title: CD4+_TCR

city: Leiden

first: Jannie

last: Borst

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center (LUMC)

description:
Library name: CD4+_TCR
5 donors pooled

data_processing:
CellRanger (10X Genomics, v7.0.1)
scRNAseq reads were aligned to the human reference genome GRCh38.2020 and barcode counting was performed using ‘cellranger count’.
TCRseq reads were aligned to the human reference genome GRCh38.2020 and consensus TCR sequences were determined using ‘cellranger vdj’
Assembly: GRCh38.2020
Supplementary files format and content: Tab-separated value files and matrix files

source_name: decidua basalis, maternal peripheral blood, umbilical cord blood

extract_protocol:
scRNAseq libraries were prepared using a 10X Chromium single cell 5’ v2 chemistry kit (10X Genomics), according to the manufacturer’s protocol.
scRNAseq libraries were prepared using a 10X Chromium single cell 5’ v2 chemistry kit (10X Genomics), according to the manufacturer’s protocol.
TCRseq libraries were prepared using a 10X Chromium single cell V(D)J enrichment kit for mouse T cells (10X Genomics), according to the manufacturer’s protocol.

treatment_protocol: CD4+ T cells were isolated by magnetic antibody-based purification from decidua parietalis, decidua basalis, maternal periphral blood and cord blood from n=3 healthy donors that underwent caesarean section at term healthy pregnancy. A small fraction was analyzed by flow cytometry to check frequencies of decidual Tregs which were comparable between donors. On the day for submission for scRNAseq, cells were thawed, pooled in equal representation of each of the three donors per tissue and stained for CD4, CD25, CD8, CD127 and CD26 and for flow cytometrically sorted to obtain Tregs (CD25hiCD26low in decidua and CD25hiCD127low in blood) and Tconvs (CD25low/int in decidua and CD25lowCD127+ in blood). Samples were kept at 4°C throughout the procedure and collected on ice. After cell sorting, Tregs and Tconvs were combined in a 1:1 ratio per tissue to ensure equal representation of both cell types in the scRNAseq data. To discern cells from the different tissues, they were each labeled with a distinct 5’ hashtag oligonucleotide (HTO)-conjugated antibody (TotalSeqTM-C0251 - C0254, BioLegend). Cell viability was confirmed to exceed 80% in all samples. Next, all samples were combined for scRNAseq by 10 X Chromium (10 X Genomics).


title: CD4+_GEX

status: Public on Jul 23 2026

type: SRA

description:
Library name: CD4+_GEX
4 donors pooled

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: decidua basalis, maternal peripheral blood, umbilical cord blood


title: SMAD6KO_GFP_R2

city: L'Hospitalet de Llobregat

first: Jose Luis

last: Rocamora

address: Avinguda de la Granvia de l’Hospitalet, 199

country: Spain

institute: IDIBELL

description: Library name: SMAD6KO_GFP_R2

library_source: transcriptomic

data_processing:
Base calling and quality assessment performed with FastQC v0.11.7
Adapter trimming and quality trimming performed with Trimmomatic v0.38 (removed low-quality bases <Q3 from read ends; sliding window trimming with window size 4 and mean quality 15; reads <36 bp after trimming were discarded)
Trimmed reads aligned to the human reference genome (GRCh37) using HISAT2 v2.1.0
Transcript assembly and quantification performed with StringTie v2.1.3b, using NCBI annotation release 105.20190906
Gene/transcript expression levels calculated as read count, FPKM, and TPM.
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text file containing, for each of 24,253 expressed genes annotated with Gene_ID, Transcript_ID, Gene_Symbol, Description, gene_biotype, and cross-references to Protein_ID, HGNC, MIM, and IMGT/GENE-DB: per-sample read counts, FPKM, and TPM values for all 8 samples (HDMEC, SMAD6KO_GFP groups, 4 replicates each); per-group mean expression; rlog-normalized expression values; and differential expression statistics (fold change, baseMean, lfcSE, Wald statistic, raw p-value, and Benjamini-Hochberg adjusted p-value) for comparison pairs (SMAD6KO_GFP vs. HDMEC).

source_name: hTERT neonatal dermal microvascular endothelial cells

growth_protocol: Cells were cultured in 1 % gelatin-coated plates with EGM-2 medium (PromoCell) supplemented with 10 % FBS, 1% penicillin/streptomycin, 1% L-glutamine and 1% pyruvate; referred as complete EGM. Cells were always maintained at 37 °C in 5 % CO2 atmosphere.

extract_protocol:
Maxwell® RSC Instrument following manufacturer's protocol.
Library Kit TruSeq stranded mRNA following manufacturer's protocol

treatment_protocol: No treatment

tag: cell line

tag: cell type

value: Dermal Microvascular Endothelial Cell

tag: genotype

value: SMAD6 Knock-out

tag: treatment

value: No treatment


title: SMAD6KO_GFP_R1

description: Library name: SMAD6KO_GFP_R1

value: hTERT neonatal dermal microvascular endothelial cells


title: SMAD6KO_GFP_R4

description: Library name: SMAD6KO_GFP_R4


title: CD4+_CITE

description:
Library name: CD4+_CITE
3 donors pooled


title: HDMEC_R4

description: Library name: HDMEC_R4

value: WT


title: SMAD6KO_GFP_R3

description: Library name: SMAD6KO_GFP_R3


title: HDMEC_R3

description: Library name: HDMEC_R3


title: HDMEC_R2

description: Library name: HDMEC_R2


title: HDMEC_R1

description: Library name: HDMEC_R1


title: hRPE_ChIATAC,rep3

city: Hangzhou

first: tang

middle: dong

last: mei

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

description: Library name: sample3

library_source: genomic

data_processing:
Data was processed using ChIA-PIPE pipeline.
Assembly: hg38
Supplementary files format and content: bw files

molecule: genomic DNA

source_name: human primary RPE

extract_protocol:
Human donor eyes, consented for research, were obtained from the Eye hospital and were approved by the Ethics Committee of Optometry Hospital affiliated to Wenzhou Medical University (2022-121-K-92-01). iPSCs were passaged onto Matrigel-coated dish in retinal differentiation medium (RDM, DMEM/F12 with 1% B27 (Gibco, 12587010), 1% N2 (Gibco, 17502048) and 1×NEAA (Gibco, 11140050). 10 mM nicotinamide (Selleck, S1899, Houston, Tx, USA), 10 ng/ml IGF1 (Sino Biological, 10598-HNAE, Beijing, China), 10 ng/ml bFGF (Sino Biological, 10014-HNAE), 1 M A-83-01 (Selleck, S7692) and 1 M IWR-1 (Selleck, S7086) were added to RDM for 0-4 days. 10 mM nicotinamide and 10 ng/ml bFGF were replaced by 100 ng/ml Activin A (Sino Biological, 10429-HNAH) and the concentration of IGF1 increased to 20 ng/ml, and A-83-01 was not added for 4-6 days. IGF1 and IWR-1 were replaced by 1 M SU5402 (Selleck, S7667) for 6-8 days. 1 M CHIR99021 (Selleck, S1263) was added to RDM for 8-14 days. From days 14, cells were maintained in RPE supporting medium (RSM, DMEM/F12 with 15% knockout serum replacement, 5% FBS, 1×NEAA and 10 mM nicotinamide) until they matured and formed pigmented monolayers. iPSC-RPE cells were passaged with EDTA (Gibco, 25200072) and were replaced on the Matrigel-coated dish and at P3 were used in this study.
When cells grew to 80% confluency, 2% FA and 2 mM EGS were added to crosslink cells respectively. 50,000 fixed cells were used for one library. After cells lysis and nuclear permeabilization, the nuclei were digested by restriction digestion of Alu1 and HpyCH4V (NEB, R0620L), then were performed A-tailing and proximity-ligation. Chromatin fragments were tagmented by Tn5 transposase, then immobilized on M280 streptavidin dynabeads. PCR amplification was performed on beads and products were purified by AMPure XP beads. DNA libraries were sequenced on Illumina NovaS4 by paired-end 150 bp.

value: human primary RPE


title: hRPE_H3K27me3,rep4

description: Library name: sample16

data_processing:
The raw reads were trimmed using Trim Galore to remove adapters and the portion of low quality (https://github.com/FelixKrueger/TrimGalore) with default parameters. Trimmed reads were aligned to the human hg38 reference genome using Bowtie2
Duplicated reads were removed with gatk MarkDuplicates (Picard) (https:// github.com/broadinstitute/picard) and uniquely mapped nonredundant reads (MAPQ>30) were passed to MACS2 for peak calling with setting ‘macs2 callpeak -t –nomodel –keep-dup all -q 0.001’.
BigWig file were generated using bamCoverage with the RPKM normalization method.
Assembly: hg38
Supplementary files format and content: bigWig , narrowPeak
Library strategy: CUT&Tag

extract_protocol:
Human donor eyes, consented for research, were obtained from the Eye hospital and were approved by the Ethics Committee of Optometry Hospital affiliated to Wenzhou Medical University (2022-121-K-92-01). iPSCs were passaged onto Matrigel-coated dish in retinal differentiation medium (RDM, DMEM/F12 with 1% B27 (Gibco, 12587010), 1% N2 (Gibco, 17502048) and 1×NEAA (Gibco, 11140050). 10 mM nicotinamide (Selleck, S1899, Houston, Tx, USA), 10 ng/ml IGF1 (Sino Biological, 10598-HNAE, Beijing, China), 10 ng/ml bFGF (Sino Biological, 10014-HNAE), 1 M A-83-01 (Selleck, S7692) and 1 M IWR-1 (Selleck, S7086) were added to RDM for 0-4 days. 10 mM nicotinamide and 10 ng/ml bFGF were replaced by 100 ng/ml Activin A (Sino Biological, 10429-HNAH) and the concentration of IGF1 increased to 20 ng/ml, and A-83-01 was not added for 4-6 days. IGF1 and IWR-1 were replaced by 1 M SU5402 (Selleck, S7667) for 6-8 days. 1 M CHIR99021 (Selleck, S1263) was added to RDM for 8-14 days. From days 14, cells were maintained in RPE supporting medium (RSM, DMEM/F12 with 15% knockout serum replacement, 5% FBS, 1×NEAA and 10 mM nicotinamide) until they matured and formed pigmented monolayers. iPSC-RPE cells were passaged with EDTA (Gibco, 25200072) and were replaced on the Matrigel-coated dish and at P3 were used in this study.
Histone modifications of ARPE-19, iPSC-RPE, hRPE and iPSC were captured by CUT&Tag using hyperactive universal CUT&Tag assay kit for Illumina (Vazyme, TD903, Nanjing, China). 50,000 viable cells were collected for each library and incubated with concanavalin A-coated magnetic beads. The beads binding cells were captured by H3K4me1 (CST, 5326, Danvers, MA, USA), H3K4me3 (CST, 9751), H3K27ac (CST, 8173), H3K27me3 (CST, 9733) antibodies, then incubated with hyperactive pA/G-Transposon. The tagmented DNA was purified and PCR amplificated for sequencing.


