title: lefko1 0 min rep2

description: Library name: G2


title: Col-0 72 h rep2

status: Public on Dec 14 2025

type: SRA

city: Athens

first: Anastasios

last: Alatzas

address: IERA ODOS 75

country: Greece

institute: Agricultural University of Athens

description: Library name: F2

library_source: transcriptomic

data_processing:
Raw sequencing data were filtered using SOAPnuke software (version 1.5.6)
The clean reads were mapped onto the Arabidopsis reference genome (TAIR10) by means of HISAT2 software (version 2.2.1)
Clean reads were aligned to the reference gene set using Bowtie2 (version 2.4.5)
Gene expression level was calculated with RSEM (version 1.3.1)
DEGs were identified with DESeq2 (version 1.34.0)
Alternative splicing and differential alternative splicing were detected by using rMAT (version 3.2.5)
Assembly: Arabidopsis_thaliana_3702.arabidopsis.TAIR10.v2201
Supplementary files format and content: .txt files include the FPKM values of the samples

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were germonated in MS medium in the dark for 5 days

extract_protocol:
Total RNA was extracted by using the phenol-sodium dodecyl sulfate (SDS) extraction method and treated with DNase
The cDNA libraries were constructed and sequenced in DNBSEQ platform (BGI, Hong Kong)

treatment_protocol: The dark-grown seedlings were transfered to light and sampling was performed at 10min, 60min, 3h, 24h and 72h

tag: tissue

value: seedlings

tag: genotype

tag: treatment

value: light 72 h


title: Col-0 72 h rep3

description: Library name: F3


title: lefko1 10 min rep1

description: Library name: H1

value: light 10 min


title: Col-0 72 h rep1

description: Library name: F1


title: Col-0 24 h rep3

description: Library name: E3

value: light 24 h


title: lefko1 60 min rep1

description: Library name: I1

value: light 60 min


title: Col-0 24 h rep2

description: Library name: E2


title: Col-0 3 h rep3

description: Library name: D3

value: light 3 h


title: Col-0 60 min rep2

description: Library name: C2


title: Col-0 3 h rep2

description: Library name: D2


title: Col-0 24 h rep1

description: Library name: E1


title: Col-0 60 min rep3

description: Library name: C3


title: Col-0 10 min rep3

description: Library name: B3


title: lefko1 24 h rep2

description: Library name: K2


title: Col-0 3 h rep1

description: Library name: D1


title: Col-0 60 min rep1

description: Library name: C1


title: Variable glycaemic condition, biological replicate 1

city: Brisbane

first: Yuanzhao

last: Cao

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: The University Of Queensland

data_processing:
RNA-seq samples with 3 biological replicates for each group were aligned to hg38 using STAR aligner (Dobin et al., 2013) with the default option, yielding more than 294M uniquely mapped reads in total with an average of 92.84% mapping rate. Gene-level read counts were quantified using htseq-count (Anders et al., 2015) using the NCBI hg38 RefSeq gene annotation.
Assembly: NCBI hg38 RefSeq
Supplementary files format and content: Raw counts for each sample

organism: Homo sapiens

source_name: hiPSC WTC11

extract_protocol:
RNA was extracted using RNeasy Mini Kit with on-column DNase digestion using the RNase-Free DNase Set
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Prep Kit following manufacturer's protocol

tag: cell line

value: hiPSC WTC11

tag: cell type

value: HiPSC-derived cardiomyocytes

value: WT

value: DMEM no glucose plus fatty acid media + variable glucose +endothelin -1 + Cortisol


title: Variable glycaemic condition, biological replicate 3


title: Variable glycaemic condition, biological replicate 2


title: Col-0 10 min rep1

description: Library name: B1


title: Col-0 10 min rep2

description: Library name: B2


title: lefko1 0 min rep1

description: Library name: G1

value: dark


title: Constant glycaemic condition, biological replicate 1

value: DMEM no glucose plus fatty acid media + constant glucose +endothelin -1 + Cortisol


title: Col-0 0 min rep1

description: Library name: A1


title: Col-0 0 min rep3

description: Library name: A3


title: Constant glycaemic condition, biological replicate 3


title: shPAP2_1

city: Guangzhou

first: Siyao

last: Guo

address: No.58 Zhongshan Er Road

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

description: RNA-seq project2_fpkm.txt

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads with low-quality base (base quality less than or equal to 15) ratio  more than 20%; (3) Removing reads with unknown base ratio more than 5%.
Bowtie2 was applied to align the clean reads to the gene set.
Expression level of gene was calculated by RSEM.
Differential expression analysis was performed using the DESeq2.
Assembly: GRCh38
Supplementary files format and content: Count value of genes calculated by RSEM.

molecule: polyA RNA

source_name: Leukemia

extract_protocol:
RNA was extracted according to TRIzol protocol.
The RNA-seq library was prepared by fragmenting the RNAs, synthesizing cDNA fragments, repairing double-stranded cDNA ends, and ligating adaptors. The final library was obtained through PCR amplification. RNA libraries were prepared for sequencing according to standard BGISeq-500 library construction protocol.

value: Leukemia


title: shPAP2_2

description: RNA-seq project2_fpkm.txt


title: Constant glycaemic condition, biological replicate 2


title: shPAP1_2

description: RNA-seq project2_fpkm.txt


title: Maturation medium condition, biological replicate 1

value: DMEM no glucose plus fatty acid media


title: Maturation medium condition, biological replicate 2


title: NC_2

description: RNA-seq project2_fpkm.txt


title: 20 RNA

status: Public on Dec 15 2025

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

country: USA

institute: University of Illinois at Chicago

description: Library name: 20 RNA

library_source: transcriptomic single cell

data_processing:
Raw reads were demultiplexed and single-nucleus gene expression and peak enrichment were quantified simultaneously using CellRanger-arc count (10X Genomics). Single cells were filtered to ensure data used in the downstream analysis is high quality: cells with >10% mitochondrial expression, indicative of dead or dying cells; cells with low numbers of genes expressed (<1000 genes) or low total UMI RNA counts (<2000 UMI counts); and cells with low peak numbers (<200 peaks) or total ATAC counts (<500 counts) were removed. Clustering was performed on the RNA-seq data, anticipating that gene expression would have a higher dynamic range than open chromatin, using the Seurat package in R. Single - droplet multiplets were detected using the union of two independent methods: Scrublet (https://doi.org/10.1016/j.cels.2018.11.005) and DoubletDetection (http://doi.org/10.5281/zenodo.2678041). Following determination of cell types, we re-called peaks separately for each cell type using Seurat, merging peaks across all cell types to obtain a more complete measurement of the open chromatin peaks for rarer cell types.
Assembly: hg38
Supplementary files format and content: Aggregated_atac_fragments.tsv.gz: gzipped tab-separated text file, ATAC-seq fragment alignments
Supplementary files format and content: barcodes.tsv.gz: gzipped tab-separated text file, barcodes for combined multi-sample and multi-omics matrix.
Supplementary files format and content: features.tsv.gz: gzipped tab-separated text file, feature names for combined multi-sample and multi-omics matrix.
Supplementary files format and content: matrix.mtx.gz: gzipped tab-separated text file, Matrix Market format, expression matrix for combined multi-sample and multi-omics matrix.
Supplementary files format and content: recall_peaks.bed: peak coordinates of re-analyzed peak calls
Supplementary files format and content: sample_numbering_manifest.txt: manifest matching cell barcode suffixes in Aggregated_atac_fragments.tsv.gz and barcodes.tsv.gz to sample IDs
Supplementary files format and content: seurat_object.rds: Seurat object with analyzed data

source_name: Dentate gyrus

extract_protocol:
The dentate gyrus was isolated from Fresh Frozen blocks of 36 participants representing 5 diagnostic groups (YA, NCI, MCI, AD and SA). Tissue was then immediately moved to homogenization; For each sample, a separate homogenizer and douncing pestles (loose and tight) were used. Each sample was homogenized in 1ml pre-chilled lysis buffer (0.1% NP-40 Alternative (or NP-40), 10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, 40U/mL of RNAse inhibitor) by mechanical douncing for 20 times with the loose pestle followed by 20 times with the tight pestle to obtain a single cell suspension. Cell suspensions were then incubated on ice for 5 minutes. The homogenate was then filtered through 70 µm filters (Milentyi Biotec 130-041-407) and 40 µm filters (Milentyi Biotec 130-041-406), moved to 1.5 ml tubes and centrifuged at 4C for 5 minutes at 500 RCF.   Supernatants were removed and the nuclei pellet was washed 3 times with wash buffer (10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2), 0.01% BSA, 40U/mL of RNAse inhibitor). After the last wash, supernatants were removed, and the nuclei pellet was resuspended in resuspension buffer and mixed with 900 µl of Sucrose Cushion buffer. To remove the additional debris, resuspended nuclei were then loaded above a 3 Sucrose Cushion gradient (2.7 ml Nuclei PURE 2M Sucrose Cushion Solution with 300 μl Nuclei PURE Sucrose Cushion Buffer) and the sucrose gradient containing the nuclei was Centrifuged at 13,000 rcf for 45 min at 4°C. The supernatant was then carefully removed and the samples were immediately processed following the Single Cell protocol from 10x Genomics.
The 10X Genomics Multiome library preparation and sequencing was done at Northwestern University NUseq facility core with the support of NIH Grant (1S10OD025120). Nuclei number was analyzed using Nexcelom Cellometer Auto2000 with AOPI fluorescent staining method. The nuclei were first undergone transposition with ATAC enzyme for one hour at 37°C.  we loaded 16,000 transposed nuclei into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM Chip J (10X Genomics, PN-1000230), and according to the manufacturer’s protocol, single cell gel beads were generated in the emulsion (GEM). Barcoded DNA and cDNA were PCR amplified and subjected to library construction. The single nuclei ATAC-seq library was generated using the Chromium Next GEM Single Cell Multiome ATAC + Gene expression kit (10X Genomics, PN-1000281) and single Index Kit N Set A (10X Genomics, PN-1000212) according to the manufacturer’s manual. In addition, the amplified cDNA was used for the gene expression library using dual Index Kit TT Set A (10X Genomics, PN-1000215). Quality control for the constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) and Qubit DNA HS assay kit for qualitative and quantitative analysis, respectively. For the snATAC-seq library, the multiplexed libraries were pooled and sequenced on Illumina Novaseq sequencer with 100 cycles kits using the following read length: 50 bp Read1 and 49 bp Read2. For the snRNA-seq library, the libraries were sequenced on Illumina Novaseq sequencer with 100 cycles kits using the following read length: 28 bp Read 1 for cell barcode and UMI and 90 bp Read 2 for transcript expression. The targeted sequencing depth for snATAC-seq and snRNA-seq is 25,000 and 20,000 reads per cell, respectively.

