C_168_experimental

description: Library name: LP_22C_168


title: LP_1A_168_experimental

description: Library name: LP_1A_168


title: HC8_GEX

description:
mRNA
GEX ('5 mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: HC7_BCR

description:
B cell receptor sequences (BCR)
BCR: contig annotations and cell barcode information


title: LP_11B_168_experimental

description: Library name: LP_11B_168


title: GAT, FL, VGC, LAR, Mouse 11

description: Library name: 318_GAT_FL-LAR-11_L1_1

value: GAT

value: VGC-LAR


title: LF_94J_168_experimental

description: Library name: LF_94J_168


title: LP_60F_168_experimental

description: Library name: LP_60F_168


title: HC7_TCR

value: Blood


title: LF_93J_96_control

description: Library name: LF_93J_96


title: Heart, VGC, LAR, Mouse 20

description: Library name: 313_Heart_VC-LAR-20_L1_1

value: Heart

value: female


title: Lung, FL, VGC, LAR, Mouse 16

description: Library name: 311_Lung_FL-LAR-16_L1_1

value: Lung

value: BALB/cAnNTac


title: LF_81I_168_experimental

description: Library name: LF_81I_168


title: HC8_TCR


title: HC7_HTO

value: TotalSeq-C0279 anti-human Hashtag 19 Antibody


title: LF_73H_96_control

description: Library name: LF_73H_96

value: whole body


title: HC7_ADT

value: TotalSeq-C0045 anti-human CD4 Antibody, TotalSeq-C0080 anti-human CD8a Antibody, TotalSeq-C0063 anti-human CD45RA Antibody, TotalSeq-C0087 anti-human CD45RO Antibody, TotalSeq-C0148 anti-human CD197 (CCR7) Antibody


title: LF_71H_168_experimental

description: Library name: LF_71H_168


title: LF_66G_96_control

description: Library name: LF_66G_96


title: LP_44E_168_experimental

description: Library name: LP_44E_168


title: LF_61G_168_experimental

description: Library name: LF_61G_168


title: HC7_GEX


title: Heart, FL, TERM, Mouse 1

description: Library name: 308_Heart_FL-_ISS_Term-_1_L1_1

value: FL-TERM

value: 3 months


title: Thymus, VGC, TERM, Mouse 16

description: Library name: 309_Thymus_VGC-_ISS_Term-_16_L1_1

value: Thymus


title: LF_57F_168_experimental

description: Library name: LF_57F_168


title: LP_16B_96_control

description: Library name: LP_16B_96


title: LF_53F_96_control

description: Library name: LF_53F_96


title: HC6_BCR


title: BAT, VGC, LAR, Mouse 3

description: Library name: 307_BAT_VC-LAR-3_L1_1

value: BAT


title: LF_45E_168_experimental

description: Library name: LF_45E_168


title: SCAT, FL, VGC, LAR, Mouse 3

description: Library name: 312_SCAT_FL-LAR-3_L1_1

source_name: SCAT

value: SCAT


title: HC6_TCR

value: PBMC


title: LF_83I_96_control

description: Library name: LF_83I_96


title: LF_40D_96_control

description: Library name: LF_40D_96


title: LF_43E_96_control

description: Library name: LF_43E_96


title: HC6_HTO

value: TotalSeq-C0278 anti-human Hashtag 18 Antibody


title: MAT, FL, VGC, LAR, Mouse 11

description: Library name: 304_MAT_FL-LAR-11_L1_1

value: MAT

value: 8 months


title: LF_32D_168_experimental

description: Library name: LF_32D_168


title: Kidney, VGC, LAR, Mouse 1

description: Library name: 305_Kidney_VC-LAR-1_L1_1

value: Kidney

value: VGC-LAR


title: HC6_ADT

value: Blood


title: LF_2A_168_experimental

description: Library name: LF_2A_168


title: LF_21C_168_experimental

description: Library name: LF_21C_168


title: Thymus, HGC, TERM, Mouse 3

description: Library name: 303_Thymus_HGC-_ISS_Term-_3_L1_1

value: HGC-TERM

value: female


title: HC6_GEX


title: LF_17B_96_control

description: Library name: LF_17B_96


title: Spleen, HGC, TERM, Mouse 1

description: Library name: 302_Spleen_HGC-_ISS_Term-_1_L1_1

value: Spleen

value: BALB/cAnNTac


title: LF_15B_168_experimental

description: Library name: LF_15B_168

value: whole body


title: HC5_TCR

description:
T cell receptor sequences (TCR)
TCR: contig annotations and cell barcode information


title: LF_10A_96_control

description: Library name: LF_10A_96


title: LF_52F_168_experimental

description: Library name: LF_52F_168


title: CF_96J_96_control

description: Library name: CF_96J_96


title: GAT, HGC, LAR, Mouse 11

description: Library name: 301_GAT_HC-LAR-11_L1_1

source_name: GAT

value: GAT

value: HGC-LAR


title: MAT, VGC, TERM, Mouse 1

description: Library name: 306_MAT_VGC-_ISS_Term-_1_L1_1

value: VGC-TERM

value: 3 months


title: CF_9A_96_control

description: Library name: CF_9A_96


title: HC5_HTO

value: TotalSeq-C0280 anti-human Hashtag 20 Antibody


title: Lung, VGC, TERM, Mouse 11

description: Library name: 300_Lung_VGC-_ISS_Term-_11_L1_1

value: Lung


title: CF_93J_168_experimental

description: Library name: CF_93J_168


title: HC5_ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: PBMC

value: TotalSeq-C0045 anti-human CD4 Antibody, TotalSeq-C0080 anti-human CD8a Antibody, TotalSeq-C0063 anti-human CD45RA Antibody, TotalSeq-C0087 anti-human CD45RO Antibody, TotalSeq-C0148 anti-human CD197 (CCR7) Antibody