title: hRPE_H3K27me3,rep3

description: Library name: sample15


title: hRPE_H3K27ac,rep4

description: Library name: sample14


title: hRPE_H3K27ac,rep3

description: Library name: sample13


title: hRPE_H3K4me3,rep4

description: Library name: sample10


title: hRPE_H3K4me1,rep3

description: Library name: sample11


title: hRPE_H3K4me3,rep3

description: Library name: sample9


title: hRPE_H3K4me1,rep4

description: Library name: sample12


title: hRPE_RNA,rep4

description:
Library name: Sample 8
Column name in humna_RPE_TPM.txt:hRPE2

data_processing:
The raw reads were trimmed using Trim Galore to remove adapters and the portion of low quality with default parameters.
Trimmed reads were aligned to the human hg38 reference genome using HISAT2. Reads with mapping quality score less than 30 were filtered.million (TPM) values were calculated for each gene then.
Raw count for each gene were quantified using HTSeq with parameters for reverse strandedness (-s reverse).
Transcript per million (TPM) values were calculated for each gene.
Assembly: hg38
Supplementary files format and content: txt file include TPM values for each Sample

extract_protocol:
Human donor eyes, consented for research, were obtained from the Eye hospital and were approved by the Ethics Committee of Optometry Hospital affiliated to Wenzhou Medical University (2022-121-K-92-01). iPSCs were passaged onto Matrigel-coated dish in retinal differentiation medium (RDM, DMEM/F12 with 1% B27 (Gibco, 12587010), 1% N2 (Gibco, 17502048) and 1×NEAA (Gibco, 11140050). 10 mM nicotinamide (Selleck, S1899, Houston, Tx, USA), 10 ng/ml IGF1 (Sino Biological, 10598-HNAE, Beijing, China), 10 ng/ml bFGF (Sino Biological, 10014-HNAE), 1 M A-83-01 (Selleck, S7692) and 1 M IWR-1 (Selleck, S7086) were added to RDM for 0-4 days. 10 mM nicotinamide and 10 ng/ml bFGF were replaced by 100 ng/ml Activin A (Sino Biological, 10429-HNAH) and the concentration of IGF1 increased to 20 ng/ml, and A-83-01 was not added for 4-6 days. IGF1 and IWR-1 were replaced by 1 M SU5402 (Selleck, S7667) for 6-8 days. 1 M CHIR99021 (Selleck, S1263) was added to RDM for 8-14 days. From days 14, cells were maintained in RPE supporting medium (RSM, DMEM/F12 with 15% knockout serum replacement, 5% FBS, 1×NEAA and 10 mM nicotinamide) until they matured and formed pigmented monolayers. iPSC-RPE cells were passaged with EDTA (Gibco, 25200072) and were replaced on the Matrigel-coated dish and at P3 were used in this study.
Total RNA was extracted using KAPA RNA prep kits (Roche, KK8560，Basel, Switzerland) from iPSC-RPE, hRPE and iPSC cells. Total RNA was subjected to ribosome removal, DNase digestion, fragmentation, and PCR amplification. Then libraries were sequenced on an Illuminar NovaSeq 6000.


title: hRPE_ATAC, rep4

description: Library name: sample4

data_processing:
The raw reads were trimmed using Trim Galore to remove adapters and the portion of low quality (https://github.com/FelixKrueger/TrimGalore) with default parameters. Trimmed reads were aligned to the human hg38 reference genome using Bowtie2
Duplicated reads were removed with gatk MarkDuplicates (Picard) (https:// github.com/broadinstitute/picard) and uniquely mapped nonredundant reads (MAPQ>30) were passed to MACS2 for peak calling with setting ‘macs2 callpeak -t –nomodel –keep-dip all –shift -100 –extsize 200’ .
BigWig file were generated using bamCoverage with the RPKM normalization method.
Assembly: hg38
Supplementary files format and content: bigWig , narrowPeak

extract_protocol:
Human donor eyes, consented for research, were obtained from the Eye hospital and were approved by the Ethics Committee of Optometry Hospital affiliated to Wenzhou Medical University (2022-121-K-92-01). iPSCs were passaged onto Matrigel-coated dish in retinal differentiation medium (RDM, DMEM/F12 with 1% B27 (Gibco, 12587010), 1% N2 (Gibco, 17502048) and 1×NEAA (Gibco, 11140050). 10 mM nicotinamide (Selleck, S1899, Houston, Tx, USA), 10 ng/ml IGF1 (Sino Biological, 10598-HNAE, Beijing, China), 10 ng/ml bFGF (Sino Biological, 10014-HNAE), 1 M A-83-01 (Selleck, S7692) and 1 M IWR-1 (Selleck, S7086) were added to RDM for 0-4 days. 10 mM nicotinamide and 10 ng/ml bFGF were replaced by 100 ng/ml Activin A (Sino Biological, 10429-HNAH) and the concentration of IGF1 increased to 20 ng/ml, and A-83-01 was not added for 4-6 days. IGF1 and IWR-1 were replaced by 1 M SU5402 (Selleck, S7667) for 6-8 days. 1 M CHIR99021 (Selleck, S1263) was added to RDM for 8-14 days. From days 14, cells were maintained in RPE supporting medium (RSM, DMEM/F12 with 15% knockout serum replacement, 5% FBS, 1×NEAA and 10 mM nicotinamide) until they matured and formed pigmented monolayers. iPSC-RPE cells were passaged with EDTA (Gibco, 25200072) and were replaced on the Matrigel-coated dish and at P3 were used in this study.
chromatin accessibility of ARPE-19, iPSC-RPE, hRPE and iPSC were captured by hyperactive ATAC-seq library prep kit for Illumina (Vazyme, TD711). 50,000 viable cells were collected for each library and tagmented by tagment enzyme. The tagmented DNA was purified and PCR amplificated for sequencing.


title: hRPE_ATAC, rep3

description: Library name: sample3


title: Batch1_DMSO3

city: Stanford

first: Meenakshi

last: Chakraborty

state: CA

address: 269 Campus Drive

country: USA

institute: Stanford University

description: Library name: Batch1_DMSO3

data_processing:
TrimGalore v0.6.10
Kallisto 0.48.0
Assembly: GRCh38
Supplementary files format and content: h5 files are outputs from kallisto
Supplementary files format and content: tsv files are outputs from kallisto

source_name: brain

extract_protocol:
Cells were frozen in TRIzol, and chloroform was added after the samples were thawed. Following centrifugation, RNA was isolated from the aqueous phase using the Qiagen RNeasy Mini Kit. Samples were then treated with TURBO DNase (Fisher Scientific), followed by RNA cleanup according to the "RNA Cleanup" protocol in the RNeasy Mini Kit handbook and subsequent ethanol precipitation.
mRNA libraries were prepared by Novogene from the extracted RNA, using a polyA enrichment strategy.

value: brain


title: Pressure-trained ECT (MCTR_Endo_plus)

city: Kyoto

first: Hidetoshi

last: Masumoto

state: Japan

address: 54 Shogoin Kawahara-cho, Sakyo-ku

country: Japan

institute: KYOTO UNIVERSITY

description:
Library name: ChRN0535
Hydrostatic pressure-trained engineered cardiac tissue showing endothelial cell-associated maturation response (MCTR_Endo_plus).

data_processing:
Raw base call files were demultiplexed and converted to FASTQ files using Cell Ranger v7.1.0.
Sequencing reads were aligned to the human reference genome GRCh38 using Cell Ranger count v7.1.0.
Gene-barcode count matrices were generated using Cell Ranger v7.1.0.
Quality control, normalization, clustering, differential expression analysis, and UMAP visualization were performed using Seurat.
Assembly: GRCh38
Supplementary files format and content: Processed data consist of gene-by-cell count matrices generated using Cell Ranger v7.1.0 and provided in HDF5 (.h5) format. These files contain expression counts for all detected genes and cells and were used for downstream analyses including clustering, differential expression analysis, and UMAP visualization.
Supplementary files format and content: Processed data files correspond to the samples ChRN0534, ChRN0535, and ChRN0536 and are provided as raw_feature_bc_matrix.h5 files.

molecule: polyA RNA

source_name: 201B6 human iPSC

growth_protocol: Engineered cardiac tissues (ECTs) were generated from human induced pluripotent stem cell (hiPSC)-derived cardiovascular cells as described in the associated manuscript. Tissues were cultured under standard conditions at 37°C in a humidified atmosphere containing 5% CO2. Hydrostatic pressure training was applied as indicated for each experimental group.

extract_protocol:
ECTs were dissociated into single-cell suspensions using enzymatic digestion. Viable cells were collected and used for single-cell RNA sequencing library preparation.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Gene Expression platform (10x Genomics) according to the manufacturer's instructions and sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: Control ECTs were maintained under standard culture conditions. Pressure-trained ECTs were subjected to cyclic hydrostatic pressure stimulation at 50 kPa for 1 hour per day for 3 consecutive days following 2 weeks of pre-culture.

value: 201B6 human iPSC

value: engineered cardiac tissue

value: wild type

value: Hydrostatic pressure training (MCTR_Endo_plus)

tag: pressure

value: 50 kPa

tag: duration

value: 1 h/day × 3 days

tag: batch


title: Pressure-trained ECT (MCTR_Endo_minus)

description:
Library name: ChRN0536
Hydrostatic pressure-trained engineered cardiac tissue lacking endothelial cell-associated maturation response (MCTR_Endo_minus).

value: Hydrostatic pressure training (MCTR_Endo_minus)


title: hRPE_RNA,rep3

description:
Library name: Sample 7
Column name in human_RPE_TPM.txt:hRPE1


title: Control ECT

description:
Library name: ChRN0534
Control engineered cardiac tissue derived from human iPSC-derived cardiovascular cells.

value: Control

value: 0 kPa


title: STA9090+BGT226 treated ACC cells HSB2

city: Bethesda

first: Naris

last: Nilubol

state: MD

address: Building 10 - Room 45952

department: Surgical Oncology Program

institute: National Cancer Institute

description: Library name: HSB2

data_processing:
Basecalling was performed with RTA v3.4.4.
Demultiplexing was performed with bcl2fastq v2.20 using no lane splitting and barcode mismatch allowance of 1.
Reads were trimmed for adapters and low-quality bases using Cutadapt v1.18.
Trimmed reads were aligned to hg38 using STAR v2.7.0f.
Gene expression quantification was performed using RSEM v1.3.1 from STAR transcriptome BAM output.
Assembly: hg38
Supplementary files format and content: Tab-delimited raw gene-level count matrix generated using STAR/RSEM. Rows represent genes identified by Ensembl gene ID and gene symbol; columns represent samples.