value: Dentate gyrus

tag: diagnosis

value: SA

tag: age at_death

tag: pmi


title: RF DDLS8817 (-)CR31B-3

city: New York

first: Prathibha

last: Mohan

state: NY

address: 1275 York Avenue

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

description:
Ribofootprint
sarcoma_count_tab_RNA_run1_rm0row.txt
sarcoma_ribodiff_run1.genename.txt

data_processing:
library strategy: ribosome footprinting
Sequence Alignment:
The human genome sequence GRCh37 was downloaded from Ensembl public database: http:// www.ensembl.org. Ribosome footprint (RF) reads were aligned to reference genome GRCh37 using STAR26. STAR clips the linker sequence (5’- CTGTAGGCACCATCAAT-3’), which is technically introduced during RF library construction, and trims the remaining sequence from the 3’ end while aligning the reads to reference sequence. Briefly, we set the parameters for PALMapper as follows: maximum number of mismatches: 2; minimum aligning length: 15; maximum intron length (splice alignment): 10000. We only use the uniquely aligned reads for further analysis. To remove ribosomal RNA, the footprint reads were also aligned to a ribosome sequence database using STAR with the same parameters except not allowing splice alignment. We retrieved the human ribosome sequences from SILVA30 databases. The FASTA file was used as reference sequence to align against. The rRNA-aligned reads were filtered out from GRCh37-aligned reads.After removing the ribosomal RNA, we still observed a portion of reads that were dominated by linker sequence and Illumina P7 adapter. These reads can also be trimmed during mapping and cause false alignment. Therefore, we searched a string of 1~8 nt from linker sequence around the trimming site (±2 bp) allowing 1 nt mismatch. We removed the read if there was no such linker sequence. Finally, we filtered out reads ≤ 24-bp and ≥ 36-bp, and the remaining reads with aligned length from 25- to 35-bp were used to analyse the translational effects of CR31B.Total mRNA sequencing reads were aligned to the GRCh37 reference using STAR31. We performed the splice alignment and only use the uniquely aligned reads with maximum 3 mismatches. rRNA contaminating reads were also filtered out using the same strategy described before.
Footprint Profile Analysis using Ribodiff:
For each gene, we only counted the number of aligned reads that were mapped within exonic regions. The genome annotation was downloaded from Ensembl database. We used our recently developed tool Ribodiff to analyze the ribosome footprinting data. Ribodiff uses a negative binomial based generalized linear model to detect the significant difference of footprint read counts in two conditions, taking the RNA-Seq transcriptional measurements as the confounding factor. Therefore it is capable of identifying the genes having translational control that is independent of the transcriptional regulation. The statistical test is a chi-squared test on the deviances of the H0 and H1 model fitting. Benjamini–Hochberg procedure was used to obtain the false discovery rate. The ribosomal distribution curves for a single gene were plotted in a similar way but without normalizing the read coverage, and the coverage was smoothed using ‘moving average’ smoothing algorithm.
Motif analysis:
The transcripts of each gene were quantified based on the total mRNA-seq data using MISO26,32. The 5’UTR of most abundant transcript was collected for predicting motifs. Both the significant genes with increased or decreased TE and altered ribosomal distribution and the corresponding background gene sets were predicted by DREME26. We considered the predicted consensus sequences with P < 1×10-4 as significant motifs. Motif occurrences were called using FIMO26 with default parameters for strand specific prediction in human and other species using gene orthologs.
Assembly: GRCh37

source_name: DDLS 8817

growth_protocol: DDLS8817 cell lines were cultured in DMEM media supplemented with 10% fetal bovine serum and 10nM Penicillin/Streptomycin and 10mM Glutamine or as per the ATCC recommended medium.

extract_protocol: DDLS8817cells were treated with DMSO or (-)CR31B (10nM -  2hr) followed by cycloheximide treatment for 10 minutes. Total RNA and ribosome-protected fragments were isolated following published protocol (Ingolia et al 2012). Deep sequencing libraries were generated from these fragments and sequenced on the HiSeq 2000 platform. Genome annotation was from the Ensembl database release 75 (http:// www.ensembl.org).

treatment_protocol: Cells wre treated with DMSO (CT) or DOX (2mg/ml for 12 hr).

value: DDLS 8817

value: Dedifferentiated lipsarcoma


title: Col-0 0 min rep2

description: Library name: A2

value: seedlings


title: RF DDLS8817 (-)CR31B-2


title: NC_1

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads with low-quality base (base quality less than or equal to 15) ratio  more than 20%; (3) Removing reads with unknown base ratio more than 5%.
Bowtie2 was applied to align the clean reads to the gene set.
Expression level of gene was calculated by RSEM.
Differential expression analysis was performed using the DESeq2.
Assembly: GRCh38
Supplementary files format and content: FPKM value of genes calculated by RSEM.

value: control


title: RF DDLS8817 (-)CR31B-1


title: shPAP1_1

value: PAPOLA knockdown


title: RF DDLS8817 DMSO-2

value: DMSO


title: Total DDLS8817 (-)CR31B-3

description:
sarcoma_count_tab_RNA_run1_rm0row.txt
sarcoma_ribodiff_run1.genename.txt

data_processing:
Sequence Alignment:
The human genome sequence GRCh37 was downloaded from Ensembl public database: http:// www.ensembl.org. Ribosome footprint (RF) reads were aligned to reference genome GRCh37 using STAR26. STAR clips the linker sequence (5’- CTGTAGGCACCATCAAT-3’), which is technically introduced during RF library construction, and trims the remaining sequence from the 3’ end while aligning the reads to reference sequence. Briefly, we set the parameters for PALMapper as follows: maximum number of mismatches: 2; minimum aligning length: 15; maximum intron length (splice alignment): 10000. We only use the uniquely aligned reads for further analysis. To remove ribosomal RNA, the footprint reads were also aligned to a ribosome sequence database using STAR with the same parameters except not allowing splice alignment. We retrieved the human ribosome sequences from SILVA30 databases. The FASTA file was used as reference sequence to align against. The rRNA-aligned reads were filtered out from GRCh37-aligned reads.After removing the ribosomal RNA, we still observed a portion of reads that were dominated by linker sequence and Illumina P7 adapter. These reads can also be trimmed during mapping and cause false alignment. Therefore, we searched a string of 1~8 nt from linker sequence around the trimming site (±2 bp) allowing 1 nt mismatch. We removed the read if there was no such linker sequence. Finally, we filtered out reads ≤ 24-bp and ≥ 36-bp, and the remaining reads with aligned length from 25- to 35-bp were used to analyse the translational effects of CR31B.Total mRNA sequencing reads were aligned to the GRCh37 reference using STAR31. We performed the splice alignment and only use the uniquely aligned reads with maximum 3 mismatches. rRNA contaminating reads were also filtered out using the same strategy described before.
Footprint Profile Analysis using Ribodiff:
For each gene, we only counted the number of aligned reads that were mapped within exonic regions. The genome annotation was downloaded from Ensembl database. We used our recently developed tool Ribodiff to analyze the ribosome footprinting data. Ribodiff uses a negative binomial based generalized linear model to detect the significant difference of footprint read counts in two conditions, taking the RNA-Seq transcriptional measurements as the confounding factor. Therefore it is capable of identifying the genes having translational control that is independent of the transcriptional regulation. The statistical test is a chi-squared test on the deviances of the H0 and H1 model fitting. Benjamini–Hochberg procedure was used to obtain the false discovery rate. The ribosomal distribution curves for a single gene were plotted in a similar way but without normalizing the read coverage, and the coverage was smoothed using ‘moving average’ smoothing algorithm.
Motif analysis:
The transcripts of each gene were quantified based on the total mRNA-seq data using MISO26,32. The 5’UTR of most abundant transcript was collected for predicting motifs. Both the significant genes with increased or decreased TE and altered ribosomal distribution and the corresponding background gene sets were predicted by DREME26. We considered the predicted consensus sequences with P < 1×10-4 as significant motifs. Motif occurrences were called using FIMO26 with default parameters for strand specific prediction in human and other species using gene orthologs.
Assembly: GRCh37


title: peritoneal immune cells, KO

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

description:
Library name: KO
10x Genomics

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.3.0) was used for generation of Seurat object.
The count matrix was normalized with NormalizeData function.
tSNE and UMAP were performed by R package Seurat (version 4.3.0).
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: peritoneal immune cells

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

treatment_protocol: For the S-100 induced chronic AIH model, mouse livers were perfused with pre-cold PBS and homogenized using a TissueLyser (QIAGEN). Homogenates were centrifuged at 100,000×g for 1 hour at 4°C, and the resulting supernatants (S-100) were emulsified with an equal volume of complete Freund’s adjuvant (CFA; Sigma-Aldrich, Cat# F5881).Alb-WT Bicd2fl/fl and Alb-Cre Bicd2fl/fl mice were immunized with 2.5 mg S-100 weekly via intraperitoneal injection for 3 consecutive weeks. To obtain hepatic immune cells, liver tissues were minced and grinded in pre-cold FACS buffer (PBS containing 1% FBS), followed by filtration through a 70 μm cell strainer. Lymphocytes were isolated through 40/70% Percoll (Cytiva, Cat# 17089109) by gradient centrifuging 800 × g for 20 min. Cells located at the inter-layer were collected.

value: peritoneal immune cells

value: KO

value: HFD


title: Total DDLS8817 (-)CR31B-1


title: Maturation medium condition, biological replicate 3

value: hiPSC WTC11

value: HiPSC-derived cardiomyocytes

value: WT


title: RF DDLS8817 DMSO-3


title: peritoneal immune cells, WT

description:
Library name: WT
10x Genomics


title: Human keratinocyte SOCS6 overexpression control 3

city: Changsha

first: Zeng

last: Jinrong

address: No.138 Tongzipo Rd, Yuelu District, Changsha, Hunan, China, 410013

institute: the Third Xiangya Hospital, Central South University

description: Library name: OE_C_3

data_processing:
Raw reads were quality-controlled with fastp (v0.20.0), then aligned to the Homo sapiens reference genome (GRCh38) using HISAT2 (v2.2.1). Gene-level expression was quantified via featureCounts (v2.0.1) based on annotated genomic intervals, and transcript-level expression was estimated using StringTie (v2.1.6).
Assembly: GRCh38
Supplementary files format and content: CSV files include raw counts for each sample

source_name: skin

extract_protocol:
Healthy foreskin tissue from circumcision (donors with no history of atopic dermatitis [AD] or inflammatory skin diseases) was used to isolate human primary keratinocytes (KCs). The tissues were preserved at 4℃ and transported to the laboratory on ice within 6 hours. After washing, the subcutaneous tissue was removed and the remaining tissue was cut into small pieces. The tissue pieces were digested with neutral protease at 4℃ overnight, followed by trypsin digestion with shaking at 37℃ for 7 minutes. Digestion was terminated with serum, and the cell suspension was filtered and centrifuged. Complete medium was prepared, and the cells were resuspended, seeded, and cultured at 37℃. Subsequent RNA extraction and sequencing were performed on KCs with SOCS6 knockdown or overexpression.
RNA-seq

value: skin

value: keratinocyte cells

value: SOCS6 overexpression control


title: Human keratinocyte SOCS6 overexpression control 2

description: Library name: OE_C_2


title: Human keratinocyte SOCS6 overexpression control 1

description: Library name: OE_C_1


title: Total DDLS8817 DMSO-2


title: RF DDLS8817 DMSO-1


title: Total DDLS8817 DMSO-3


title: Alb-WT Bicd2fl/fl, rep2

description:
Library name: WT2
10x Genomics

data_processing:
Illumina Casava2.19 software used for basecalling.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm39
Supplementary files format and content: FPKM

source_name: liver

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen) and reverse transcribed into cDNA with GoScriptTM Reverse Transcription System (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

treatment_protocol: For the S-100 induced chronic AIH model, mouse livers were perfused with pre-cold PBS and homogenized using a TissueLyser (QIAGEN). Homogenates were centrifuged at 100,000×g for 1 hour at 4°C, and the resulting supernatants (S-100) were emulsified with an equal volume of complete Freund’s adjuvant (CFA; Sigma-Aldrich, Cat# F5881).Alb-WT Bicd2fl/fl and Alb-Cre Bicd2fl/fl mice were immunized with 2.5 mg S-100 weekly via intraperitoneal injection for 3 consecutive weeks.