title: CF_82I_168_experimental

description: Library name: CF_82I_168


title: MAT, HGC, LAR, Mouse 14

description: Library name: 299_MAT_HC-LAR-14_L1_1

value: MAT


title: CF_75H_96_control

description: Library name: CF_75H_96


title: CF_86I_96_control

description: Library name: CF_86I_96


title: LF_30C_96_control

description: Library name: LF_30C_96


title: BAT, VGC, LAR, Mouse 1

description: Library name: 298_BAT_VC-LAR-1_L1_1

value: BAT


title: HC5_GEX


title: Diaphragm, HGC, TERM, Mouse 12

description: Library name: 297_Diaphragm_HGC-_ISS_Term-_12_L1_1

value: Diaphragm

value: 8 months


title: CF_69G_96_control

description: Library name: CF_69G_96


title: CF_72H_168_experimental

description: Library name: CF_72H_168


title: HC4_BCR

value: Blood


title: GAT, FL, TERM, Mouse 11

description: Library name: 296_GAT_FL-_ISS_Term-_11_L1_1

value: FL-TERM

value: female


title: CF_58F_96_control

description: Library name: CF_58F_96


title: HC5_BCR


title: CF_52F_168_experimental

description: Library name: CF_52F_168


title: CF_46E_96_control

description: Library name: CF_46E_96


title: Spleen, FL, TERM, Mouse 13

description: Library name: 295_Spleen_FL-_ISS_Term-_13_L1_1

value: Spleen

value: BALB/cAnNTac


title: HC4_HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: TotalSeq-C0260 anti-human Hashtag 10 Antibody


title: CF_34D_96_control

description: Library name: CF_34D_96

value: whole body


title: Liver, VGC, LAR, Mouse 1

description: Library name: 294_Liver_VC-LAR-1_L1_1

source_name: Liver

value: Liver

value: VGC-LAR


title: CF_43E_168_experimental

description: Library name: CF_43E_168


title: HC4_ADT


title: CF_31D_168_experimental

description: Library name: CF_31D_168


title: CF_25C_96_control

description: Library name: CF_25C_96


title: HC4_GEX


title: CF_22C_168_experimental

description: Library name: CF_22C_168


title: CF_20B_96_control

description: Library name: CF_20B_96


title: CF_1A_168_experimental

description: Library name: CF_1A_168


title: SCAT, FL, TERM, Mouse 3

description: Library name: 292_SCAT_FL-_ISS_Term-_3_L1_1

value: SCAT

value: 3 months


title: Diaphragm, FL, TERM, Mouse 3

description: Library name: 293_Diaphragm_FL-_ISS_Term-_3_L1_1


title: HC3_BCR

value: PBMC


title: CBN_98J_96_control

description: Library name: CBN_98J_96


title: CF_11B_168_experimental

description: Library name: CF_11B_168


title: HC3_TCR


title: CF_62G_168_experimental

description: Library name: CF_62G_168


title: SCAT, FL, TERM, Mouse 14

description: Library name: 291_SCAT_FL-_ISS_Term-_14_L1_1


title: Lung, FL, VGC, LAR, Mouse 5

description: Library name: 290_Lung_FL-LAR-5_L1_1

value: Lung


title: HC3_HTO

value: TotalSeq-C0252 anti-human Hashtag 2 Antibody


title: CBN_84I_96_control

description: Library name: CBN_84I_96


title: CBN_93J_168_experimental

description: Library name: CBN_93J_168


title: CBN_82I_168_experimental

description: Library name: CBN_82I_168


title: HC4_TCR


title: BAT, FL, VGC, LAR, Mouse 16

description: Library name: 289_BAT_FL-LAR-16_L1_1

value: BAT


title: CBN_7A_96_control

description: Library name: CBN_7A_96


title: CBN_80H_96_control

description: Library name: CBN_80H_96


title: HC3_ADT

value: TotalSeq-C0045 anti-human CD4 Antibody, TotalSeq-C0080 anti-human CD8a Antibody, TotalSeq-C0063 anti-human CD45RA Antibody, TotalSeq-C0087 anti-human CD45RO Antibody, TotalSeq-C0148 anti-human CD197 (CCR7) Antibody


title: Lung, HGC, LAR, Mouse 12

description: Library name: 288_Lung_HC-LAR-12_L1_1

value: HGC-LAR

value: 8 months


title: CBN_71H_168_experimental

description: Library name: CBN_71H_168


title: HC2_BCR

value: Blood


title: CBN_65G_96_control

description: Library name: CBN_65G_96


title: CBN_62G_168_experimental

description: Library name: CBN_62G_168


title: Heart, FL, VGC, LAR, Mouse 16

description: Library name: 287_Heart_FL-LAR-16_L1_1

value: Heart

value: female


title: HC3_GEX

description:
mRNA
GEX ('5 mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CBN_49E_96_control

