title: Ucn3_RNAs_2_Mother

description: Library name: Ucn3_RNA_2_Mother


title: A549 cells, RELA ChIP, Ad-IκBαΔN, I+B, 1h, rep 2

status: Public on Jan 12 2026

type: SRA

city: Calgary

first: Alex

last: Gao

state: Alberta

address: 3330 Hospital Dr NW

department: Physiology and Pharmacology

country: Canada

institute: University of Calgary

description: Library name: Sample 24

library_source: genomic

data_processing:
Demultiplexing was performed using bcl2fastq conversion software (v2.18.0.12) and read quality was assessed using FastQC (v0.10.1).
Good-quality reads were mapped to GRCh38 reference genome using bowtie2 (v2.4.4) and the resultant BAM files were sorted and indexed using samtools (v) prior to peak calling using MACS2 (v2.2.7.1). MACS-identified peaks for GR and RELA were assessed by DiffBind R package (v3.2) to calculate differential binding in response to each treatment compared to no stimulation.
Due to the variability between the Ad-IκBαΔN ChIP samples in the number of reads that were successfully mapped to the reference genome, BAM files were normalized to account for such differences before the post-normalization “.bigwig” files were used for graphical representation in heatmaps and data summarization.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes peak names, locations, binding intensity, and behaviour upon combination treatment
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: The human pulmonary type II cell line, A549, was grown under standard culture condition using Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 2mM L-glutamine. Cells were incubated at 37°C in 5% CO2 and were grown to confluence either in 100mm, or 6/12/24-well plates, as appropriate. Prior to experiments, cells were incubated overnight in basal media that was serum- and additive-free.

extract_protocol:
Protein-DNA cross-linking was performed by adding methanol-free formaldehyde to 1% in the culture medium and incubating for 10 min at room temperature. Formaldehyde was then quenched at room temperature for 5 min with 125mM glycine prior to washing cells for 5 min with ice-cold PBS and scraping into ice-cold lysis buffer (5mM PIPES pH 8.0, 1mM EDTA, 85mM KCl, 5% glycerol, 0.5% NP-40) supplemented with protease inhibitor cocktail (PIC). Cell suspensions were incubated at 4°C for 3 h with continuous agitation. Nuclei were collected by centrifugation (600 g, 5 min, 4°C) and resuspended in ice-cold nuclei lysis buffer (NLB) (1xPBS containing 1mM EDTA, 5% glycerol, 0.5% sodium deoxycholate, 0.1% SDS, 1% NP-40) supplemented with PIC. Samples were sonicated at 4°C using a Bioruptor set for 28 – 30 high-power bursts with 30 s on-off cycles. Lysates were cleared by centrifugation (maximum speed for 15 min at 4°C) and supernatants used for immunoprecipitation. Protein G magnetic Dynabeads were preincubated with primary antibody (2.5µl/sample) overnight at 4 °C in NLB supplemented with PIC and 5 mg/ml BSA. After washing twice with ice-cold NLB plus PIC, the Dynabeads were incubated with cleared lysates overnight at 4°C in NLB supplemented with PIC and BSA. Beads were given 4 washes with ice-cold NLB containing 500mM NaCl, followed by 4 washes with ice-cold LiCl buffer (20mM Tris at pH 8.0, 1 mM EDTA, 250mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate). Crosslinks were reversed by incubation in TE buffer (10mM Tris-HCl,1mM EDTA, pH 8.0) supplemented with 0.7% SDS and 0.2 mg/ml proteinase K for 3h at 55 °C, then 16 h at 65°C. DNA was purified with a ChIP DNA Clean & Concentrator kit.
ChIP-seq libraries were prepared using the NEB Ultra II kit.

treatment_protocol: Budesonide was dissolved in DMSO as a 10mM stock. Unless specifically indicated, budesonide was used at 300nM on cells, representing a concentration that was maximally effective/near maximal on a 2×GRE reporter and gene expression in A549 cells. Final DMSO concentrations on cells were ≤ 0.1%. Recombinant human IL1B was dissolved in phosphate-buffered saline (PBS) containing 0.1% bovine serum albumin (BSA). IL1B was previously found to be maximally or near maximally effective on NF-κB reporters and gene expression at 1ng/ml and this concentration was used in all experiments unless specifically indicated. Following overnight incubation in serum free medium, cells were changed to fresh serum free medium and either not stimulated (NS) or treated with, IL1B, budesonide (Bud) or IL1B plus budesonide (I+B) for the indicated times prior to harvesting for RNA extraction. Data are from two independent experiments.

tag: cell line

tag: cell type

value: lung carcinoma epithelial cells

tag: genotype

value: WT

tag: treatment

value: I+B

tag: condition

value: Ad-IκBαΔN

tag: chip antibody

value: RELA (Cell Signaling, #8242S)


title: A549 cells (input), rep 1

description: Library name: Sample 25


title: Ucn3_RNAs_2_VirginFemale

city: Cambridge

first: Brandon

last: Logeman

state: MA

address: 16 Divinity

country: USA

institute: Harvard University

description: Library name: Ucn3_RNA_2_VirginFemale

library_source: transcriptomic single cell

data_processing:
Illumina sequencing reads were aligned to mm10 using the 10x Genomics CellRanger pipeline with default parameters.
Assembly: mm10
Supplementary files format and content: RNAseq files exist as Feature Barcode Market Exchange Matrices (MEX) files. ATACseq files exist as indexed Fragment files.

molecule: nuclear RNA

organism: Mus musculus

source_name: brain

extract_protocol:
For all samples, the preoptic area of the hypothalamus was dissected and snap frozen in liquid nitrogen. Tissue samples from five animals per sample were pooled and Dounce homogenized before isolating GFP-expressing nuclei via FANS.
Library construction was performed according to 10x Genomics protocols.

tag: tissue

value: brain

tag: sample group


title: 1b.1.018.epi

city: St Louis

first: Margaret

middle: L

last: Axelrod

state: MO

address: 660 South Euclid Avenue, Campus Box 8118

department: Pathology and Immunology

institute: Washington University in St. Louis

description: Library name: 1b.1.018.epi

library_source: transcriptomic

data_processing:
Sequencing (fastq) files were initially processed through the proprietary GeoMx NGS Pipeline. The raw reads were trimmed, paired-end reads were merged, and then these reads were aligned to the corresponding identification barcodes based on their tag sequence identifiers, which correspond to genes in the transcriptome. The number of tags were counted to determine number of transcripts, corresponding to level of RNA expression. PCR duplicates were removed by sorting the unique molecular identifiers. Data was normalized using Q3 normalization. Low quality reads (low percent aligned reads, low percent stitched reads, low nuclei count) were excluded from analysis.
Assembly: hg38
Supplementary files format and content: Raw linear counts are included as the processed data file

molecule: total RNA

source_name: Cervix

extract_protocol:
ROIs were segregated using a nuclear counterstain and anti-cytokeratin immunofluorescence probes (clone AE1/AE3, Novus NBP2-33200) to separate RNA captured from tumor epithelium (cytokeratin-positive) from RNA in the adjacent SIME (cytokeratin negative). Aspirates from 93 ROIs were collected (25 benign cervix, 21 Silva A, 22 Silva B, and 25 Silva C)
Library preparation was performed according to the manufacturer’s instructions. During the library preparation process, the photocleaved oligonucleotides with tag sequence identifiers, unique molecular identifiers, and sequencing primer reads were PCR amplified. Unique dual indexes and flow cell sequences were added. Library concentration was quantified by Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced on the Illumina NovaSeq X Plus (Illumina, Inc., San Diego, CA, USA), targeting 1.5 billion reads per library.

value: Cervix

value: epi

tag: silva pattern

value: C

tag: risk

value: High

tag: caseid


title: Ucn3_RNAs_2_Father

description: Library name: Ucn3_RNA_2_Father


title: 1b.1.019.epi

description: Library name: 1b.1.019.epi


title: 1b.1.016.stroma

description: Library name: 1b.1.016.stroma

value: stroma


title: Ucn3_RNAs_2_VirginMale

description: Library name: Ucn3_RNA_2_VirginMale


title: 1b.1.017.epi

description: Library name: 1b.1.017.epi


title: Ucn3_RNAs_1_Mother

description: Library name: Ucn3_RNA_1_Mother


title: A549 cells, RELA ChIP, Ad-GFP, I+B, 1h, rep 2

description: Library name: Sample 22

value: Ad-GFP


title: A549 cells, RELA ChIP, Ad-IκBαΔN, I+B, 1h, rep 1

description: Library name: Sample 23


title: 1b.1.015.epi

description: Library name: 1b.1.015.epi


title: GATA1FL_1, IgG , replica 1

city: Memphis

first: Rashid

last: Mehmood

state: Tennessee

address: 324 NIGHT SAIL DR N APT 112, UNIT # 04-112

department: Hematology

institute: St Jude Children's Research Hospital

description:
Library name: GATA1FL_IgG_1
CUT&RUN

data_processing:
raw reads were processed using the community driven nfcore cutandrun version 3.1 pipeline
Assembly: hg38
Supplementary files format and content: .bigWig
Library strategy: CUT&Run

growth_protocol: Expansion condition: SFEM II containing 3 U/mL EPO, 50 ng/mL hSCF, 1 μM dexamethasone and 1 μg/mL doxycycline; Differentiation condition: IMDM containing 2% FBS, 3% human AB serum, 3 U/mL EPO, 10 μg/mL insulin, 3 U/mL heperin, 1mg/mL human holo-transferrin, 50 ng/mL hSCF and 1 μg/mL doxycline.

extract_protocol:
CUT&RUN DNA was purified from HUDEP1 clones expressing either the full-length GATA1 (GATA1FL) or the short isoform (GATA1s_1D5 and GATA1s_1KI9) under expansion or differentiation (on day 4 or 24 hours) conditions, respectively. The CUT&RUN process was conducted using CUTANA™ ChIC/CUT&RUN Kit (REF#14-1048).
CUT&RUN libraries were constructed according to the CUTANA™ CUT&RUN Library Prep Kit (REF#14-1001 and 14-1002) protocol.

value: erythroid progenitor cell line

value: expansion


title: 1b.1.014.epi

description: Library name: 1b.1.014.epi


title: A549 cells, RELA ChIP, Ad-GFP, I+B, 1h, rep 1

description: Library name: Sample 21


title: 1b.1.014.stroma

description: Library name: 1b.1.014.stroma


title: 1b.1.013.stroma

description: Library name: 1b.1.013.stroma


title: 1b.1.010.stroma

description: Library name: 1b.1.010.stroma

value: A

value: Low


title: A549 cells, RELA ChIP, Ad-GFP, IL1B, 1h, rep 1

description: Library name: Sample 17


title: 1b.1.011.epi

description: Library name: 1b.1.011.epi

value: B


title: 1b.1.009.stroma

description: Library name: 1b.1.009.stroma


title: 1b.1.016.epi

description: Library name: 1b.1.016.epi


title: Ucn3_RNAs_1_Father

description: Library name: Ucn3_RNA_1_Father


title: A549 cells, RELA ChIP, Ad-GFP, IL1B, 1h, rep 2

description: Library name: Sample 18

value: lung carcinoma epithelial cells


title: 1b.1.015.stroma

description: Library name: 1b.1.015.stroma


title: Ucn3_RNAs_1_VirginFemale

description: Library name: Ucn3_RNA_1_VirginFemale


title: 1b.1.011.stroma

description: Library name: 1b.1.011.stroma


title: Ucn3_RNAs_1_VirginMale

description: Library name: Ucn3_RNA_1_VirginMale


title: 1b.1.010.epi

description: Library name: 1b.1.010.epi


title: A549 cells, RELA ChIP, Ad-IκBαΔN, NS, 1h, rep 2

description: Library name: Sample 16

value: WT

value: NS


title: 1b.1.012.epi

description: Library name: 1b.1.012.epi


title: 1b.1.009.epi

description: Library name: 1b.1.009.epi


title: 1b.1.012.stroma

description: Library name: 1b.1.012.stroma


title: 1b.1.008.epi

description: Library name: 1b.1.008.epi


title: Gal_RNAs_2_Father

description: Library name: Gal_RNA_2_Father


title: 1b.1.013.epi

description: Library name: 1b.1.013.epi


title: Gal_RNAs_2_VirginFemale

description: Library name: Gal_RNA_2_VirginFemale


title: Gal_RNAs_1_Father

description: Library name: Gal_RNA_1_Father


title: A549 cells, RELA ChIP, Ad-IκBαΔN, IL1B, 1h, rep 2

description: Library name: Sample 20

value: Ad-IκBαΔN


title: 1b.1.007.stroma

description: Library name: 1b.1.007.stroma


title: A549 cells, RELA ChIP, Ad-IκBαΔN, IL1B, 1h, rep 1

description: Library name: Sample 19

value: RELA (Cell Signaling, #8242S)