value: liver

value: Alb-WT Bicd2fl/fl

value: S-100 induced AIH


title: Alb-WT Bicd2fl/fl, rep4

description:
Library name: WT4
10x Genomics


title: Alb-WT Bicd2fl/fl, rep1

description:
Library name: WT1
10x Genomics


title: Alb-WT Bicd2fl/fl, rep3

description:
Library name: WT3
10x Genomics


title: Total DDLS8817 DMSO-1

value: DDLS 8817

value: Dedifferentiated lipsarcoma


title: Alb-Cre Bicd2fl/fl, rep4

description:
Library name: KO4
10x Genomics

value: Alb-Cre Bicd2fl/fl


title: Human keratinocyte SOCS6 overexpression 2

description: Library name: OE_2

value: SOCS6 overexpression


title: heptoid gland adenoma (HGA), 7 - technical replicate no. 2

city: Berlin

first: Alexander

middle: F. H.

last: Haake

address: Robert-von-Ostertag-Straße 15

department: Department of Veterinary Medicine

country: Germany

institute: Freie Universität Berlin

description: Library name: h28.2

data_processing:
The FASTQ sequencing files were preprocessed (adapter trimmed, filtered) using Cutadapt and aligned to the NCBI Reference Sequence (RefSeq) assembly for the dog (Canis lupus familiaris) UU_Cfam_GSD_1.0 with the STAR aligner. Read counts per gene were generated with two rounds of featureCounts to mitigate the effect of too short 3' UTR annotations. Reads that remained unassigned in the first round were subjected to the second round of featureCounts on an adjusted annotation with a 3' extension by 2 kilobases. Differential gene expression analysis for the comparison apocrine gland anal sac adenocarcinoma (AGASAC) versus hepatoid gland adenoma (HGA) was performed with R using DESeq2. Significance thresholds were drawn at a log2(fold change) of ≤ -1 or ≥ 1 and an adjusted p-value of ≤ 0.05.
https://www.lexogen.com/wp-content/uploads/2019/03/015UG009V0251_QuantSeq_Illumina.pdf
Assembly: UU_Cfam_GSD_1.0 (NCBI RefSeq assembly: GCF_011100685.1)
Supplementary files format and content: tab-delimited text file including raw and normalised counts and differential gene expression data for each sample

organism: Canis lupus familiaris

source_name: archival FFPE tumour tissue

extract_protocol:
Total RNA was extracted utilising the PureLinkTM FFPE Total RNA Isolation Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA). After DNase I treatment 500 - 1000 ng total RNA was used for library construction.
QuantSeq 3' mRNA-Seq FWD Library Preparation Kit (Lexogen GmbH, Vienna, Austria) was used according to the manufacturer's guidelines (user guide 015UG009V0251) using the low-quality RNA protocol.

value: archival FFPE tumour tissue

tag: Sex

value: male

tag: breed

value: Golden Retriever

tag: age (years)


title: Alb-Cre Bicd2fl/fl, rep3

description:
Library name: KO3
10x Genomics


title: heptoid gland adenoma (HGA), 7 - technical replicate no. 1

description: Library name: h28.1


title: Total DDLS8817 (-)CR31B-2


title: Alb-Cre Bicd2fl/fl, rep2

description:
Library name: KO2
10x Genomics


title: Human keratinocyte SOCS6 knockdown control 3

description: Library name: KD_C_3

value: SOCS6 knockdown control


title: heptoid gland adenoma (HGA), 6 - technical replicate no. 3

description: Library name: h24.3

value: female

value: Hunting dog-mix


title: Alb-Cre Bicd2fl/fl, rep1

description:
Library name: KO1
10x Genomics


title: 9NA-Nrf1 Btz 3

type: RNA

city: Tokyo

first: Yukiko

last: Yoshida

address: 2-1-6, Kamikitazawa, Setagaya-ku

department: Department of Basic Medical Sciences

country: Japan

institute: Tokyo Motrolopotan Institute of Medical Science

description: Gene expression after 15 h treated with 20 nM Btz

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit and hybridized with a Human Gene Expression 4x44K v2 Microarray (Agilent Technologies). Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: The slides were scanned  immediately after washing on SureScan Microarray Scanner (Agilent Technologies) using one color scan setting for 4x44k array slides (Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was obtained using the Agilent Feature Extraction software (version 12.1.1.1) with set to default for all parameters.

source_name: NGLY1-KO HeLa cells expressing NRF1 N/A treated with Btz rep3

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: HeLa  cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM:Sigma-Aldrich, Cat# D5796) supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich, Cat# 173012 Lot# 0001658760) and penicillin /streptomycin /glutamine (Gibco, Cat# 10378-016). Cells were cultured at 37˚C in a 5% CO2 incubator.

extract_protocol: RNA was were purified using an RNease Mini Kit (Qiagen).

treatment_protocol: Cells were treated with bortezomib ( Btz, LC laboratories, Cat# B-1408) for 15 h.

value: HeLa cell


title: Human keratinocyte SOCS6 overexpression 3

description: Library name: OE_3

value: skin


title: heptoid gland adenoma (HGA), 1 - technical replicate no. 2

description: Library name: h2.2

tag: condition

value: neutered

value: Boxer-mix


title: Human keratinocyte SOCS6 knockdown control 2

description: Library name: KD_C_2

value: keratinocyte cells


title: heptoid gland adenoma (HGA), 6 - technical replicate no. 1

description: Library name: h24.1


title: Human keratinocyte SOCS6 knockdown 2

description: Library name: KD_2

value: SOCS6 knockdown


title: GC-1 spg cells, Vector_3_QN202402240001-23

first: Rui

last: Hua

state: GuangDong

address: 838 Guangzhou North Avenue

department: Department of Obstetrics and Gynecology

institute: Nanfang Hospital, Southern Medical University

description: Library name: Sample 6

data_processing:
using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Geneabundance was expressed as fragments per kilobase ofexon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: testis

growth_protocol: GC-1 spg cells were maintained in DMEM supplemented with 10% premium fetal bovine serum and 1% penicillin-streptomycin in a humidified atmosphere of 5% CO₂ at 37°C.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Germany). One microgram of total RNA was used as input material for sequencing library construction.
Paired-end libraries were synthesized by using the Stranded mRNA-seq Lib Prep Kit for lllumina (ABclonal, China) following Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 10 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments thengo through an end repair process, the addition ofa single ‘A’base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 3.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).

value: testis

value: GC-1 spg

value: Germ Cell

value: Vector Control

value: Non-obstructive azoospermia


title: GC-1 spg cells, Vector_2_QN202402240001-23

description: Library name: Sample 5


title: heptoid gland adenoma (HGA), 1 - technical replicate no. 1

description: Library name: h2.1

value: archival FFPE tumour tissue


title: GC-1 spg cells, Ov_SNHG1_3_QN202402240001-23

description: Library name: Sample 3

value: SNHG1 Overexpression


title: shPAPOLA2

data_processing:
Raw reads were first filtered for reads that having the characteristic subsequence [A] × 10 + [G] × 9, or the reverse complementary sequence [C] × 9 + [T] × 10, resulting from addition of a GI tail to the poly(A) tail. Reads were oriented such that each read starts with the sequencing adapter sequence, followed by the UMI, the GI tail, the poly(A) tail and the sequence of the cDNA molecule.
Reads were mapped to human hg38 genome using STARLong
Reads were assigned to Ensembl GRCh38 annotation gene models for all samples using FeatureCounts
Assembly: GRCh38
Supplementary files format and content: TPM value of genes calculated by RSEM.
Library strategy: FLAM-Seq

extract_protocol:
RNA was extracted according to TRIzol protocol.
The RNA-seq library was prepared by Poly(A)+ RNA preparation, GI tailing of RNA, cDNA synthesis,  cDNA library amplification and Sequencing library preparation. Libraries were prepared for sequencing according to SMRTbell Template Prep Kit protocol.

value: Leukemia

tag: shRNA


title: Human keratinocyte SOCS6 knockdown 3

description: Library name: KD_3


title: cont Btz 3

source_name: NGLY1-KO HeLa cells treated with Btz rep3


title: 9ND-Nrf1 Btz 2

source_name: NGLY1-KO HeLa cells expressing NRF1 N/D treated with Btz rep2


title: Human keratinocyte SOCS6 knockdown 1

description: Library name: KD_1


title: shPAPOLA1


title: Human keratinocyte SOCS6 overexpression 1

description: Library name: OE_1

value: SOCS6 overexpression


title: 9ND-Nrf1 Btz 3

source_name: NGLY1-KO HeLa cells expressing NRF1 N/D treated with Btz rep3


title: cont Btz 2

source_name: NGLY1-KO HeLa cells treated with Btz rep2


title: shPAPOLA

extract_protocol:
Immunoprecipitated samples were subjected to Proteinase K digestion at 55°C for 1 hour. Total RNAs were extracted from both the input and immunoprecipitated samples by adding 5 volumes of TRIzol reagent, followed by Direct-zol RNA Miniprep (Zymo).
Libraries for high-throughput sequencing were constructed using the TruSeq Stranded v2 mRNA Sample Prep Kit (Illumina) and were quantified by a BioAnalyzer High Sensitivity DNA chip.