description: Library name: CBN_49E_96


title: Spleen, HGC, LAR, Mouse 12

description: Library name: 286_Spleen_HC-LAR-12_L1_1

source_name: Spleen

value: Spleen

value: BALB/cAnNTac


title: CBN_51F_168_experimental

description: Library name: CBN_51F_168

value: whole body


title: HC2_HTO

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody


title: CBN_60F_96_control

description: Library name: CBN_60F_96


title: CBN_44E_168_experimental

description: Library name: CBN_44E_168


title: GAT, HGC, TERM, Mouse 14

description: Library name: 285_GAT_HGC-_ISS_Term-_14_L1_1

value: GAT

value: HGC-TERM


title: Heart, HGC, TERM, Mouse 2

description: Library name: 284_Heart_HGC-_ISS_Term-_2_L1_1

value: 3 months


title: HC2_TCR

value: PBMC


title: Heart, FL, VGC, LAR, Mouse 8

description: Library name: 283_Heart_FL-LAR-8_L1_1

value: VGC-LAR


title: CBN_15B_96_control

description: Library name: CBN_15B_96


title: CBN_1A_168_experimental

description: Library name: CBN_1A_168


title: HC2_ADT


title: Diaphragm, FL, VGC, LAR, Mouse 1

description: Library name: 282_Diaphragm_FL-LAR-1_L1_1

value: Diaphragm


title: CBN_37D_96_control

description: Library name: CBN_37D_96


title: CBN_12B_168_experimental

description: Library name: CBN_12B_168


title: BG_87I_96_control

description: Library name: BG_87I_96


title: HC2_GEX


title: HC1_TCR


title: CBN_22C_168_experimental

description: Library name: CBN_22C_168


title: Lung, VGC, LAR, Mouse 1

description: Library name: 281_Lung_VC-LAR-1_L1_1

value: Lung


title: BG_82I_168_experimental

description: Library name: BG_82I_168


title: Liver, HGC, TERM, Mouse 2

description: Library name: 280_Liver_HGC-_ISS_Term-_2_L1_1

value: Liver


title: BG_74H_96_control

description: Library name: BG_74H_96


title: HC1_HTO


title: BG_96J_168_experimental

description: Library name: BG_96J_168


title: Thymus, HGC, LAR, Mouse 14

description: Library name: 279_Thymus_HC-LAR-14_L1_1

value: Thymus

value: HGC-LAR


title: BG_72H_168_experimental

description: Library name: BG_72H_168


title: BG_68G_96_control

description: Library name: BG_68G_96


title: HC1_GEX

value: Blood


title: BG_62G_168_experimental

description: Library name: BG_62G_168


title: BG_57F_96_control

description: Library name: BG_57F_96


title: Spleen, FL, TERM, Mouse 2

description: Library name: 278_Spleen_FL-_ISS_Term-_2_L1_1

value: FL-TERM


title: HC1_BCR

description:
B cell receptor sequences (BCR)
BCR: contig annotations and cell barcode information


title: BG_5A_96_control

description: Library name: BG_5A_96


title: CBN_31D_168_experimental

description: Library name: CBN_31D_168


title: Kidney, HGC, LAR, Mouse 3

description: Library name: 277_Kidney_HC-LAR-3_L1_1

value: Kidney

value: female

value: 8 months


title: BG_51F_168_experimental

description: Library name: BG_51F_168

value: whole body


title: BG_41E_168_experimental

description: Library name: BG_41E_168


title: Lung, HGC, TERM, Mouse 13

description: Library name: 276_Lung_HGC-_ISS_Term-_13_L1_1

value: BALB/cAnNTac


title: Heart, VGC, TERM, Mouse 1

description: Library name: 275_Heart_VGC-_ISS_Term-_1_L1_1

value: Heart

value: VGC-TERM


title: BG_38D_96_control

description: Library name: BG_38D_96


title: ATG5 KO SEAM biol rep 2

city: Birmingham

first: Gamze

last: Kocak

address: Edgbaston

country: United Kingdom

institute: University of Birminghham

data_processing:
The raw data generated was converted from .bcl to fastQ and demultiplexed by DRAGEN v4.2.7.
Assembly: hg18
Supplementary files format and content: Tab-delimited text files includes TPM values for each sample.

source_name: hESC-derived multi-zonal ocular cells

extract_protocol:
Total RNA extraction from cells was performed using TRIzol reagent followed by DNase treatment using the RNase-free DNase set. The amount of input RNA is determined by the quantity of RNA samples.
Ilumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit is used for the construction of NGS libraries from the samples with acceptable quality parameters.

value: hESC-derived multi-zonal ocular cells

value: KO

value: SEAM differentiation


title: ATG5 KO SEAM biol rep 3


title: BG_32D_168_experimental

description: Library name: BG_32D_168


title: BG_25C_96_control

description: Library name: BG_25C_96


title: MAT, VGC, LAR, Mouse 11

description: Library name: 274_MAT_VC-LAR-11_L1_1

value: MAT

value: VGC-LAR


title: ATG5 KO SEAM biol rep 1


title: BG_1A_168_experimental

description: Library name: BG_1A_168


title: ATG5 WT SEAM biol rep 3

value: WT


title: Liver, VGC, TERM, Mouse 4

description: Library name: 273_Liver_VGC-_ISS_Term-_4_L1_1

value: Liver

value: 3 months


title: BG_18B_96_control

description: Library name: BG_18B_96


title: BG_11B_168_experimental

description: Library name: BG_11B_168


title: ATG5 WT SEAM biol rep 2


title: BG_101C_168_experimental

description: Library name: BG_101C_168


title: SCAT, HGC, TERM, Mouse 2

description: Library name: 272_SCAT_HGC-_ISS_Term-_2_L1_1

value: SCAT

value: HGC-TERM


title: HC1_ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: Blood

value: PBMC

value: TotalSeq-C0045 anti-human CD4 Antibody, TotalSeq-C0080 anti-human CD8a Antibody, TotalSeq-C0063 anti-human CD45RA Antibody, TotalSeq-C0087 anti-human CD45RO Antibody, TotalSeq-C0148 anti-human CD197 (CCR7) Antibody