title: Gal_RNAs_2_Mother

description: Library name: Gal_RNA_2_Mother

value: brain


title: Gal_RNAs_2_VirginMale

description: Library name: Gal_RNA_2_VirginMale


title: A549 cells, RELA ChIP, Ad-IκBαΔN, NS, 1h, rep 1

description: Library name: Sample 15


title: 1b.1.006.stroma

description: Library name: 1b.1.006.stroma

value: Cervix


title: 1b.1.008.stroma

description: Library name: 1b.1.008.stroma


title: Gal_RNAs_1_Mother

description: Library name: Gal_RNA_1_Mother


title: A549 cells, RELA ChIP, Ad-GFP, NS, 1h, rep 2

description: Library name: Sample 14


title: Gal_RNAs_1_VirginFemale

description: Library name: Gal_RNA_1_VirginFemale


title: 1b.1.004.stroma

description: Library name: 1b.1.004.stroma


title: A549 cells, RELA ChIP, Ad-GFP, NS, 1h, rep 1

description: Library name: Sample 13


title: 1b.1.004.epi

description: Library name: 1b.1.004.epi

value: epi


title: 1b.1.003.epi

description: Library name: 1b.1.003.epi


title: 1b.1.003.stroma

description: Library name: 1b.1.003.stroma


title: 1b.1.002.stroma

description: Library name: 1b.1.002.stroma


title: A549 cells, GR ChIP, Ad-IκBαΔN, I+B, 1h, rep 1

description: Library name: Sample 11

value: I+B

value: GR356 (Sasse et al., 2019)


title: 1b.1.001.stroma

description: Library name: 1b.1.001.stroma

value: stroma


title: 1b.1.005.epi

description: Library name: 1b.1.005.epi


title: 1b.1.002.epi

description: Library name: 1b.1.002.epi


title: Brs3_RNAs_2_Mother

description: Library name: Brs3_RNA_2_Mother


title: 1b.1.005.stroma

description: Library name: 1b.1.005.stroma


title: 1b.1.001.epi

description: Library name: 1b.1.001.epi


title: A549 cells, GR ChIP, Ad-IκBαΔN, I+B, 1h, rep 2

description: Library name: Sample 12


title: Gal_RNAs_1_VirginMale

description: Library name: Gal_RNA_1_VirginMale


title: A549 cells, GR ChIP, Ad-GFP, I+B, 1h, rep 1

description: Library name: Sample 9

value: Ad-GFP


title: Brs3_RNAs_2_Father

description: Library name: Brs3_RNA_2_Father


title: 1A.049.epi

description: Library name: 1A.049.epi

value: normal

value: Normal


title: Brs3_RNAs_2_VirginFemale

description: Library name: Brs3_RNA_2_VirginFemale


title: 1A.049.stroma

description: Library name: 1A.049.stroma


title: A549 cells, GR ChIP, Ad-GFP, I+B, 1h, rep 2

description: Library name: Sample 10


title: A549 cells, GR ChIP, Ad-IκBαΔN, Bud 1h, rep 1

description: Library name: Sample 7

value: Bud


title: Brs3_RNAs_1_Father_L002

description:
Library name: Brs3_RNA_1_Father_L002
Brs3_Father_1_barcodes.tsv
Brs3_Father_1_features.tsv
Brs3_Father_1_matrix.mtx
Brs3_Father_1_metadata.tsv


title: Brs3_RNAs_2_VirginMale

description: Library name: Brs3_RNA_2_VirginMale


title: A549 cells, GR ChIP, Ad-IκBαΔN, Bud 1h, rep 2

description: Library name: Sample 8


title: A549 cells, GR ChIP, Ad-GFP, Bud, 1h, rep 2

description: Library name: Sample 6


title: 1A.048.epi

description: Library name: 1A.048.epi


title: 1A.047.stroma

description: Library name: 1A.047.stroma

value: High


title: Brs3_RNAs_1_Mother_L002

description:
Library name: Brs3_RNA_1_Mother_L002
Brs3_Mother_1_barcodes.tsv
Brs3_Mother_1_features.tsv
Brs3_Mother_1_matrix.mtx
Brs3_Mother_1_metadata.tsv


title: A549 cells, GR ChIP, Ad-IκBαΔN, NS, 1h, rep 1

description: Library name: Sample 3


title: 1A.045.epi

description: Library name: 1A.045.epi


title: 1A.043.stroma

description: Library name: 1A.043.stroma

value: B


title: 1A.043.epi

description: Library name: 1A.043.epi


title: 1A.048.stroma

description: Library name: 1A.048.stroma


title: 1A.042.stroma

description: Library name: 1A.042.stroma


title: Brs3_RNAs_1_VirginMale_L002

description:
Library name: Brs3_RNA_1_VirginMale_L002
Brs3_VirginMale_1_barcodes.tsv
Brs3_VirginMale_1_features.tsv
Brs3_VirginMale_1_matrix.mtx
Brs3_VirginMale_1_metadata.tsv


title: 1A.047.epi

description: Library name: 1A.047.epi


title: Brs3_RNAs_1_Father_L001

description: Library name: Brs3_RNA_1_Father_L001


title: A549 cells, GR ChIP, Ad-GFP, Bud, 1h, rep 1

description: Library name: Sample 5

value: lung carcinoma epithelial cells


title: 1A.045.stroma

description: Library name: 1A.045.stroma


title: 1b.1.006.epi

description: Library name: 1b.1.006.epi

value: A

value: Low


title: 1b.1.007.epi

description: Library name: 1b.1.007.epi


title: 1A.041.stroma

description: Library name: 1A.041.stroma


title: 1A.044.epi

description: Library name: 1A.044.epi


title: Gata1s, H3K18la, replica 3

first: Te

last: Ling

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

description:
Library name: G1s5_H3K18la_3
CUT&RUN

data_processing:
Followed the nf-core/cutandrun Nextflow pipeline (revision 3.2.2) using default/standard processing steps for CUT&RUN data, including read QC, trimming, alignment, filtering, and peak calling.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Run

source_name: E13.5 fetal liver

extract_protocol:
CUT&RUN DNA was purified from wild-type and Gata1s erythroblasts using antibodies against H3K27ac, H3K27la, and H3K18la. The CUT&RUN process was performed using the CUTANA™ ChIC/CUT&RUN Kit (REF#14-1048).
CUT&RUN libraries were constructed according to the CUTANA™ CUT&RUN Library Prep Kit (REF#14-1001 and 14-1002) protocol.

value: E13.5 fetal liver

value: erythroblasts


title: D3_sictrl

city: London

first: Paul

last: Evans

address: Charterhouse square

country: United Kingdom

institute: QMUL

description: Library name: D3_sictrl

data_processing:
Fastq files were processed using the nf.core rna-seq pipeline (version 3.6.0) (https://nf-co.re/rnaseq/3.6) incorporating salmon pseudo-alignment and quantification (v 1.5.2).
Assembly: hg38
Supplementary files format and content: quant.sf files produce by salmon. Name: The transcript ID. Length: The effective length of the transcript, accounting for factors like read mapping and fragment length distribution. EffectiveLength: An adjusted length, taking into account the fragment length distribution. TPM (Transcripts Per Million): The normalized transcript abundance, representing transcripts per million mapped reads. This is a commonly used metric for comparing transcript expression across samples. NumReads: The estimated number of reads that map to the transcript.

source_name: aorta

growth_protocol: Cells were cultured and maintained in EGM2 media (Promocell)

extract_protocol:
Total RNA was extracted from HAoECs using the RNeasy Mini Kit (Qiagen, 74104)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: siRNA was used at a concentration of 25nM and cells were exposed to flow for 72hours

value: aorta

value: Primary human aortic endothelial cells (HAoEC)

value: Scrambled siRNA


title: Brs3_RNAs_1_Mother_L001

description: Library name: Brs3_RNA_1_Mother_L001

value: brain


title: 1A.044.stroma

description: Library name: 1A.044.stroma

value: Cervix


title: 1A.039.stroma

description: Library name: 1A.039.stroma

value: stroma


title: D2_sictrl

description: Library name: D2_sictrl


title: 1A.039.epi

description: Library name: 1A.039.epi

value: epi


title: 1A.046.stroma

description: Library name: 1A.046.stroma

value: normal


title: A549 cells, GR ChIP, Ad-IκBαΔN, NS, 1h, rep 2

description: Library name: Sample 4

value: WT

value: NS

value: Ad-IκBαΔN

value: GR356 (Sasse et al., 2019)


title: Brs3_RNAs_1_VirginFemale_L002

description:
Library name: Brs3_RNA_1_VirginFemale_L002
Brs3_VirginFemale_1_barcodes.tsv
Brs3_VirginFemale_1_features.tsv
Brs3_VirginFemale_1_matrix.mtx
Brs3_VirginFemale_1_metadata.tsv


title: D1_sictrl

description: Library name: D1_sictrl


title: A549 cells, GR ChIP, Ad-GFP, NS, 1h, rep 1

description: Library name: Sample 1

value: lung carcinoma epithelial cells

value: Ad-GFP


title: Brs3_RNAs_1_VirginFemale_L001

description: Library name: Brs3_RNA_1_VirginFemale_L001


title: 1A.037.stroma

description: Library name: 1A.037.stroma

value: A

value: Low


title: Brs3_RNAs_1_VirginMale_L001

description: Library name: Brs3_RNA_1_VirginMale_L001


title: 1A.040.stroma

description: Library name: 1A.040.stroma

value: Normal


title: D4_sictrl

description: Library name: D4_sictrl

value: aorta


title: 1A.042.epi

description: Library name: 1A.042.epi

value: B

value: High


title: 1A.037.epi

description: Library name: 1A.037.epi


title: A549 cells, GR ChIP, Ad-GFP, NS, 1h, rep 2

description: Library name: Sample 2


title: 1A.036.stroma

description: Library name: 1A.036.stroma


title: 1A.040.epi

description: Library name: 1A.040.epi


title: 1A.046.epi

description: Library name: 1A.046.epi


title: Gata1s, H3K18la, replica 2

description:
Library name: G1s4_H3K18la_2
CUT&RUN

value: E13.5 fetal liver

value: erythroblasts


title: 1A.036.epi

description: Library name: 1A.036.epi

value: Cervix


title: 1A.035.epi

description: Library name: 1A.035.epi

value: epi


title: D1_siPelp1

description: Library name: D1_siPelp1

value: Primary human aortic endothelial cells (HAoEC)