value: shPAPOLA


title: GC-1 spg cells, Ov_SNHG1_2_QN202402240001-23

description: Library name: Sample 2


title: 9NA-Nrf1 Btz 2

source_name: NGLY1-KO HeLa cells expressing NRF1 N/A treated with Btz rep2


title: shNS

value: shNS


title: cont Btz 1

source_name: NGLY1-KO HeLa cells treated with Btz rep1

value: HeLa cell


title: OP, replicate 1, Visium CytAssist

city: Nanjing

first: Ying

last: Tang

address: Dingjiaqiao 87

institute: southeast university

description: 10x Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv: list of spatial barcodes
Supplementary files format and content: features.tsv: list of gene IDs
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format
Library strategy: Visium CytAssist Spatial

source_name: lung tissue of OP patient

extract_protocol:
The histology workflow utilized the Visium CytAssist Spatial Gene Expression for FFPE. Cryosections, cut at a thickness of 5 μm, were mounted onto testing chips.
Visium spatial gene expression analysis was conducted using the Visium CytAssist Spatial Gene Expression for FFPE kits (10x Genomics, PN-1000520). The tissue slices underwent crosslinking treatment followed by probe hybridization and probe connection on the crosslinked sections. After connecting the probes, RNA from the tissue section was enzymatically digested using RNase with tissue removal enzyme (10x Genomics, PN-3000387) to release the probes from the cells. These released probes, which were captured by the capture sequences on the Visium CytAssist Spatial Gene Expression slide using the Visium CytAssist instrument, were then extended and eluted. Subsequently, the eluted probes were transferred to new tubes for further use.

value: lung tissue of OP patient

value: OP tissue

value: H&E stained lung tissue

value: healthy

value: H&E stained


title: Human keratinocyte SOCS6 knockdown control 1

description: Library name: KD_C_1

value: skin

value: keratinocyte cells

value: SOCS6 knockdown control


title: 9ND-Nrf1 Btz 1

source_name: NGLY1-KO HeLa cells expressing NRF1 N/D treated with Btz rep1


title: GC-1 spg cells, Vector_1_QN202402240001-23

description: Library name: Sample 4

value: testis

value: GC-1 spg

value: Germ Cell

value: Vector Control


title: shNS

source_name: Leukemia

value: Leukemia


title: KO2

description: Library name: Sample 5

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Assembly: GRCh38
Supplementary files format and content: Read count for each Sample

source_name: bone marrow

extract_protocol:
RNA was extracted according to TRIzol protocol.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

value: bone marrow

value: PAPOLA KO


title: KO3

description: Library name: Sample 6


title: MCF7 ColTracks N4

city: Orsay

first: Kevin

last: MOREAU

address: Rue Henri Becquerel – CS 90030

country: France

institute: CNRS

description:
Library name: Sample6
D1570T38

data_processing:
Trim-galore 0,6,7 with cutadapt 4,1 were used for trimming, then FastQC v0,11,9 was used to assess the quality.
Reads were aligned with STAR 2,7,6a on hg38 (gencode v34)
Raw counts were used as input in DESeq2 to identify differentially expressed genes between MCF-7 cells grown in presence or not of collagen-tracks. Results were filtered based on p-value < 0.05 and a Log2FC> |1.5| for further analysis such as Gene Ontology and STRING interactome pathway analyses. Everything was done under R environment (4,2,1)
Assembly: HG38
Supplementary files format and content: Raw counts for each sample in a tab delimited table.

growth_protocol: MCF7 cells were cultivated on DMEM high glucose glutamax, 10% fetal bovine serum at 37° and 5% CO2 in humidified atmosphere

extract_protocol:
mRNAs were extracted from cultured cells using the Nucleospin RNA kit (Macherey Nagel) according to the manufacturer’s instructions. RNA quality control was perfomed by Bioanalyser
Stranded mRNA prep Ligation-Illumina on Total RNA

treatment_protocol: MCF7 cells were seeded on a collagen matrix (0,5mg/ml in DPBS, 4h polimerization 37°) or on collagen-matrix decorated collagen-tracks during 72h

value: epithelial cells

value: WT

value: WT on collagen+ collagen-Tracks


title: Immune cells, LCMV-treated, 7 days post injection

city: Seoul

first: Hyungseok

last: Seo

address: Gwannak-ro 1

department: Pharmacy

country: South Korea

institute: Seoul National University

description:
Library name: LCMV 7dpi
10X Genomics

data_processing:
The Cell Ranger v8.0.1 (10X Genomics) pipeline was used to process demultiplexing, alignment and gene counting from scRNA-seq data. FASTQ files were generated using ‘cellranger mkfastq’ command and aligned to the mouse reference genome (mm10).
Assembly: Mouse mm10
Supplementary files format and content: Cell ranger count matrix for filtered single cells in each sample

source_name: Whole Brain

extract_protocol:
Mice were anesthetized with isoflurane and underwent cardiovascular perfusion with PBS, followed by isolation of the brain. The brain was homogenized by mechanical force on 100-μm strainer. The suspension was pelleted by centrifugation at 300 x g for 5 min and resuspended in digestion buffer [1.5mg/ml Collagenase D, 10U/ml DNase I in RPMI], subsequently transferred to a gentleMACS C tube. Enzymatic digestion was performed under stirring at 160 rpm, 37 °C for 30 min. Cells were resuspended in 5ml of 30% Percoll diluted in RPMI and 2ml of PBS was carefully added on top of the layer. Immune cells were purified by density gradient centrifugation at 500 x g (with lowest acceleration and low brake) for 20 min at 18 °C. After the myelin layer and the supernatant were removed, pelleted immune cells were washed and resuspended in DPBS.
Libraries were prepared using the Chromium Next GEM Single Cell 5’ Kit v2 (dual index) (10X Genomics) following manufacturer’s instructions.

treatment_protocol: LPS 2mg/kg or LCMV 2x105 PFU, i.p. injection

value: Whole Brain

value: Immune cells

tag: host strain

tag: age

value: 6-8 weeks old

value: male

value: LCMV (2x105 PFU)


title: Immune cells, LCMV-treated, 30 days post injection

description:
Library name: LCMV 30dpi
10X Genomics


title: Normal human keratinocytes_rep2

description: IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.

hyb_protocol: Cy3 and Cy5 labeled cRNAs were  combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Hierarchical clustering heatmap analysis was performed for differentially m6A-methylated RNAs. Differentially m6A-methylated mRNAs were analyzed for GO and pathway enrichment.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and/or Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.

source_name: IP RNA

label_protocol: Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated "IP" fraction contained enriched m6A methylated RNAs, and the supernatant " Sup" fraction contained unmodified RNAs."IP" and "Sup" RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: Collected samples are maintained in liquid nitrogen

extract_protocol: Total RNA extracted using Trizol reagent.The purity and amount of total RNA samples

value: Normal human keratinocytes

value: Female

source_name: SUP RNA


title: 9NA-Nrf1 Btz 1

source_name: NGLY1-KO HeLa cells expressing NRF1 N/A treated with Btz rep1

value: HeLa cell


title: Normal human keratinocytes_rep1


title: MCF7 ColTracks N2

description:
Library name: Sample4
D1570T37


title: GC-1 spg cells, Ov_SNHG1_1_QN202402240001-23

description: Library name: Sample 1

value: testis

value: GC-1 spg

value: SNHG1 Overexpression

value: Non-obstructive azoospermia


title: Immune cells, RPMI-treated, 7 days post injection

description:
Library name: RPMI
10X Genomics

value: RPMI


title: MCF7 N4

description:
Library name: Sample5
D1570T35

value: WT on collagen


title: MCF7 N2

description:
Library name: Sample3
D1570T34

value: epithelial cells


title: Atopic dermatitis keratinocytes_rep3

value: Atopic dermatitis keratinocytes


title: Con3

description: Library name: Sample 3

value: bone marrow

value: Leukemia

value: PAPOLA flox/flox


title: Atopic dermatitis keratinocytes_rep2


title: Immune cells, PBS-treated, 3 days post injection

description:
Library name: PBS
10X Genomics

value: Whole Brain

value: Immune cells

value: 6-8 weeks old

value: PBS


title: Con2

description: Library name: Sample 2


title: MCF7 ColTracks N1

description:
Library name: Sample2
D1570T36

value: WT

value: WT on collagen+ collagen-Tracks


title: Immune cells, LPS-treated, 30 days post injection

description:
Library name: LPS 30dpi
10X Genomics

value: male

value: LPS (2mg/kg)


title: Normal human keratinocytes_rep3

value: Normal human keratinocytes

value: Male


title: Atopic dermatitis keratinocytes_rep1


title: MCF7 N1

description:
Library name: Sample1
D1570T33


title: AtPPSR1 overepxression, 0 µM Pi, 24 h, root, rep2

status: Public on Dec 13 2025

city: Saskatoon

first: Jieyu

last: Chen

state: SK

address: Collaborative Science Research Building, 112 Science Place

department: Department of Biology

country: Canada

institute: University of Saskatchewan

description: Library name: OE_C0_root_rep2

data_processing:
Raw RNA-Seq reads were processed to remove adaptor and low-quality sequences using Trimmomatic and polyA/T tails using PRINSEQ++.
The processed reads were then aligned to the rRNA database to remove possible contaminating rRNA reads.
The resulting cleaned RNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TAIR10), using HISAT2 (version 2.2.1).
Raw counts for protein-coding genes were calculated based on the alignments and normalized to fragments per kilobase of exon per million mapped fragments (FPKM).
Differentially expressed genes (DEGs) were identified using the DESeq2 R package. Genes with an adjusted P <0.05, identified by DESeq2, were considered as differentially expressed.
Assembly: The resulting cleaned RNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TAIR10), using HISAT2 (version 2.2.1).
Supplementary files format and content: Matrix table files include normalized counts for each sample.

source_name: root

growth_protocol: The autoclaved 0.7% (w/v) agar containing 200 µM Pi, in addition to other nutrient components (1.25 mM KNO3, 0.5 mM MgSO4, 0.5 mM Ca(NO3)2, 10 µM FeEDDHA, 17.5 µM H3BO3, 3.5 µM MnCl2, 0.25 µM ZnSO4, 0.05 µM NaMoO4, 2.5 µM NaCl, and 0.0025 µM CoCl2), was filled into 10-µL pipette tips. Tips were cut before being placed into tip boxes filled with equivalent sufficient-Pi solution, with pH value adjusted to 5.5-5.8. Seeds were surface sterilized and vernalized before sowing equally onto the tips in different treatments. Seedling roots were immersed into the hydroponic solution for seven days; all seedlings were transferred onto floats in magenta boxes containing sufficient-Pi solution (four plants per magenta box) when the rosette reached 50% of the final size. The solution was replenished weekly. All plants were grown in a growth chamber at 22°C under a 16-h light/8-h dark photoperiod at a photon flux density of 150 µmol m−2 s−1.