source_name: Adrenocortical Carcinoma

extract_protocol:
RNA extraction was carried out using the RNeasy Mini Kit (74104, Thermofisher Scientific) according to the manufacturer's protocol
Libraries were prepared using Illumina Stranded Total RNA Ligation with Ribo-Zero Plus and sequenced as paired-end reads on an Illumina NovaSeq 6000 SP flowcell. Read structure was R1:101, i7:10, i5:10, R2:101. Libraries were stranded.

value: Adrenocortical Carcinoma


title: STA9090+BGT226 treated ACC cells HSB3

description: Library name: HSB3


title: STA9090+BGT226 treated ACC cells HSB1

description: Library name: HSB1


title: STA9090+PIK75 treated ACC cells HSP3

description: Library name: HSP3


title: STA9090+PIK75 treated ACC cells HSP1

description: Library name: HSP1


title: BGT226 treated ACC cells HB3

description: Library name: HB3


title: STA9090+PIK75 treated ACC cells HSP2

description: Library name: HSP2


title: PIK75 treated ACC cells HP3

description: Library name: HP3


title: BGT226 treated ACC cells HB1

description: Library name: HB1


title: BGT226 treated ACC cells HB2

description: Library name: HB2


title: PIK75 treated ACC cells HP2

description: Library name: HP2


title: STA9090 treated ACC cells HS3

description: Library name: HS3


title: STA9090 treated ACC cells HS2

description: Library name: HS2


title: Untreated ACC cells HC3

description: Library name: HC3


title: Untreated ACC cells HC2

description: Library name: HC2


title: STA9090 treated ACC cells HS1

description: Library name: HS1


title: Untreated ACC cells HC1

description: Library name: HC1


title: scTCRseq STAT3GOF CD8+ T cells 7

city: Philadelphia

first: Montana

last: Knight

state: PA

address: 3615 Civic Center Blvd

department: Department of Biomedical and Health Informatics

institute: Children's Hospital of Philadelphia

description: Library name: STAT3GOF7_TCR

data_processing:
Sequencing data mapped with CellRanger v7.1.0 to the GRCh38 human reference (both genome and VDJ). Data further filtered and processed using Seurat v4.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: H5 files represent the results of mapping the scRNA-seq data to the human genome. CSV files are the results of mapping the scTCR-seq data. RDS file is data aggregated into a seurat object (does include custom cell annotations).
Library strategy: scTCR-Seq

source_name: CD8+ T cells

extract_protocol:
Cryopreserved human PBMCs were thawed as indicated in the manuscript, counted, and 0.5E6-1E6 cells were transferred to a new tube, washed with PBS and centrifuged, followed by an incubation with 50μL of Live/Dead Aqua, CD14/CD16/CD19 V500, CD3 APC-R700, CD4 AF488 and CD8a BV605 antibodies in FACS Buffer with 10% Brilliant Stain Buffer for 30 minutes at RT. Cells were then washed and resuspended using FACS buffer followed by a straining through a 35um nylon mesh strainer. Cells were sorted for live CD8+ T cells into eppendorf tubes with RPMI + 10% FBS. Cells were then washed two times with RPMI + 10% FBS to remove EDTA.
Library prep done with 10X Chromium Next GEM Single Cell 5’ Kit v2 and Chromium Single Cell Human TCR Amplification Kit.

value: CD8+ T cells


title: scTCRseq STAT3GOF CD8+ T cells 5

description: Library name: STAT3GOF5_TCR


title: scTCRseq STAT3GOF CD8+ T cells 3

description: Library name: STAT3GOF3_TCR


title: scTCRseq STAT3GOF CD8+ T cells 2

description: Library name: STAT3GOF2_TCR


title: scTCRseq STAT3GOF CD8+ T cells 6

description: Library name: STAT3GOF6_TCR


title: scTCRseq STAT3GOF CD8+ T cells 1

description: Library name: STAT3GOF1_TCR


title: scTCRseq healthy CD8+ T cells 5

description: Library name: HC5_TCR


title: scTCRseq STAT3GOF CD8+ T cells 4

description: Library name: STAT3GOF4_TCR


title: scTCRseq healthy CD8+ T cells 4

description: Library name: HC4_TCR


title: scTCRseq healthy CD8+ T cells 3

description: Library name: HC3_TCR


title: scTCRseq healthy CD8+ T cells 1

description: Library name: HC1_TCR


title: scTCRseq healthy CD8+ T cells 2

description: Library name: HC2_TCR


title: scRNAseq STAT3GOF CD8+ T cells 7

description: Library name: STAT3GOF7_GEX

data_processing:
Sequencing data mapped with CellRanger v7.1.0 to the GRCh38 human reference (both genome and VDJ). Data further filtered and processed using Seurat v4.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: H5 files represent the results of mapping the scRNA-seq data to the human genome. CSV files are the results of mapping the scTCR-seq data. RDS file is data aggregated into a seurat object (does include custom cell annotations).


title: scRNAseq STAT3GOF CD8+ T cells 6

description: Library name: STAT3GOF6_GEX


title: scRNAseq STAT3GOF CD8+ T cells 5

description: Library name: STAT3GOF5_GEX


title: scRNAseq STAT3GOF CD8+ T cells 4

description: Library name: STAT3GOF4_GEX


title: scRNAseq STAT3GOF CD8+ T cells 3

description: Library name: STAT3GOF3_GEX


title: scRNAseq healthy CD8+ T cells 5

description: Library name: HC5_GEX


title: scRNAseq STAT3GOF CD8+ T cells 1

description: Library name: STAT3GOF1_GEX


title: Batch3_Panto2

description: Library name: Batch3_Panto2


title: scRNAseq healthy CD8+ T cells 3

description: Library name: HC3_GEX


title: scRNAseq STAT3GOF CD8+ T cells 2

description: Library name: STAT3GOF2_GEX


title: scRNAseq healthy CD8+ T cells 2

description: Library name: HC2_GEX


title: scRNAseq healthy CD8+ T cells 1

description: Library name: HC1_GEX


title: scRNAseq healthy CD8+ T cells 4

description: Library name: HC4_GEX


title: mAbCD73,rep3

city: Guangzhou

first: Shuo

last: Wan

state: Guangdong

address: No.601, West Huangpu Avenue

institute: Jinan University

description: Library name: sample18

data_processing:
The raw data is filtered for low-quality sequences, including the following contents Part:
(1) Remove the adapter sequence in the Reads;
(2) Remove N ( N represents fuzzy base information ) Reads (default) with a certain number of bases 5bp)；
(3) Reads containing more than a certain percentage (default 40%) of low-mass bases (mass value ≤20) are removed;
(4) Sliding window quality clipping: The sliding window size is set to a certain size (default 4bp), and the average quality is lower than the special one the fixed value (default 20) is trimmed;
The above steps are for both Reads 1 and Reads 2.
HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) software is used to compare transcriptome sequencing Reads to the reference genome. Clean Reads are matched to the reference genome to obtain alignment feature information and stored in SAM format (Sequence Alignment/Map format). The SAM sequence alignment format standard was developed by Sange, which is mainly used for sequencing sequence alignment to display information features on the genome. Based on the comparison results, the BAM file is sorted using Samtools, filtered repeated.  Expression analysis is the premise of difference analysis, and the essence of expression analysis is based on the comparison of each sample The Reads Count value of different genes is counted, that is, the number of Reads compared to that gene is also counted. The underlying information for subsequent differential gene analysis, if the gene is highly expressed, so does its Reads coverage. We use HTSeq for Reads Count calculations, HTSeq provides the union, intersection_strict, intersection_nonempty three models determine that a Reads belongs to a gene Reads, etc., and finally the comparison results of the sequence on the reference genome are statistically displayed and graphed.
Supplementary files format and content: *.txt

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted from the sample using the TRIzol™ Reagent, followed by RNA purity with Nano Drop, RNA concentration with Qubit RNA BR (Broad-Range) Assay Kit, and RNA integrity with RNA Screen Tape.
Based on the total amount of total RNA, 0.1-1ug of total RNA was taken and the mRNA was isolated using the Albertec Poly(A) mRNA Capture Module (Cat. No. RK20340) Kit, and then the mRNA library was constructed with the Arbotec Fast RNA-seq Lib Prep Kit V2 (Cat. No. RK20306) Library Building Kit.

value: Peripheral blood

value: NK cells

value: Primary cells

value: the supernatant of HK1+EBV treated with 10ug/ml CD73 antibody for two hours, then 500ng/mL AMP


title: Ctrl,rep3

description: Library name: sample15

value: WT

value: the supernatant of HK1+EBV treated with 10ug/ml control antibody for two hours, then 500ng/mL AMP


title: Ctrl,rep1

description: Library name: sample13


title: HK1+EBV,rep1

description: Library name: sample10

value: the supernatant of  HK1+EBV treated with 500ng/mL AMP


title: HK1+EBV,rep3

description: Library name: sample12


title: HK1,rep3

description: Library name: sample9

value: the supernatant of  HK1 treated with 500ng/mL AMP


title: HK1,rep2

description: Library name: sample8


title: ADO (5mM),rep3

description: Library name: sample6

value: 5mM ADO treatment


title: HK1,rep1

description: Library name: sample7


title: ADO (5mM),rep2

description: Library name: sample5


title: ADO (0mM),rep3

description: Library name: sample3

value: 0mM ADO treatment


title: ADO (5mM),rep1

description: Library name: sample4


title: PIK75 treated ACC cells HP1

description: Library name: HP1


title: ADO (0mM),rep2

description: Library name: sample2


title: ADO (0mM),rep1

description: Library name: sample1


title: HK1EBV_A

description: Library name: sample10

data_processing:
The raw data is filtered for low-quality sequences, including the following contents Part:
(1) Remove the adapter sequence in the Reads;
(2) Remove N ( N represents fuzzy base information ) Reads (default) with a certain number of bases 5bp);
(3) Reads containing more than a certain percentage (default 40%) of low-mass bases (mass value ≤20) are removed;
(4) Sliding window quality clipping: The sliding window size is set to a certain size (default 4bp), and the average quality is lower than the special one the fixed value (default 20) is trimmed;
The above steps are for both Reads 1 and Reads 2.
HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) software is used to compare transcriptome sequencing Reads to the reference genome. Clean Reads are matched to the reference genome to obtain alignment feature information and stored in SAM format (Sequence Alignment/Map format). The SAM sequence alignment format standard was developed by Sange, which is mainly used for sequencing sequence alignment to display information features on the genome. Based on the comparison results, the BAM file is sorted using Samtools, filtered repeated.  Expression analysis is the premise of difference analysis, and the essence of expression analysis is based on the comparison of each sample The Reads Count value of different genes is counted, that is, the number of Reads compared to that gene is also counted. The underlying information for subsequent differential gene analysis, if the gene is highly expressed, so does its Reads coverage. We use HTSeq for Reads Count calculations, HTSeq provides the union, intersection_strict, intersection_nonempty three models determine that a Reads belongs to a gene Reads, etc., and finally the comparison results of the sequence on the reference genome are statistically displayed and graphed.
Supplementary files format and content: *.txt