value: Pelp1 siRNA


title: 1A.034.stroma

description: Library name: 1A.034.stroma

value: stroma


title: 1A.034.epi

description: Library name: 1A.034.epi


title: D3_siAebp1

description: Library name: D3_siAebp1

value: Aebp1 siRNA


title: 1A.038.epi

description: Library name: 1A.038.epi

value: normal


title: D2_siAebp1

description: Library name: D2_siAebp1


title: 1A.033.epi

description: Library name: 1A.033.epi


title: D4_siPelp1

description: Library name: D4_siPelp1


title: 1A.030.stroma

description: Library name: 1A.030.stroma


title: 1A.038.stroma

description: Library name: 1A.038.stroma


title: D3_siPelp1

description: Library name: D3_siPelp1


title: WT, H3K18la, replica 3

description:
Library name: WT4_H3K18la_3_
CUT&RUN


title: D1_siAebp1

description: Library name: D1_siAebp1


title: D4_siAebp1

description: Library name: D4_siAebp1


title: Gata1s, IgG, replica 1

description:
Library name: G1s5_IgG
CUT&RUN


title: 1A.030.epi

description: Library name: 1A.030.epi


title: 1A.029.stroma

description: Library name: 1A.029.stroma


title: 1A.027.stroma

description: Library name: 1A.027.stroma

value: C


title: 1A.041.epi

description: Library name: 1A.041.epi


title: Gata1s, H3K27la, replica 1

description:
Library name: G1s1_H3K27la_1
CUT&RUN


title: 1A.035.stroma

description: Library name: 1A.035.stroma


title: 1A.026.stroma

description: Library name: 1A.026.stroma


title: Gata1s, H3K18la, replica 1

description:
Library name: G1s3_H3K18la_1
CUT&RUN


title: Gata1s, H3K27la, replica 2

description:
Library name: G1s3_H3K27la_2
CUT&RUN


title: Gata1s, H3K27la, replica 3

description:
Library name: G1s4_H3K27la_3
CUT&RUN


title: WT, H3K27la, replica 2

description:
Library name: WT2_H3K27la_2
CUT&RUN


title: 1A.024.stroma

description: Library name: 1A.024.stroma


title: 1A.024.epi

description: Library name: 1A.024.epi


title: Gata1s, H3K27ac, replica 2

description:
Library name: G1s2_H3K27ac_2
CUT&RUN


title: 1A.029.epi

description: Library name: 1A.029.epi


title: 1A.032.stroma

description: Library name: 1A.032.stroma


title: Gata1s, H3K27ac, replica 1

description:
Library name: G1s1_H3K27ac_1
CUT&RUN


title: Gata1s, H3K27ac, replica 3

description:
Library name: G1s3_H3K27ac_3
CUT&RUN


title: siT1_OSS_2

description: Library name: siT1_OSS_2

value: Twist1 siRNA

tag: flow condition

value: LOSS


title: D2_siPelp1

description: Library name: D2_siPelp1


title: siNT_OSS_4

description: Library name: siNT_OSS_4

value: Scrambled siRNA


title: siT1_OSS_3

description: Library name: siT1_OSS_3


title: WT, H3K18la, replica 2

description:
Library name: WT3_H3K18la_2
CUT&RUN


title: WT, H3K27la, replica 1

description:
Library name: WT1_H3K27la_1
CUT&RUN


title: 1A.032.epi

description: Library name: 1A.032.epi

value: A

value: Low


title: 1A.033.stroma

description: Library name: 1A.033.stroma


title: 1A.026.epi

description: Library name: 1A.026.epi


title: 1A.027.epi

description: Library name: 1A.027.epi


title: siT1_OSS_4

description: Library name: siT1_OSS_4

value: aorta


title: siNT_OSS_3

description: Library name: siNT_OSS_3


title: 1A.025.epi

description: Library name: 1A.025.epi

value: High


title: siT1_OSS_1

description: Library name: siT1_OSS_1


title: 1A.023.stroma

description: Library name: 1A.023.stroma


title: WT, H3K18la, replica 1

description:
Library name: WT2_H3K18la_1
CUT&RUN

value: E13.5 fetal liver


title: 1A.025.stroma

description: Library name: 1A.025.stroma


title: WT, H3K27la, replica 3

description:
Library name: WT3_H3K27la_3
CUT&RUN

value: erythroblasts


title: 1A.023.epi

description: Library name: 1A.023.epi

value: Cervix


title: 1A.022.stroma

description: Library name: 1A.022.stroma


title: WT, H3K27ac, replica 2

description:
Library name: WT2_H3K27ac_2
CUT&RUN


title: 1A.021.stroma

description: Library name: 1A.021.stroma


title: siNT_OSS_1

description: Library name: siNT_OSS_1


title: 1A.022.epi

description: Library name: 1A.022.epi

value: epi


title: siNT_OSS_2

description: Library name: siNT_OSS_2

value: Primary human aortic endothelial cells (HAoEC)


title: WT, H3K27ac, replica 3

description:
Library name: WT3_H3K27ac_3
CUT&RUN


title: 1A.021.epi

description: Library name: 1A.021.epi


title: Sample TA02, T-lymphoblastic leukaemia/lymphoma (Hi-C)

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Department of Pathology

institute: University of Michigan Medical School

description: Library name: HIC_TA02

data_processing:
Hi-C sequencing data was processed using the Arima-SV-Pipeline (v1.3), comprising HiCUP (v0.8.0) to calculate quality control metrics and perform read alignment and filtering, hic_breakfinder to call rearrangement breakpoints, and Juicer Tools (v1.6) to produce multi-resolution Hi-C matrices from mapped and filtered read pairs. FFPE samples were processed using default pipeline parameters for the Arima-HiC+ for FFPE restriction enzyme chemistry. Alignment was performed against the GRCh38 human reference genome.
Assembly: GRCh38
Supplementary files format and content: Genome-wide Hi-C matrices in .hic file format

source_name: tumor

extract_protocol:
FFPE tissue from 2-5 unstained slides cut at 5-10µm were processed using the Arima HiC+ for FFPE kit (Product Number A311038, Arima Genomics, Carlsbad, CA) as per manufacturer protocols to produce Illumina-compatible sequencing libraries. Briefly, 5µm unstained FFPE tissue sections were first de-waxed and rehydrated, and then subjected to Hi-C sample preparation using Arima HiC+ for FFPE kit.
Following Hi-C sample preparation,  Illumina-compatible sequencing libraries were constructed by shearing the proximally ligated DNA and then size selecting DNA fragments using SPRI beads. The size-selected DNA fragments containing proximity ligation junctions were then enriched using Enrichment Beads (provided in the Arima HiC+ for FFPE kit) and converted to Illumina-compatible sequencing libraries. The resulting Hi-C libraries underwent standard quality control (qPCR and BioAnalyzer).

value: tumor


title: 1A.020.epi

description: Library name: 1A.020.epi


title: 1A.019.stroma

description: Library name: 1A.019.stroma

value: stroma


title: 1A.020.stroma

description: Library name: 1A.020.stroma


title: WT, H3K27ac, replica 1

description:
Library name: WT1_H3K27ac_1
CUT&RUN


title: 1A.018.epi

description: Library name: 1A.018.epi


title: Sample TA01, T-lymphoblastic leukaemia/lymphoma (Hi-C)

description: Library name: HIC_TA01


title: 1A.017.stroma

description: Library name: 1A.017.stroma

value: Normal


title: Sample PM01, Primary mediastinal large B-cell lymphoma (Hi-C)

description: Library name: HIC_PM01


title: 1A.016.stroma

description: Library name: 1A.016.stroma

value: normal


title: 1A.019.epi

description: Library name: 1A.019.epi

value: C


title: 1A.016.epi

description: Library name: 1A.016.epi


title: WT, IgG, replica 1

description:
Library name: WT2_IgG
CUT&RUN


title: Sample PL14, Solitary plasmacytoma of bone (Hi-C)

description: Library name: HIC_PL14


title: Liver, Mdr2-/-, lycorine-1

city: nanjing

first: Ying

last: Zheng

address: 639 Longmian Avenue, Jiangning District

country: China

institute: China pharmaceutical university

description:
Library name: Mdr2-/- lycorine-1
Mdr2 knockout, lycorine treatment

data_processing:
CLC Genomics Workbench V11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length faction: 0.8 similarity faction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: Liver

growth_protocol: 8-week-old Mdr2-HKO mice were treated with vehicle or lycorine for 2 weeks.

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (Qiagen). 1.3μg total RNA was used for the construction of suquencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufaturer's protocols.

treatment_protocol: Mouse liver tissues, rapidly frozen in liquid nitrogen, were stored at -80°C for subsequent RNA extraction.

value: Liver

value: Mdr2 knockout

value: Lycorine


title: Liver, Mdr2-/-, lycorine-2

description:
Library name: Mdr2-/- lycorine-2
Mdr2 knockout, lycorine treatment


title: Liver, Mdr2-/-, lycorine-3

description:
Library name: Mdr2-/- lycorine-3
Mdr2 knockout, lycorine treatment


title: 1A.018.stroma

description: Library name: 1A.018.stroma


title: 1A.015.epi

description: Library name: 1A.015.epi


title: Sample PL12, Multiple myeloma (Hi-C)

description: Library name: HIC_PL12


title: 1A.015.stroma

description: Library name: 1A.015.stroma


title: Sample PL13, Multiple myeloma (Hi-C)

description: Library name: HIC_PL13


title: Liver, Mdr2-/-, vehicle-3

description:
Library name: Mdr2-/- vehicle-3
Mdr2 knockout, vehicle treatment

value: Vehicle


title: 1A.017.epi

description: Library name: 1A.017.epi


title: 1A.014.epi

description: Library name: 1A.014.epi


title: 1A.012.stroma

description: Library name: 1A.012.stroma

value: A

value: Low


title: Sample PL09, Multiple myeloma (Hi-C)

description: Library name: HIC_PL09


title: 1A.013.stroma

description: Library name: 1A.013.stroma


title: 1A.012.epi

description: Library name: 1A.012.epi


title: Murine B16F10 melanoma cells, Polianthes tuberosa L. extract-treated group, replicate3

city: WuXi

first: Li

last: qiaozhen

address: Meicun street

institute: Jiangnan University

description:
Library name: TES3
Column name in gene_count.xls: TES3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.22.0 (the default parameters) Trimmed sequence reads were mapped to hg38 using hisat2 v2.2.0 (the default parameters). Read count was calculated and normalized by featurecount v2.0.6 (-p)
Assembly: mm39
Supplementary files format and content: Excel read count of genes for each sample

molecule: polyA RNA

source_name: B16F10 melanoma cells

extract_protocol:
RNA extraction was performed simultaneously for all samples using the NucleoSpin RNA Plus kit (Macherey-Nagel), following the manufacturer’s protocol.
RNA sequencing was conducted by Novogene using Illumina platforms based on sequencing-by-synthesis (SBS) technology.

value: B16F10 melanoma cells


title: Liver, Mdr2-/-, vehicle-1

description:
Library name: Mdr2-/- vehicle-1
Mdr2 knockout, vehicle treatment


title: Liver, Mdr2-/-, vehicle-2

description:
Library name: Mdr2-/- vehicle-2
Mdr2 knockout, vehicle treatment


title: Sample PL10, Multiple myeloma (Hi-C)

description: Library name: HIC_PL10


title: Sample PL11, Multiple myeloma (Hi-C)

description: Library name: HIC_PL11


title: Murine B16F10 melanoma cells, Polianthes tuberosa L. extract-treated group, replicate2

description:
Library name: TES2
Column name in gene_count.xls: TES2


title: 1A.013.epi

description: Library name: 1A.013.epi


title: Murine B16F10 melanoma cells, Polianthes tuberosa L. extract-treated group, replicate1

description:
Library name: TES1
Column name in gene_count.xls: TES1


title: Murine B16F10 melanoma cells, control, replicate2

description:
Library name: blank2
Column name in gene_count.xls: blank2


title: Sample PL07, Multiple myeloma (Hi-C)

description: Library name: HIC_PL07


title: 1A.014.stroma

description: Library name: 1A.014.stroma


title: 1A.008.stroma

description: Library name: 1A.008.stroma


title: Sample PL06, Solitary plasmacytoma of bone (Hi-C)

description: Library name: HIC_PL06


title: 1A.007.stroma

description: Library name: 1A.007.stroma


title: Murine B16F10 melanoma cells, control, replicate3

description:
Library name: blank3
Column name in gene_count.xls: blank3


title: Sample PL08, Multiple myeloma (Hi-C)

description: Library name: HIC_PL08


title: Sample PL05, Multiple myeloma (Hi-C)

description: Library name: HIC_PL05


title: 1A.008.epi

description: Library name: 1A.008.epi


title: 1A.011.stroma

description: Library name: 1A.011.stroma

value: B


title: 1A.010.stroma

description: Library name: 1A.010.stroma


title: Sample PL03, Solitary plasmacytoma of bone (Hi-C)

description: Library name: HIC_PL03


title: Sample PL02, Multiple myeloma (Hi-C)

description: Library name: HIC_PL02


title: 1A.006.epi

description: Library name: 1A.006.epi


title: 1A.009.epi

description: Library name: 1A.009.epi


title: 1A.010.epi

description: Library name: 1A.010.epi


title: In vitro cultured alveolar macrophages, emricasan, 6h, rep 1

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: Emri_1

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in 101-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver.2.3.5.1 and SAMtools ver.1.11.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: alveolar macrophages

extract_protocol:
Total RNA extraction from the cells were performed using FastGene™ RNA Kit (NIPPON Genetics) according to the manufactures protocol.
Library preparation was performed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: In vitro cultured alveolar macrophages (prepared from C57BL/6J mice) were cultured with emricasan (40 μM) or 0.05% DMSO (control) for 6 hours.

