title: ICE_sample3_rep1

value: cornea endothelium

value: primary cell

value: corneal endothelial cell


title: ICE_sample2_rep2

status: Public on Jan 12 2026

type: SRA

city: Beijing

first: Jiaxin

last: Zhang

address: No.49 Garden North Road

department: Ophthalmology

country: China

institute: Peking University Third Hospital

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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

tag: cell line

tag: cell type

tag: disease state

value: Iridocorneal endothelial (ICE) syndrome


title: PAO1_CLAP_IP replicate B

city: Boston

first: Simon

last: Dove

state: Massachusetts

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

department: Infectious Diseases

country: USA

institute: Boston Children's Hospital

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

library_source: other

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.

tag: strain

tag: genotype

value: WT

tag: treatment

value: Growth:OD ≈ 2.0 in LB

tag: ip antibody

value: Magne Halo tagged beads (Promega G728A)


title: 4T1 cells, Control, 1

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 1

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

organism: Mus musculus

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: PAO1ΔphaF_pPhaF-CTD-V_IP replicate C

description:
Library name: Sample 4C
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: anti-VSVG mAb (Merck V4888)


title: ICE_sample3_rep3


title: ICE_sample1_rep2


title: PAO1ΔphaF_pPhaF-CTD_IP replicate B

description:
Library name: Sample 3B
RNA after application of CLIP-seq

value: PAO1 with phaF deletion (pPhaF-CTD)


title: 20uM-3

city: Nanjing

first: Po

last: Hu

address: 138 Xianlin Rd

institute: Nanjing University of Chinese Medicine

description: treatment

data_processing:
fastp v.0.19.7 was used to process the raw data in fastq format to get clean data (parameter qualified_quality_phred 15；cut_mean_quality 20；length_required 75).
Clean reads were mapped to the NCBI Rfam database, and rRNA sequences were removed by Bowtie2(v2.33)（parameter default）.
Sequence reads after ribosome removal were aligned to the Homo sapiens reference genome GRCh38 from ensembl database by Hisat2 (v2.1.0)（parameter default）.
Salmon software v1.2.1 was used to obtain the expression for each gene（parameter default）.
EdgeR software v3.20.2 was used to obtain the differentially expressed genes（parameter fold change>2;FDR<0.05）.
Supplementary files format and content: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Blood

growth_protocol: Jurkat cells were cultured in RPMI-1640 medium (Gibco, USA). The mediums were supplemented with 10% fetal bovine serum (Gibco), 100 U/mL of benzylpenicillin, and 100 U/mL of streptomycin in a humidified environment with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using HiPure Universal RNA Mini Kit（Magen）. 0.6 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Next® Ultra™ Nondirectional RNA Library Prep Kit for Illumina® (New England Biolabs, MA, USA) following manufacturer's protocols.

treatment_protocol: Comparative gene expression profiling analysis of RNA-seq data for the Jurkat cells treated with  20 μmol/L isoliensinine for 12 h.

value: Blood

value: Jurkat

value: Tcellacutelymphoblastic leukemia

value: 20 umol/L isoliensinine for 12 h


title: ICE_sample1_rep1

value: cornea endothelium

value: primary cell


title: 4T1 cells, sdAb#07.81, 24 h-2

address: 杭州师范大学仓前校区慎12-205

description: Library name: Sample 4


title: WT replica 2

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: WT_2

library_source: transcriptomic single cell

data_processing:
raw reads were processed using 10x Genemoics cellranger count pipeline, filtered count mattrix were used in seurat for downstream analysis.
Assembly: mm10
Supplementary files format and content: cellranger filtered read count mattrix are included as processed data

source_name: E13.5 fetal liver

extract_protocol:
To isolate total E13.5 fetal liver cells, livers from E13.5 embryos were harvested, and single-cell suspensions were prepared by gentle pipetting in cold 1× PBS supplemented with 10% FBS. Dead cells were removed prior to library preparation.
Expression libraries were constructed according to the Chromium 10X single cell 5′ reagent protocol.

value: E13.5 fetal liver

value: total fetal liver cells


title: 4T1 cells, sdAb#07.81, 24 h-1

address: 杭州师范大学仓前校区慎12-205

description: Library name: Sample 3


title: 20uM-2

description: treatment

value: WT


title: FHC,sh-METTL1-2

city: Changsha

first: Lichao

last: Yang

state: Hunan

address: renmin middle road

institute: The Second Xiangya Hospital, Central South University

description: Library name: sh-METTL1-1

data_processing:
Raw sequencing reads were subjected to quality control using FastQC.
Adapters and low-quality reads were trimmed prior to alignment.
Clean reads were aligned to the human reference genome using STAR.
Gene-level read counts were generated using featureCounts.
Assembly: GRCh38
Supplementary files format and content: Processed data files include gene-level raw count matrices for each sample.

source_name: human intestinal epithelial cells

growth_protocol: FHC cells were cultured in Dulbecco’s modified Eagle’s medium/Ham’s F-12 (DMEM/F12) supplemented with 10% fetal bovine serum and maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted from FHC cells using TRIzol reagent according to the manufacturer’s instructions. RNA concentration and integrity were assessed before library preparation.
RNA sequencing libraries were constructed using the Illumina TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions. Briefly, poly(A)+ RNA was enriched from total RNA, fragmented, and reverse-transcribed to generate cDNA libraries, which were subsequently indexed and amplified for paired-end sequencing.

treatment_protocol: FHC cells were infected with lentiviral short hairpin RNA targeting METTL1 (sh-METTL1) or a non-targeting control shRNA (sh-Ctrl). Stable knockdown cells were selected and validated prior to RNA extraction.