value: nasopharyngeal carcinoma cell line

value: EBV treatment


title: HK1_C

description: Library name: sample9

value: control


title: HK1_A

description: Library name: sample7


title: CNE2EBV_C

description: Library name: sample6


title: HK1_B

description: Library name: sample8


title: CNE2EBV_A

description: Library name: sample4


title: CNE2_C

description: Library name: sample3


title: CNE2_B

description: Library name: sample2


title: pho4(A) pho4(B) strain T=0 (pH 5.5), replicate C

status: Public on Jul 24 2026

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

institute: UNIVERSITAT AUTONOMA BARCELONA

description: Library name: AB_T0_C

data_processing:
Raw reads (fastq format) were transformed into clean reads through fastp  (Chen et al., 2018, PMID: 30423086). The HISAT2 (v2.2.1) was used to align paired-end clean reads to the K. phaffii GS115 reference genome (assembly GCA_000027005.1) to generate BAM files.
Differential gene expression analysis was carried out with the BAM files using DESeq2 (Love et al., 2014, PMID:25516281) and stablishing a |log2(FoldChange)| >= 1 and a p-value <= 0.01, unless otherwise stated.
Assembly: GCA_000027005.1
Supplementary files format and content: File "All_data_FPKM.xlsx" excel file with "Fragment per kilobase Million" data for each sample.
Supplementary files format and content: File "LowvsHigh Pi.xlsx", excel file with diverse comparisons for the low vs high phosphate experiments
Supplementary files format and content: File "Alkali_stress.xlsx", Excel file with diverse comparisons of the pH 5.5 to pH 8.0 time-course experiments

organism: Komagataella phaffii GS115

source_name: whole cell

growth_protocol: For evaluation of the transcriptional response of K. phaffii to alkalinization of the medium cells were grown overnight on YPGly medium. Cultures were then diluted in 100 ml of fresh medium at OD600=0.2 (~ 107 cells/ml) and grown until an OD600 around 0.6. At this point, two 50 ml-aliquots were centrifuged (5 min at 1000xg). For assessment of the effects of phosphate starvation, cells were grown for ~40 h on 20 ml of synthetic medium prepared with Formedium premade mix (ref. CYN0803, Yeast Nitrogen Base without Amino Acids and Phosphate) supplemented with 15 mM KCl, 2% glycerol and 7.35 mM KH2PO4, and adjusted to pH 5.8.

extract_protocol:
Total RNA extraction was carried out as described in (Albacar et al., 2023, PMID: 37013612 ) from three independent cultures of wild-type, pho4(A) (strain PJA-004), pho4(B) (strain PJA-021) and pho4(A) pho4(B) (PJA-026) cells. RNA concentration was assessed by Qubit assay (ThermoFisher) and its integrity with an Agilent 5400 Fragment Analyzer System.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, synthesis of the first strand cDNA was achieved by means of random hexamer primers, followed by the second strand cDNA synthesis using dTTP. After end repair, A-tailing, and adapter ligation, fragments were size selected, PCR amplified, and purified. Libraries were then pooled and subjected to sequencing in a NovaSeq X Plus equipment (Illumina) by Novogene Co., Ltd.

treatment_protocol: For alkalinization experiments, two 50 ml-aliquots were centrifuged (5 min at 1000xg). One aliquot was resuspended in the same volume of fresh YPGly medium plus 50 mM TAPS pH 5.5 (control cells) or in YPGly supplemented with 50 mM TAPS adjusted to pH 8.0 (stressed cells). Samples (15 ml) were taken immediately after resuspension in medium at pH 5.5 (T=0) and, for each stressed culture, after 15, 30 and 60 min, placed on ice and immediately centrifuged (5 min at 1000 xg) at 4 °C. Then one ml of cold H2O was added, and cells were transferred to pre-cooled 1.5 ml screw cap tubes and centrifuged (2 min at 1000 xg) at 4 °C. Finally, the supernatant was removed, and samples were frozen with liquid N2 and stored at -80 ºC. For cultures to be subjected to Pi starvation (low Pi), cells (10 OD600) were centrifuged and washed twice with medium without KH2PO4, whereas for control cultures (high Pi) 2.5 OD600 were taken and washed twice with medium containing 7.35 mM KH2PO4. In all cases, cells were resuspended in 50 ml the appropriate medium and growth resumed for 24 h.  Then, ~5 OD600 of each culture was collected and processed as described above.

value: whole cell


title: SCAF2928t_27424_TCR

first: Huaitian

last: Liu

address: Building 37, Room 3050

department: CCR

institute: NCI

data_processing:
The demultiplexing, the primary analysis output, gene counting and TCR and BCR counting were performed by Cell Ranger Software. Base calling was performed using RTA 3.9.2, demultiplexing was performed using cellranger v6.1.1 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v6.1.1 (STAR 2.7.2a). Sequenced reads were aligned to the 10x Genomics provided human reference sequence (refdata-gex-GRCh38-2020-A).
PBMCs from the 59 patients yielded ≥ 3 cells per isolation with a total of 322897 cells that were merged using the Merge() function. After merging, cells with less than 200 nFeature RNA or more than 10% mitochondrial reads were excluded using Seurat v4.3.0
The V(D)J sequencing data were analyzed with the djvdj R package for single-cell V(D)J data.
Assembly: GRCh38
Supplementary files format and content: H5 file containing per-molecule information for all molecules that contain a valid barcode, a valid UMI, and were assigned with high confidence to a gene or Feature Barcode.
Supplementary files format and content: Filtered_contig_annotations.csv contains annotations of each high-confidence cell barcode.
Library strategy: TCR-Seq

source_name: Prostate cancer patient

extract_protocol:
Whole blood was collected and Lymphocyte separation medium was added and then the samples were centrifuged at 1400 rpm for 30 min. The lymphocyte layer was transferred to a new tube, 1X phosphate-buffered saline (PBS) was added and then centrifuged.The supernatant was discarded and the remaining sample was resuspended in PBS and centrifuged at 800 rpm for 8 mins. The supernatant was again discarded and the sample was then resuspend in freezing media: RPMI + 20% human AB serum.The cells in the samples were counted and frozen in 900 µl of freezing media and 100 µl of DMSO per cryovial.Vials were stored in liquid nitrogen.
Library construction was performed at the Single Cell Analysis Facility, a core service with the Center for Cancer Research at the NCI, Bethesda, MD. scRNA-seq libraries were prepared with the Chromium Next GEM Single Cell 5’Reagent Kits V2 (10X Genomics; PN-1000263, PN-1000265, PN-1000190, PN-1000252, PN-1000253) following the manufacturer’s instruction. Briefly, cells were partitioned into nanoliter-scale Gel-beads-in-Emulsion (GEMs), generated by combining barcoded Gel Beads, a Master Mix containing  cells, and Partitioning Oil onto Chromium Next GEM Chip K. After successful completion of uniform emulsion consistency, the reverse transcription was run overnight to amplify full length cDNA. Simplified cDNA was then used to amplify full-length V(D)J segments, followed V(D)J library construction and 5' gene expression library construction. All the steps including TCR and BCR enrichment libraries and QC steps were performed as described in the 10X Genomics 5’ v2 Single Cell User Guide.

value: Blood

tag: race

value: African American (AA)

tag: lethal prostate_cancer_group

value: Nonlethal


title: CNE2_A

description: Library name: sample1


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB085FON)

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR345WTX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR345WTX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB085FON

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

source_name: Homo sapiens female adult (33 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: dev stage

value: adult

tag: age

value: 33 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

tag: link

value: ENCBS484APA at ENCODE; https://www.encodeproject.org/ENCBS484APA/


title: iPSC_H3K27me3,rep2

description: Library name: sample32

source_name: human iPSCs

tag: tissue

value: human iPSCs


title: iPSC_H3K27me3,rep1

description: Library name: sample31


title: iPSC_H3K27ac,rep2

description: Library name: sample30


title: iPSC_H3K4me1,rep2

description: Library name: sample28


title: iPSC_H3K4me1,rep1

description: Library name: sample27


title: iPSC_H3K4me3,rep1

description: Library name: sample25


title: iPSC_H3K4me3,rep2

description: Library name: sample26


title: ARPE-19_H3K27me3,rep2

description: Library name: sample24

tag: cell line


title: ARPE-19_H3K27me3,rep1

description: Library name: sample23


title: ARPE-19_H3K27ac,rep2

description: Library name: sample22


title: ARPE-19_H3K27ac,rep1

description: Library name: sample21


title: ARPE-19_H3K4me1,rep2

description: Library name: sample20


title: ARPE-19_H3K4me1,rep1

description: Library name: sample19


title: ARPE-19_H3K4me3,rep1

description: Library name: sample17


title: ARPE-19_H3K4me3,rep2

description: Library name: sample18


title: iPSC-RPE_H3K4me1,rep1

description: Library name: sample11

source_name: induced pluripotent stem cell-derived RPE


title: iPSC-RPE_H3K4me3,rep2

description: Library name: sample10

value: induced pluripotent stem cell-derived RPE


title: iPSC-RPE_H3K4me3,rep1

description: Library name: sample9


title: iPSC-RPE_H3K27ac,rep1

description: Library name: sample13


title: hRPE_H3K27me3,rep2

description: Library name: sample8

value: human primary RPE


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB462BZK)

description:
https://www.encodeproject.org/experiments/ENCSR339FTN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR339FTN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB462BZK

source_name: Homo sapiens male adult (42 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: male