value: alveolar macrophages

value: WT

value: emricasan


title: 1A.007.epi

description: Library name: 1A.007.epi

value: Cervix

value: epi


title: Sample PL04, Multiple myeloma (Hi-C)

description: Library name: HIC_PL04

value: tumor


title: Murine B16F10 melanoma cells, control, replicate1

description:
Library name: blank1
Column name in gene_count.xls: blank1


title: 1A.011.epi

description: Library name: 1A.011.epi


title: 1A.006.stroma

description: Library name: 1A.006.stroma

value: stroma

value: Normal


title: In vitro cultured alveolar macrophages, emricasan, 6h, rep 2

description: Library name: Emri_2


title: In vitro cultured alveolar macrophages, control, 6h, rep 1

description: Library name: Ctrl_1

value: ctrl


title: Sample PL01, Solitary plasmacytoma of bone (Hi-C)

description: Library name: HIC_PL01


title: 1A.004.epi

description: Library name: 1A.004.epi


title: 1A.005.epi

description: Library name: 1A.005.epi


title: αβ, SP, CRISPR, ADT

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description:
Library name: Sample 24
antibody-derived oligonucleotide (ADT), hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
RNA-seq and CITE-seq were demultiplexed using CellRanger (v8.0.0) software from 10x Genomics.
TCR-seq αβ and γδ contigs were processed separately. αβ scTCR libraries were generated by using the CellRanger multi pipeline (v8.0.0). γδ scTCR libraries were generated by using the CellRanger vdj pipeline (v3.0.2), then cell aggregation and annotation of the contig outputs were performed using scirpy Python package (v0.12.0).
For the CRISPR experiment, RNA-seq and CITE-seq were demultiplexed using CellRanger (v9.0.1) software from 10x Genomics.
For the CRISPR experiment, both αβ and γδ scTCR libraries were generated by using the CellRanger multi pipeline (v9.0.1). γδ scTCR libraries were then further pre-processed in scirpy (v0.15.2) as described earlier, with an additional re-annotation step of the unfiltered contig outputs using dandelion Python package (v0.5.4).
Assembly: GRCh38 genome (version 2020-A)
Assembly: For the CRISPR experiment: GRCh38 genome (version 2024-A)
Supplementary files format and content: scRNA/CITE-seq: matrix.mtx, features.tsv, barcodes.tsv. // matrix files include transcript count from each single-cell GEX/ADT library, barcodes tsv files includes the barcodes present in that single-cell GEX/ADT library and features tsv file includes the ID of the genes/proteins detected in that single-cell GEX/ADT library
Supplementary files format and content: scTCR-seq: TCR_filtered_contig_annotations.csv, TCR_all_contig_annotations.csv. // CSV files include single-cell barcoded CDR3 sequences.
Library strategy: CITE-seq

molecule: protein

source_name: spleen

extract_protocol:
The single cell suspensions were stained with CITE-seq antibodies (ADTs and HTOs). Then γδ and αβ T cells were sorted from the thymi and peripheral organs (spleen, liver and lung) of HIS mice transplanted with human HSPCs. Single cells were encapsulated in GEMs ("Gel bead in EMulsion") using the Chromium Next GEM Single Cell 5' Kit v2.
After knocking-out (KO) DNTT in the input HSPCs of HIS mice by CRISPR, the single cell suspensions were stained with CITE-seq antibodies (ADTs and HTOs). Then γδ and αβ T cells were sorted from the thymi and spleens of HIS mice transplanted with human HSPCs. Single cells were encapsulated in GEMs using the Chromium Next GEM Single Cell 5' Kit v2 or the GEM-X Universal 5’ Gene Expression v3.
Separate sc libraries were generated for gene expression (GEX), antibody-derived tags (ADT), and V(D)J TCR according to the user guidelines (CG000330).
All steps were carried out using manufacturer-supplied reagents, except for custom primers speciﬁc for TRDC and TRGC constant gene segments (Eurogentec) as described in the paper.
For the CRISPR experiment, separate sc libraries were generated for gene expression (GEX), antibody-derived tags (ADT), and V(D)J TCR according to the user guidelines (CG000734).
For the CRISPR experiment, all steps were carried out using manufacturer-supplied reagents, except for custom primers speciﬁc for TRDC and TRGC constant gene segments (Eurogentec) as described in the paper.

treatment_protocol: DNTT was knocked-out (KO) in the input CD34+ HSPCs of some HIS mice by CRISPR.

value: spleen

tag: strain

value: NOD.Cg-KitW-41J Tyr+ Prkdcscid Il2rgtm1Wjl/ThomJ

tag: age

value: 12 weeks old

value: alpha beta T cell

value: mixed sample (control or DNTT-KO)

tag: library type

value: ADT, HTO

tag: hto

value: Hashtag1 (control mouse), Hashtag2 (control mouse), Hashtag3 (control mouse), Hashtag4 (control mouse), Hashtag5 (control mouse), Hashtag6 (KO mouse), Hashtag7 (KO mouse), Hashtag8 (KO mouse), Hashtag9 (KO mouse), Hashtag10 (KO mouse)


title: 1A.005.stroma

description: Library name: 1A.005.stroma

value: A

value: Low


title: 1A.001.stroma

description: Library name: 1A.001.stroma

value: B


title: Sample MC01, Mantle cell lymphoma (Hi-C)

description: Library name: HIC_MC01


title: In vitro cultured alveolar macrophages, control, 6h, rep 2

description: Library name: Ctrl_2

value: alveolar macrophages

value: WT


title: 1A.009.stroma

description: Library name: 1A.009.stroma

value: Cervix

value: normal


title: 1A.001.epi

description: Library name: 1A.001.epi

value: epi


title: 1A.002.stroma

description: Library name: 1A.002.stroma

value: stroma


title: Sample MC02, Mantle cell lymphoma, blastoid variant (Hi-C)

description: Library name: HIC_MC02

value: tumor


title: 1A.003.epi

description: Library name: 1A.003.epi


title: Sample HL01, Classic Hodgkin lymphoma (Hi-C)

description: Library name: HIC_HL01


title: siYBX1,rep3

city: Bethesda

first: Markus

last: Hafner

state: Maryland

address: 50 South Drive

institute: NIAMS/NIH

description: Library name: siYBX1,rep3

data_processing:
Sequencing quality was assessed using FastQC (v0.11.8). Reads were aligned to the human reference genome (hg38) with STAR (v2.7.9a) using default parameters and the option --quantMode GeneCounts to obtain raw read counts per gene, based on the ncbiRefSeq annotation. Differential expression analyses were conducted with R (v4.4.2) and DESeq2 (v1.46.0) using median-of-ratios normalized read counts and Benjamini-Hochberg adjusted p-values. Genes were considered differentially expressed based on the following criteria: baseMean > 10, adjusted p-value < 0.05 and log2(fold change[treated/control]) > 1 (up-regulated) or < -1 (down-regulated).
Assembly: hg38
Supplementary files format and content: raw count matrix

source_name: Kidney

extract_protocol: About 6 x 105 cells were seeded in 60-mm plates and transfected the next day with 50 pmol of siRNA targeting YBX1 (ThermoFisher Scientific, Cat.#4390824, siRNA ID s9731) or a control siRNA (ThermoFisher Scientific, Cat.#4390843) preincubated for 20 min at room temperature with 5 µL of Lipofectamine RNAiMAX transfection reagent (ThermoFisher Scientific, Cat.#13778150) in OPTI-MEM medium. Cells were collected and split in two 72 h after transfection. Total proteins were extracted with RIPA buffer on one half of the cells and used for western blot to assess the silencing efficiency. Total RNAs were extracted on the second half of the cells with TRIzol™ Reagent (ThermoFisher Scientific, Cat.#15596018) and treated with DNAse I using the Direct-zol RNA Miniprep kit (Zymo research, Cat.#R2052) according to the manufacturer’s instructions. Each siRNA transfection was performed in biological triplicate.

value: Kidney

value: YBX1 Knockdown


title: siYBX1,rep1

description: Library name: siYBX1,rep1


title: γδ, TH, CRISPR, ADT

description:
Library name: Sample 21
antibody-derived oligonucleotide (ADT), hashtag-derived oligonucleotide (HTO)

source_name: thymus

value: thymus

value: NOD.Cg-KitW-41J Tyr+ Prkdcscid Il2rgtm1Wjl/ThomJ

value: 12 weeks old

value: gamma delta T cell

value: Hashtag9 (control mice), Hashtag10 (KO mice)


title: 1A.004.stroma

description: Library name: 1A.004.stroma

value: A


title: 1A.003.stroma

description: Library name: 1A.003.stroma

value: Low


title: Sample MC03, Mantle cell lymphoma (Hi-C)

description: Library name: HIC_MC03


title: αβ, TH, CRISPR, TCR

description: Library name: Sample 19

data_processing:
RNA-seq and CITE-seq were demultiplexed using CellRanger (v8.0.0) software from 10x Genomics.
TCR-seq αβ and γδ contigs were processed separately. αβ scTCR libraries were generated by using the CellRanger multi pipeline (v8.0.0). γδ scTCR libraries were generated by using the CellRanger vdj pipeline (v3.0.2), then cell aggregation and annotation of the contig outputs were performed using scirpy Python package (v0.12.0).
For the CRISPR experiment, RNA-seq and CITE-seq were demultiplexed using CellRanger (v9.0.1) software from 10x Genomics.
For the CRISPR experiment, both αβ and γδ scTCR libraries were generated by using the CellRanger multi pipeline (v9.0.1). γδ scTCR libraries were then further pre-processed in scirpy (v0.15.2) as described earlier, with an additional re-annotation step of the unfiltered contig outputs using dandelion Python package (v0.5.4).
Assembly: GRCh38 genome (version 2020-A)
Assembly: For the CRISPR experiment: GRCh38 genome (version 2024-A)
Supplementary files format and content: scRNA/CITE-seq: matrix.mtx, features.tsv, barcodes.tsv. // matrix files include transcript count from each single-cell GEX/ADT library, barcodes tsv files includes the barcodes present in that single-cell GEX/ADT library and features tsv file includes the ID of the genes/proteins detected in that single-cell GEX/ADT library
Supplementary files format and content: scTCR-seq: TCR_filtered_contig_annotations.csv, TCR_all_contig_annotations.csv. // CSV files include single-cell barcoded CDR3 sequences.
Library strategy: TCR-Seq

value: alpha beta T cell

value: mixed sample (control or DNTT-KO)

value: VDJ


title: Sample DL08, Diffuse large B-cell lymphoma/high grade B-cell lymphoma (GCB) (Hi-C)

description: Library name: HIC_DL08


title: αβ, SP, CRISPR, TCR

description: Library name: Sample 20

value: spleen


title: Sample DL07, Diffuse large B-cell lymphoma/high grade B-cell lymphoma (GCB) (Hi-C)

description: Library name: HIC_DL07


title: 1A.002.epi

description: Library name: 1A.002.epi

value: Cervix

value: B


title: γδ, SP, CRISPR, TCR

description: Library name: Sample 18


title: Sample DL06, Diffuse large B-cell lymphoma (GCB) (Hi-C)

description: Library name: HIC_DL06


title: V45M5G_4

city: El Paso

first: Enrique

middle: Ivan

last: Ramos

state: Texas

address: 5001 El Paso Dr.