value: human intestinal epithelial cells


title: PAO1-PhaF-V_IP replicate C

description:
Library name: Sample 2C
RNA after application of CLIP-seq

value: phaF-VSVG

value: Growth:OD ≈ 2.0 in LB


title: WT replica 3

description: Library name: WT_3


title: FHC,sh-METTL1-3

description: Library name: sh-METTL1-2


title: FHC,sh-Ctrl-2

description: Library name: sh-Ctrl-2

value: sh-Control


title: Gata1s, replica 4

description: Library name: GATA1s_4


title: FHC,sh-Ctrl-3

description: Library name: sh-Ctrl-3


title: ICE_sample1_rep3

value: corneal endothelial cell

value: Iridocorneal endothelial (ICE) syndrome


title: PAO1ΔphaF_pPhaF-CTD-V_IP replicate A

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

value: PAO1 with phaF deletion

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

value: anti-VSVG mAb (Merck V4888)


title: PAO1ΔphaF_pPhaF-CTD_IP replicate C

description:
Library name: Sample 3C
RNA after application of CLIP-seq

value: PAO1 with phaF deletion (pPhaF-CTD)


title: FHC,sh-Ctrl-1

description: Library name: sh-Ctrl-1


title: Normal_sample3_rep3

value: Normal


title: Normal_sample3_rep4


title: WT, replica 1

description: Library name: WT_1


title: 4T1 cells, Control, 2

address: 杭州师范大学仓前校区慎12-205

description: Library name: Sample 2

value: breast caner

value: triple-negative breast cancer cell

value: sdAb


title: Normal_sample3_rep2

value: cornea endothelium

value: primary cell


title: Gata1s, replica 3

description: Library name: GATA1s_3

value: E13.5 fetal liver

value: total fetal liver cells


title: Normal_sample3_rep1


title: 0uM-1

description: control

value: Blood

value: Jurkat

value: Tcellacutelymphoblastic leukemia

value: WT

value: 0 umol/L isoliensinine for 12 h


title: Normal_sample2_rep2

value: corneal endothelial cell


title: 20uM-1

description: treatment

value: 20 umol/L isoliensinine for 12 h


title: ICE_sample2_rep1

value: Iridocorneal endothelial (ICE) syndrome


title: 0uM-2

description: control


title: PAO1ΔphaF_pPhaF-CTD_IP replicate A

description:
Library name: Sample 3A
RNA after application of CLIP-seq

value: PAO1 with phaF deletion

value: PAO1 with phaF deletion (pPhaF-CTD)

value: Growth:OD ≈ 2.0 in LB

value: anti-VSVG mAb (Merck V4888)


title: Normal_sample1_rep2

value: Normal


title: PAO1-PhaF-V_IP replicate B

description:
Library name: Sample 2B
RNA after application of CLIP-seq

value: phaF-VSVG


title: PAO1-PhaF-V_IP replicate A

description:
Library name: Sample 2A
RNA after application of CLIP-seq


title: Normal_sample2_rep1

value: cornea endothelium

value: primary cell


title: CD45+ Plaur KO ADT

city: RTP

first: Brian

middle: Nicholas

last: Papas

address: 111 TW Alexander Drive

department: DIR

institute: NIEHS

description: Library name: HN4_mRNA_PlaurKO_CD45+_ADT

data_processing:
Reads basecalled using cellranger-7.1.0 mkfastq
Cell Ranger v7.0.0 "count" function to map reads and assign cell barcodes
Assembly: mm10
Supplementary files format and content: Cell Ranger Output files: barcodes.tsv.gz, features.tsv.gz, matrix.tsv.gz
Library strategy: CITE-seq

molecule: polyA RNA

source_name: Lung

extract_protocol:
Lungs were minced and digested, and flow cytometric sorting (BD FACSAria II) was used to prepare circulating CD45.2+ leukocytes from WT and Plaur–/– mice.
Approximately 16,000 live cells at or above 4×10^5 live cells/mL with 70% or higher viability were loaded into the Single Cell Chip followed by forming 10,000 single cell emulsion in Chromium Controller (10x Genomics). The first strand of cDNA for antibody derived transcripts (ADT) and gene derived transcripts is synthesized according to manufacturer’s instructions (10x Genomics, catalogue #PN-1000268). Then the cDNA is amplified according to the Total A-seq instruction (BioLegend) for samples with Total-seq A antibodies and the Chromium single cell 3′ library and gel bead kit v3.1 (Protocol CG000315, 10x Genomics). The Gene Expression and the ADT Libraries were prepared separately following manufacturer’s instructions. The two types of libraries were mixed at 10:1 molar ratio (Gene Expression library to ADT library) and sequenced by the NIEHS Epigenomics and DNA Sequencing Core Laboratory on NovaSeq 6000 (Illumina) with paired-end sequencing (Read1: 28;  Read2: 90). A total of 288,184,128 reads were obtained.

value: Lung

value: Total Lung Cell Lysate

value: Plaur KO

tag: library type

value: ADT

tag: adt

value: CD11b_TotalA, CD14_TotalA, CCR3_TotalA, Ly-6C_TotalA, ST2_TotalA


title: PAO1_IP replicate B

description:
Library name: Sample 1B
RNA after application of CLIP-seq

value: WT


title: CD45+ WT ADT

description: Library name: HN3_mRNA_WT_CD45+_ADT


title: 0uM-3

description: control

value: Blood

value: Jurkat

value: Tcellacutelymphoblastic leukemia

value: 0 umol/L isoliensinine for 12 h


title: sorted pre-B cells, non_relapse, r1

city: Stanford

first: Yuxuan

last: Liu

state: California

address: 265 Campus Drive

department: Pediatrics

institute: Stanford University

description:
Library name: UPN20
columa name in Raw_counts_DDPR_samples.csv: UPN20

data_processing:
Sequence reads trimmed for adaptor sequence and mapped to GRCh38.
Read counts were extract and normalized to VST using DESeq2 package.
Assembly: Assembly: GRCh38
Supplementary files format and content: tab-delimited files contain raw counts for each sample

source_name: diagnostic bone marrow sample

growth_protocol: Six diagnostic samples of known pS6 status from our previously published cohort (Good et al. Nat Med 2018) (n=3 pS6+ from patients who would relapse; n=3 pS6- from patients who are in continuous remission) were thawed in warm RPMI-1640 medium with 10% FBS.