extract_protocol:
RNA was prepared using TRIZOL method following the manufacturer's recommendations.
Strand-specific RNA sequencing libraries were constructed using poly(A)-enriched RNA. mRNA was captured using oligo(dT) beads and fragmented during elution. First-strand cDNA synthesis was performed using reverse transcriptase and random hexamers with dNTPs. Second-strand cDNA synthesis was carried out using a dUTP nucleotide mix. Following end repair, dA-tailing, and adapter ligation, the dUTP-containing second strand was selectively degraded by uracil DNA glycosylase (UDG), ensuring that only first-strand cDNA was retained for PCR amplification. The final library represents the sense strand of the original RNA transcript.

treatment_protocol: For Pi-stress treatment, the wild-type (ecotype: Col-0), ppsr1 T-DNA knockout, and AtPPSR1 overexpression plants were grown under Pi-sufficient (200 μM Pi) for four weeks and then given a 24-h treatment of either Pi-sufficient or Pi-deficient (0 μM Pi) conditions. Then the roots and mature rosette leaves were harvested, separately, for RNA extraction. A total of three independent biological replicates were performed.

value: root

value: AtPPSR1 overepxression

value: Pi-deficient, 0 µM Pi

tag: time

tag: batch


title: AtPPSR1 overepxression, 0 µM Pi, 24 h, root, rep3

description: Library name: OE_C0_root_rep3

tag: tissue


title: AtPPSR1 overepxression, 0 µM Pi, 24 h, root, rep1

description: Library name: OE_C0_root_rep1

tag: genotype


title: Immune cells, LPS-treated, 3 days post injection

description:
Library name: LPS 3dpi
10X Genomics

tag: treatment


title: AtPPSR1 overepxression, 200 µM Pi, 24 h, root, rep1

description: Library name: OE_C200_root_rep1

value: Pi-sufficient, 200 µM Pi


title: KO1

description: Library name: Sample 4

value: bone marrow

tag: cell line

value: PAPOLA KO


title: AtPPSR1 overepxression, 200 µM Pi, 24 h, root, rep2

description: Library name: OE_C200_root_rep2


title: ppsr1 knockout, 0 µM Pi, 24 h, root, rep3

description: Library name: KO_C0_root_rep3

value: ppsr1 T-DNA knockout


title: ppsr1 knockout, 0 µM Pi, 24 h, root, rep1

description: Library name: KO_C0_root_rep1


title: Col-0, 0 µM Pi, 24 h, root, rep3

description: Library name: WT_C0_root_rep3


title: ppsr1 knockout, 200 µM Pi, 24 h, root, rep1

description: Library name: KO_C200_root_rep1


title: ppsr1 knockout, 0 µM Pi, 24 h, root, rep2

description: Library name: KO_C0_root_rep2


title: ppsr1 knockout, 200 µM Pi, 24 h, root, rep2

description: Library name: KO_C200_root_rep2


title: Col-0, 0 µM Pi, 24 h, root, rep2

description: Library name: WT_C0_root_rep2


title: ppsr1 knockout, 200 µM Pi, 24 h, root, rep3

description: Library name: KO_C200_root_rep3


title: Col-0, 200 µM Pi, 24 h, root, rep1

description: Library name: WT_C200_root_rep1


title: Col-0, 0 µM Pi, 24 h, root, rep1

description: Library name: WT_C0_root_rep1


title: Col-0, 200 µM Pi, 24 h, root, rep3

description: Library name: WT_C200_root_rep3


title: Col-0, 200 µM Pi, 24 h, root, rep2

description: Library name: WT_C200_root_rep2


title: AtPPSR1 overepxression, 0 µM Pi, 24 h, leaf, rep3

description: Library name: OE_C0_leaf_rep3

source_name: leaf

value: leaf


title: AtPPSR1 overepxression, 0 µM Pi, 24 h, leaf, rep1

description: Library name: OE_C0_leaf_rep1


title: AtPPSR1 overepxression, 200 µM Pi, 24 h, leaf, rep3

description: Library name: OE_C200_leaf_rep3


title: AtPPSR1 overepxression, 0 µM Pi, 24 h, leaf, rep2

description: Library name: OE_C0_leaf_rep2


title: ppsr1 knockout, 0 µM Pi, 24 h, leaf, rep1

description: Library name: KO_C0_leaf_rep1


title: AtPPSR1 overepxression, 200 µM Pi, 24 h, leaf, rep2

description: Library name: OE_C200_leaf_rep2


title: ppsr1 knockout, 0 µM Pi, 24 h, leaf, rep2

description: Library name: KO_C0_leaf_rep2


title: ppsr1 knockout, 0 µM Pi, 24 h, leaf, rep3

description: Library name: KO_C0_leaf_rep3


title: AtPPSR1 overepxression, 200 µM Pi, 24 h, root, rep3

description: Library name: OE_C200_root_rep3


title: Con1

description: Library name: Sample 1

tag: cell type

value: Leukemia

value: PAPOLA flox/flox


title: ppsr1 knockout, 200 µM Pi, 24 h, leaf, rep3

description: Library name: KO_C200_leaf_rep3


title: AtPPSR1 overepxression, 200 µM Pi, 24 h, leaf, rep1

description: Library name: OE_C200_leaf_rep1


title: ppsr1 knockout, 200 µM Pi, 24 h, leaf, rep2

description: Library name: KO_C200_leaf_rep2


title: Col-0, 0 µM Pi, 24 h, leaf, rep3

description: Library name: WT_C0_leaf_rep3


title: ppsr1 knockout, 200 µM Pi, 24 h, leaf, rep1

description: Library name: KO_C200_leaf_rep1


title: Col-0, 0 µM Pi, 24 h, leaf, rep2

description: Library name: WT_C0_leaf_rep2


title: Col-0, 0 µM Pi, 24 h, leaf, rep1

description: Library name: WT_C0_leaf_rep1


title: Col-0, 200 µM Pi, 24 h, leaf, rep3

description: Library name: WT_C200_leaf_rep3


title: Col-0, 200 µM Pi, 24 h, leaf, rep1

description: Library name: WT_C200_leaf_rep1


title: Col-0, 200 µM Pi, 24 h, leaf, rep2

description: Library name: WT_C200_leaf_rep2


title: PreFFX+nivolumab, Pt_2P

city: Los Angeles

first: Jason

middle: Michael

last: Link

state: CA

address: 650 Charles E Young Dr S

department: Surgery

institute: University of California, Los Angeles

description: Library name: Pt_2P

data_processing:
The reads were mapped by STAR 2.7.9a and read counts per gene were quantified using the human genome GRCh38. In Partek Flow, read counts were normalized by CPM +1.0E-4
Assembly: GRCh38
Supplementary files format and content: txt file of normalized counts

source_name: Pancreatic Ductal Adenocarcinoma

extract_protocol:
Pre-treatment tumor biopsy or post-treatment tumor resection specimens were formalin fixed and embedded in paraffin. Tissue sections were cut to slides and pathologist-guided, tumor-enriched regions were macroscopically scraped.
Libraries for RNA-Seq were prepared with KAPA stranded RNA HyperPrep Kit with RiboErase (HMR)
Sequencing was performed on Illumina NovaSeq6000 for a PE 2x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software

value: Pancreatic Ductal Adenocarcinoma


title: PostFFX+nivolumab, Pt_22a

description: Library name: Pt_22a

value: FOLFIRINOX+nivolumab


title: PostFFX+nivolumab, Pt_26

description: Library name: Pt_26


title: PostFFX+nivolumab, Pt_27

description: Library name: Pt_27


title: PostFFX+nivolumab, Pt_20

description: Library name: Pt_20


title: PostFFX+nivolumab, Pt_25

description: Library name: Pt_25


title: PreFFX+nivolumab, Pt_12P

description: Library name: Pt_12P


title: PreFFX+nivolumab, Pt_18P

description: Library name: Pt_18P


title: PostFFX+nivolumab, Pt_24

description: Library name: Pt_24


title: PreFFX+nivolumab, Pt_19P

description: Library name: Pt_19P


title: PostFFX+nivolumab, Pt_14

description: Library name: Pt_14


title: PostFFX+nivolumab, Pt_9

description: Library name: Pt_9


title: PostFFX+nivolumab, Pt_19

description: Library name: Pt_19


title: PreFFX+nivolumab, Pt_6P

description: Library name: Pt_6P


title: PostFFX+nivolumab, Pt_10

description: Library name: Pt_10


title: PreFFX+nivolumab, Pt_21P

description: Library name: Pt_21P


title: PostFFX+nivolumab, Pt_21

description: Library name: Pt_21


title: PostFFX+nivolumab, Pt_3

description: Library name: Pt_3


title: PostFFX, Pt_F3

description: Library name: Pt_F3

value: FOLFIRINOX


title: PostFFX, Pt_F2

description: Library name: Pt_F2


title: PostFFX, Pt_F1

description: Library name: Pt_F1


title: PostFFX+nivolumab, Pt_6

description: Library name: Pt_6


title: PostFFX+nivolumab, Pt_13

description: Library name: Pt_13


title: PostFFX+nivolumab, Pt_15

description: Library name: Pt_15


title: PostFFX+nivolumab, Pt_12

description: Library name: Pt_12


title: PostFFX+nivolumab, Pt_11

description: Library name: Pt_11


title: PostFFX+nivolumab, Pt_4

description: Library name: Pt_4


title: PostFFX+nivolumab, Pt_1

description: Library name: Pt_1


title: PostFFX+nivolumab, Pt_16

description: Library name: Pt_16


title: PostFFX, Pt_F6

description: Library name: Pt_F6


title: PostFFX, Pt_F5

description: Library name: Pt_F5


title: PostFFX, Pt_F8

description: Library name: Pt_F8


title: PostFFX, Pt_F4

description: Library name: Pt_F4


title: PostFFX+nivolumab, Pt_18

description: Library name: Pt_18


title: ET11, A549, rep1

city: Urbana

first: Elizabeth

middle: Anne

last: Thayer

address: 407 S Goodwin Ave

department: Microbiology

institute: University of Illinois at Urbana-Champaign

description:
Library name: ET11_A549_1
column name in et01b28_bulkseq_counts.txt: ET11_1

data_processing:
Adaptors were trimmed from the 3'-end of the reads.
The fastq files were generated and demultiplexed using bcl2fastq v2.20 Conversion Software (Illumina)
Reads were aligned using STAR/2.7.6a
Count matrix was made for each gene in each datafile then compiled into one count matrix for the entire experiment.
Assembly: NCBI GRCh38 with Ensembl99
Supplementary files format and content: tab-delimited textfile containing a full raw count matrix for all the samples (columns) and genes (rows)

source_name: cell line

growth_protocol: A549 cells were maintained in DMEM supplemented with 8.3% fetal bovine serum in an incubator at 37℃ with 5%CO2

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN).
The libraries were prepared using Illumina's "TruSeq Stranded mRNAseq Sample Prep kit' per the manufacturer's protocol. The libraries were pooled and sequencined on one S4 lane for 151 cycles from both ends of the fragments on a NovaSeq 6000.