department: Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center El Paso

description: Library name: 15

data_processing:
Paired-end raw reads were uploaded into Genialis Expressions web-based application for RNA sequencing analysis (Genialis, Inc., Boston, MA). Their "General RNA-seq pipeline (featureCounts)" pipeline was used to analyze our raw data with their default settings. Description for this pipeline is adopted from their website as follow: “First, reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming. Next, preprocessed reads are aligned by STAR aligner. Aligned reads are summarized to gene-level counts by the featureCounts tool. FastQC reports, alignment statistics, QoRTs QC, RNA-SeQC and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool. RNA-SeQC is initiated only when ENSEMBL annotation is selected.” Trimmed reads were aligned to human genome (hg38) (Ensembl release version 109) with STAR aligner. We would like to note that we performed data analysis around October 2024 to April 2025; Genialis Expressions application version might have changed a little bit since then according to vendor’s routine maintenance. Output data for featureCounts, PCA, and DESeq2 was downloaded to generate figures and downstream analyses.
Assembly: hg38, Ensembl release version 109
Supplementary files format and content: txt files of raw counts for each sample (featureCounts data output)

source_name: MDA-MB-157 GFP ind OE

growth_protocol: MDA-MB-157 cells were maintained in DMEM high glucose medium (DMEM, 10% fetal bovine serum, 1% pen/strep) and incubated at 37°C in 5% CO2, with the addition of new medium every 2-3 days.

extract_protocol:
RNA was isolated using EZ-10 DNAway RNA Mini-Preps Kit (Bio Basic, Canada). TapeStation (Agilent Technologies 4200) was used to analyze the RNA integrity of the preparation, and RNA quantification was done using Nanodrop (Thermo Scientific, USA).
Isolated RNA samples with >9 RIN (RNA Integrity Number) were utilized for RNA-seq library preparation. RNA-seq libraries for total RNA-sequencing were prepared and sequenced at Novogene Corporation (Sacramento, CA). After sample preparation, sample QC was carried out by Nanodrop, agarose gel electrophoresis, and Agilent 2100. Following the QC, enrichment of eukaryotic mRNA with oligo (dT) beads was conducted. The mRNA was then fragmented at random by the use of a fragmentation buffer. After fragmentation, the cDNA was synthesized using random hexamer primers, followed by the addition of a second-strand synthesis buffer (Illumina), dNTPs, RNase H, and DNA polymerase I to initiate the second-strand synthesis. Once terminal repair, A-tailing, and sequencing adaptor ligation steps are finished, the double-stranded cDNA library is completed through size selection and PCR enrichment. The libraries then go through QC checks, which include Qubit 2.0, Agilent 2100, and real-time PCR. Finally, the quantified libraries are pooled according to the concentration and data amount required, and fed into Illumina sequencers (NovaSeq X Plus).

treatment_protocol: MDA-MB-157 cells were seeded (0.7 x 10^5 cells/well) in 6-well culture plates in DMEM high glucose medium. After 24 h, medium was switched to DMEM low glucose medium for 48 h before being treated with appropriate glucose concentration (1, 5, or 15 g/L) and co-treated with doxycyline (250 ng/mL) for 4 h.

value: MDA-MB-157 GFP ind OE

value: Human epithelial breast cancer cells

value: Dox + 15 g/L glucose for 4 h


title: αβ, TH, CRISPR, ADT

description:
Library name: Sample 23
antibody-derived oligonucleotide (ADT), hashtag-derived oligonucleotide (HTO)

value: ADT, HTO


title: Sample DL09, Diffuse large B-cell lymphoma/high grade B-cell lymphoma (GCB) (Hi-C)

description: Library name: HIC_DL09

value: tumor


title: γδ, SP, CRISPR, ADT

description:
Library name: Sample 22
antibody-derived oligonucleotide (ADT), hashtag-derived oligonucleotide (HTO)

value: NOD.Cg-KitW-41J Tyr+ Prkdcscid Il2rgtm1Wjl/ThomJ

value: Hashtag1 (control mouse), Hashtag2 (control mouse), Hashtag3 (control mouse), Hashtag4 (control mouse), Hashtag5 (control mouse), Hashtag6 (KO mouse), Hashtag7 (KO mouse), Hashtag8 (KO mouse), Hashtag9 (KO mouse), Hashtag10 (KO mouse)


title: siCTRL,rep1

description: Library name: siCTRL,rep1

value: Kidney

value: WT

value: siCTRL


title: Sample DL03, Diffuse large B-cell lymphoma/high grade B-cell lymphoma (GCB) (Hi-C)

description: Library name: HIC_DL03


title: V44M5161_2

description: Library name: 10

source_name: MDA-MB-157 MIR503HG ind OE

value: MDA-MB-157 MIR503HG ind OE

value: Dox + 5 g/L glucose for 4 h


title: V45M5161_2

description: Library name: 16


title: V45M5G_3

description: Library name: 14


title: V44M5161_4

description: Library name: 12


title: siYBX1,rep2

description: Library name: siYBX1,rep2

value: YBX1 Knockdown


title: V45M5161_3

description: Library name: 17


title: Sample DC06, Primary diffuse large B-cell lymphoma of the CNS (Hi-C)

description: Library name: HIC_DC06


title: αβ, SP, CRISPR, GEX

description: Library name: Sample 16

data_processing:
RNA-seq and CITE-seq were demultiplexed using CellRanger (v8.0.0) software from 10x Genomics.
TCR-seq αβ and γδ contigs were processed separately. αβ scTCR libraries were generated by using the CellRanger multi pipeline (v8.0.0). γδ scTCR libraries were generated by using the CellRanger vdj pipeline (v3.0.2), then cell aggregation and annotation of the contig outputs were performed using scirpy Python package (v0.12.0).
For the CRISPR experiment, RNA-seq and CITE-seq were demultiplexed using CellRanger (v9.0.1) software from 10x Genomics.
For the CRISPR experiment, both αβ and γδ scTCR libraries were generated by using the CellRanger multi pipeline (v9.0.1). γδ scTCR libraries were then further pre-processed in scirpy (v0.15.2) as described earlier, with an additional re-annotation step of the unfiltered contig outputs using dandelion Python package (v0.5.4).
Assembly: GRCh38 genome (version 2020-A)
Assembly: For the CRISPR experiment: GRCh38 genome (version 2024-A)
Supplementary files format and content: scRNA/CITE-seq: matrix.mtx, features.tsv, barcodes.tsv. // matrix files include transcript count from each single-cell GEX/ADT library, barcodes tsv files includes the barcodes present in that single-cell GEX/ADT library and features tsv file includes the ID of the genes/proteins detected in that single-cell GEX/ADT library
Supplementary files format and content: scTCR-seq: TCR_filtered_contig_annotations.csv, TCR_all_contig_annotations.csv. // CSV files include single-cell barcoded CDR3 sequences.

value: 12 weeks old

value: alpha beta T cell

value: mixed sample (control or DNTT-KO)

value: mRNA


title: siCTRL,rep3

description: Library name: siCTRL,rep3


title: Sample DL05, Diffuse large B-cell lymphoma/high grade B-cell lymphoma (GCB) (Hi-C)

description: Library name: HIC_DL05


title: V45M5161_4

description: Library name: 18


title: V44M5G_2

description: Library name: 7

value: MDA-MB-157 GFP ind OE


title: V41M5161_4

description: Library name: 6

value: Human epithelial breast cancer cells

value: Dox + 1 g/L glucose for 4 h


title: V45M5G_2

description: Library name: 13

value: Dox + 15 g/L glucose for 4 h


title: V41M5161_2

description: Library name: 4


title: V44M5161_3

description: Library name: 11


title: Sample DC04, Primary diffuse large B-cell lymphoma of the CNS (Hi-C)

description: Library name: HIC_DC04

value: tumor


title: V44M5G_3

description: Library name: 8


title: αβ, TH, CRISPR, GEX

description: Library name: Sample 15

value: thymus

value: NOD.Cg-KitW-41J Tyr+ Prkdcscid Il2rgtm1Wjl/ThomJ


title: γδ, TH, CRISPR, TCR

description: Library name: Sample 17

value: gamma delta T cell

value: VDJ


title: V41M5161_3

description: Library name: 5


title: Sample DC05, Primary diffuse large B-cell lymphoma of the CNS (Hi-C)

description: Library name: HIC_DC05


title: γδ, TH, CRISPR, GEX

description: Library name: Sample 13


title: V41M5G_2

description: Library name: 1


title: V41M5G_3

description: Library name: 2


title: γδ, SP, CRISPR, GEX

description: Library name: Sample 14

value: spleen


title: γδ, PO, ADT

description:
Library name: Sample 10
antibody-derived oligonucleotide (ADT), hashtag-derived oligonucleotide (HTO)

source_name: spleen, liver, lung

value: spleen, liver, lung

value: 14-16 weeks old

value: ADT, HTO

value: Hashtag1 (spleen), Hashtag2 (lung), Hashtag3 (liver)


title: siCTRL,rep2

description: Library name: siCTRL,rep2

value: Kidney

value: WT

value: siCTRL


title: CAL-51, p27-, Rep3

city: Worcester

first: Junhui

last: Li

address: 364 Plantation St

institute: University of Massachusetts Medical School

description:
Library name: p27low3
CAL-51, p27-, Rep3

data_processing:
The analysis were performed on the OneStopRNASeq platform.
Specifically, paired-end RNASeq reads were aligned to hg38 with STAR
Gene expression were quantified with featureCounts
Genome annotation file used was gencode.vM25.primary_assembly
Differential analysis processed with DESeq2
Assembly: hg38
Supplementary files format and content: Gene expression matrix: This is a tabular file that represents the gene expression levels for each sample in the dataset. It typically includes rows representing genes or transcripts and columns representing individual samples. The values in the matrix can be raw read counts, normalized expression values (e.g., TPM or FPKM), or log-transformed expression values.
Supplementary files format and content: Differential expression analysis results: These files contain the results of differential gene expression analysis, identifying genes that show significant expression differences between different conditions or groups. The files may include statistics such as fold change, p-values, adjusted p-values, and gene annotations.

source_name: breast carcinoma

extract_protocol:
RNA was extracted from the indicated cells using a NucleoSpin RNA kit
Library for RNA-Seq was prepared according to KAPA Stranded mRNA Hyper prep polyA selected kit with 201–300 bp insert size using 250ng RNA as input

value: breast carcinoma


title: Sample DC03, Diffuse large B-cell lymphoma of the CNS from Richter's transformation of B-cell CLL (Hi-C)

description: Library name: HIC_DC03


title: Sample DL04, Diffuse large B-cell lymphoma/high grade B-cell lymphoma (Non-GCB) (Hi-C)

description: Library name: HIC_DL04


title: Sample DC02, Primary diffuse large B-cell lymphoma of the CNS (Hi-C)

description: Library name: HIC_DC02


title: αβ, PO, TCR

description: Library name: Sample 8

value: alpha beta T cell


title: CAL-51, p27-, Rep1

description:
Library name: p27low1
CAL-51, p27-, Rep1


title: CAL-51, p27+, Rep3

description:
Library name: p27high3
CAL-51, p27+, Rep3


title: V41M5G_4

description: Library name: 3

value: MDA-MB-157 GFP ind OE

value: Human epithelial breast cancer cells

value: Dox + 1 g/L glucose for 4 h


title: Sample BL01, Burkitt lymphoma (Hi-C)

description: Library name: HIC_BL01

value: tumor


title: CAL-51, p27+, Rep1

description:
Library name: p27high1
CAL-51, p27+, Rep1


title: comBO_d35 granular gel_MM3

city: Oxford

first: Yuqi

last: Shen

state: Oxfordshiore

address: MRC WIMM, University of Oxford

department: Radcliffe Department of Medicine

institute: University of Oxford

description:
Library name: Sample 12
scRNA-seq of d35 granular gel-based comBO engrafted with myeloma patient CD138+ cells

data_processing:
scRNA-seq raw data was processed first using the CellRanger pipeline (10x Genomics, v.7.0.0), post-processed using CellBender (v.0.3.0), Souporcell (v.3.0.0) and analysed with Seurat (v.5.1.0). Predicted ligand receptor (LR) analysis was performed using CellChat (v1.6.1). Differential abundance was computed with the miloR package (v.2.0), integration performed using Harmony (v.1.2.0) and plotting performed using the scCustomise package (v.2.1.2).
Assembly: GRCh38-2020-A
Supplementary files format and content: R objects containing annotated SingleCellaR objects.