extract_protocol:
Sorted cells were collected in 1 mL of cell-staining media containing RNAase inhibitors (VRC, Promega; RNAsin, New England Biolabs) and RNA was extracted using RNeasy Micro kit (Qiagen) following manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using SMARTER Ultra low kit (Takara Bio/Clonotech Laboratories) for sequencing

treatment_protocol: To enrich leukemic pre-B cells from patient samples, samples were stained with 7-color FACS panel at room temp. Pre-B cells are enriched in the population with low CD45 expression, positive for CD34, CD38 and CD10 and high expression of CD19, CD24 and CD43.

value: diagnostic bone marrow sample

value: B-ALL


title: Normal_sample1_rep1

value: corneal endothelial cell


title: sorted pre-B cells, non_relapse, r3

description:
Library name: UPN30
columa name in Raw_counts_DDPR_samples.csv: UPN30


title: Gata1s, replica 1

description: Library name: GATA1s_1

value: E13.5 fetal liver

value: total fetal liver cells


title: PAO1_IP replicate A

description:
Library name: Sample 1A
RNA after application of CLIP-seq

value: Growth:OD ≈ 2.0 in LB

value: anti-VSVG mAb (Merck V4888)


title: CD45- Plaur KO, GEX

description: Library name: HN2_mRNA_PlaurKO_CD45-

data_processing:
Reads basecalled using cellranger-7.1.0 mkfastq
Cell Ranger v7.0.0 "count" function to map reads and assign cell barcodes
Assembly: mm10
Supplementary files format and content: Cell Ranger Output files: barcodes.tsv.gz, features.tsv.gz, matrix.tsv.gz

extract_protocol:
Lungs were minced and digested, and flow cytometric sorting (BD FACSAria II) was used to CD45.2– structural cells from WT and Plaur–/– mice.
Approximately 16,000 live cells at or above 4×10^5 live cells/mL with 70% or higher viability were loaded into the Single Cell Chip followed by forming 10,000 single cell emulsion in Chromium Controller (10x Genomics). The first strand of gene derived transcripts is synthesized according to manufacturer’s instructions (10x Genomics, catalogue #PN-1000268The Gene Expression Libraries were prepared following manufacturer’s instructions. The libraries were sequenced by the NIEHS Epigenomics and DNA Sequencing Core Laboratory on NovaSeq 6000 (Illumina) with paired-end sequencing (Read1: 28;  Read2: 90). A total of 228,525,028 reads were obtained.

value: Lung


title: Gata1s, replica 2

description: Library name: GATA1s_2


title: CD45+ WT GEX

description: Library name: HN3_mRNA_WT_CD45+_GEX

value: Total Lung Cell Lysate

value: mRNA


title: bulk_mRNA-seq_PR8_21DPI_B6_brain_2, mRNA-seq

city: New Orleans

first: Xuebin

last: Qin

state: LA

address: 1430 Tulane Avenue

department: Pathology

institute: Tulane University

description:
Library name: Sample 42
10x Genomics
162_Brain_21_DPII

data_processing:
Fastq files generated by Illumina BaseSpace DRAGEN Analysis Software (Version 1.2.1) were applied for further data analyses. Raw reads were assessed using FastQC before alignment to mm10 by STAR. Transcript assembly and abundance estimation were performed with Htseq.
Assembly: mm10
Supplementary files format and content: matrix files of Htseq raw counts

source_name: Brain

extract_protocol:
Tissue samples for MA30 and PR8 infection were preserved in 1mL Trizol (15596026; Invitrogen) and extracted with a RNeasy Mini Kit (Cat. No.74104; QIAGEN) according to the manufactures’ instructions. Nanodrop was used to test the concentration and purity of the RNA prior to qPCR and bulk RNAseq.
Final cDNA libraries containing TruSeq RNA CD indexes (Illumina, 20019792) were quantitated using a Qubit dsDNA HS assay kit (Thermo Fisher Scientific, Q32854). The quality of the libraries was determined by running each on an Agilent TapeStation 4150 using an Agilent D1000 ScreenTape (Agilent: 5067-5582). Smear analysis was performed using Agilent TapeStation Software (Version 4.1.1) with a range of 200-600bp to determine the average size of each library. Size and concentration were then used to calculate the molarity of each library. Libraries were pooled at a final concentration of 750pM with a spike-in of 2% PhiX control library v3 (Illumina, FC-110-3001). A mixture of pooled libraries was loaded on an Illumina NextSeq P1 (300) reagent cartridge (Illumina, 20050264). Paired-end and dual indexing sequence, 150x8x8x150, was performed on NextSeq2000, yielding approximately 20M paired-end reads per sample.

value: Brain

value: PR8, 21 DPI


title: bulk_mRNA-seq_PR8_21DPI_B6_brain_4, mRNA-seq

description:
Library name: Sample 44
10x Genomics
172_Brain_21_DPII


title: Normal_sample1_rep3

value: cornea endothelium

value: primary cell

value: Normal


title: bulk_mRNA-seq_PR8_21DPI_B6_brain_1, mRNA-seq

description:
Library name: Sample 41
10x Genomics
161_Brain_21_DPII


title: HCCLM3 cells, LINC00862-2

city: Weifang

first: Yingying

last: Jiang

state: Shandong

address: 7166 Baotong west Road

institute: Weifang Medical University

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:hisat2-2.0.4) 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. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) 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: hg38
Supplementary files format and content: tab-delimited excel file including raw counts for each sample
Supplementary files format and content: tab-delimited excel file including FPKM values for each sample