value: cell line

value: human alveolar epithelial cells

tag: clone


title: ET11, A549, rep2

description:
Library name: ET11_A549_2
column name in et01b28_bulkseq_counts.txt: ET11_2


title: ET11, A549, rep3

description:
Library name: ET11_A549_3
column name in et01b28_bulkseq_counts.txt: ET11_3


title: ET9, A549, rep3

description:
Library name: ET9_A549_3
column name in et01b28_bulkseq_counts.txt: ET9_3


title: ET9, A549, rep1

description:
Library name: ET9_A549_1
column name in et01b28_bulkseq_counts.txt: ET9_1


title: ET10, A549, rep2

description:
Library name: ET10_A549_2
column name in et01b28_bulkseq_counts.txt: ET10_2


title: ET10, A549, rep3

description:
Library name: ET10_A549_3
column name in et01b28_bulkseq_counts.txt: ET10_3


title: ET7, A549, rep3

description:
Library name: ET7_A549_3
column name in et01b28_bulkseq_counts.txt: ET7_3


title: ET9, A549, rep2

description:
Library name: ET9_A549_2
column name in et01b28_bulkseq_counts.txt: ET9_2


title: PostFFX, Pt_F7

description: Library name: Pt_F7


title: ET8, A549, rep2

description:
Library name: ET8_A549_2
column name in et01b28_bulkseq_counts.txt: ET8_2


title: ET8, A549, rep3

description:
Library name: ET8_A549_3
column name in et01b28_bulkseq_counts.txt: ET8_3


title: ET6, A549, rep3

description:
Library name: ET6_A549_3
column name in et01b28_bulkseq_counts.txt: ET6_3


title: ET6, A549, rep2

description:
Library name: ET6_A549_2
column name in et01b28_bulkseq_counts.txt: ET6_2


title: ET7, A549, rep2

description:
Library name: ET7_A549_2
column name in et01b28_bulkseq_counts.txt: ET7_2


title: PostFFX+nivolumab, Pt_5

description: Library name: Pt_5


title: ET10, A549, rep1

description:
Library name: ET10_A549_1
column name in et01b28_bulkseq_counts.txt: ET10_1


title: ET5, A549, rep3

description:
Library name: ET5_A549_3
column name in et01b28_bulkseq_counts.txt: ET5_3


title: ET6, A549, rep1

description:
Library name: ET6_A549_1
column name in et01b28_bulkseq_counts.txt: ET6_1


title: ET5, A549, rep1

description:
Library name: ET5_A549_1
column name in et01b28_bulkseq_counts.txt: ET5_1


title: ET4, A549, rep3

description:
Library name: ET4_A549_3
column name in et01b28_bulkseq_counts.txt: ET4_3


title: PostFFX, Pt_F9

description: Library name: Pt_F9


title: ET3, A549, rep3

description:
Library name: ET3_A549_3
column name in et01b28_bulkseq_counts.txt: ET3_3


title: ET3, A549, rep1

description:
Library name: ET3_A549_1
column name in et01b28_bulkseq_counts.txt: ET3_1


title: ET2, A549, rep3

description:
Library name: ET2_A549_3
column name in et01b28_bulkseq_counts.txt: ET2_3


title: ET8, A549, rep1

description:
Library name: ET8_A549_1
column name in et01b28_bulkseq_counts.txt: ET8_1


title: ET1, A549, rep3

description:
Library name: ET1_A549_3
column name in et01b28_bulkseq_counts.txt: ET1_3


title: ET2, A549, rep1

description:
Library name: ET2_A549_1
column name in et01b28_bulkseq_counts.txt: ET2_1


title: ET2, A549, rep2

description:
Library name: ET2_A549_2
column name in et01b28_bulkseq_counts.txt: ET2_2


title: ET1, A549, rep1

description:
Library name: ET1_A549_1
column name in et01b28_bulkseq_counts.txt: ET1_1


title: ET7, A549, rep1

description:
Library name: ET7_A549_1
column name in et01b28_bulkseq_counts.txt: ET7_1


title: Parental (WT), A549, rep2

description:
Library name: WT_A549_2
column name in et01b28_bulkseq_counts.txt: WT_2

value: WT


title: Parental (WT), A549, rep3

description:
Library name: WT_A549_3
column name in et01b28_bulkseq_counts.txt: WT_3


title: Patient_K_OMALIZUMAB_WEEK_24;SR8537

city: Liège

first: Sara

last: Gerday

address: Av. Hippocrate 1/11

country: Belgium

institute: GIGA Research Institute

description:
Library name: Patient_K_OMALIZUMAB_WEEK_24
FEMALE

data_processing:
Quality of bulk RNA-Seq data was assessed with FastQC (v0.11.8).
The FASTQ files were aligned to the reference human genome assembly (GRCh38.p13) with STAR (2.7.0c version). The reference genome sequence and annotation (GTF) files were obtained from ENSEMBL (release 108) to generate genome indexes.
STAR was instructed to output genomic alignments in transcriptomic coordinates (binary alignment files). Binary alignment files (.bam) were then used to produce gene and transcript expression levels with RSEM (v1.3.1).
Assembly: The FASTQ files were aligned to the reference human genome assembly (GRCh38.p13) with STAR (2.7.0c version). The reference genome sequence and annotation (GTF) files were obtained from ENSEMBL (release 108) to generate genome indexes.
Supplementary files format and content: Text file includes gene and transcript expression levels for each sample.

source_name: Whole Blood

extract_protocol:
Blood samples were aliquoted into 1 mL per tube and treated with filtered (0.2μM, Cytiva, Cat. No. 10462205) 10X RBC Lysis Buffer Multi-species (eBioscience, Cat. No. 00-4300-54) for optimal lysis of erythrocytes. White blood cells were collected by centrifugation at 500 x g for five minutes at 4°C. The resulting pellets were re- suspended and homogenized in 1 mL of QIAzol Lysis Reagent (Qiagen, Cat. No. 79306) and stored at − 80°C. On the day of RNA extraction, samples were thawed and allowed to return to room temperature. For every milliliter of QIAzol, 0.2 mL of the phase separation reagent chloroform (Fisher Scientific, Cat. No. 10784143) was added. The samples were then homogenized by vigorously shaking to an emulsion. After an incubation time of two minutes at RT, samples were centrifuged at 10.000 x g for fifteen minutes at 4°C to separate the phases. The upper aqueous phase ( ∼ 500 μL) was transferred to a new microcentrifuge tube. In this tube, 500 μL of isopropanol (Fisher Scientific, Cat. No. 10111733) and 2 μL of GlycoBlue (Fisher Scientific-Invitrogen, Cat. No. 10391565), to increase pellet visibility, were added. After an incubation time of ten minutes at RT, samples were centrifuged at 10.000 x g for fifteen minutes at 4°C. Supernatant was then removed and the pellet was washed with 500 μL of 75% cold ethanol (Sigma-Aldrich, Cat. No. 1085430250) to precipitate the RNA. Samples were again centrifuged at 10.000 x g for one minute at 4°C and each pellet was re-suspended in RNase-free water after air drying. RNase-free conditions were maintained at all times. Total RNA extraction was followed by column-based RNA purification with the RNA Clean & Concentrator-5 kit (Zymo Research, Cat. No. R1013). Before clean- up, the DNase digestion procedure was performed using the DNase I Set. DNase I reaction mix (50 μL) was prepared and incubated at RT for fifteen minutes. Following the purification protocol, two volumes of RNA Binding Buffer (100 μL) and an equal volume (150 μL) of 100% ethanol (Sigma-Aldrich, Cat. No. 1085430250) were added to each sample and transferred to a Zymo-Spin IC column. The columns were first centrifuged at 10.000 × g for thirty seconds. This was followed by one wash with RNA Prep Buffer and two washes with RNA Wash Buffer, following the manufacturer’s instructions. Final elution of 15 μL each, with centrifugation at 10.000 x g for thirty seconds at RT, was performed with RNase-free water. The purified and concentrated RNA samples were stored at − 80°C. RNase-free conditions were maintained at all times.
Sequencing libraries were prepared with the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina, Cat. No. 20040529), following the manu- facturer’s protocol. The input amount of total RNA was 500 ng per sample. The sequencing libraries were quantified by qPCR using the KAPA SYBR FAST qPCR Master Mix and primers targeting the Illumina P5 and P7 flow cell oligo sequences (Roche Diagnostics, Cat. No. 07959389001). Libraries were then pooled in equimolar amounts. The amount of libraries loaded onto the flow cell was 1 nM. The clustered flow cells underwent paired-end sequencing (2 × 150 bp) on a NovaSeq 6000 Sequencing System (Illumina, Cat. No. 20012850), with the NovaSeq S4 Reagent Kit 300 cycles v1.5 kit (Illumina, Cat. No. 20028312), yielding an average of 33 x 106 reads per sample.

value: Whole Blood

value: Peripheral blood leukocytes

value: OMALIZUMAB


title: Patient_L_OMALIZUMAB_WEEK_0;SR7902

description:
Library name: Patient_L_OMALIZUMAB_WEEK_0
FEMALE


title: Patient_L_OMALIZUMAB_WEEK_24;SR8058

description:
Library name: Patient_L_OMALIZUMAB_WEEK_24
FEMALE


title: Patient_J_OMALIZUMAB_WEEK_24;SR8187

description:
Library name: Patient_J_OMALIZUMAB_WEEK_24
MALE


title: Patient_K_OMALIZUMAB_WEEK_0;SR8439

description:
Library name: Patient_K_OMALIZUMAB_WEEK_0
FEMALE


title: ET5, A549, rep2

description:
Library name: ET5_A549_2
column name in et01b28_bulkseq_counts.txt: ET5_2


title: Patient_J_OMALIZUMAB_WEEK_0;SR8034

description:
Library name: Patient_J_OMALIZUMAB_WEEK_0
MALE


title: Patient_I_OMALIZUMAB_WEEK_0;SR8341

description:
Library name: Patient_I_OMALIZUMAB_WEEK_0
FEMALE


title: Patient_I_OMALIZUMAB_WEEK_24;SR8438

description:
Library name: Patient_I_OMALIZUMAB_WEEK_24
FEMALE


title: ET4, A549, rep2

description:
Library name: ET4_A549_2
column name in et01b28_bulkseq_counts.txt: ET4_2


title: Patient_H_OMALIZUMAB_WEEK_24;SR8382

description:
Library name: Patient_H_OMALIZUMAB_WEEK_24
FEMALE


title: ET4, A549, rep1

description:
Library name: ET4_A549_1
column name in et01b28_bulkseq_counts.txt: ET4_1