source_name: hiPSC-derived bone marrow organoid engrafted with CD138+ cells derived from multiple myeloma patient 3 for 2 weeks

growth_protocol: human iPSCs were subjected to a series of cytokine cocktails to guide multi-lineage differentiation at 5% O2, including mesodermal induction prior to commitment to vascular and myeloid lineage generation, followed by a lymphoid phase, and finally individual organoid culture.

extract_protocol:
Chromium Next GEM Single Cell 3ʹ Kit v3.1 for Sample 1-4. Chromium Next GEM Single Cell 3' HT Kits v3.1 for Sample 5-12.
Libraries for samples 1-4 were prepared using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (Dual Index). Library preparation for samples 5-12 followed the manufacturer’s instructions for the Chromium Next GEM Single Cell 3ʹ HT Kit v3.1 (Dual Index).

value: Bone marrow haematopoietic and stromal cells


title: γδ, TH, ADT

description:
Library name: Sample 9
antibody-derived oligonucleotide (ADT), hashtag-derived oligonucleotide (HTO)

value: thymus

value: NOD.Cg-KitW-41J Tyr+ Prkdcscid Il2rgtm1Wjl/ThomJ

value: gamma delta T cell

value: ADT


title: CAL-51, p27+, Rep2

description:
Library name: p27high2
CAL-51, p27+, Rep2


title: comBO_d35 granular gel_MM1

description:
Library name: Sample 10
scRNA-seq of d35 granular gel-based comBO engrafted with myeloma patient CD138+ cells

source_name: hiPSC-derived bone marrow organoid engrafted with CD138+ cells derived from multiple myeloma patient 1 for 2 weeks


title: CAL-51, p27-, Rep2

description:
Library name: p27low2
CAL-51, p27-, Rep2


title: V44M5G_4

description: Library name: 9

value: Dox + 5 g/L glucose for 4 h


title: αβ, TH, ADT

description:
Library name: Sample 11
antibody-derived oligonucleotide (ADT), hashtag-derived oligonucleotide (HTO)

value: 14-16 weeks old


title: Sample BN01, B-cell lymphoma NOS (Hi-C)

description: Library name: HIC_BN01


title: Sample DC01, Primary diffuse large B-cell lymphoma of the CNS (Hi-C)

description: Library name: HIC_DC01


title: αβ, PO, ADT

description:
Library name: Sample 12
antibody-derived oligonucleotide (ADT), hashtag-derived oligonucleotide (HTO)

value: spleen, liver, lung

value: ADT, HTO

value: Hashtag1 (spleen), Hashtag2 (lung), Hashtag3 (liver)


title: Sample BA02, B-lymphoblastic leukaemia/lymphoma (Hi-C)

description: Library name: HIC_BA02


title: comBO_d35 granular gel_MM2

description:
Library name: Sample 11
scRNA-seq of d35 granular gel-based comBO engrafted with myeloma patient CD138+ cells

source_name: hiPSC-derived bone marrow organoid engrafted with CD138+ cells derived from multiple myeloma patient 2 for 2 weeks


title: αβ, TH, GEX

description: Library name: Sample 3

value: mRNA


title: γδ, PO, TCR

description: Library name: Sample 6

value: VDJ


title: αβ, TH, TCR

description: Library name: Sample 7

value: alpha beta T cell


title: MiaPaCa-2 cells, siACO1,  replicate 3

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

description:
Library name: Sample 12
Column name in rawCount_allSample.txt: A21

data_processing:
Base calling and generation of FASTQ files were performed using standard CASAVA pipeline.
RNA-seq quality was checked by running FastQC, and TrimGalore was used for adapter and quality trimming. RNA-seq reads were mapped against GRCm39 using STAR (v 2.7.0e) aligner with default parameters.
Differential gene expression analysis was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files of normalized abundance measurements.

growth_protocol: Cells were maintained in medium recommended by the supplier.

extract_protocol:
Total RNA was extracted using PureLink RNA isolation (Life Technologies, 12183025) and treated with DNase (Life Technologies, AM2222).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The end repair, A-tailing, adapter ligation, size selection, amplification, and purification were performed.

treatment_protocol: siRNA transfection using standard protocol.

value: pancreatic cancer


title: γδ, PO, GEX

description: Library name: Sample 2


title: comBO_d35 granular gel_HD

description:
Library name: Sample 9
scRNA-seq of d35 granular gel-based comBO engrafted with healthy donor CD34+ cells

source_name: hiPSC-derived bone marrow organoid engrafted with healthy donor CD34+ cells for 2 weeks


title: comBO_d20 bulk gel_biol rep4

description:
Library name: Sample 4
scRNA-seq of d20 bulk hydrogel-based comBO

source_name: hiPSC-derived bone marrow organoid

value: hiPSC-derived bone marrow organoid


title: comBO_d35 granular gel_biol rep1

description:
Library name: Sample 7
scRNA-seq of d35 granular gel-based comBO


title: comBO_d35 granular gel_biol rep2

description:
Library name: Sample 8
scRNA-seq of d35 granular gel-based comBO


title: γδ, TH, GEX

description: Library name: Sample 1


title: Sample AL02, ALK-positive anaplastic large cell lymphoma (Hi-C)

description: Library name: HIC_AL02


title: MiaPaCa-2 cells, siACLY,  replicate 2

description:
Library name: Sample 8
Column name in rawCount_allSample.txt: A14

value: siACLY


title: comBO_d35 bulk gel_biol rep1

description:
Library name: Sample 5
scRNA-seq of d35 bulk hydrogel-based comBO


title: WT_B2

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

description: Library name: Ig589_B2

data_processing:
Gene expression count matrices were exported by cell barcode using R. Single cell gene expression counts were normalised using Sanity with default values. Single cells were excluded if mitochondrial reads accounted for more than 20% of the reads. Differentially expressed genes between Pre589+ and Pre589- B2 cells were determined using limma on log transcription quotients from Sanity. After Bonferroni correction, genes with a family-wise error rate (FWER) < 0.05 were called as significantly differentially expressed. Gene set enrichment analysis (GSEA), was performed on Hallmark (mh) and Cell Signature (m8) ontologies, and terms with FWER < 0.05 were defined as significantly enriched.
Assembly: GRCm38.p6
Supplementary files format and content: tsv.gz
Supplementary files format and content: mtx.gz

source_name: B cell

extract_protocol:
9G4 antibody (purified rat anti-human IGHV4-34*01; IgM Biosciences) was conjugated to Alexa Fluor 647 (AF647) using an antibody labelling kit (Life Technologies), according to the manufacturer’s instructions. Mouse bone marrow and spleen single cell suspensions were washed and kept in FACS buffer (PBS/5% FCS/0.02% sodium azide). All antibody incubation steps were completed on ice and in the dark, with centrifugations at 2000 rpm for 3 minutes at 4°C. Cells were incubated with anti-CD16/32 (ebioscience) Fc block for 15 minutes, washed twice incubated for 30-45 minutes, with a cocktail of flow cytometry antibodies (including 9G4) in PBS. After two washes, cells were fixed for 15 minutes in PBS/5% formalin (2% formaldehyde; Sigma) and resuspended in FACS buffer, for acquisition on the Symphony (BD) flow cytometer.
A total of 27,000 and 28,000 peritoneal cavity B2 cells were bulk sorted into 1.5ml tubes containing sterile PBS/10% FCS from n=2 sex- and age-matched pre589-tg mice. A total of 10,000 cells were captured in the 5’ V(D)J+GEX 10x reaction using the Chromium Single-Cell 5’ Gel Beads and v2 Library kits (10X Genomics). Quality control of libraries was assessed with an Agilent BioAnalyzer High Sensitivity DNA chip, pooled, and quantified using qPCR (KAPA Library Quantification Kit). Denatured libraries were loaded onto an Illumina NovaSeq 6000 and sequenced using a 150-cycle High-Output Kit.

value: B cell


title: MiaPaCa-2 cells, siACO1,  replicate 2

description:
Library name: Sample 11
Column name in rawCount_allSample.txt: A20


title: MiaPaCa-2 cells, siACO1,  replicate 1

description:
Library name: Sample 10
Column name in rawCount_allSample.txt: A19


title: comBO_d35 bulk gel_biol rep2

description:
Library name: Sample 6
scRNA-seq of d35 bulk hydrogel-based comBO

value: Bone marrow haematopoietic and stromal cells


title: MiaPaCa-2 cells, siACLY,  replicate 1

description:
Library name: Sample 7
Column name in rawCount_allSample.txt: A13


title: MiaPaCa-2 cells, siSLC25A1,  replicate 3

description:
Library name: Sample 6
Column name in rawCount_allSample.txt: A9


title: MiaPaCa-2 cells, siACLY,  replicate 3

description:
Library name: Sample 9
Column name in rawCount_allSample.txt: A15


title: comBO_d20 bulk gel_biol rep2

description:
Library name: Sample 2
scRNA-seq of d20 bulk hydrogel-based comBO


title: MiaPaCa-2 cells, siSLC25A1,  replicate 2

description:
Library name: Sample 5
Column name in rawCount_allSample.txt: A8


title: Sample AL01, ALK-negative anaplastic large cell lymphoma (Hi-C)

description: Library name: HIC_AL01

source_name: tumor

value: tumor


title: Sample BA01, B-lymphoblastic leukaemia/lymphoma (Hi-C)

description: Library name: HIC_BA01


title: αβ, PO, GEX

description: Library name: Sample 4

value: NOD.Cg-KitW-41J Tyr+ Prkdcscid Il2rgtm1Wjl/ThomJ


title: comBO_d20 bulk gel_biol rep3

description:
Library name: Sample 3
scRNA-seq of d20 bulk hydrogel-based comBO


title: γδ, TH, TCR

description: Library name: Sample 5

value: thymus

value: gamma delta T cell


title: MiaPaCa-2 cells, siControl,  replicate 3

description:
Library name: Sample 3
Column name in rawCount_allSample.txt: A3

value: siControl


title: comBO_d20 bulk gel_biol rep1

description:
Library name: Sample 1
scRNA-seq of d20 bulk hydrogel-based comBO


title: stimulated B cells, BTKi treated at t=0h #3

city: Mainz

first: Neuroimmunology

last: Mainz

address: Langenbeckstr. 1

department: Neurology

country: Germany

institute: University Medical Center of the Johannes Gutenberg University Mainz

data_processing:
Sequence quality was assessed using FASTQC (v 0.12.1),
reads were quasi-mapped to GRCh38 using salmon (v1.10.2), with default parameters,
the transcriptome index was built using salmon's function index,
transcript-level count matrices were generated using the tximport package.
Assembly: GRCh38
Supplementary files format and content: salmon files

source_name: B cells

extract_protocol:
RNA isolation was performed using the RNeasy Micro Kit (Qiagen)
Barcoded mRNA-seq cDNA libraries were prepared from 100 ng of total RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual with a final amplification of 12 PCR cycles. Quantity was assessed using Invitrogen’s Qubit HS assay kit and library size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay.
RNA Seqeuncing (PE150)

treatment_protocol: After Isolation, B cells were stimulated with sCD40L, BCR-cross linking Antibody and IL-4 with or without BTKi (Evobrutinib)

value: B cells

value: WT

value: 40X4+ BTKi 1µM

tag: btki treatment

tag: rna-isolation (after_b_cell_isolation)


title: stimulated B cells, vehicle treated #3

tag: cell type

value: 40X4 +vehicle


title: PB-N2-KO-2

city: Hangzhou

first: Saiyong

last: Zhu

state: Zhejiang

address: 866 Yuhangtang Rd.