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, 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, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). 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 Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: Cells were transfected with LINC00862-vector or Emtpy-vector

value: Hepatoma cells

value: LINC00862 overexpression


title: sorted pre-B cells, relapse, r3

description:
Library name: UPN26
columa name in Raw_counts_DDPR_samples.csv: UPN26

value: diagnostic bone marrow sample


title: PAO1_IP replicate C

description:
Library name: Sample 1C
RNA after application of CLIP-seq

value: WT


title: bulk_mRNA-seq_MA30_21DPI_B6_brain_4, mRNA-seq

description:
Library name: Sample 40
10x Genomics
543_Ma30_Brain21

value: MA30, 21 DPI


title: bulk_mRNA-seq_MA30_21DPI_B6_brain_2, mRNA-seq

description:
Library name: Sample 38
10x Genomics
532_Ma30_Brain21


title: T274M/+-6

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

description: Library name: CNC87_B3

data_processing:
The quality of the sequences in FASTQ format was assessed using the FastQC (v.0.11.5) tool.
Adapter removal and trimming of read ends with a Phred quality score of less than 25 were carried out using Trim Galore (v.0.5.0) and Cutadapt (v.1.10). Trimmed reads less than 40 bp in length were excluded from downstream analysis.
The reads were screened for the presence of rRNA and mtRNA sequences using FastQ-Screen (v.0.10.0).
RSeQC package (v.2.6.2) was used to assess read distribution, positional read duplication, gene body coverage, junction saturation and to confirm the strandedness of the reads.
Assembly: The reads were aligned to the reference genome (GRCh38.p13) with Gencode v44 annotations using the STAR aligner (v.2.6.0.c).
Supplementary files format and content: STAR alignemnts were processed to extract read counts for genes using htseq-count (v.0.6.1p2).

source_name: brain

extract_protocol:
Total RNA was extracted using the Rneasy Mini kit. RNA samples were checked on the Agilent Bioanalyzer 2100 RNA Nano chip for RNA integrity (RIN > 7) and quantified using the Qubit RNA HS Assay.
RNA library preparation was performed following the NEBNext Ultra II Directional RNA Library Preparation protocol to generate stranded data. In brief, 200 ng of total RNA was used as the input material and enriched for poly-A mRNA using magnetic oligo d(T) beads, fragmented into the 200-300-bases range for 10 minutes at 94°C and converted to double stranded cDNA. cDNA proceeded to library preparation and dual-index Illumina adapters were added through PCR. Final libraries were validated on the Fragment Analyzer using the High Sensitivity NGS Kit or on the Bioanalyzer 2100 DNA High Sensitivity chip to check for size and absence of primer dimers and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol.

value: brain

value: isogenic iPSC lines

value: neurons


title: HCCLM3 cells, LINC00862-3


title: CD45+ Plaur KO GEX

description: Library name: HN4_mRNA_PlaurKO_CD45+_GEX

value: Plaur KO


title: bulk_mRNA-seq_PR8_21DPI_B6_brain_3, mRNA-seq

description:
Library name: Sample 43
10x Genomics
171_Brain_21_DPII


title: CD45- WT, GEX

description: Library name: HN1_mRNA_WT_CD45-

value: Lung


title: sorted pre-B cells, non_relapse, r2

description:
Library name: UPN27
columa name in Raw_counts_DDPR_samples.csv: UPN27

value: B-ALL


title: bulk_mRNA-seq_PR8_8-9DPI_B6_brain_4, mRNA-seq

description:
Library name: Sample 36
10x Genomics
251_Brain_8_9_DPII

value: PR8, 8-9 DPI


title: PTEN(i)pe-/-

first: Gilles

last: Laverny

address: 1 rue Laurent fries

country: France

institute: IGBMC

description: the same libraries were run sequenced two times (R1 & R2, and L1 & L2)

data_processing:
Image analysis, base calling and demultiplexing were performed using RTA 2.7.7 and Cell Ranger 3.0.1 mkfastq
Alignment, barcode and UMI filtering and counting were performed using Cell Ranger 3.0.1 count and mouse reference 3.0.0 (mm10 and Ensembl release 93)
Assembly: mm10
Supplementary files format and content: Filtered (contains only detected cellular barcodes) feature-barcode matrix (each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)) in Market Exchange Format (MEX) and gzipped.
Supplementary files format and content: csv files with metadata and barcode sequences corresponding respectively to row and column indices from the matrix.

source_name: Prostate

extract_protocol:
Mice prostates were mechanically and enzymatically dissociated. Single living cells were obtained by FACS sorting.
Cell number and viability were determined by a Trypan Blue exclusion assay on a Neubauer Chamber. Samples consisted of  > 95% viable cells were processed on the Chromium Controller from 10X Genomics (Leiden, The Netherlands). Ten thousand cells were loaded per well to yield approximately 5 to 6,000 captured cells into nanoliter-scale Gel Beads-in-Emulsion (GEMs). Single cell 3’ mRNA seq library were generated according to Chromium Single Cell 3' Reagent Kits User Guide (v2 Chemistry) from 10X Genomics (ref CG00052 Rev E). Briefly, GEMs were generated by combining barcoded gel beads, a RT master mix containing cells, and partitioning oil onto Chromium Chip A. Following full length cDNA synthesis and barcoding from poly-adenylated mRNA, GEM were broken and pooled before cDNA amplification by PCR using 10 cycles. After enzymatic fragmentation and size selection, sequencing library were constructed by adding Illumina (Paris, France) P5 and P7 primers as well as sample index via end repair, A tailing, adaptor ligation and PCR with 12 cycles. Library quantification and quality control was performed using Bioanalyzer 2100 (Agilent Technologies, Santa Clara CA).