title: AR_99J_96_control

description: Library name: AR_99J_96

value: whole body


title: Diaphragm, FL, TERM, Mouse 16

description: Library name: 271_Diaphragm_FL-_ISS_Term-_16_L1_1

value: Diaphragm

value: FL-TERM

value: female

value: BALB/cAnNTac

value: 8 months


title: BG_100J_96_control

description: Library name: BG_100J_96


title: ATG5 WT SEAM biol rep 1

value: hESC-derived multi-zonal ocular cells

value: SEAM differentiation


title: AR_97J_168_experimental

description: Library name: AR_97J_168


title: BG_45E_96_control

description: Library name: BG_45E_96


title: AR_85I_96_control

description: Library name: AR_85I_96


title: hBMSC, miR-127-3p mimic, rep3

city: Araçatuba

first: Victor Gustavo Balera

last: Brito

email: vgb.brito@unesp.br, brito@wustl.edu

state: SP

address: Marechal Rondon, km 527/8

department: Basic sciences

country: Brazil

institute: São Paulo State University

data_processing:
Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited text files include raw counts for each sample

source_name: bone marrow from male donnor

growth_protocol: Human bone marrow-derived mesenchymal stromal cells (hBMSC) were purchased from Lonza(C) and cultured in growth medium [low glucose DMEM supplemented with 10% fetal bovine serum, 1 ng/mL basic fibroblast growth factor (bFGF), 2 mM glutamine, and antibiotics(100 U/mL penicillin and 100 μg/mL streptomycin)] up to passage 5.

extract_protocol:
Total RNA was extracted using the Total RNA Purification Kit (Norgen Biotek Corp). Samples were DNAse I treated (Invitrogen, Thermo Fisher), and used for libreary preparation.
Total RNA integrity was determined using Agilent Bioanalyzer and library preparation was performed with 500 ng of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol: Human bone marrow-derived mesenchymal stromal cells (hBMSC) at passage 5 were seeded at 0.1 million cells/well in 24-well plates. Twenty-four hours after seeding, the cells were transfected with 30 nM of miR-127-3p mimic or a negative control RNA (miRVana TM), using Lipofectamine RNAiMAX, following the manufacturer's instructions. A non-transfected group served as an additional control. Twenty-four hours post-transfection, the culture medium was changed to osteogenic medium (alpha MEM supplemented with 10% fetal bovine serum, 50 µM ascorbic acid 2-phosphate, 10 mM β-glycerophosphate, 10 nM dexamethasone, 100 U/mL penicillin, and 100 μg/mL streptomycin). Medium was changes every 2 days, and after 7 days of osteogenic induction, total RNA was isolated, and the over-expression of miR-127-3p was confirmed by RT-qPCR. The RNA samples were then used for RNA-sequencing.

value: bone marrow from male donnor

value: mesenchymal stromal cells

value: miR-127-3p mimic


title: hBMSC, miR-127-3p mimic, rep2

value: bone marrow-derived mesenchymal stromal cells


title: BAT, FL, TERM, Mouse 2

description: Library name: 270_BAT_FL-_ISS_Term-_2_L1_1

source_name: BAT

value: BAT

value: 3 months


title: BAT, HGC, LAR, Mouse 2

description: Library name: 269_BAT_HC-LAR-2_L1_1

value: HGC-LAR


title: AR_82I_168_experimental

description: Library name: AR_82I_168


title: BAT, FL, VGC, LAR, Mouse 13

description: Library name: 268_BAT_FL-LAR-13_L1_1

value: VGC-LAR


title: AR_8A_96_control

description: Library name: AR_8A_96


title: AR_72H_168_experimental

description: Library name: AR_72H_168


title: AR_77H_96_control

description: Library name: AR_77H_96


title: AR_67G_96_control

description: Library name: AR_67G_96


title: AR_61G_168_experimental

description: Library name: AR_61G_168


title: AR_53F_96_control

description: Library name: AR_53F_96


title: hBMSC, negative control, rep3

value: Negative control


title: AR_52F_168_experimental

description: Library name: AR_52F_168

value: whole body


title: AR_47E_96_control

description: Library name: AR_47E_96


title: Lung, FL, TERM, Mouse 13

description: Library name: 266_Lung_FL-_ISS_Term-_13_L1_1

value: Lung


title: AR_41E_168_experimental

description: Library name: AR_41E_168


title: AR_39D_96_control

description: Library name: AR_39D_96


title: Kidney, VGC, TERM, Mouse 12

description: Library name: 267_Kidney_VGC-_ISS_Term-_12_L1_1

value: Kidney

value: VGC-TERM


title: Lung, HGC, LAR, Mouse 16

description: Library name: 265_Lung_HC-LAR-16_L1_1

value: female

value: BALB/cAnNTac


title: hBMSC, non-transfected, rep3

value: Non-transfected


title: hBMSC, non-transfected, rep2


title: AR_2A_168_experimental

description: Library name: AR_2A_168


title: Spleen, VGC, TERM, Mouse 2

description: Library name: 264_Spleen_VGC-_ISS_Term-_2_L1_1

value: Spleen


title: AR_29C_96_control

description: Library name: AR_29C_96


title: AR_22C_168_experimental

description: Library name: AR_22C_168


title: Pancreas, HGC, LAR, Mouse 3

description: Library name: 263_Pancreas_HC-LAR-3_L1_1

source_name: Pancreas

value: Pancreas

value: 8 months


title: hBMSC, non-transfected, rep1

value: bone marrow from male donnor

value: mesenchymal stromal cells


title: AR_12B_168_experimental

description: Library name: AR_12B_168


title: AR_20B_96_control

description: Library name: AR_20B_96


title: AR_31D_168_experimental

description: Library name: AR_31D_168


title: BAT, HGC, LAR, Mouse 5

description: Library name: 261_BAT_HC-LAR-5_L1_1

value: BAT


title: iPSC-derived granulocyte, CD45+CD14-CD11b+CD16+CD66b+, day 20, line 28L, biol rep 2

city: Cincinnati

first: Kentaro

last: Iwasawa

state: OH

address: 3333 BURNET AVENUE

department: Division of Gastroenterology, Hepatology and Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: iPSC_Granulo2_45Pos14Neg11bPos16Pos66bPos