title: Patient_F_OMALIZUMAB_WEEK_24;SR8436

description:
Library name: Patient_F_OMALIZUMAB_WEEK_24
MALE


title: Patient_G_OMALIZUMAB_WEEK_0;SR7927

description:
Library name: Patient_G_OMALIZUMAB_WEEK_0
FEMALE


title: Patient_H_OMALIZUMAB_WEEK_0;SR8267

description:
Library name: Patient_H_OMALIZUMAB_WEEK_0
FEMALE


title: Patient_G_OMALIZUMAB_WEEK_24;SR8098

description:
Library name: Patient_G_OMALIZUMAB_WEEK_24
FEMALE


title: Patient_F_OMALIZUMAB_WEEK_0;SR8358

description:
Library name: Patient_F_OMALIZUMAB_WEEK_0
MALE


title: ET3, A549, rep2

description:
Library name: ET3_A549_2
column name in et01b28_bulkseq_counts.txt: ET3_2


title: Patient_E_OMALIZUMAB_WEEK_24;SR8265

description:
Library name: Patient_E_OMALIZUMAB_WEEK_24
MALE


title: ET1, A549, rep2

description:
Library name: ET1_A549_2
column name in et01b28_bulkseq_counts.txt: ET1_2


title: Patient_E_OMALIZUMAB_WEEK_0;SR8146

description:
Library name: Patient_E_OMALIZUMAB_WEEK_0
MALE


title: Parental (WT), A549, rep1

description:
Library name: WT_A549_1
column name in et01b28_bulkseq_counts.txt: WT_1


title: Patient_C_OMALIZUMAB_WEEK_0;SR8351

description:
Library name: Patient_C_OMALIZUMAB_WEEK_0
FEMALE


title: Patient_B_OMALIZUMAB_WEEK_24;SR8402

description:
Library name: Patient_B_OMALIZUMAB_WEEK_24
FEMALE


title: Patient_D_OMALIZUMAB_WEEK_0;SR7913

description:
Library name: Patient_D_OMALIZUMAB_WEEK_0
MALE


title: Patient_B_OMALIZUMAB_WEEK_0;SR8338

description:
Library name: Patient_B_OMALIZUMAB_WEEK_0
FEMALE


title: Patient_A_OMALIZUMAB_WEEK_24;SR8057

description:
Library name: Patient_A_OMALIZUMAB_WEEK_24
FEMALE


title: Patient_A_OMALIZUMAB_WEEK_0;SR7883

description:
Library name: Patient_A_OMALIZUMAB_WEEK_0
FEMALE


title: Patient_I_MEPOLIZUMAB_WEEK_24;SR8200

description:
Library name: Patient_I_MEPOLIZUMAB_WEEK_24
FEMALE

value: MEPOLIZUMAB


title: Patient_I_MEPOLIZUMAB_WEEK_0;SR7986

description:
Library name: Patient_I_MEPOLIZUMAB_WEEK_0
FEMALE


title: Patient_F_MEPOLIZUMAB_WEEK_24;SR8548

description:
Library name: Patient_F_MEPOLIZUMAB_WEEK_24
FEMALE


title: Patient_H_MEPOLIZUMAB_WEEK_24;SR8202

description:
Library name: Patient_H_MEPOLIZUMAB_WEEK_24
FEMALE


title: Patient_G_MEPOLIZUMAB_WEEK_24;SR8324

description:
Library name: Patient_G_MEPOLIZUMAB_WEEK_24
FEMALE


title: Patient_G_MEPOLIZUMAB_WEEK_0;SR8151

description:
Library name: Patient_G_MEPOLIZUMAB_WEEK_0
FEMALE


title: Patient_E_MEPOLIZUMAB_WEEK_24;SR8565

description:
Library name: Patient_E_MEPOLIZUMAB_WEEK_24
MALE


title: Patient_H_MEPOLIZUMAB_WEEK_0;SR7985

description:
Library name: Patient_H_MEPOLIZUMAB_WEEK_0
FEMALE


title: Patient_E_MEPOLIZUMAB_WEEK_0;SR8352

description:
Library name: Patient_E_MEPOLIZUMAB_WEEK_0
MALE


title: Patient_N_BENRALIZUMAB_WEEK_24;SR8072

description:
Library name: Patient_N_BENRALIZUMAB_WEEK_24
FEMALE

value: BENRALIZUMAB


title: Patient_C_OMALIZUMAB_WEEK_24;SR8604

description:
Library name: Patient_C_OMALIZUMAB_WEEK_24
FEMALE


title: Patient_D_MEPOLIZUMAB_WEEK_24;SR8560

description:
Library name: Patient_D_MEPOLIZUMAB_WEEK_24
FEMALE


title: Patient_D_OMALIZUMAB_WEEK_24;SR8029

description:
Library name: Patient_D_OMALIZUMAB_WEEK_24
MALE


title: Patient_C_MEPOLIZUMAB_WEEK_24;SR8532

description:
Library name: Patient_C_MEPOLIZUMAB_WEEK_24
FEMALE


title: Patient_B_MEPOLIZUMAB_WEEK_24;SR8558

description:
Library name: Patient_B_MEPOLIZUMAB_WEEK_24
FEMALE


title: Patient_N_BENRALIZUMAB_WEEK_0;SR7901

description:
Library name: Patient_N_BENRALIZUMAB_WEEK_0
FEMALE


title: Patient_C_MEPOLIZUMAB_WEEK_0;SR8414

description:
Library name: Patient_C_MEPOLIZUMAB_WEEK_0
FEMALE


title: Patient_B_MEPOLIZUMAB_WEEK_0;SR8411

description:
Library name: Patient_B_MEPOLIZUMAB_WEEK_0
FEMALE


title: Patient_A_MEPOLIZUMAB_WEEK_24;SR8207

description:
Library name: Patient_A_MEPOLIZUMAB_WEEK_24
FEMALE


title: Patient_M_BENRALIZUMAB_WEEK_0;SR8068

description:
Library name: Patient_M_BENRALIZUMAB_WEEK_0
FEMALE


title: Patient_M_BENRALIZUMAB_WEEK_24;SR8225

description:
Library name: Patient_M_BENRALIZUMAB_WEEK_24
FEMALE


title: Patient_A_MEPOLIZUMAB_WEEK_0;SR7980

description:
Library name: Patient_A_MEPOLIZUMAB_WEEK_0
FEMALE


title: Patient_F_MEPOLIZUMAB_WEEK_0;SR8421

description:
Library name: Patient_F_MEPOLIZUMAB_WEEK_0
FEMALE


title: Patient_L_BENRALIZUMAB_WEEK_24;SR8233

description:
Library name: Patient_L_BENRALIZUMAB_WEEK_24
MALE


title: Patient_L_BENRALIZUMAB_WEEK_0;SR8052

description:
Library name: Patient_L_BENRALIZUMAB_WEEK_0
MALE


title: Patient_K_BENRALIZUMAB_WEEK_0;SR8230

description:
Library name: Patient_K_BENRALIZUMAB_WEEK_0
MALE


title: Patient_K_BENRALIZUMAB_WEEK_24;SR8367

description:
Library name: Patient_K_BENRALIZUMAB_WEEK_24
MALE


title: Patient_J_BENRALIZUMAB_WEEK_0;SR7984

description:
Library name: Patient_J_BENRALIZUMAB_WEEK_0
MALE


title: Patient_I_BENRALIZUMAB_WEEK_24;SR8288

description:
Library name: Patient_I_BENRALIZUMAB_WEEK_24
FEMALE


title: Patient_I_BENRALIZUMAB_WEEK_0;SR8067

description:
Library name: Patient_I_BENRALIZUMAB_WEEK_0
FEMALE


title: Patient_H_BENRALIZUMAB_WEEK_24;SR8226

description:
Library name: Patient_H_BENRALIZUMAB_WEEK_24
FEMALE


title: Patient_H_BENRALIZUMAB_WEEK_0;SR8051

description:
Library name: Patient_H_BENRALIZUMAB_WEEK_0
FEMALE


title: Patient_G_BENRALIZUMAB_WEEK_24;SR8258

description:
Library name: Patient_G_BENRALIZUMAB_WEEK_24
MALE


title: Patient_F_BENRALIZUMAB_WEEK_24;SR8243

description:
Library name: Patient_F_BENRALIZUMAB_WEEK_24
FEMALE


title: Patient_G_BENRALIZUMAB_WEEK_0;SR8115

description:
Library name: Patient_G_BENRALIZUMAB_WEEK_0
MALE


title: Patient_E_BENRALIZUMAB_WEEK_24;SR8284

description:
Library name: Patient_E_BENRALIZUMAB_WEEK_24
FEMALE


title: Patient_E_BENRALIZUMAB_WEEK_0;SR8069

description:
Library name: Patient_E_BENRALIZUMAB_WEEK_0
FEMALE


title: Patient_D_BENRALIZUMAB_WEEK_0;SR7933

description:
Library name: Patient_D_BENRALIZUMAB_WEEK_0
FEMALE


title: Patient_D_BENRALIZUMAB_WEEK_24;SR8108

description:
Library name: Patient_D_BENRALIZUMAB_WEEK_24
FEMALE


title: Patient_C_BENRALIZUMAB_WEEK_24;SR8280

description:
Library name: Patient_C_BENRALIZUMAB_WEEK_24
MALE


title: Patient_C_BENRALIZUMAB_WEEK_0;SR8167

description:
Library name: Patient_C_BENRALIZUMAB_WEEK_0
MALE


title: Patient_B_BENRALIZUMAB_WEEK_24;SR8229

description:
Library name: Patient_B_BENRALIZUMAB_WEEK_24
MALE


title: Patient_A_BENRALIZUMAB_WEEK_24;SR8171

description:
Library name: Patient_A_BENRALIZUMAB_WEEK_24
FEMALE


title: Patient_B_BENRALIZUMAB_WEEK_0;SR8102

description:
Library name: Patient_B_BENRALIZUMAB_WEEK_0
MALE


title: Patient_A_BENRALIZUMAB_WEEK_0;SR7961

description:
Library name: Patient_A_BENRALIZUMAB_WEEK_0
FEMALE


title: Control_3

first: Liuchao

last: Zhang

state: Jiangsu

address: 300 Guangzhou Road, Nanjing

institute: Nanjing medical universuty

description: Library name: simple3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.Raw reads of fastq format  were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar. Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Assembly: Human (Homo sapiens), GRCh38.p13
Supplementary files format and content: The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: IOMM-Lee

value: meningioma


title: Control_1

description: Library name: simple1


city: 北京

first: yixue

last: Luo

state: 北京市

address: Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, China

institute: 清华大学

description:
Library name: dif_3D_day4_1
denoting the sample named Day6_dif_1 and presenting the differentiation of cell clusters on day6 for 4 days rep1

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include genecount values for each Sample

source_name: organoids generated from human induced pluripotent stem cell

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.


title: KMT2C-KD_2

description: Library name: simple5


title: Patient_F_BENRALIZUMAB_WEEK_0;SR8041

description:
Library name: Patient_F_BENRALIZUMAB_WEEK_0
FEMALE


title: Patient_J_BENRALIZUMAB_WEEK_24;SR8186

description:
Library name: Patient_J_BENRALIZUMAB_WEEK_24
MALE


title: NPC05

city: Shanghai

first: Xin

last: Huang

address: No.83, Fenyang Rd.