value: 42 year

value: ENCBS088ZAD at ENCODE; https://www.encodeproject.org/ENCBS088ZAD/


title: hRPE_H3K27me3,rep1

description: Library name: sample7


title: hRPE_H3K27ac,rep2

description: Library name: sample6


title: iPSC-RPE_H3K27ac,rep2

description: Library name: sample14


title: hRPE_H3K27ac,rep1

description: Library name: sample5


title: hRPE_H3K4me1,rep2

description: Library name: sample4


title: hRPE_H3K4me1,rep1

description: Library name: sample3


title: hRPE_H3K4me3,rep1

description: Library name: sample1


title: hRPE_H3K4me3,rep2

description: Library name: sample2


title: ARPE-19_ChIA-PET,rep2

description: Library name: sampple4

extract_protocol:
Human donor eyes, consented for research, were obtained from the Eye hospital and were approved by the Ethics Committee of Optometry Hospital affiliated to Wenzhou Medical University (2022-121-K-92-01).
When cells grew to 80% confluency, 1% formaldehyde (FA) (Sigma, 47608, St. Louis, MO, USA) and 2 mM ethylene glycol bis (succinimidyl succinate) (EGS) (Thermo Scientific, 21565, Waltham, MA, USA) were added to crosslink cells respectively. 10 million of fixed ARPE-19 or hRPE were used to generate one library. After cells lysis and nuclear permeabilization, the nuclei were digested by restriction digestion of Alu1 (NEB, R0137L, Ipswich, MA, USA) and performed A-tailing and proximity-ligation and sonication into 2-3 kb chromatin DNA. Chromatin fragments were incubated with anti-RNA polymerase II RPB1 (BioLegend, 8WG16, San Diego, CA, USA) or anti-CTCF (HUABIO, ET1703-90) coated protein G beads (Invitrogen, 10009D). Antibody captured chromatin DNA was tagmented by Tn5 transposase (Illumina, FC-121-1031, San Diego, CA, USA), then immobilized on M280 streptavidin dynabeads (Invitrogen, 11205D). PCR amplification was performed on beads and products were purified by AMPure XP beads (Invitrogen, 11206D) and subjected to size selection (300-600 bp) by BluePipin instrument with cassette kit (Sage Science, BDF2010, Beverly, MA, USA). DNA libraries were sequenced on Illumina NovaS4 by paired-end 150 bp.


title: ARPE-19_ChIA-PET,rep1

description: Library name: sampple3


title: hRPE_ChIA-PET,rep2

description: Library name: sampple2


title: hRPE_ChIA-PET,rep1

description: Library name: sampple1


title: iPSC_ChIATAC,rep2

description: Library name: sample6


title: iPSC_ChIATAC,rep1

description: Library name: sample5


title: iPSC-RPE_ChIATAC,rep1

description: Library name: sample3


title: hRPE_ChIATAC,rep2

description: Library name: sample2


title: iPSC_RNA,rep2

description:
Library name: Sample 6
Column name in humna_RPE_TPM.txt:iPSC2


title: hRPE_ChIATAC,rep1

description: Library name: sample1


title: iPSC-RPE_ChIATAC,rep2

description: Library name: sample4


title: iPSC_RNA,rep1

description:
Library name: Sample 5
Column name in human_RPE_TPM.txt:iPSC1


title: iPSC-RPE_RNA,rep2

description:
Library name: Sample 4
Column name in humna_RPE_TPM.txt:iPSC-RPE2


title: hRPE_RNA,rep2

description:
Library name: Sample 2
Column name in humna_RPE_TPM.txt:hRPE2


title: iPSC-RPE_RNA,rep1

description:
Library name: Sample 3
Column name in human_RPE_TPM.txt:iPSC-RPE1


title: iPSC_ATAC, rep2

description: Library name: sample8


title: ARPE-19_ATAC, rep2

description: Library name: sample6


title: ARPE-19_ATAC, rep1

description: Library name: sample5


title: iPSC-RPE_ATAC, rep2

description: Library name: sample4


title: iPSC-RPE_ATAC, rep1

description: Library name: sample3


title: hRPE_ATAC, rep1

description: Library name: sample1


title: hRPE_ATAC, rep2

description: Library name: sample2


title: HCT116, siIGF2BP3, ER stress, 4

city: Vienna

first: Aleksandra

middle: S

last: Anisimova

address: Dr. Bohr Gasse 9

country: Austria

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

description: Library name: siIGF2BP3_TM_4

data_processing:
SLAMseq reads were processed and aligned to human genome hg38 using the nf-core/slamseq analysis pipeline v1.0.0 (Neumann et al., 2019; Ewels et al., 2020) with default parameters.
Assembly: hg38
Supplementary files format and content: csv, gene total and T-C read count, slamdunk output

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

extract_protocol:
Total RNA was extracted using the KingFisher Flex Purification System (Thermo) with the High-Performance RNA Isolation kit (Molecular Tools Shop, Vienna BioCenter). During the isolation RNA was treated with RNase-free DNase I (NEB).
SLAMseq samples were prepared according to the standard SLAMseq protocol described in (Herzog et al., Nature Methods, 2017; Ameres, Herzog, and  Reichholf, Protocol Exchange, 2017). Briefly, total RNA was alkylated with 10 mM iodoacetamide in alkylation buffer (50 mM sodium phosphate buffer pH 8.0, 50% DMSO) at 50°C for 15 min and purified using the KingFisher Flex Purification System. Sequencing libraries were prepared with QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen). Libraries were sequenced on a NovaSeq SP on SR100 (Illumina) at the Vienna BioCenter NGS facility with 30 million reads per sample on average.

treatment_protocol: Endoplasmic reticulum (ER) stress was induced with 5 µg/mL tunicamycin (TM) for 4 hours (1:1000 DMSO was used as a control). ). 4-thiouridine (s4U) was added to cell culture media at 250 µM 2 hours prior collection.

tag: cell type

value: human colorectal carcinoma

value: Tunicamycin (TM)


title: HCT116, siIGF2BP3, ER stress, 1

description: Library name: siIGF2BP3_TM_1

tag: treatment


title: HCT116, siIGF2BP3, ER stress, 3

description: Library name: siIGF2BP3_TM_3


title: HCT116, siIGF2BP3, ER stress, 2

description: Library name: siIGF2BP3_TM_2


title: HCT116, siIGF2BP3, DMSO control, 4

description: Library name: siIGF2BP3_DMSO_4

value: DMSO control


title: HCT116, siIGF2BP3, DMSO control, 3

description: Library name: siIGF2BP3_DMSO_3


title: HCT116, siIGF2BP3, DMSO control, 2

description: Library name: siIGF2BP3_DMSO_2


title: HCT116, siIGF2BP3, DMSO control, 1

description: Library name: siIGF2BP3_DMSO_1


title: HCT116, siIGF2BP2, siIGF2BP3, ER stress, 4

description: Library name: siIGF2BP23_TM_4


title: HCT116, siIGF2BP2, siIGF2BP3, ER stress, 3

description: Library name: siIGF2BP23_TM_3


title: HCT116, siIGF2BP2, siIGF2BP3, ER stress, 1

description: Library name: siIGF2BP23_TM_1


title: HCT116, siIGF2BP2, siIGF2BP3, ER stress, 2

description: Library name: siIGF2BP23_TM_2


title: HCT116, siIGF2BP2, siIGF2BP3, DMSO control, 4

description: Library name: siIGF2BP23_DMSO_4


title: HCT116, siIGF2BP2, siIGF2BP3, DMSO control, 3

description: Library name: siIGF2BP23_DMSO_3


title: HCT116, siIGF2BP2, siIGF2BP3, DMSO control, 1

description: Library name: siIGF2BP23_DMSO_1


title: HCT116, siIGF2BP2, ER stress, 4

description: Library name: siIGF2BP2_TM_4


title: HCT116, siIGF2BP2, ER stress, 3

description: Library name: siIGF2BP2_TM_3


title: HCT116, siIGF2BP2, ER stress, 2

description: Library name: siIGF2BP2_TM_2


title: HCT116, siIGF2BP2, ER stress, 1

description: Library name: siIGF2BP2_TM_1


title: HCT116, siIGF2BP2, DMSO control, 3

description: Library name: siIGF2BP2_DMSO_3


title: HCT116, siIGF2BP2, DMSO control, 4

description: Library name: siIGF2BP2_DMSO_4


title: HCT116, siIGF2BP2, DMSO control, 2

description: Library name: siIGF2BP2_DMSO_2


title: HCT116, siIGF2BP2, DMSO control, 1

description: Library name: siIGF2BP2_DMSO_1


title: HCT116, siControl, ER stress, 3

description: Library name: siControl_TM_3


title: HCT116, siControl, ER stress, 2

description: Library name: siControl_TM_2


title: hRPE_RNA,rep1

description:
Library name: Sample 1
Column name in human_RPE_TPM.txt:hRPE1


title: iPSC_ATAC, rep1

description: Library name: sample7


title: HCT116, siControl, ER stress, 1

description: Library name: siControl_TM_1


title: HCT116, siControl, DMSO control, 3

description: Library name: siControl_DMSO_3


title: HCT116, siControl, DMSO control, 4

description: Library name: siControl_DMSO_4


title: HCT116, siControl, DMSO control, 2

description: Library name: siControl_DMSO_2


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, ER stress, auxin, 4

description: Library name: WTmAIDIGF2BP3_TM_IAA_4

growth_protocol: HCT116 conditionally expressing doxycycline-inducible (tetON) OsTIR1 were obtained from the Masato Kanemaki lab (Natsume et al. 2016).   HCT116 cells were cultured in McCoy’s 5A (modified) medium (Sigma, M9309) supplemented with 10% fetal bovine serum (Gibco, 10437028), 2 mM L-Glutamine (Sigmam, G7513), 1% Pen/Step (Sigma, P0781) in a humidified incubator at 37°C and 5% CO2. Generation of the HCT116 mAID-IGF2BP3 cell line (endogenously tagged, homozygous) was done accordingly to the protocol described in Yesbolatova et al.,  2019.

treatment_protocol: To induce expression of OsTIR1 cells were treated with 200 ng/mL doxycycline for 24 hours. mAID-IGF2BP3 depletion was induced with IAA added to the cell culture media at 500 μM for 9 hours and ER stress was induced with 5 µg/mL tunicamicin (TM) for 5 hours (1:1000 DMSO was used as a control). 4-thiouridine (s4U) was added to cell culture media at 250 µM for 2 hours. All indicated treatment times are hours prior to collection. One ~80% confluent well of 24-well plate was used per condition, experiment was performed in quadruplicate.