data_processing:
Samples were sequenced at a depth of 20M paired-end (40M total) reads per sample reads per sample by Medgenome Inc.
The FASTQ files from paired-end sequencing were initially processed (including trimming, filtering low-quality reads, and removing adaptors) using the command line tool fast (Chen et al. 2018, Bioinformatics)
Quantification is performed via psuedoalignment using the R package Kallisto against the human reference transcriptome hg38 (Bray et al. 2016, Nat Biotech)
Gene counts are then estimated from the resulting transcript abundances using the R package tximport (Soneson et al, 2015, F1000Res)
Samples are combined into a final counts matrix. The function mnnCorrect from the R package Batchelor was adapted to correct the counts for batch effects using a mutual nearest neighbors method60. Differentially expressed genes were then identified between populations of interest using R package DESeq2 (Love at al, 2014, Genome Biol) and visualized using volcano plots. The corrected counts matrix is log-transformed for principal component analysis, and principal components are calculated and visualized. The top and bottom 100 genes from the first four principal components are subsets from the normalized counts and used for generating the expression heatmap.
Assembly: hg38
Supplementary files format and content: comma-separated values files include CPM values for each Sample

extract_protocol:
RNA was harvested using Arcturus™ PicoPure™ RNA Isolation Kit (ThermoFisher) or Rneasy mini plus kit (Qiagen, only iPSC-derived monocytes and iPSC-derived granulocytes). Takara SMART-Seq v4 Ultra low Input RNA kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols by Medgenome Inc.

value: iPSC-derived granulocytes

value: wildtype

value: No treatment

tag: time

value: Day 20


title: iPSC-derived granulocyte, CD45+CD14-CD11b+CD16+CD66b+, day 20, line 28L, biol rep 1

description: iPSC_Granulo1_45Pos14Neg11bPos16Pos66bPos


title: Long read scRNA-seq mouse hippocampus sequencing with RPS2-STAMP rep3

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

description:
Library name: biol rep 3
Single-cell long-read sequencing of Ribo-STAMP-expressing mouse hippocampus

data_processing:
Aligned with pbmm2 to mm10 + tdTomato reference
CPM and log normalization for reads. Raw edits were normalized by Stamp expression via regression. EditsC = total Edited Cs in transcript / (total Cs in transcript annotation * total reads) and Cell assignments are based on short-read scRNA-seq from same samples which were filtered for doublets and low-quality cells.
Assembly: mm10
Supplementary files format and content: Read count matrices: gene-level and transcript-level read counts in TSV format (longread_read_count_matrix_*_gene_id.tsv, longread_read_count_matrix_*_gene_name.tsv, longread_read_count_matrix_*_transcript_id.tsv)
Supplementary files format and content: Edit count matrices: gene-level and transcript-level edit counts in TSV format (longread_number_edits_matrix_*_gene_id.tsv, longread_number_edits_matrix_*_gene_name.tsv, longread_number_edits_matrix_*_transcript_id.tsv)
Supplementary files format and content: AnnData objects: normed and filtered counts by transcript (longread_normed_counts_transcript_adata_*.h5ad), filtered and STAMP-normalized edits by transcript (longread_normed_edits_adata_*.h5ad), and filtered edit-to-coverage ratio by transcript (longread_EditsC_transcript_adata_*.h5ad)

source_name: Hippocampus

growth_protocol: P22 C57BL/6J mice stereotactically injected with EF1a-Ribo-STAMP virus in dorsal hippocampus. Processed 72h post-injection at P25.

extract_protocol:
Hippocampi dissected from perfused brains, enzymatically dissociated with Papain/DNaseI, filtered, and resuspended at 1200 cells/µl.
10x Genomics Chromium Next GEM Single Cell 3' v3.4. Target: 10,000 cells/replicate. Libraries sequenced on PacBio Revio.

value: Hippocampus

value: Mixed

value: Injection in dHC with 800 nL EF1a-Ribo STAMP virus

tag: batch


title: Long read scRNA-seq mouse hippocampus sequencing with RPS2-STAMP rep2

description:
Library name: biol rep 2
Single-cell long-read sequencing of Ribo-STAMP-expressing mouse hippocampus


title: hBMSC, negative control, rep2

value: bone marrow-derived mesenchymal stromal cells

value: Negative control


title: PDAC, Human Tumor, sample106

city: Chapel Hill

first: Jen Jen

last: Yeh

state: North Carolina

address: 450 West drive

institute: The University of North Carolina at Chapel Hill

description: Library name: ST5425

data_processing:
Space Ranger (v2.1.0) was used, following10X Genomics guidelines, to process the raw data and generate gene count files.
“spaceranger mkfastq” with default settings was used to convert BCL files to FASTQ files.
“spaceranger count” was applied with default settings and required input files, including FASTQ files, brightfield microscope image, CytAssist image, as well as the manual alignment JASON file.
Seurat (v5.1.0) was used for subsequent data processing.
Assembly: Human GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Library strategy: Spatial Transcriptomics

source_name: Primary PDAC

extract_protocol:
Spatial transcriptomics was done using the 10X Genomics Visium Cytassist platform using 5 µm tissue sections that were mounted onto a glass slide. Tumor areas of interest were aligned with a 6.5 x 6.5 mm capture area on a Cytassist Spatial Gene Expression slide. Following the manufacturer protocol, sections were deparaffinized, H&E stained, imaged, and then decrosslinked to release mRNAs which bind to the spatially barcoded oligos on the 4992 spots of each capture area, at a spatial resolution of 55 µm. Once probe pairs hybridized and ligated to the RNA, the single-stranded ligation product was released from the tissue and captured on the Visium slide.
Probe products were reverse transcribed and extended to incorporate a unique molecular identifier (UMI) and the spatial barcode. Following amplification, libraries were constructed from the cDNA. qPCR of pre-amplification material was used to determine cycle number for the sample index PCR to generate the final library. After a SPRIselect bead cleanup, generated libraries were sequenced on the Illumina NextSeq2000 platform using a P3 100 cycle kit at a depth of ~300M reads per section, resulting in >60,000 reads per spot.