department: Life Sciences Institute

institute: Zhejiang University

description: Library name: Sample 11

data_processing:
Illumina Casava1.8 software was used for basecalling.
Raw reads were trimmed by fastp (v0.22.0) with default parameters.
Clean reads were aligned to hg38 genome using HISAT2 (v2.2.1) with default parameters.
Transcript assembly was carried out by stringtie (v2.1.7) and expression of transcripts sharing each gene_id was quantified as transcripts Per Million (TPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: MEL1 hESC line

growth_protocol: ePPs were cultured on feeder in EF6I medium: DMEM containing 1:50 B27, 50 ng/ml EGF, 10 ng/ml bFGF, 10 μM 616452, and 1 μM I-BET151 (APExBIO).  R6 medium: DMEM containing 1:50 B27, 0.05% BSA (Yeasen), 10 μM zinc sulfate (Vetec), 10 μg/ml heparin (Sigma), 10 μM 616452 (TargetMol), 1 μM T3 (Sigma), 0.2 μM LDN-193189 (Tocris), 0.2 μM Compound E (MedChem Express), 0.5 mM vitamin C, and 10 μM forskolin (TargetMol).

extract_protocol:
Total RNA was extracted and purified using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme)
RNA-seq library preparation and sequencing were performed by LC-Bio Technology.

tag: cell line

value: MEL1 hESC line

value: ePP-derived islets


title: Ctrl_rep3

city: Wuhan

first: Yin

address: Zhang Road No. 99 Jiefang Road 238

institute: Renmin Hospital of Wuhan University

description: Library name: Sample 6

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of Mus_musculus.GRCm39 using STRA software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: xlsx files include all_reads_counts in sheet 1 and all_samples_rpkm in sheet 2 for each sample.

source_name: Retina

extract_protocol:
Total RNAs were extracted from retinas using TRIzol Reagent (Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: Retina

tag: genotype

value: C57BL/6J, WT


title: stimulated B cells, BTKi treated at t=48h #3

tag: treatment


title: Transcriptome of cumulus cell at 12h_3

city: Ube

first: Amon

last: Shiroshita

state: Yamaguchi

address: Minamikogushi 1-1-1

institute: Yamaguchi university

description:
Library name: CC_12h_rep3
Transcriptome profiling during ovulation.

data_processing:
CLC Genomics Workbench v22.0.1
Assembly: GRCm38
Supplementary files format and content: csv file contains gene-level raw read counts for each sample.

source_name: ovary

extract_protocol:
RNA was harvested using RNeasy Micro Kit (Qiagen) and RNeasy Mini Kit (Qiagen). Total RNA was used for library construction.
RNA libraries were constructed using a stranded mRNA library prep kit and sequenced on the Illumina NovaSeq 6000 platform.

value: ovary

value: hCG 12h


title: CS_rep3

description: Library name: Sample 3

value: C57BL/6J, conditional REP1 knockout


title: PB-N2-WT-2

description: Library name: Sample 8


title: Ctrl_rep2

description: Library name: Sample 5


title: Mouse colon, IL-10 KO+FMT 1

city: Galveston

first: Kevin

middle: M.

last: Lopez

address: 301 University Blvd

department: Internal Medicine

institute: University of Texas Medical Branch at Galveston

description: Library name: Sample_4127

data_processing:
Cluster formation of the library DNA templates was performed using the TruSeq PE Cluster Kit v3 and the Illumina cBot workstation
Paired-end 50 base sequencing by synthesis was performed using TruSeq SBS kit v3 on an Illumina HiSeq 1000
Alignment of sequence reads was performed using the Spliced Transcript Alignment to a Reference program version 2.4.2a, using default parameters
Differential expression was evaluated using Cufflinks/Cuffdiff software, v2.2.1
Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment within the gene lists of interest were performed using Enrichr
Assembly: GRCm39
Supplementary files format and content: counts

source_name: Colon

growth_protocol: Six-week-old male C57BL/6J mice and homozygous Il10-/- 129(B6)-Il10tm1Cgn/J mice were housed under specific pathogen-free (SPF) conditions in the UTMB Animal Facility with a 12-hour light/dark cycle, a temperature range of 24-26°C, and a relative humidity of 40-70%.

extract_protocol:
Mice were euthanized under anesthesia and their colon tissues snap-frozen in liquid nitrogen. Total RNAs were isolated from pulverized frozen colon tissue using the PureLink RNA Mini Kit (Thermo Fisher).
RNA libraries were prepared using the Illumina TruSeq RNA Sample Preparation kit per manufacturer's protocol.

treatment_protocol: For C57BL/6J mice, there were three groups of 10 mice receiving the following treatments: (1) vehicle control mice, (2)  DSS mice given 2% DSS in drinking water for 4 cycles of 7 days each with intermittent 2-week intervals of normal drinking water, and (3) DSS mice given the same DSS treatment plus fecal microbiota transplantation from healthy 8-week-old mice from the vehicle control group (1). For 129(B6)-Il10tm1Cgn/J mice, there were three groups of 10 mice receiving the following treatments: (1) wild-type, (2) IL-10 homozygous knockout, and (3) IL-10 homozygous knockout plus fecal microbiota transplantation from wild-type mice of group (1).

value: Colon

value: Colonocytes

value: IL-10 KO

value: FMT


title: Mouse colon, IL-10 KO+FMT 2

description: Library name: Sample_4128


title: PB-N2-WT-3

description: Library name: Sample 9


title: Transcriptome of cumulus cell at 12h_2

description:
Library name: CC_12h_rep2
Transcriptome profiling during ovulation.

value: mural granulosa cell


title: naive B cells #3


title: PB-N2-KO-1

description: Library name: Sample 10


title: Mouse colon, IL-10 KO+FMT 5

description: Library name: Sample_4131


title: PB-N2-KO-3

description: Library name: Sample 12


title: PB-N2-WT-1

description: Library name: Sample 7


title: Mouse colon, IL-10 KO 4

description: Library name: Sample_4137


title: CS_rep1

description: Library name: Sample 1


title: stimulated B cells, BTKi treated at t=48h #2


title: MiaPaCa-2 cells, siControl, replicate 1

description:
Library name: Sample 1
Column name in rawCount_allSample.txt: A1

value: pancreatic cancer

value: siControl


title: Mouse colon, IL-10 KO+FMT 4

description: Library name: Sample_4130


title: Mouse colon, IL-10 KO+FMT 3

description: Library name: Sample_4129


title: unstimulated B cells #3

value: B cells

value: WT


title: Ctrl_rep1

description: Library name: Sample 4


title: Mouse colon, IL-10 KO 5

description: Library name: Sample_4138


title: PB-C16-WT-3

description: Library name: Sample 3


title: PB-C16-KO-1

description: Library name: Sample 4


title: MiaPaCa-2 cells, siSLC25A1,  replicate 1

description:
Library name: Sample 4
Column name in rawCount_allSample.txt: A7


title: stimulated B cells, vehicle treated #2

value: 40X4 +vehicle


title: Transcriptome of cumulus cell at 4h_1

description:
Library name: CC_4h_rep1
Transcriptome profiling during ovulation.

value: hCG 4h


title: PB-C16-WT-2

description: Library name: Sample 2

value: MEL1 hESC line

value: ePP-derived islets


title: Transcriptome of cumulus cell at 12h_1

description:
Library name: CC_12h_rep1
Transcriptome profiling during ovulation.


title: Transcriptome of cumulus cell at 0h_3

description:
Library name: CC_0h_rep3
Transcriptome profiling during ovulation.

value: hCG 0h


title: PB-C16-KO-3

description: Library name: Sample 6


title: Mouse colon, IL-10 KO 1

description: Library name: Sample_4132


title: Transcriptome of cumulus cell at 0h_2

description:
Library name: CC_0h_rep2
Transcriptome profiling during ovulation.

value: ovary


title: MiaPaCa-2 cells, siControl,  replicate 2

description:
Library name: Sample 2
Column name in rawCount_allSample.txt: A2


title: PB-C16-KO-2

description: Library name: Sample 5


title: Transcriptome of cumulus cell at 4h_3

description:
Library name: CC_4h_rep3
Transcriptome profiling during ovulation.


title: stimulated B cells, BTKi treated at t=48h #1

value: 40X4+ BTKi 1µM


title: CS_rep2

description: Library name: Sample 2

value: Retina

value: C57BL/6J, conditional REP1 knockout


title: Mouse colon, IL-10 KO 3

description: Library name: Sample_4136

value: Colon

value: Colonocytes


title: PB-C16-WT-1

description: Library name: Sample 1


title: Transcriptome of cumulus cell at 0h_1

description:
Library name: CC_0h_rep1
Transcriptome profiling during ovulation.


title: FLAG VMP1 IP#3

first: yang

last: wenwen

address: No. 163 Xianlin Avenue, Qixia District, Nanjing

institute: life science school of nanjing university,china

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38.p14 (GCA_000001405.29)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: renal tubular epithelial cell

value: Transfect the Flag-VMP6 plasmid,RIP (RNA immunoprecipitation) was performed using Flag antibody magnetic beads


title: Mouse colon, Naïve 1

description: Library name: Sample_5072


title: Mouse colon, Naïve 4

description: Library name: Sample_4118


title: Mouse colon, IL-10 KO 2

description: Library name: Sample_4133

value: IL-10 KO


title: FLAG VMP1 IP#2

value: Transfect the Flag-VMP5 plasmid,RIP (RNA immunoprecipitation) was performed using Flag antibody magnetic beads


title: Transcriptome of mural granulosa cells cell at 12h_3

description:
Library name: MGC_12h_rep3
Transcriptome profiling during ovulation.

value: mural granulosa cell

value: hCG 12h


title: unstimulated B cells #2

value: B cells

value: WT


title: Mouse colon, Naïve 3

description: Library name: Sample_4117


title: unstimulated B cells #1


title: Mouse colon, DSS+FMT 3

description: Library name: Sample_5037

value: DSS+FMT


title: positive control#3

value: Transfect the Flag-VMP3 plasmid,Direct use of total cell lysate


title: naive B cells #2


title: stimulated B cells, BTKi treated at t=0h #2


title: Mouse colon, DSS+FMT 2

description: Library name: Sample_5032


title: Transcriptome of cumulus cell at 4h_2

description:
Library name: CC_4h_rep2
Transcriptome profiling during ovulation.

value: hCG 4h


title: FLAG VMP1 IP#1

value: Transfect the Flag-VMP4 plasmid,RIP (RNA immunoprecipitation) was performed using Flag antibody magnetic beads


title: stimulated B cells, vehicle treated #1

value: 40X4 +vehicle


title: Mouse colon, Naïve 2

description: Library name: Sample_5074


title: positive control#2

value: Transfect the Flag-VMP2 plasmid,Direct use of total cell lysate


title: sh-hnRNPA1-1

first: Lan

last: Lin

address: 299 Bayi Road, Wuchang District

department: School of Life Sciences

institute: Wuhan University

data_processing:
The raw data underwent quality control filtering using FastQC and Trim Galore software.Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads.
STAR software was employed for reference genome alignment
quantification using RSEM software
resulting in the determination of gene expression as Transcripts Per Million (TPM) values.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HeLa

growth_protocol: Human HeLa  cells were obtained from ATCC and cultured in DMEM(HyClone, SH30022.01) and 10% FBS(C04001-500, Vivacell), 100 ml will receive an additional 1 ml of Penicillin-Streptomycin Solution(03-031-1B)