value: Prostate

value: single living cells

value: Pten(i)pe-/- (Prostatic luminal cell-specific Pten gene invalidation)


title: bulk_mRNA-seq_MA30_21DPI_B6_brain_3, mRNA-seq

description:
Library name: Sample 39
10x Genomics
535_Ma30_Brain21

value: Brain


title: HCCLM3 cells, NC-3

value: NC


title: sorted pre-B cells, relapse, r1

description:
Library name: UPN8
columa name in Raw_counts_DDPR_samples.csv: UPN8


title: HCCLM3 cells, LINC00862-1

value: Hepatoma cells


title: T274M/+-7

description: Library name: CNC87_B5


title: 21C-Lk54-7

city: Clemson

first: Rooksana

middle: Elizabeth

last: Noorai

state: South Carolina

address: 105 Collings St, BRC 157

department: Clemson University Genomics and Bioinformatics Facility

institute: Clemson University

description: Library name: 21C-Lk54-7

data_processing:
seqtk v1.3-r106
FastQC v0.11.6
Trimmomatic v0.36
GSNAP v2018-07-04
edgeR v3.22.5
Assembly: GCA_000149245.3_CNA3
Supplementary files format and content: Normalized counts text file, tab separated

organism: Cryptococcus neoformans

source_name: Yeast culture

growth_protocol: 5 ml of overnight cultures were refreshed and incubated in 50 ml YPD for 4 hours to reach an OD600 of ~1.0. The cultures were incubated in 25 ml YPD at room temperature (~24°C).

extract_protocol:
RNA extraction was performed with Bio-Rad Aurum Total RNA Mini Kit (Cat # 732-6820).
Library preparation was completed using the Illumina TruSeq Stranded kit (Illumina, San Diego, CA, USA).

value: Yeast culture

value: Septin 12 mutant

value: Fungal cell


title: PTEN/VDR(i)pe-/-

value: Pten/Vdr(i)pe-/- (Prostatic luminal cell-specific Pten and VDR gene invalidation)


title: sorted pre-B cells, relapse, r2

description:
Library name: UPN9
columa name in Raw_counts_DDPR_samples.csv: UPN9

value: diagnostic bone marrow sample


title: T274M/+-5

description: Library name: CNC87_B2

value: brain

value: isogenic iPSC lines


title: bulk_mRNA-seq_MA30_21DPI_B6_brain_1, mRNA-seq

description:
Library name: Sample 37
10x Genomics
528_Ma30_Brain21

value: MA30, 21 DPI


title: Urolithin A, 50μM, biological rep4

city: Athens

first: Konstantinos

last: Palikaras

address: Mikras Asias 75

department: Physiology

country: Greece

institute: Medical School, National and Kapodistrian University of Athens

data_processing:
Data were filtered using HISAT2
Filtered reads were mapped to reference transcriptome using FeatureCounts v.1.6.2
Assembly: WBcel235
Supplementary files format and content: .csv file
Supplementary files format and content: matix table containing gene IDs,mapping data and read counts

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: N2 C. elegans animals were grown in OP50-seeded plates at 20°C.

extract_protocol:
Total RNA was extracted from homogenized worm pellets using Nucleozol (Macherey-Nagel).
Libraries were prepared using the DNBSEQ Eukaryotic Stranded Transcriptome library - Stranded mRNA Library

treatment_protocol: UA samples were treated with 50μM Urolithin A, supplemeted to the growth medium.

value: Whole animal

value: wild type (N2)

value: Urolithin A, 50μM


title: HCCLM3 cells, NC-1


title: HCCLM3 cells, NC-2


title: Urolithin A, 50μM, biological rep3


title: wild type

value: Prostate

value: wild type


title: G256W/+-6

description: Library name: CNC2_B3

value: neurons


title: 21C-Lk54-4

description: Library name: 21C-Lk54-4


title: Urolithin A, 50μM, biological rep2


title: Urolithin A, 50μM, biological rep1


title: Control, biological rep4

value: untreated


title: bulk_mRNA-seq_PR8_8-9DPI_B6_brain_3, mRNA-seq

description:
Library name: Sample 35
10x Genomics
246_Brain_8_9_DPII

value: Brain

value: PR8, 8-9 DPI


title: 21C-LK162-7

description: Library name: 21C-LK162-7

value: Yeast culture


title: G256W/+-4

description: Library name: CNC2_B1


title: T274M/+-4

description: Library name: CNC87_B1


title: G256W/+-7

description: Library name: CNC2_B5


title: Control, biological rep2


title: L292_293/+-7

description: Library name: CNC14_B5


title: Control, biological rep1


title: bulk_mRNA-seq_MA30_7DPI_B6_brain_4, mRNA-seq

description:
Library name: Sample 30
10x Genomics
531_Ma30_Brain5_7

value: MA30, 7DPI


title: G256W/+-5

description: Library name: CNC2_B2


title: Control, biological rep3


title: bulk_mRNA-seq_MA30_7DPI_B6_brain_5, mRNA-seq

description:
Library name: Sample 31
10x Genomics
534_Ma30_Brain5_7


title: 21C-LK162-3

description: Library name: 21C-LK162-3

value: Fungal cell


title: bulk_mRNA-seq_MA30_7DPI_B6_brain_3, mRNA-seq

description:
Library name: Sample 29
10x Genomics
525_Ma30_Brain5_7


title: 21C-Lk54-1

description: Library name: 21C-Lk54-1

value: Septin 12 mutant


title: bulk_mRNA-seq_PR8_8-9DPI_B6_brain_2, mRNA-seq

description:
Library name: Sample 34
10x Genomics
244_Brain_8_9_DPII


title: 21C-LK162-1

description: Library name: 21C-LK162-1


title: bulk_mRNA-seq_MA30_7DPI_B6_brain_6, mRNA-seq

description:
Library name: Sample 32
10x Genomics
539_Ma30_Brain5_7


title: Spt16 Rpb1 ChIP-seq, ChIP DNA: spt6Δ2-238 pob3-E154K, IAA rep 2

first: James

middle: L

last: Warner

state: MA

address: 77 Avenue Louis Pasteur, Room 358

department: Genetics

institute: Harvard Medical School

description: Library name: 666_95_8WG16_rep2

library_source: genomic

data_processing:
Reads were aligned to the S.cerevisiae and S. pombe genomes using Bowtie2 (Langmead and Salzburg 2012) and sorted using samtools (Danecek et al. 2021).
Spike-in normalization factors were calculated using a custom python script (https://github.com/winston-lab/warner_chip_seq) using the number of reads mapping to the S. pombe genome.
Spike-in normalized coverage tracks were generated using deeptools bamCoverage (Ramirez et al 2016).
ChIP enrichment over input samples for ratio coverage tracks was calculated using deeptools bigwigCompare (Ramirez et al 2016).
Assembly: S. cerevisiae R64.2.1/sacCer3
Supplementary files format and content: Spike-in normalized coverage tracks generated using deeptools (Ramirez et al 2016) are provided in BIGWIG format (files ending _si.bw).
Supplementary files format and content: ChIP enrichment over input coverage tracks are provided in BIGWIG format (files ending _ratio.bw).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in SC-Trp at 30°C wth shaking to an OD600 of ≈ 0.6 prior to treament.