value: Primary PDAC


title: PDAC, Human Tumor, sample28

description: Library name: ST5473


title: iPSC-derived monocytes, CD45+CD14+, day 20, line 28L, biol rep 2

value: iPSC-derived monocytes


title: PDAC, Human Tumor, sample120

description: Library name: ST11592

value: FOLFIRINOX


title: hBMSC, miR-127-3p mimic, rep1

value: miR-127-3p mimic


title: SCAT, HGC, TERM, Mouse 12

description: Library name: 260_SCAT_HGC-_ISS_Term-_12_L1_1

value: SCAT

value: HGC-TERM

value: female

value: BALB/cAnNTac

value: 8 months


title: iPSC-derived monocytes, CD45+CD14+, day 20, line 28L, biol rep 1

value: wildtype


title: PDAC, Human Tumor, sample20

description: Library name: ST5068


title: Liver, FL, TERM, Mouse 12

description: Library name: 259_Liver_FL-_ISS_Term-_12_L1_1

value: Liver

value: FL-TERM


title: hBMSC, negative control, rep1

value: bone marrow from male donnor

value: mesenchymal stromal cells


title: MAT, VGC, LAR, Mouse 16

description: Library name: 257_MAT_VC-LAR-16_L1_1

value: MAT

value: VGC-LAR


title: Long read scRNA-seq mouse hippocampus sequencing with RPS2-STAMP rep1

description:
Library name: biol rep 1
Single-cell long-read sequencing of Ribo-STAMP-expressing mouse hippocampus

value: Hippocampus

value: Mixed

value: Injection in dHC with 800 nL EF1a-Ribo STAMP virus


title: PDAC, Human Tumor, sample53

description: Library name: ST11588

value: Primary PDAC

value: FOLFIRINOX


title: PDAC, Human Tumor, sample118

description: Library name: ST10772


title: hFLO, CD14+ CD16+ CD163-, day 30, line 72_3, Mono, biol rep 2

value: hFLO-Monocytes

value: No treatment

value: Day 30


title: PDAC, Human Tumor, sample112

description: Library name: ST10708


title: Primary Hepatocyte, not FACS-sorted (Yecuris, 20-0001/Donor HHF13023), techn. rep 2

source_name: primary

value: primary

value: Primary Hepatocytes

value: Day 1


title: hFLO, CD45+ CD14+ CD16+ CD163-, day 30, line 72_3, Mono, biol rep 1

value: wildtype


title: NAIVE_4

city: Seattle

first: Jakob

middle: Helmuth

last: von Moltke

state: Washington

address: 750 Republican Street

department: Immunology

institute: University of Washington

description: Library name: lib61721

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads.
Assembly: GRCm39
Supplementary files format and content: .csv file (all_genes.csv) containing filtered and normalized log2 read counts

source_name: mesenteric lymph nodes

extract_protocol:
cells sorted directly into Nextera XT lysis buffer
With multiplexing primers according to Nextera XT manufacturer's protocol

treatment_protocol: 200 Heligmosomoides polygyrus bakeri L3 larvae by oral gavage; 2 mg pyrantel pamoate by oral gavage on D14 and D15

value: mesenteric lymph nodes

value: CD4 T cells

value: 200 Heligmosomoides polygyrus bakeri L3 larva; pyrantel pamoate drug clear D14 and D15; harvest 28 days after drug clear


title: MLN_3

description: Library name: lib65173


title: NAIVE_1

description: Library name: lib61718


title: NAIVE_3

description: Library name: lib61720


title: Pancreas, VGC, LAR, Mouse 3

description: Library name: 256_Pancreas_VC-LAR-3_L1_1

value: Pancreas

value: female

value: BALB/cAnNTac

value: 8 months


title: Diaphragm, VGC, TERM, Mouse 1

description: Library name: 254_Diaphragm_VGC-_ISS_Term-_1_L1_1

value: Diaphragm

value: VGC-TERM

value: 3 months


title: Thymus, HGC, TERM, Mouse 2

description: Library name: 255_Thymus_HGC-_ISS_Term-_2_L1_1

source_name: Thymus

value: Thymus

value: HGC-TERM


title: Thymus, HGC, LAR, Mouse 11

description: Library name: 262_Thymus_HC-LAR-11_L1_1

value: HGC-LAR


title: Thymus, HGC, LAR, Mouse 16

description: Library name: 258_Thymus_HC-LAR-16_L1_1


title: MFAT_4

description: Library name: lib65161

source_name: mesenteric fat

value: mesenteric fat


title: MFAT_2

description: Library name: lib65159


title: MLN_2

description: Library name: lib65172


title: PBMC-derived, IL4/IL13-polarized macrophage, not FACS-sorted, biol rep 2

value: primary

value: Primary macrophages

value: IL4 and IL13


title: Pancreas, HGC, TERM, Mouse 1

description: Library name: 251_Pancreas_HGC-_ISS_Term-_1_L1_1


title: MFAT_1

description: Library name: lib65158


title: MLN_1

description: Library name: lib65170

value: mesenteric lymph nodes


title: Thymus, FL, TERM, Mouse 3

description: Library name: 253_Thymus_FL-_ISS_Term-_3_L1_1

value: FL-TERM


title: MFAT_3

description: Library name: lib65160

value: CD4 T cells

value: 200 Heligmosomoides polygyrus bakeri L3 larva; pyrantel pamoate drug clear D14 and D15; harvest 28 days after drug clear