tag: genotype

value: Tet-OsTIR1-PURO, mAID-IGF2BP3

value: Doxycycline, tunicamycin (TM),  auxin


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, ER stressl, auxin, 3

description: Library name: WTmAIDIGF2BP3_TM_IAA_3


title: HCT116, siControl, DMSO control, 1

description: Library name: siControl_DMSO_1


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, ER stress, auxin, 2

description: Library name: WTmAIDIGF2BP3_TM_IAA_2


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, ER stress, DMSO control, 4

description: Library name: WTmAIDIGF2BP3_TM_DMSO_4

value: Doxycycline, tunicamycin (TM),  DMSO control


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, ER stress, auxin, 1

description: Library name: WTmAIDIGF2BP3_TM_IAA_1


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, ER stress, DMSO control, 3

description: Library name: WTmAIDIGF2BP3_TM_DMSO_3


title: mAbCD73,rep2

description: Library name: sample17

value: Peripheral blood

value: NK cells

value: Primary cells

value: WT

value: the supernatant of HK1+EBV treated with 10ug/ml CD73 antibody for two hours, then 500ng/mL AMP


title: mAbCD73,rep1

description: Library name: sample16


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, ER stress, DMSO control, 1

description: Library name: WTmAIDIGF2BP3_TM_DMSO_1


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, DMSO control, auxin, 4

description: Library name: WTmAIDIGF2BP3_Control_IAA_4

value: Doxycycline, DMSO control,  auxin


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, ER stress, DMSO control, 2

description: Library name: WTmAIDIGF2BP3_TM_DMSO_2


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, DMSO control, auxin, 3

description: Library name: WTmAIDIGF2BP3_Control_IAA_3


title: Ctrl,rep2

description: Library name: sample14

value: the supernatant of HK1+EBV treated with 10ug/ml control antibody for two hours, then 500ng/mL AMP


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, DMSO control, auxin, 1

description: Library name: WTmAIDIGF2BP3_Control_IAA_1


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, DMSO control, auxin, 2

description: Library name: WTmAIDIGF2BP3_Control_IAA_2


title: HK1+EBV,rep2

description: Library name: sample11

value: the supernatant of  HK1+EBV treated with 500ng/mL AMP


title: HCT116, siIGF2BP2, siIGF2BP3, DMSO control, 2

description: Library name: siIGF2BP23_DMSO_2


title: HCT116 tetON OsTIR1 mAID-IGF2BP3 mAID-IGF2BP3, DMSO control, DMSO control, 1

description: Library name: WTmAIDIGF2BP3_Control_DMSO_1

value: Doxycycline, DMSO control,  DMSO control


title: HCT116 tetON OsTIR1 mAID-IGF2BP3 mAID-IGF2BP3, DMSO control, DMSO control, 2

description: Library name: WTmAIDIGF2BP3_Control_DMSO_2


title: HCT116 tetON OsTIR1, ER stress, auxin, 4

description: Library name: WT_TM_IAA_4


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, DMSO control, DMSO control, 4

description: Library name: WTmAIDIGF2BP3_Control_DMSO_4


title: HCT116 tetON OsTIR1 mAID-IGF2BP3, DMSO control, DMSO control, 3

description: Library name: WTmAIDIGF2BP3_Control_DMSO_3


title: HCT116 tetON OsTIR1, ER stressl, auxin, 3

description: Library name: WT_TM_IAA_3


title: HCT116 tetON OsTIR1, ER stress, auxin, 2

description: Library name: WT_TM_IAA_2


title: HK1EBV_B

description: Library name: sample11

value: nasopharyngeal carcinoma cell line

value: EBV treatment


title: HK1EBV_C

description: Library name: sample12


title: HCT116 tetON OsTIR1, ER stress, auxin, 1

description: Library name: WT_TM_IAA_1

value: human colorectal carcinoma


title: HCT116 tetON OsTIR1, ER stress, DMSO control, 3

description: Library name: WT_TM_DMSO_3


title: HCT116 tetON OsTIR1, ER stress, DMSO control, 2

description: Library name: WT_TM_DMSO_2


title: HCT116 tetON OsTIR1, ER stress, DMSO control, 4

description: Library name: WT_TM_DMSO_4


title: CNE2EBV_B

description: Library name: sample5


title: HCT116 tetON OsTIR1, DMSO control, auxin, 4

description: Library name: WT_Control_IAA_4


title: HCT116 tetON OsTIR1, ER stress, DMSO control, 1

description: Library name: WT_TM_DMSO_1


title: HCT116 tetON OsTIR1, DMSO control, auxin, 3

description: Library name: WT_Control_IAA_3


title: HCT116 tetON OsTIR1, DMSO control, auxin, 2

description: Library name: WT_Control_IAA_2


title: HCT116 tetON OsTIR1, DMSO control, auxin, 1

description: Library name: WT_Control_IAA_1


title: HCT116 tetON OsTIR1, DMSO control, DMSO control, 4

description: Library name: WT_Control_DMSO_4


title: HCT116 tetON OsTIR1, DMSO control, DMSO control, 3

description: Library name: WT_Control_DMSO_3


title: HCT116 tetON OsTIR1, DMSO control, DMSO control, 2

description: Library name: WT_Control_DMSO_2


title: HCT116, siControl, ER stress, 4

description: Library name: siControl_TM_4

value: Tunicamycin (TM)


title: HCT116 tetON OsTIR1, DMSO control, DMSO control, 1

description: Library name: WT_Control_DMSO_1


title: sgIGF2BP3, siIGF2BP3, 3

description: Library name: IGF2BP3_siIGF2BP3_3

data_processing:
Basecalling was performed using Real-Time Analysis (RTA) v1.18.54.4. BCL files were converted to demultiplexed fastq files with bcl2fastq v2.20.0.422.
The quality-, adapter-, and polyA-trimmed reads were aligned to human genome hg38 using GENCODE annotation (release 36) with STAR v2.7.5c. As the reads originate from SLAMseq protocol and have T to C transitions, 5 mismatches were allowed.
Assembly: hg38
Supplementary files format and content: csv, gene total read counts

source_name: RKO

growth_protocol: RKO cells expressing doxycycline-inducible Cas9 were a kind gift from Johannes Zuber (IMP, Vienna, Austria) (de Almeida et al., 2021 ). RKO cells were cultured in RPMI-1640 media (Sigma, R8758) supplemented with 10% fetal bovine serum (Gibco, 10437028), 2 mM L-Glutamine (Sigmam, G7513), 1% Pen/Step (Sigma, P0781), 1x non-essential amino acids (Thermo Scientific, 11140050), and 1 mM sodium pyruvate (Gibco, 11360070) in a humidified incubator at 37°C and 5% CO2. RKO-Dox-Cas9 (iCas9) cell lines for doxycycline-inducible knockout of IGF2BP3 or IGF2BP2 were established  using lentiviral transduction with lentiviral particles (produced as described in (Hornegger, H. et al. ) containing Dual-sgRNA_hU6-mU6 vectors described in (de Almeida et al., 2021 ) expressing two sgRNAs against IGF2BP3 (5′ TGGCACCGACTGATAGAGCT 3′ and 5′ GAAGATACTTTCTAGGTCCG 3′), or against IGF2BP2 (5′ ATATGTGACGTTGACAACGG 3′ and 5′ GTGCGCTGAGGTTCAACCCT 3′), or against non-coding locus AAVS1 (5’ CGCTGTGCCCCGATGCACAC 3’ and 5′ GGCGCGTCGCTCGCTCGCTC 3′) from human and mouse U6 promoters and eBFP2 from a PGK promoter. The eBFP2-positive cells were FACS sorted at BD FACSMelody™ Cell Sorter at Max Perutz Labs BioOptics FACS Facility.

extract_protocol:
Total RNA was extracted using the KingFisher Flex Purification System (Thermo) with the High-Performance RNA Isolation kit (Molecular Tools Shop, Vienna BioCenter). During the isolation RNA was treated with RNase-free DNase I (NEB).
SLAMseq samples were prepared according to the standard SLAMseq protocol described in (Herzog et al., Nature Methods, 2017; Ameres, Herzog, and  Reichholf, Protocol Exchange, 2017). Briefly, total RNA was alkylated with 10 mM iodoacetamide in alkylation buffer (50 mM sodium phosphate buffer pH 8.0, 50% DMSO) at 50°C for 15 min and purified using the KingFisher Flex Purification System. Sequencing libraries were prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7765L). Libraries were sequenced on a NovaSeq SP on SR100 (Illumina) at the Vienna BioCenter NGS facility with 30 million reads per sample on average.

treatment_protocol: IGF2BP3 or IGF2BP2 depletion was induced in RKO iCas9 cells with 250 ng/mL doxycycline for 72 hours. For siRNA knockdown, cells were transfected with ON-TARGETplus Human IGF2BP2 (Dharmacon, L-017705-00-0005) or IGF2BP3 (Dharmacon, L-003976-00-0005) SMARTpool siRNAs  at 75 nM for 48 hours using DharmaFECT 2 (Dharmacon, T-2002-01). ON-TARGETplus nontargeting siRNA #1 (Dharmacon, D-001810-01-05) was used as a control. 4-thiouridine (s4U) was added to cell culture media at 250 µM for 2 hours. One ~80% confluent well of 24-well plate was used per condition, experiment was performed in quadruplicate.