institute: Fudan University

description:
Library name: Sample 4
single cell RNA-Seq

data_processing:
The feature-barcode matrices were obtained by aligning reads to the human genome (GRCh38) using STARsolo with default parameter
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Proliferative vitreoretinopathy membranes, Male, Proliferative vitreoretinopathy stage C

extract_protocol:
The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces on ice After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35 μm cell strainer. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer. The single-cell suspension was further enriched with a MACS dead cell removal kit (Miltenyi Biotec).
BD Rhapsody system  were used to capture the single cells and construct the scRNA-Seq libraries


title: ZWB04

description:
Library name: Sample 3
single cell RNA-Seq

value: Proliferative vitreoretinopathy membranes, Male, Proliferative vitreoretinopathy stage C


title: KMT2C-KD_1

description: Library name: simple4


title: USC2 cells_CTX-439_3

city: Kyoto

first: Shunsuke

last: Kawahara

address: 54 Kawahara-cho, Shogoin

department: Obstetrics and Gynecology

institute: Kyoto University Hospital

description:
Library name: Sample 31
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform (RRID: 223 SCR_016387, Illumina) to generate 100 bp paired-end reads.
Raw reads were preprocessed using fastp (version 0.23.2) and aligned to the human reference genome GRCh38 using STAR (version 2.7.10a) and RSEM (version 1.3.1).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw read counts for every gene in each sample.

source_name: Endometrium

extract_protocol:
Total RNA was extracted from frozen tumors using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Endometrium

value: patient-derived xenograft (PDX)

value: unknown


title: Control_2

description: Library name: simple2


title: USC2 cells_CTX-439_4

description:
Library name: Sample 32
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: WHN03

description:
Library name: Sample 2
single cell RNA-Seq


title: XZH02

description:
Library name: Sample 1
single cell RNA-Seq


title: KMT2C-KD_3

description: Library name: simple6


title: USC2 cells_CTX-439_2

description:
Library name: Sample 30
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: JT06

description:
Library name: Sample 5
single cell RNA-Seq


title: Patient_D_MEPOLIZUMAB_WEEK_0;SR8406

description:
Library name: Patient_D_MEPOLIZUMAB_WEEK_0
FEMALE


description:
Library name: Day6_B_1
cell clusters on day6 in the persistent presence of blebbistatin rep1

value: organoids generated from human induced pluripotent stem cell


description:
Library name: Day6_B_2
cell clusters on day6 in the persistent presence of blebbistatin rep2


description:
Library name: dif_3D_day4_2
denoting the sample named Day6_dif_1 and presenting the differentiation of cell clusters on day6 for 4 days rep2


title: USC2 cells_CTX-439_1

description:
Library name: Sample 29
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: USC2 cells_control_1

description:
Library name: Sample 25
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO, same dosage as CTX-439 group) as control.


title: USC2 cells_control_2

description:
Library name: Sample 26
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO, same dosage as CTX-439 group) as control.


title: USC1 cells_CTX-439_4

description:
Library name: Sample 24
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: USC2 cells_control_3

description:
Library name: Sample 27
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO, same dosage as CTX-439 group) as control.


title: USC1 cells_CTX-439_3

description:
Library name: Sample 23
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: USC1 cells_CTX-439_2

description:
Library name: Sample 22
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: USC1 cells_control_4

description:
Library name: Sample 20
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO, same dosage as CTX-439 group) as control.


title: USC1 cells_CTX-439_1

description:
Library name: Sample 21
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: USC1 cells_control_3

description:
Library name: Sample 19
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO, same dosage as CTX-439 group) as control.


title: USC1 cells_control_2

description:
Library name: Sample 18
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO, same dosage as CTX-439 group) as control.


title: USC1 cells_control_1

description:
Library name: Sample 17
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO, same dosage as CTX-439 group) as control.


title: ARK2 cells_CTX-439_4

description:
Library name: Sample 16
ARK2 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: ARK2 cells_CTX-439_3

description:
Library name: Sample 15
ARK2 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: ARK2 cells_CTX-439_2

description:
Library name: Sample 14
ARK2 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: ARK2 cells_CTX-439_1

description:
Library name: Sample 13
ARK2 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: ARK2 cells_control_4

description:
Library name: Sample 12
ARK2 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO) as control.

value: vehicle (DMSO, same dosage as CTX-439 group)


title: ARK2 cells_control_2

description:
Library name: Sample 10
ARK2 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO) as control.


title: ARK2 cells_control_3

description:
Library name: Sample 11
ARK2 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO) as control.


title: ARK1 cells_CTX-439_1

description:
Library name: Sample 5
ARK1 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: USC2 cells_control_4

description:
Library name: Sample 28
Patient-derived xenograft (PDX) model of uterine serous carcinoma. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO, same dosage as CTX-439 group) as control.


title: ARK1 cells_control_3

description:
Library name: Sample 3
ARK1 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO) as control.


title: ARK2 cells_control_1

description:
Library name: Sample 9
ARK2 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO) as control.


title: ARK1 cells_CTX-439_3

description:
Library name: Sample 7
ARK1 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: ARK1 cells_control_1

description:
Library name: Sample 1
ARK1 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO) as control.


title: ARK1 cells_control_4

description:
Library name: Sample 4
ARK1 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO) as control.


title: INTS3_NELFC-KD_R2

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

description:
Library name: INTS3_NELFC-KD_R2
ChIP-seq

library_source: genomic

data_processing:
Adapters were trimmed with Cutadapt with the following options: --minimum-length 10 -q 15, 10 -j 16 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA. Trimmed reads were mapped to the Drosophila melanogaster BDGP6.32 and human GRCh38.p13 reference genome with STAR and the parameters: --runThreadN 16 --readFilesCommand gunzip -c -k –alignIntronMax 1 --outFilterMultimapNmax 20 --limitBAMsortRAM 20000000000 --outSAMtype BAM SortedByCoordinate. SAMtools was used to retain the properly mapped reads and to remove PCR duplicates. Reads mapping to the human DAC Exclusion List Regions (accession: ENCSR636HFF) were removed with BEDtools. For spike-in normalization, CSTF64 and INTS3 Drosophila peaks were called against their respective Inputs with MACS379 callpeak and the options -B -f BAMPE -g 1.5e8 -q 0.01 –scale-to small –call-summits. Each peak was then defined as peak summit – 150 bp to peak summit + 150 bp. Only peaks found to overlap between the DMSO and IAA 4h conditions were kept, using the overlapping region as the peak region. BEDtools multicov was then used to quantify Input, CSTF64, and INTS3 signals across their respective peaks, normalised for the library size and the length of the peak region, and used for calculating the spike-in normalization factor for the IAA 4h condition, with the DMSO condition put to 1. After subsampling the human bam files to the smallest library with SAMtools view, spike-in normalized bigwig files were created with deepTools2 bamCoverage tool with the parameters -bs 10 -p max –scaleFactor Normalization_Factor -e.
Assembly: hg38
Supplementary files format and content: bigWig files

molecule: genomic DNA

growth_protocol: Cells were cultured in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS) and penicillin/streptomycin. All the cells were maintained in a humidified incubator at 5% CO2, 37oC.

extract_protocol:
Cells were cultivated on 150 mm dishes until 50% confluency, fixed by addition of 1% formaldehyde (Sigma) for 15 min at 37°C and quenched by 125mM glycine for 10 min at 37°C. The cells were collected by scraping, washed 3 times with cold PBS, resuspended in 1.5 mL L1 buffer (50 mM Tris pH 8.0; 2 mM EDTA pH 8.0; 0,1% NP40; 10% glycerol; protease inhibitors (Nacalai Tesque)) per 107 cells, and lysed on ice for 5 min. The nuclei were collected by centrifugation at 800g for 5m at 4°C and lysed in 1.5 mL of L2 buffer (0,2% SDS; 10 mM EDTA; 50 mM Tris pH 8.0; protease inhibitors (Nacalai Tesque)). The suspension was sonicated in 15 mL conical tubes in a cooled Bioruptor 2 (Diagenode) for 15 min at low settings. Sonicated chromatin was centrifuged for 10 min at 1,4000 rpm and collected the supernatant. The shared chromatin was diluted 10x in the dilution buffer.  For calibration, 4 ng of spike-in chromatin (Active Motif) was added to each IP sample. 60 µg of Protein A Dynabeads (Thermo Fisher Scientific) for each sample were pre-washed twice with dilution buffer (0,5% NP40; 200 mM NaCl; 50 mM Tris pH 8.0; protease inhibitors). The chromatin was incubated with pre-washed beads for 1h at 4°C to clear unspecific binding proteins to the beads. 3μg of the pre-cleared chromatin was incubated with 6 μg of α-CSTF64 (A301-092A, Bethyl) or α-INTS3 (16620-1-AP, Proteintech) and 4.4 μg of spike-in specific antibody (Active Motif), O/N at 4°C on rotator. Next, 60 μL pre-washed beads were added to the chromatin+antibody sample and incubated for 1-2hr at 4°C on rotator. After the incubation, the beads were washed 2 times with buffer A (0.05% SDS; 0.5% TritonX; 2 mM EDTA; 150 mM NaCl; 20 mM Tris pH 8.0), 3 times with buffer B (0.02% SDS; 0.5% NP40; 2 mM EDTA; 250 mM NaCl; 20 mM Tris pH 8.0), 2 times with buffer C (0.05% DOC; 0.5% NP40; 2 mM EDTA; 500 mM NaCl; 20 mM Tris pH 8.0) and finally once again with buffer D (1 mM EDTA; 10 mM Tris pH 8.0). The immunoprecipitated DNA fragments were eluted from the beads with 100ul elution buffer (1% SDS, 100mM NaHCO3) for 15 min at 30°C, and repeated this step twice. After elution, for de-crosslinking, the DNA fragments were incubated for 4h at 65°C in the presence of 10µg RNase A (EN0531, Thermo Fisher Scientific) on thermo mixer (eppendorf). The immunoprecipitated DNA was then purified with the DNA Clean & Concentrator Kit (ZYMO) according to manufacturer’s protocol and used for library preparation.
NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) was used to prepare libraries for sequencing, following manufacturer’s instructions.

treatment_protocol: Cells were treated with 500 µM Auxin or DMSO for 4 h to degrade the AID-tagged protein.

tag: antibody

value: 16620-1-AP, Proteintech

value: Colorectal adenocarcinoma

value: NELF-C-AID OsTIR1

value: Auxin 4h


title: INTS3_DMSO_R1

description:
Library name: INTS3_DMSO_R1
ChIP-seq

value: DMSO 4h


title: DLD-1 Input_NELFC-KD_R2

description:
Library name: Input_NELFC-KD_R2
ChIP-seq


title: INTS3_DMSO_R2

description:
Library name: INTS3_DMSO_R2
ChIP-seq