title: NAIVE_2

description: Library name: lib61719


title: PBMC-derived, IL4/IL13-polarized macrophage, not FACS-sorted, biol rep 1

value: wildtype

value: Day 1


title: Brain, HGC, TERM, Mouse 9

description: Library name: 252_Brain_HGC-_ISS_Term-_9_L1_1

source_name: Brain

value: Brain

value: female

value: BALB/cAnNTac


title: PBMC-derived, LPS-polarized macrophage, not FACS-sorted, biol rep 2

value: LPS


title: SILP_4

description: Library name: lib65157

source_name: small intestine lamina propria

value: small intestine lamina propria


title: PBMC-derived, LPS-polarized macrophage, not FACS-sorted, biol rep 1


title: hFLO, CD45+ CD14+ CD16+, day 30, line 72_3, MonoMac, biol rep 3

value: hFLO-Monocytes and -Macrophages

value: No treatment

value: Day 30


title: Kidney, FL, VGC, LAR, Mouse 11

description: Library name: 250_Kidney_FL-LAR-11_L1_1

source_name: Kidney

value: Kidney

value: VGC-LAR

value: 8 months


title: SILP_1

description: Library name: lib65154


title: Primary Hepatocyte, not FACS-sorted (Yecuris, 20-0001/Donor HHF13023), techn. rep 1

value: primary

value: Primary Hepatocytes


title: SILP_2

description: Library name: lib65155

value: CD4 T cells


title: SI_CD4_5_3

description:
Library name: lib61712
27_4006_SILP-CD4

value: 200 Heligmosomoides polygyrus bakeri L3 larva; pyrantel pamoate drug clear D14 and D15; harvest 28 days after drug clear


title: hFLO, CD45+ CD14+ CD16+, day 30, line 72_3, MonoMac, biol rep 1

value: wildtype


title: SI_CD4_5_2

description:
Library name: lib61711
26_4005_SILP-CD4


title: SI_CD4_5_1

description:
Library name: lib61710
25_4004_SILP-CD4


title: Lung, VGC, TERM, Mouse 5

description: Library name: 248_Lung_VGC-_ISS_Term-_5_L1_1

source_name: Lung

value: Lung

value: VGC-TERM

value: 3 months


title: Kidney, HGC, TERM, Mouse 2

description: Library name: 247_Kidney_HGC-_ISS_Term-_2_L1_1

value: HGC-TERM

value: female

value: BALB/cAnNTac


title: SILP_3

description: Library name: lib65156

value: small intestine lamina propria


title: SI_CD4_13_4

description:
Library name: lib61701
16_4135_SILP-CD4


title: SI_CD4_13_2

description:
Library name: lib61699
14_4133_SILP-CD4


title: CD68+ primary liver macrophage (ThermoFisher Scientific, HUKCCS/HK8408)

value: Primary liver macrophages

value: No treatment

value: Day 1


title: hFLO, CD45+ CD14- CD16+, day 30, line 72_3

value: hFLO-granulocytes

value: Day 30


title: SI_CD4_13_3

description:
Library name: lib61700
15_4134_SILP-CD4


title: SI_CD4_13_1

description:
Library name: lib61698
13_4132_SILP-CD4


title: Lung, HGC, LAR, Mouse 13

description: Library name: 245_Lung_HC-LAR-13_L1_1

value: HGC-LAR


title: Kidney, HGC, LAR, Mouse 11

description: Library name: 246_Kidney_HC-LAR-11_L1_1

value: Kidney

value: 8 months


title: E11.5, rep3

city: Houston

first: Ziyue

last: Yang

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Library name: 12_1190E

data_processing:
The FASTQ files were downloaded from BaseSpace Sequence Hub (Illumina). The quality control, alignment, and annotation were done following COMPSRA pipeline88 with the parameters -ref mm10 -qc -ra TGGAATTCTCGGGTGCCAAGG -rb 4 -rh 20 -rt 20 -rr 20 -rlh 8,17 -aln -mt star -ann -ac 1, and then mapped reads were quantified with -fun -fm -fms 1-12 -fdclass 1,2 -fdann -pro COMPSRA_MERGE. Raw read counts for individual miRNAs with the same seed sequence89 were summed up to calculate raw counts for each miRNA family.
Assembly: GRCm39
Supplementary files format and content: txt, raw read count

source_name: Pancreas, E11.5

extract_protocol:
Cells were sorted into Trizol LS and RNA was extracted using miRNeasy micro kit (Qiagen 217084)
Small RNA libraries were generated with the NEXTflex Small RNA-Seq kit v3(NOVA5132, Bioo Scientific). After PCR amplification, small RNA libraries were purified via TBE-PAGE (4565014, Biorad).