value: RKO

value: Dox-inducible Cas9, GFP, sgIGF2BP3 - BFP

value: no treatment


title: sgIGF2BP3, siIGF2BP3, 4

description: Library name: IGF2BP3_siIGF2BP3_4


title: sgIGF2BP3, siIGF2BP3, 2

description: Library name: IGF2BP3_siIGF2BP3_2


title: sgIGF2BP3, siControl, 4

description: Library name: IGF2BP3_siControl_4


title: sgIGF2BP3, siIGF2BP3, 1

description: Library name: IGF2BP3_siIGF2BP3_1


title: sgIGF2BP3, siControl, 3

description: Library name: IGF2BP3_siControl_3


title: iPSC_H3K27ac,rep1

description: Library name: sample29

value: human iPSCs


title: sgIGF2BP3, siControl, 2

description: Library name: IGF2BP3_siControl_2


title: sgIGF2BP3, siControl, 1

description: Library name: IGF2BP3_siControl_1


title: sgIGF2BP3, Dox, 3

description: Library name: IGF2BP3_DOX_3

value: DOX


title: sgIGF2BP3, Dox, 4

description: Library name: IGF2BP3_DOX_4


title: sgIGF2BP3, Dox, 1

description: Library name: IGF2BP3_DOX_1


title: sgIGF2BP3, DMSO control, 4

description: Library name: IGF2BP3_DMSO_4

value: DMSO control


title: sgIGF2BP3, Dox, 2

description: Library name: IGF2BP3_DOX_2


title: sgIGF2BP3, DMSO control, 3

description: Library name: IGF2BP3_DMSO_3


title: sgIGF2BP2, siIGF2BP2, 3

description: Library name: IGF2BP2_siIGF2BP2_3

value: Dox-inducible Cas9, GFP, sgIGF2BP2 - BFP


title: sgIGF2BP2, siIGF2BP2, 4

description: Library name: IGF2BP2_siIGF2BP2_4


title: sgIGF2BP3, DMSO control, 2

description: Library name: IGF2BP3_DMSO_2


title: Batch2_AKG1

description: Library name: Batch2_AKG1

value: brain


title: sgIGF2BP3, DMSO control, 1

description: Library name: IGF2BP3_DMSO_1


title: sgIGF2BP2, siControl, 3

description: Library name: IGF2BP2_siControl_3


title: iPSC-RPE_H3K27me3,rep2

description: Library name: sample16

value: induced pluripotent stem cell-derived RPE


title: sgIGF2BP2, siIGF2BP2, 1

description: Library name: IGF2BP2_siIGF2BP2_1


title: sgIGF2BP2, siIGF2BP2, 2

description: Library name: IGF2BP2_siIGF2BP2_2


title: sgIGF2BP2, siControl, 2

description: Library name: IGF2BP2_siControl_2


title: sgIGF2BP2, Dox, 4

description: Library name: IGF2BP2_DOX_4


title: sgIGF2BP2, siControl, 1

description: Library name: IGF2BP2_siControl_1


title: sgIGF2BP2, Dox, 3

description: Library name: IGF2BP2_DOX_3


title: sgIGF2BP2, Dox, 2

description: Library name: IGF2BP2_DOX_2


title: sgIGF2BP2, DMSO control, 2

description: Library name: IGF2BP2_DMSO_2


title: sgIGF2BP2, Dox, 1

description: Library name: IGF2BP2_DOX_1


title: sgIGF2BP2, DMSO control, 1

description: Library name: IGF2BP2_DMSO_1


title: sgIGF2BP2, DMSO control, 3

description: Library name: IGF2BP2_DMSO_3


title: sgAAVS1, Dox, 4

description: Library name: AAVS1_DOX_4

value: Dox-inducible Cas9, GFP, sgAAVS1 - BFP


title: sgAAVS1, Dox, 3

description: Library name: AAVS1_DOX_3


title: sgAAVS1, Dox, 1

description: Library name: AAVS1_DOX_1


title: sgAAVS1, DMSO control, 2

description: Library name: AAVS1_DMSO_2


title: sgAAVS1, Dox, 2

description: Library name: AAVS1_DOX_2


title: sgAAVS1, DMSO control, 4

description: Library name: AAVS1_DMSO_4


title: sgAAVS1, DMSO control, 3

description: Library name: AAVS1_DMSO_3


title: sgAAVS1, DMSO control, 1

description: Library name: AAVS1_DMSO_1


title: Ribo-Seq, siIGF2BP3, ER stress, 2

description: Library name: siIGF2BP3_TM_2

library_source: other

data_processing:
For GEO submission original demultiplexed files representig three replicates were additionally demultiplexed to separate single samples according 5'adapter indexes using cutadapt 5.0 allowing up to one mismatch per adapter sequence. For data processing UMI and sample indexes were transferred to the read name with UMI-tools 1.1.6 (as UMI and cell barcode respectively) and trimmed of the adapater sequence. Note that first two nucleotides at the 5' end of the read originate from the RT primer and have to be trimmed.  The quality- and adapter-trimmed reads were aligned to human genome hg38 using GENCODE annotation (release 36) with STAR v2.7.5c allowing up to one mismatch per read. The alignments were demultiplexed to separate single samples according 5'adapter indexes and deduplicated using UMI-tools 1.1.6. Gene read counts were obtained with featureCounts v2.0.1.
Assembly: hg38
Supplementary files format and content: csv, gene read count table
Library strategy: Ribo-Seq

molecule: other

extract_protocol:
One ~80% confluent well of a 6-well plate per condition (three biological replicates per condition) was washed with ice-cold PBS (Sigma) supplemented with 100 mg/mL cycloheximide, lysed on a plate on ice with 350 μL of ice-cold lysis buffer (20 mM HEPES pH 7.3, 150 mM KCl, 5 mM MgCl2, 1% Triton X-100, 100 mg/mL cycloheximide, 1 mM DTT, 1x EDTA-free protease inhibitor cocktail), scraped, and transferred to 1.5 mL RNase-free tube. Cell lysates were passed three times through the 27G needle, incubated on ice for 10 min with intermittent vortexing, and clarified on a table-top centrifuge at maximum speed (20,000 g) for 20 min at 4°C. Total RNA concentration in the lysate was estimated using OD A260 measurement on Nanodrop. The lysate concentrations were brought to 240 ng/μL, 15 μL aliquots were taken for matching RNA-Seq. 200 μL of the lysate were supplemented with 5 mM CaCl2, 2 U/μL DNase I (NEB), 0.65 μg of micrococcal nuclease (Sigma, 10107921001), and 0.7 U of RNase I (Ambion) and incubated at room temperature for one hour on a rotator. The lysate was layered on 10%-50% sucrose gradient and centrifugated at 35,000 g for 3 hours at 4°C in a SW40Ti rotor. Polysome fractions were separated on a BioComp  fractionator and monosome fractions were collected.
Ribo-Seq libraries were prepared as described in (McGlincy and Ingolia, 2017) with the following changes. rRNA was depleted from samples after adapter ligation using human riboPOOL probes (siTOOLs) according to the manufacturer’s instructions, purified with Oligo Clean & Concentrator kit, and eluted in 12 μL of RNase-free water. Reverse transcription was done with SuperScript III (Invitrogen). Oligonucleotides used for Ribo-Seq are listed below. Preadenylated 5' adapter sequence is NNNNNNNNNNAGATCGGAAGAGCACACGTCTGAA. First five nucleotides of the adapter are UMI, while next five nuclotides are a sample index allowing multiplexing during library preparation. Samples barcodes are: ATCGT - siControl_DMSO, CGTAA - siIGF2BP2_DMSO, CTAGA - siIGF2BP3_DMSO, GATCA - siControl_TM, TAGAC - siIGF2BP2_TM, TCTAG - siIGF2BP3_TM. Reverse transcription primer sequence RNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG/iSp18/GTGACTGGAGTTCAGACGTGTGCTC. Libraries were sequenced on a NovaSeq SP on SR100 (Illumina) at the Vienna BioCenter NGS facility with 60 million reads per sample on average.

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


title: Ribo-Seq, siIGF2BP3, DMSO control, 3

description: Library name: siIGF2BP3_DMSO_3


title: Ribo-Seq, siIGF2BP3, ER stress, 3

description: Library name: siIGF2BP3_TM_3


title: Ribo-Seq, siIGF2BP3, ER stress, 1

description: Library name: siIGF2BP3_TM_1


title: Ribo-Seq, siIGF2BP2, ER stress, 3

description: Library name: siIGF2BP2_TM_3


title: Ribo-Seq, siIGF2BP3, DMSO control, 2

description: Library name: siIGF2BP3_DMSO_2


title: Ribo-Seq, siIGF2BP2, ER stress, 1

description: Library name: siIGF2BP2_TM_1


title: Ribo-Seq, siIGF2BP2, DMSO control, 3

description: Library name: siIGF2BP2_DMSO_3


title: Ribo-Seq, siIGF2BP3, DMSO control, 1

description: Library name: siIGF2BP3_DMSO_1


title: Ribo-Seq, siIGF2BP2, DMSO control, 2

description: Library name: siIGF2BP2_DMSO_2


title: Ribo-Seq, siControl, DMSO control, 3

description: Library name: siControl_DMSO_3


title: Ribo-Seq, siControl, ER stress, 1

description: Library name: siControl_TM_1


title: Ribo-Seq, siIGF2BP2, DMSO control, 1

description: Library name: siIGF2BP2_DMSO_1


title: Ribo-Seq, siControl, DMSO control, 2

description: Library name: siControl_DMSO_2


title: Ribo-Seq, siControl, ER stress, 3

description: Library name: siControl_TM_3


title: siIGF2BP3, ER stress, 3

description: Library name: TM_IGF2BP3_3

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

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


title: siIGF2BP3, ER stress, 1

description: Library name: TM_IGF2BP3_1


title: siIGF2BP3, DMSO control, 2

description: Library name: DMSO_IGF2BP3_2


title: siIGF2BP3, DMSO control, 1

description: Library name: DMSO_IGF2BP3_1


title: siIGF2BP2, ER stress, 1

description: Library name: TM_IGF2BP2_1


title: siIGF2BP2, ER stress, 3

description: Library name: TM_IGF2BP2_3


title: siIGF2BP2, DMSO control, 3

description: Library name: DMSO_IGF2BP2_3


title: siControl, ER stress, 3

description: Library name: TM_siControl_3


title: siControl, ER stress, 1

description: Library name: TM_siControl_1


title: siControl, DMSO control, 1

description: Library name: DMSO_siControl_1


title: ER stress (TM), IGF2BP2 KO, clone F6, 2

description: Library name: TM_IGF2BP2KO_F6_rep2

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

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

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

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

value: IGF2BP2 KO, clone F6, Tet-OsTIR1-PURO


title: ER stress (TM), IGF2BP3 KO, clone A3, 2

description: Library name: TM_IGF2BP3KO_A3_rep2

value: IGF2BP3 KO, clone A3, Tet-OsTIR1-PURO


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB714ICB)

description:
https://www.encodeproject.org/experiments/ENCSR725BGI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR725BGI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB714ICB