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions.
RNA of samples was extracted from the tissues by Trizol method, Sequencing libraries were generated using NEBNext® Ultra™RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer's recommendations.

value: HeLa


title: Mouse colon, DSS+FMT 1

description: Library name: Sample_5031

value: Colon


title: positive control#1

value: Transfect the Flag-VMP1 plasmid,Direct use of total cell lysate


title: stimulated B cells, BTKi treated at t=0h #1

value: 40X4+ BTKi 1µM


title: Neurons , treated with vehicle, # 2

data_processing:
Sequence quality was assessed using FASTQC (v 0.12.1),
reads were quasi-mapped to GRCh38 using salmon (v1.10.2), with default parameters,
the transcriptome index was built using salmon's function index,
transcript-level count matrices were generated using the tximport package.
Assembly: GRCh38 (GCF_000001405.40)
Supplementary files format and content: salmon files

source_name: Neurons

extract_protocol:
RNA isolation was performed using the RNeasy Micro Kit (Qiagen) according to the manufacturers instructions
Barcoded mRNA-seq cDNA libraries were prepared from 100 ng of total RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual with a final amplification of 12 PCR cycles. Quantity was assessed using Invitrogen’s Qubit HS assay kit and library size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay.

treatment_protocol: human Neurons were treated for 24h as stated above

value: Neurons

value: vehicle


title: Neurons treated with BTK, # 2

value: BTKi 1µM


title: Neurons , treated with vehicle, # 1


title: Transcriptome of mural granulosa cells cell at 4h_2

description:
Library name: MGC_4h_rep2
Transcriptome profiling during ovulation.

value: ovary

value: mural granulosa cell


title: Transcriptome of mural granulosa cells cell at 4h_1

description:
Library name: MGC_4h_rep1
Transcriptome profiling during ovulation.


title: Transcriptome of mural granulosa cells cell at 12h_2

description:
Library name: MGC_12h_rep2
Transcriptome profiling during ovulation.

value: hCG 12h


title: Transcriptome of mural granulosa cells cell at 4h_3

description:
Library name: MGC_4h_rep3
Transcriptome profiling during ovulation.

value: WT


title: naive B cells #1

value: B cells


title: Transcriptome of mural granulosa cells cell at 12h_1

description:
Library name: MGC_12h_rep1
Transcriptome profiling during ovulation.


title: Mouse colon, DSS 3

description: Library name: Sample_5043

value: Colonocytes

value: DSS


title: Mouse colon, DSS 1

description: Library name: Sample_5029


title: Neurons treated with BTK, # 1


title: sh-control-2

value: sh-control


title: Mouse colon, DSS 4

description: Library name: Sample_5044


title: Transcriptome of mural granulosa cells cell at 0h_2

description:
Library name: MGC_0h_rep2
Transcriptome profiling during ovulation.

value: hCG 0h


title: sh-control-1


title: Transcriptome of mural granulosa cells cell at 0h_1

description:
Library name: MGC_0h_rep1_
Transcriptome profiling during ovulation.


title: Mouse colon, DSS 2

description: Library name: Sample_5030


title: PAO1-PhaF-Halo_CLAP_IP replicate B

city: Boston

first: Simon

last: Dove

state: Massachusetts

address: Boston Childrens Hospital, 300 Longwood Avenue EN761.1

department: Infectious Diseases

institute: Boston Children's Hospital

description:
Library name: Sample 6B
RNA after application of CLAP-seq

data_processing:
fastq records trimming (cutadapt 2.10)
bigwig file generation (deepTools version 3.5.1)
Assembly: Pseudomonas aeruginosa PAO1: NC_002516.2
Supplementary files format and content: Bigwig format

molecule: other

organism: Pseudomonas aeruginosa

growth_protocol: Bacterial strains were grown with aeration at 37˚C , shaking at 200 rpm, in LB medium

extract_protocol:
TRI Reagent was used for RNA extraction
Final libary construction was carried out based on the RNAtag-Seq methodology (Shishkin, et al., 2015)

treatment_protocol: Cells were harvested by centrifugation, washed with PBS, UV crosslinked and pellets stored at -80˚C.

value: phaF-Halo

value: Growth:OD ≈ 2.0 in LB

tag: ip antibody

value: Magne Halo tagged beads (Promega G728A)


title: ICE_sample3_rep4

city: Beijing

first: Jiaxin

last: Zhang

address: No.49 Garden North Road

department: Ophthalmology

institute: Peking University Third Hospital

data_processing:
Trimmomatic (0.39) was used to eliminate low-quality reads and trim adapter sequences.
Alignment to the hg19 reference genome was performed using STAR (2.7.5c)
Gene quantification was performed using StringTie (2.1.7) to obtain read count values for gene expression.
Assembly: hg19
Supplementary files format and content: tab-separated file includes raw counts for each sample

source_name: cornea endothelium

extract_protocol:
The Descemet membrane and corneal endothelium complex, obtained from patients with ICE syndrome or residual corneal donors, was cultured in DMEM/F12 medium supplemented with 15% Fetal Bovine Serum and 2mg/ml collagenase A. Tissue was digested in a cell culture incubator (37℃, 5% CO2) for 4-8 hours until reaching a cell mass state. Following careful removal of the supernatant, trypsin digestion was performed for 5-10 minutes. Subsequently, culture medium with double the volume of trypsin was added to neutralize the reaction. Finally, a 2ml syringe was utilized for gentle blowing and pipetting (8-10 times) to obtain a suspension of single cells or small cell aggregates.
Library was performed according to the manufacter's instructions.

tag: tissue

value: cornea endothelium

value: primary cell

value: corneal endothelial cell

tag: disease state

value: Iridocorneal endothelial (ICE) syndrome


title: PAO1-PhaF-Halo_CLAP_IP replicate C

description:
Library name: Sample 6C
RNA after application of CLAP-seq


title: 4T1 cells, sdAb#07.81, 48 h-2

city: 杭州市

first: 宣儒

last: 陈

state: 浙江省

address: 杭州师范大学仓前校区慎12-205

institute: 杭州师范大学

description: Library name: Sample 8

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Reference genome sequences and gene model annotation files of relative species were downloaded from genome website. Secondly, Hisat2 (v2.0.1) was used to indexreference genome sequence.
Clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: gz files for each Sample

source_name: breast caner

growth_protocol: Mouse breast cancer 4T1 cell line  and were cultured in RPMI 1640 supplemented with 10% FBS (SINSAGE TECH, South America), 2 mM Glutamine and 100 units/mL penicillin and 0.1 mg/mL streptomycin. All cells were maintained at 37℃ and 1% O2, 5% CO2 and passaged using 0.25% trypsin/0.02% EDTA for dissociation at 80% confluence.

extract_protocol:
The total RNAs were isolated using the Trizol reagent (Invitrogen) following the manufacturer’s protocol. RNA quality was inspected using Nanodrop (all samples had 260/280-ratio≥1.9).
Then libraries with different indexs were multiplexed and loaded on an Illumina NovaSeq 6000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: 4T1 cells were induced by treatment of 24 h or 48 h post confluent cells with 0.5 ug/ml sdAb (sdAb, Con or sdAb#07.81).

value: breast caner

value: triple-negative breast cancer cell

value: sdAb


title: Mouse colon, Control 1

description: Library name: Sample_37

value: Colon


title: PAO1-PhaF-Halo_CLAP_IP replicate A

description:
Library name: Sample 6A
RNA after application of CLAP-seq


title: ICE_sample2_rep3


title: sh-hnRNPA1-2

value: HeLa


title: Mouse colon, Control 2

description: Library name: Sample_38

value: WT


title: Transcriptome of mural granulosa cells cell at 0h_3

description:
Library name: MGC_0h_rep3
Transcriptome profiling during ovulation.

value: ovary

value: mural granulosa cell


title: OB-0-control

city: Taipei city

first: Li-Hang

last: Hsu

state: Taiwan (R.O.C)

address: No. 1, Sec. 4, Roosevelt Rd

department: Plant Pathology and Microbiology

country: Taiwan

institute: National Taiwan University

data_processing:
RNA-seq reads were processed using "Trinity v2.3.2".
Read quality was evaluated using "MultiQC v1.2".
The alignment and the read count quantification were performed with "bowtie2 v2.3.2" and "RSEM v1.2.31" respectively, and the alignment QC report was evaluated using "Qualimap v2".
The gene expression level is calculated by using FPKM method.
Genome_build: C. albicans SC5314
Supplementary_files_format_and_content: A tab-delimited text file includes FPKM, BLASTP, BLASTX, and annotation

organism: Candida albicans

source_name: C. albicans cells

growth_protocol: C. albicans cells were grown overnight at 30°C, washed twice with sterile ddH2O, diluted to 0.25 OD600/mL in 5 mL YPD broth, and then incubated at 30°C for 3 h with shaking at 200 rpm.

extract_protocol:
Cells were centrifuged at 4°C for 10 min at 3,250 rpm, and washed with ice-cold ddH2O to discard medium. Total RNA was extracted using TRIzol reagent (Invitrogen, USA). After adding 1 mL TRIzol and beads, collected cells were vortexed 30 s and put on ice 30 s for five times. Cultures were centrifuged at 4°C /12,000g for 10 min, and the supernatant was transferred to a new tube. The 200 μL of chloroform was added and mixed thoroughly, and tubes were incubated at room temperature for 3 min, centrifuged at 4°C/12,000g for 15 min, and supernatant was transferred to a new tube. Tubes were added 500 μL of isopropanol, incubated at room temperature for 10 min, centrifuged at 4°C/12,000g for 10 min, and the supernatant was discarded. Pellet containing RNA was washed twice with 75% ethanol and resuspend with RNase free water.
The mRNA was enriched with oligo(dT) magnetic beads and shortened into approximately 200-base fragments in fragmentation buffer. The first strand of cDNA was synthesized by the use of a random hexamer, buffer, dNTPs, and RNase H, and the second by the use of DNA polymerase I. The double strand cDNAs were purified with magnetic beads. After end preparation and 3’ end single nucleotide adenine addition were performed, sequencing adaptors were ligated to the fragments, and amplified by PCR. An Aglient 2100 bioanalyzer and ABI StepOnePlus real-time PCR system were used to qualify and quantify the sample library, and the library products were sequenced via an illumina HiSeq 2000 instrument.

treatment_protocol: To the experiment group, OB was added into YPD broth at a final concentration of 0.5 μg/mL during the 3 h incubation, while the control group was untreated.

value: wild type


title: 4T1 cells, sdAb-Con, 48 h-1

address: 杭州师范大学仓前校区慎12-205

description: Library name: Sample 5

value: sdAb-Con


title: 4T1 cells, sdAb#07.81, 48 h-1

address: 杭州师范大学仓前校区慎12-205

description: Library name: Sample 7


title: PAO1_CLAP_IP replicate A

description:
Library name: Sample 5A
RNA after application of CLAP-seq


title: PAO1_CLAP_IP replicate C

description:
Library name: Sample 5C
RNA after application of CLAP-seq


title: Mouse colon, Control 3

description: Library name: Sample_39

value: Colonocytes


title: 4T1 cells, sdAb-Con, 48 h-2

address: 杭州师范大学仓前校区慎12-205

description: Library name: Sample 6


title: OB-05-exp


title: ICE_sample3_rep2


title: PAO1ΔphaF_pPhaF-CTD-V_IP replicate B

description:
Library name: Sample 4B
RNA after application of CLIP-seq

source_name: PAO1 with phaF deletion

value: PAO1 with phaF deletion

value: PAO1 with phaF deletion (pPhaF-CTD-V)

value: Growth:OD ≈ 2.0 in LB

value: anti-VSVG mAb (Merck V4888)