value: Pancreas, E11.5

value: Pancreas

value: Pdx1-Cre labelled cells

value: Pdx1-Cre, tdtomato+


title: Heart, VGC, TERM, Mouse 2

description: Library name: 244_Heart_VGC-_ISS_Term-_2_L1_1

source_name: Heart

value: Heart

value: VGC-TERM

value: 3 months


title: Thymus, FL, VGC, LAR, Mouse 3

description: Library name: 249_Thymus_FL-LAR-3_L1_1

value: Thymus

value: VGC-LAR

value: female

value: BALB/cAnNTac


title: E11.5, rep2

description: Library name: 11_1190D


title: hFLO, CD45+ CD16+ CD66b+, day 30, line 72_3

description: hFLO_Granulo_45Pos16Pos66bPos, PA

value: wildtype

value: Palmitic Acid


title: Liver, FL, TERM, Mouse 11

description: Library name: 242_Liver_FL-_ISS_Term-_11_L1_1

source_name: Liver

value: Liver

value: FL-TERM


title: E10.5, rep3

description: Library name: 9_1134C

source_name: Pancreas, E10.5

value: Pancreas, E10.5


title: hFLO, CD45+ CD14+ CD16+, day 30, line 1383D6, MonoMac, biol rep 2

value: hFLO-Monocytes and -Macrophages

value: No treatment

value: Day 30


title: hFLO, CD45- EPCAM+, day 30, line 72_3 PA

value: hFLO-fetal hepatocytes


title: hFLO, CD45+ CD14+ CD16+, day 30, line 72_3


title: Sperm total RNA, Duroc boar 5, 10 months, mature

city: Hamar

first: Asmita

last: Shrestha

state: Innlandet

address: Holsetgata 22

department: Department of Biotechnology

country: Norway

institute: University of Inland Norway

description: Library name: B14_10mo_RNA

data_processing:
Quality control: FastQC v0.12.1.
Adapter trimming: Trim Galore v0.6.10 with parameters --quality 20 --stringency 3 --length 35 --paired (for RNA-seq) or single-end mode (miRNA-seq), --trim-n option enabled.
Total RNA-seq alignment: HISAT2 v2.2.1 alignment to Sus scrofa genome, SAM to BAM conversion using SAMtools v1.16.1.
Gene quantification: featureCounts (Subread v2.0.4) with parameters -p (paired-end), -t exon, -g gene_id, -s 2 (reverse stranded).
miRNA-seq processing: sRNAbench from sRNAtoolbox suite v1.0 with default parameters, annotation against miRBase v21 for Sus scrofa small non-coding RNAs.
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-delimited text files with gene/miRNA identifiers in first column and sample expression counts in subsequent columns. Column headers correspond to library names from SAMPLES section. RNA-seq file contains Ensembl gene IDs and raw counts from featureCounts. miRNA-seq file contains miRNA IDs from miRBase and raw counts from sRNAbench.

organism: Sus scrofa

source_name: spermatozoa

extract_protocol:
Fresh semen containing 200 million sperm/ml was centrifuged at 600×g for 10 min at RT. Sperm pellets were washed with PBS and subjected to somatic cell lysis using 1 mL somatic cell lysis buffer (0.1% SDS, 0.5% Triton X-100) for 30 min on ice, then washed at 200×g for 15 min at 4°C. Sperm were washed twice with PBS (600×g, 10 min, 4°C) and snap-frozen. RNA extraction: sperm lysed with 1 mL Qiazol and 120 µL TCEP, vortexed 5 min, incubated at 56°C for 60 min. RNA isolated using miRNeasy Mini Kit (Qiagen) with on-column DNase digestion, eluted in 40 µL RNase-free water.
Total RNA-seq: Using 4 µL RNA (8.8-61.2 ng), rRNA depletion performed with QiaSeq FastSelect HMR reagents following manufacturer's protocol for partially degraded RNA (RIN 2-6). Libraries prepared with NEBNext Ultra II Directional Library Prep Kit from step 4.2, adapters diluted 1:25, 16 PCR cycles amplification. miRNA-seq: Libraries prepared using QiaSeq miRNA library kit with 5.5-38.3 ng RNA input, adapters diluted per manufacturer recommendations, 18 PCR cycles amplification. All samples indexed with unique adapters.
miRNA-seq: Libraries prepared using QiaSeq miRNA library kit (Qiagen) with 5.5-38.3 ng total RNA input. Adapters diluted according to manufacturer recommendations based on RNA input amount. Libraries amplified with 18 PCR cycles. Samples indexed with unique adapters to enable multiplexing on single sequencing run.

value: spermatozoa

value: sperm

value: Duroc

value: 10 months


title: SI_CD4_5_4

description:
Library name: lib61713
28_4007_SILP-CD4

value: small intestine lamina propria

value: CD4 T cells

value: 200 Heligmosomoides polygyrus bakeri L3 larva; pyrantel pamoate drug clear D14 and D15; harvest 28 days after drug clear


title: Sperm total RNA, Duroc boar 4, 10 months, mature

description: Library name: B13_10mo_RNA


title: Lung, FL, TERM, Mouse 4

description: Library name: 243_Lung_FL-_ISS_Term-_4_L1_1

value: Lung

value: female

value: BALB/cAnNTac

value: 3 months


title: Liver, HGC, LAR, Mouse 13

description: Library name: 241_Liver_HC-LAR-13_L1_1

value: Liver

value: HGC-LAR


title: E10.5, rep2

description: Library name: 8_1134B

value: Pancreas, E10.5

value: Pancreas

value: Pdx1-Cre labelled cells

value: Pdx1-Cre, tdtomato+


title: Sperm total RNA, Duroc boar 3, 10 months, mature, replicate 2

description:
Library name: B11_10mo_RNA_rep2
Technical replicate 1 - BAM files merged after alignment with B11_10mo_RNA_rep1 BAM files before downstream analysis

value: spermatozoa


title: E10.5, rep1

description: Library name: 7_1134A


title: tissu DNA from high-grade colon adenoma 19

type: genomic

city: Besançon

first: Alexis

last: Overs

address: 16 route de Gray

country: France

institute: University of Franche-Comte

description: genomic DNA from colon high-grade adenoma

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and stadard recommended Illumina scanner setting

data_processing:
minfi package (v1.52.1) in R environnement (v4.4.2)
Average Beta

label: Cy3 and Cy5

source_name: colon adenoma

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from FFPE samples using the QIAmp DNA Mini Kit according to the manufacturer’s instructions

value: colon adenoma

value: Male

tag: laterality

value: Left

tag: disease state

value: high-grade colon adenoma


title: tissu DNA from high-grade colon adenoma 18

tag: tissue

value: Right