extract_protocol:
Cells were fixed with 1% formaldehyde for 30 minutes. Quenching, cell lysis, and chromatin extraction were performed as previously described (Gopalakrishnan et al 2019). Chromatin was sonicated using a Covaris E220e sonicator for 450 seconds per sample with a peak power of 140, a duty factor of 5, and 200 cycles per burst. Sonication was confirmed by agarose gel electrophoresis. Each chromatin sample was mixed with 10% S. pombe chromatin (strain FWP570) by protein mass for spike-in normalization.
Libraries were constructed using the NEBNext Ultra II DNA library Prep Kit for Illumina (New England Biolabs) following manufacturer specifications.

treatment_protocol: Cultures were diluted in SC-Trp to OD600 = 0.3 and treated with either DMSO (final concentration 0.05% v/v) or 3-indoleacetic acid (IAA, final concentration 25 μM) for 90 minutes at 30°C with shaking.

tag: plasmid

tag: chip antibody

value: a-Rpb1 8WG16 (EMD Millipore 05-952-I)

value: spt6D2-238-3xFLAG, SPT16-13xMYC, pob3-E154K, SPT6-V5-AID

value: 3-indoleacetic acid


title: bulk_mRNA-seq_MA30_7DPI_B6_brain_2, mRNA-seq

description:
Library name: Sample 28
10x Genomics
522_Ma30_Brain5_7


title: 21C-Lk54-3

description: Library name: 21C-Lk54-3


title: 21C-LK162-4

description: Library name: 21C-LK162-4


title: Low Protein - Standard + 10% Lys 9

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description: Library name: 64

data_processing:
Adaptor sequences and low quality reads removed
Mapped to S. scrofa genome (Sscrofa11.1)
DEG determined using DESeq2
Assembly: Sscrofa11.1
Supplementary files format and content: excel file with count data and gene symbol for each sample

organism: Sus scrofa

source_name: Muscle

extract_protocol:
RNA was extracted using RNeasy Plus Universal kit (Qiagen, Hilden, Germany) following instructions provided by the manufacturer
standard Illumina