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: adult

value: 40 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS384WYW at ENCODE; https://www.encodeproject.org/ENCBS384WYW/


title: sgIGF2BP2, siControl, 4

description: Library name: IGF2BP2_siControl_4

value: RKO

value: human colorectal carcinoma

value: no treatment


title: ER stress (TM), parental, sample 2, 2

description: Library name: TM_parental_2_rep2

value: Tunicamycin (TM)


title: sgIGF2BP2, DMSO control, 4

description: Library name: IGF2BP2_DMSO_4

value: Dox-inducible Cas9, GFP, sgIGF2BP2 - BFP

value: DMSO control


title: ER stress (TM), parental, sample 1, 2

description: Library name: TM_parental_1_rep2


title: Control, IGF2BP2 KO, clone F6, 2

description: Library name: Control_IGF2BP2KO_F6_rep2


title: Control, IGF2BP2 KO, clone B7, 2

description: Library name: Control_IGF2BP2KO_B7_rep2

value: IGF2BP2 KO, clone B7, Tet-OsTIR1-PURO


title: Control, IGF2BP3 KO, clone E4, 2

description: Library name: Control_IGF2BP3KO_E4_rep2

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


title: Ribo-Seq, siIGF2BP2, ER stress, 2

description: Library name: siIGF2BP2_TM_2


title: Control, IGF2BP3 KO, clone D12, 2

description: Library name: Control_IGF2BP3KO_D12_rep2

value: IGF2BP3 KO, clone D12, Tet-OsTIR1-PURO


title: Control, IGF2BP3 KO, clone A3, 2

description: Library name: Control_IGF2BP3KO_A3_rep2

value: IGF2BP3 KO, clone A3, Tet-OsTIR1-PURO


title: Ribo-Seq, siControl, ER stress, 2

description: Library name: siControl_TM_2


title: siIGF2BP3, ER stress, 2

description: Library name: TM_IGF2BP3_2


title: Ribo-Seq, siControl, DMSO control, 1

description: Library name: siControl_DMSO_1


title: siIGF2BP2, ER stress, 2

description: Library name: TM_IGF2BP2_2


title: siIGF2BP3, DMSO control, 3

description: Library name: DMSO_IGF2BP3_3


title: ER stress (TM), IGF2BP2 KO, clone F6, 1

description: Library name: TM_IGF2BP2KO_F6_rep1

value: IGF2BP2 KO, clone F6, Tet-OsTIR1-PURO


title: ER stress (TM), IGF2BP2 KO, clone B7, 1

description: Library name: TM_IGF2BP2KO_B7_rep1


title: siIGF2BP2, DMSO control, 1

description: Library name: DMSO_IGF2BP2_1


title: siControl, ER stress, 2

description: Library name: TM_siControl_2


title: ER stress (TM), IGF2BP3 KO, clone D12, 1

description: Library name: TM_IGF2BP3KO_D12_rep1


title: ER stress (TM), IGF2BP3 KO, clone A3, 1

description: Library name: TM_IGF2BP3KO_A3_rep1


title: ER stress (TM), parental, sample 1, 1

description: Library name: TM_parental_1_rep1


title: ER stress (TM), parental, sample 2, 1

description: Library name: TM_parental_2_rep1


title: Control, IGF2BP2 KO, clone G6, 1

description: Library name: Control_IGF2BP2KO_G6_rep1

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


title: Control, IGF2BP2 KO, clone F6, 1

description: Library name: Control_IGF2BP2KO_F6_rep1


title: ER stress (TM), IGF2BP2 KO, clone B7, 2

description: Library name: TM_IGF2BP2KO_B7_rep2


title: Control, IGF2BP2 KO, clone B7, 1

description: Library name: Control_IGF2BP2KO_B7_rep1


title: Control, IGF2BP3 KO, clone E4, 1

description: Library name: Control_IGF2BP3KO_E4_rep1


title: Control, IGF2BP3 KO, clone D12, 1

description: Library name: Control_IGF2BP3KO_D12_rep1


title: ER stress (TM), IGF2BP3 KO, clone E4, 2

description: Library name: TM_IGF2BP3KO_E4_rep2


title: Control, parental, sample 2, 1

description: Library name: Control_parental_2_rep1


title: total RNA-seq from T-helper 1 cell (ENCLB552YEV)

description:
https://www.encodeproject.org/experiments/ENCSR716NJG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR716NJG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB552YEV

source_name: Homo sapiens female adult (33 years) T-helper 1 primary cell treated with 50 U/mL Interleukin-2 for 16 hours

value: T-helper 1 cell

value: primary cell

value: female

value: adult

value: 33 year

tag: treatments

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:16; duration_units:hour;

value: ENCBS068GNE at ENCODE; https://www.encodeproject.org/ENCBS068GNE/


title: IGF2BP3 PAR-CLIP, TM 4 hours, 3

description:
Library name: S141_TM_4h_3
PAR-CLIP

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

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

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

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

value: human colorectal carcinoma

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

tag: par-clip antibody


title: IgG PAR-CLIP, TM 4 hours, 1

description:
Library name: S141_IgG_TM_4h
PAR-CLIP

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB018ZEJ)

description:
https://www.encodeproject.org/experiments/ENCSR711IBG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR711IBG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB018ZEJ

value: CD4-positive, alpha-beta T cell

value: 40 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS878DSI at ENCODE; https://www.encodeproject.org/ENCBS878DSI/


title: IgG PAR-CLIP, TM 1 hour, 1

description:
Library name: S141_IgG_TM_1h
PAR-CLIP

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


title: IGF2BP3 PAR-CLIP, TM 4 hours, 2

description:
Library name: S142_TM_4h_2
PAR-CLIP


title: IGF2BP3 PAR-CLIP, DMSO control for TM samples, 3

description:
Library name: S141_DMSO_3
PAR-CLIP

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


title: IGF2BP3 PAR-CLIP, TM 1 hour, 3

description:
Library name: S141_TM_1h_3
PAR-CLIP


title: snATAC-seq from heart left ventricle (ENCLB852ZPM)

description:
https://www.encodeproject.org/experiments/ENCSR033ENA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR033ENA
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB852ZPM
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (45 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

value: male

tag: health state

value: healthy

value: 45 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS042LKH at ENCODE; https://www.encodeproject.org/ENCBS042LKH/

value: Derived from ENCODE donor ENCDO894OKI; https://www.encodeproject.org/ENCDO894OKI/


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

description:
Library name: S142_TM_1h_1
PAR-CLIP

value: human colorectal carcinoma


title: IGF2BP3 PAR-CLIP, TM 4 hours, 1

description:
Library name: S142_TM_4h_1
PAR-CLIP

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


title: IGF2BP3 PAR-CLIP, DMSO control for TM samples, 1

description:
Library name: S142_DMSO_1
PAR-CLIP


title: IgG PAR-CLIP, Arsenite, 1

description:
Library name: S143_IgG_Arsenite
PAR-CLIP

value: 4-thiouridine (4sU) 100 μM 15h, sodium arsenate 250 μM 2h

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


title: IGF2BP3 PAR-CLIP, Arsenite, 3

description:
Library name: S143_Arsenite_3
PAR-CLIP


title: IgG PAR-CLIP, Control for Arsenite samples, 1

description:
Library name: S143_IgG_Control
PAR-CLIP

value: 4-thiouridine (4sU) 100 μM 15h, PBS 1:1000 2h


title: IGF2BP3 PAR-CLIP, Arsenite, 2

description:
Library name: S143_Arsenite_2
PAR-CLIP


title: IGF2BP3 PAR-CLIP, Arsenite, 1

description:
Library name: S143_Arsenite_1
PAR-CLIP


title: IGF2BP3 PAR-CLIP, Control for Arsenite samples, 3

description:
Library name: S143_Control_3
PAR-CLIP


title: IGF2BP3 PAR-CLIP, Control for Arsenite samples, 1

description:
Library name: S143_Control_1
PAR-CLIP


title: Peripheral_Monocytes_UC06

city: London

first: Eve

last: Hornsby

address: 4 Newark St

department: Blizard Institue/CIB

country: United Kingdom

institute: QMUL

description: 10x Genomics

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

source_name: Peripheral Blood

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

value: Peripheral Blood

tag: diagnosis

value: Ulcerative Colitis

value: Total monocytes


title: IGF2BP3 PAR-CLIP, Control for Arsenite samples, 2

description:
Library name: S143_Control_2
PAR-CLIP


title: Peripheral_Monocytes_UC05

description: 10x Genomics


title: Peripheral_Monocytes_UC04

description: 10x Genomics


title: Peripheral_Monocytes_UC02

description: 10x Genomics


title: MIAML-101-Re

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

description: human leukemic bone marrow mononuclear cells single cell Drop-seq

data_processing:
Two paired-end fastq files were converted to one query-sorted bam file using Picard tools v2.6.0 and samtools v1.2.
Sequence reads were tagged with cell and molecular barcodes, filtered for low base quality in cell or molecular barcodes, trimmed for starting sequence and polyA tail using Drop-seq tools v1.13.
The barcode-tagged, filtered and trimmed bam file is converted back to fastq file using Picard tools v2.6.0.
Alignment was performed using Star v2.5.2a.
Aligned reads were tagged with gene exons and cleaned for bead synthesis errors using Drop-seq tools v1.13.
Gene expression matrix was generated using Drop-seq tools v1.13.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw UMI counts for each cell (column) and each gene (row)

source_name: leukemic bone marrow (AML)

growth_protocol: Cryo-preserved bone marrow mononuclear cells or peripheral blood mononuclear cells from AML patients or healthy donors (STEMCELL Technologies) were thawed in a 37 °C water bath, dissociated by DNase I solution (New England Biolabs) treatment at a final concentration of 0.1 mg/mL and filtered through 40 μm cell strainers (Corning Life Sciences) to remove clumped cells. Isolated single cells were transferred into warm culture media (RPMI1640 supplemented with 10% FBS) and incubated at 37 °C for 2 hours. Then dead cells in the culture were eliminated using a dead cell removal kit from Miltenyi Biotec following the manufacturer’s protocol. The remaining viable single cells were counted and resuspended at 100 cells/ μl in a PBS-BSA solution.

extract_protocol:
Single-cell RNA sequencing was performed following the Drop-seq Online Protocol by Macosko et al (http://mccarrolllab.com/dropseq/) with minor modifications. Briefly, single cell suspension were loaded into the microfluidic device (FlowJEM) together with droplet-generating oil (Bio-Rad) and barcoded beads (MACOSKO-2011-10, Chemgenes) suspended in lysis buffer supplemented with RNase inhibitor (Lucigen) at a final concentration of 1 U/µL. Emulsions were incubated on ice for 30 minutes before droplet breakage and bead collection. Beads were subject to reverse transcription (Maxima H Minus Reverse Transcriptase: ThermoFisher; Template switch oligo: IDT) and Exo I (New England Biolabs) digestion. Next, 4000 beads were aliquoted into one PCR tube for amplification (KAPA HotStart ReadyMix: Kapa Biosystems). Products from multiple parallel PCRs were pooled together and purified using AMPure XP Beads (Beckman Coulter Life Sciences).
For each sample, 1 ng high quality cDNA was used for tagmentation and NGS library preparation using a Nextera XT kit (Illumina). High quality NGS libraries were sequenced on an Illumina NextSeq 550 (75-cycle kit) or NovaSeq 6000 (100-cycle kit) sequencers. All paired AML samples were processed and sequenced together to minimize batch effects.

tag: ex vivo treatment

value: untreated

value: bone marrow

tag: disease state

value: AML

tag: time point

value: at relapse


title: Peripheral_Monocytes_UC01

description: 10x Genomics


title: Peripheral_Monocytes_CD06

description: 10x Genomics

value: Crohn's Disease


title: Peripheral_Monocytes_CD04

description: 10x Genomics


title: Peripheral_Monocytes_CD02

description: 10x Genomics


title: Peripheral_Monocytes_CD03

description: 10x Genomics


title: Peripheral_Monocytes_CD01

description: 10x Genomics


title: Peripheral_Monocytes_HC08

description: 10x Genomics

value: Healthy Control