value: Muscle


title: L292_293/+-4

description: Library name: CNC14_B1

value: brain

value: isogenic iPSC lines


title: Low Protein - Standard + 10% Lys 11

description: Library name: 66


title: isoL292_293-5

description: Library name: CC3_B2


title: L292_293/+-6

description: Library name: CNC14_B3


title: isoL292_293-7

description: Library name: CC3_B5


title: bulk_mRNA-seq_PR8_8-9DPI_B6_brain_1, mRNA-seq

description:
Library name: Sample 33
10x Genomics
242_Brain_8_9_DPI


title: bulk_mRNA-seq_uninfected_B6_brain_2, mRNA-seq

description:
Library name: Sample 24
10x Genomics
B6_mouse_brain_2


title: L292_293/+-5

description: Library name: CNC14_B2


title: bulk_mRNA-seq_uninfected_B6_brain_4, mRNA-seq

description:
Library name: Sample 26
10x Genomics
B6_mouse_brain_4


title: Spt16 Rpb1 ChIP-seq, ChIP DNA: pob3-E154K, IAA rep 2

description: Library name: 666_93_8WG16_rep2

value: SPT6-3xFLAG, SPT16-13xMYC, pob3-E154K, SPT6-V5-AID


title: Spt16 Rpb1 ChIP-seq, ChIP DNA: spt6Δ2-238 pob3-E154K, IAA rep 1

description: Library name: 666_95_8WG16_rep1


title: Low Protein - Standard + 20% Lys 12

description: Library name: 63


title: Spt16 Rpb1 ChIP-seq, ChIP DNA: spt6Δ2-238 pob3-E154K, IAA rep 3

description: Library name: 666_95_8WG16_rep3


title: isoL292_293-6

description: Library name: CC3_B3


title: bulk_mRNA-seq_MA30_7DPI_B6_brain_1, mRNA-seq

description:
Library name: Sample 27
10x Genomics
519_Ma30_Brain5_7


title: Spt16 Rpb1 ChIP-seq, ChIP DNA: pob3-E154K, IAA rep 3

description: Library name: 666_93_8WG16_rep3


title: Low Protein - Standard + 10% Lys 12

description: Library name: 67


title: Spt16 Rpb1 ChIP-seq, ChIP DNA: pob3-E154K, IAA rep 1

description: Library name: 666_93_8WG16_rep1


title: bulk_mRNA-seq_uninfected_B6_brain_1, mRNA-seq

description:
Library name: Sample 23
10x Genomics
B6_mouse_brain_1


title: Low Protein - Standard + 10% Lys 10

description: Library name: 65


title: Low Protein - Standard + 20% Lys 10

description: Library name: 61


title: Low Protein - Standard + 20% Lys 11

description: Library name: 62


title: isoL292_293-4

description: Library name: CC3_B1


title: isoT274M-5

description: Library name: CC20_B2


title: isoT274M-7

description: Library name: CC20_B5


title: bulk_mRNA-seq_PR8_21DPI_B6_lung_4, mRNA-seq

description:
Library name: Sample 22
10x Genomics
172_Lung_21_DPI

value: Lung

value: PR8, 21 DPI


title: Spt16 Rpb1 ChIP-seq, ChIP DNA: spt6Δ2-238, IAA rep 1

description: Library name: 661_95_8WG16_rep1


title: bulk_mRNA-seq_uninfected_B6_brain_3, mRNA-seq

description:
Library name: Sample 25
10x Genomics
B6_mouse_brain_3


title: bulk_mRNA-seq_PR8_21DPI_B6_lung_3, mRNA-seq

description:
Library name: Sample 21
10x Genomics
171_lung_21_DPI


title: isoG256W-7

description: Library name: CC18_B5

value: neurons


title: bulk_mRNA-seq_PR8_21DPI_B6_lung_2, mRNA-seq

description:
Library name: Sample 20
10x Genomics
162_lung_21_DPII


title: Spt16 Rpb1 ChIP-seq, ChIP DNA: wild-type, IAA rep 2

description: Library name: 661_93_8WG16_rep2

value: SPT6-3xFLAG, SPT16-13xMYC, SPT6-V5-AID


title: Standard Protein - Standard 12

description: Library name: 59


title: isoT274M-4

description: Library name: CC20_B1


title: Spt16 Rpb1 ChIP-seq, ChIP DNA: spt6Δ2-238, IAA rep 3

description: Library name: 661_95_8WG16_rep3


title: Spt16 Rpb1 ChIP-seq, ChIP DNA: spt6Δ2-238, IAA rep 2

description: Library name: 661_95_8WG16_rep2


title: isoT274M-6

description: Library name: CC20_B3


title: bulk_mRNA-seq_MA30_21DPI_B6_lung_4, mRNA-seq

description:
Library name: Sample 18
10x Genomics
543_Ma30_Lung21

value: MA30, 21 DPI


title: Standard Protein - Standard 11

description: Library name: 58


title: Spt16 Rpb1 ChIP-seq, ChIP DNA: wild-type, IAA rep 3

description: Library name: 661_93_8WG16_rep3


title: Standard Protein - Standard 10

description: Library name: 57


title: Spt16 Rpb1 ChIP-seq, ChIP DNA: wild-type, IAA rep 1

description: Library name: 661_93_8WG16_rep1


title: Low Protein - Standard + 20% Lys 9

description: Library name: 60


title: Spt16 Myc ChIP-seq, ChIP DNA: spt6Δ2-238 pob3-E154K, IAA rep 3

description: Library name: 666_95_myc_rep3

value: a-Myc 9E10 (Santa Cruz Biotechnology sc-40)


title: bulk_mRNA-seq_PR8_21DPI_B6_lung_1, mRNA-seq

description:
Library name: Sample 19
10x Genomics
161_lung_21_DPI


title: isoG256W-6

description: Library name: CC18_B3


title: Standard Protein - Standard 9

description: Library name: 56


title: isoG256W-5

description: Library name: CC18_B2


title: isoG256W-4

description: Library name: CC18_B1


title: bulk_mRNA-seq_MA30_21DPI_B6_lung_3, mRNA-seq

description:
Library name: Sample 17
10x Genomics
535_Ma30_Lung21


title: Low Protein - Standard 12

description: Library name: 55


title: bulk_mRNA-seq_MA30_21DPI_B6_lung_2, mRNA-seq

description:
Library name: Sample 16
10x Genomics
532_Ma30_Lung21


title: Spt16 Myc ChIP-seq, ChIP DNA: spt6Δ2-238 pob3-E154K, IAA rep 1

description: Library name: 666_95_myc_rep1


title: G256W/+-1

description: Library name: 78_CNC2_B2


title: Low Protein - Standard 10

description: Library name: 53


title: bulk_mRNA-seq_PR8_8-9DPI_B6_lung_3, mRNA-seq

description:
Library name: Sample 13
10x Genomics
246_Lung_8_9_DPII

value: PR8, 8-9 DPI


title: Spt16 Myc ChIP-seq, ChIP DNA: pob3-E154K, IAA rep 2

description: Library name: 666_93_myc_rep2


title: Spt16 Myc ChIP-seq, ChIP DNA: spt6Δ2-238 pob3-E154K, IAA rep 2

description: Library name: 666_95_myc_rep2


title: bulk_mRNA-seq_MA30_21DPI_B6_lung_1, mRNA-seq

description:
Library name: Sample 15
10x Genomics
528_Ma30_Lung21


title: isoG256W-3

description: Library name: 78_CC18_B6


title: Spt16 Myc ChIP-seq, ChIP DNA: pob3-E154K, IAA rep 3

description: Library name: 666_93_myc_rep3


title: bulk_mRNA-seq_PR8_8-9DPI_B6_lung_2, mRNA-seq

description:
Library name: Sample 12
10x Genomics
244_Lung_8_9_DPII


title: isoG256W-2

description: Library name: 78_CC18_B5


title: G256W/+-3

description: Library name: 78_CNC2_B6


title: G256W/+-2

description: Library name: 78_CNC2_B5


title: Spt16 Myc ChIP-seq, ChIP DNA: pob3-E154K, IAA rep 1

description: Library name: 666_93_myc_rep1


title: Low Protein - Standard 9

description: Library name: 52


title: bulk_mRNA-seq_PR8_8-9DPI_B6_lung_4, mRNA-seq

description:
Library name: Sample 14
10x Genomics
251_Lung_8_9_DPII


title: Low Protein - Standard + 10% Lys 8

description: Library name: 51


title: Low Protein - Standard + 10% Lys 7

description: Library name: 50


title: bulk_mRNA-seq_PR8_8-9DPI_B6_lung_1, mRNA-seq

description:
Library name: Sample 11
10x Genomics
242_Lung_8_9_DPII


title: isoG256W-1

description: Library name: 78_CC18_B2


title: Low Protein - Standard 11

description: Library name: 54


title: Spt16 Myc ChIP-seq, ChIP DNA: spt6Δ2-238, IAA rep 2

description: Library name: 661_95_myc_rep2


title: Spt16 Myc ChIP-seq, ChIP DNA: spt6Δ2-238, IAA rep 3

description: Library name: 661_95_myc_rep3


title: Low Protein - Standard + 10% Lys 6

description: Library name: 49


title: bulk_mRNA-seq_MA30_7DPI_B6_lung_6, mRNA-seq

description:
Library name: Sample 10
10x Genomics
539_Ma30_Lung5_7

value: MA30, 7DPI


title: T274M/+-3

description: Library name: 72_CNC87_B6


title: bulk_mRNA-seq_MA30_7DPI_B6_lung_5, mRNA-seq

description:
Library name: Sample 9
10x Genomics
534_Ma30_Lung5_7


title: Spt16 Myc ChIP-seq, ChIP DNA: spt6Δ2-238, IAA rep 1

description: Library name: 661_95_myc_rep1


title: Low Protein - Standard + 20% Lys 8

description: Library name: 47


title: bulk_mRNA-seq_MA30_7DPI_B6_lung_3, mRNA-seq

description:
Library name: Sample 7
10x Genomics
525_Ma30_Lung5_7


title: Low Protein - Standard + 20% Lys 7

description: Library name: 46


title: isoT274M-3

description: Library name: 72_CC20_B6


title: Low Protein - Standard + 10% Lys 5

description: Library name: 48


title: T274M/+-1

description: Library name: 72_CNC87_B2


title: Spt16 Myc ChIP-seq, ChIP DNA: wild-type, IAA rep 3

description: Library name: 661_93_myc_rep3


title: Low Protein - Standard + 20% Lys 6

description: Library name: 45


title: Spt16 Myc ChIP-seq, ChIP DNA: wild-type, IAA rep 2

description: Library name: 661_93_myc_rep2


title: Spt16 Myc ChIP-seq, ChIP DNA: wild-type, IAA rep 1

description: Library name: 661_93_myc_rep1


title: isoT274M-2

description: Library name: 72_CC20_B5


title: bulk_mRNA-seq_MA30_7DPI_B6_lung_2, mRNA-seq

description:
Library name: Sample 6
10x Genomics
522_Ma30_Lung5_7


title: bulk_mRNA-seq_MA30_7DPI_B6_lung_1, mRNA-seq

description:
Library name: Sample 5
10x Genomics
519_Ma30_Lung5_7


title: bulk_mRNA-seq_MA30_7DPI_B6_lung_4, mRNA-seq

description:
Library name: Sample 8
10x Genomics
531_Ma30_Lung5_7


title: Spt16 Flag ChIP-seq, ChIP DNA: spt6Δ2-238 pob3-E154K, IAA rep 3

description: Library name: 666_95_Flag_rep3

value: a-FLAG M2 (Sigma F3165)


title: isoT274M-1

description: Library name: 72_CC20_B2


title: bulk_mRNA-seq_uninfected_B6_lung_4, mRNA-seq

description:
Library name: Sample 4
10x Genomics
809


title: Low Protein - Standard 8

description: Library name: 43


title: Low Protein - Standard + 20% Lys 5

description: Library name: 44


title: T274M/+-2

description: Library name: 72_CNC87_B5


title: Spt16 Flag ChIP-seq, ChIP DNA: spt6Δ2-238 pob3-E154K, IAA rep 2

description: Library name: 666_95_Flag_rep2


title: bulk_mRNA-seq_uninfected_B6_lung_3, mRNA-seq

description:
Library name: Sample 3
10x Genomics
807


title: bulk_mRNA-seq_uninfected_B6_lung_2, mRNA-seq

description:
Library name: Sample 2
10x Genomics
604


title: Spt16 Flag ChIP-seq, ChIP DNA: spt6Δ2-238 pob3-E154K, IAA rep 1

description: Library name: 666_95_Flag_rep1


title: Spt16 Flag ChIP-seq, ChIP DNA: pob3-E154K, IAA rep 2

description: Library name: 666_93_Flag_rep2


title: L292_293/+-2

description: Library name: 68_CNC14_B5


title: Standard Protein - Standard 8

description: Library name: 39


title: bulk_mRNA-seq_uninfected_B6_lung_1, mRNA-seq

description:
Library name: Sample 1
10x Genomics
602


title: Low Protein - Standard 6

description: Library name: 41


title: Spt16 Flag ChIP-seq, ChIP DNA: spt6Δ2-238, IAA rep 3

description: Library name: 661_95_Flag_rep3


title: isoL292_293-3

description: Library name: 68_CC3_B6


title: G4m5_4

city: London

first: Hannah

last: Painter

address: Keppel Street

country: United Kingdom

institute: LSHTM

description: Library name: X54

data_processing:
Run data were demultiplexed and converted to fastq files using Illumina’s BCL Convert Software v3.7.5.
Sequencing data was processed using nf-core/rnaseq (https://doi.org/10.5281/zenodo.7998767). Default parameters were used.
Assembly: GRCm38
Supplementary files format and content: salmon.merged.gene_counts_length_scaled.tsv; matrix of gene-level length-scaled counts for all samples
Supplementary files format and content: salmon.merged.gene_counts_scaled.tsv; matrix of gene-level library size-scaled counts for all samples
Supplementary files format and content: salmon.merged.gene_counts.tsv; matrix of gene-level raw counts for all samples
Supplementary files format and content: salmon.merged.gene_tpm.tsv; matrix of gene-level TPM values for all samples.
Supplementary files format and content: salmon.merged.transcript_counts.tsv; matrix of isoform-level raw counts for all samples.
Supplementary files format and content: salmon.merged.transcript_tpm.tsv; matrix of isoform-level TPM values for all samples

extract_protocol:
Lung accessory lobes were collected in RNAprotect tissue reagent (Qiagen) overnight before removal from the reagent and storage at -80oC until RNA extraction. RNA was extracted from the acessory lobe by homogenising the tissue in RLT buffer (+1% BME) using a Precellys 24 Tissue Homogenizer. The homogenate was centrifuged at full speed and RNA was extracted from the supernatant using the RNeasy Mini kit (Qiagen), including an on-column RNase-free DNase digestion step (Qiagen).
Total RNA quantification and integrity was confirmed using Agilent’s 4200 Tapestation (Standard Total RNA assay). For each sample, 500ng of total RNA were processed using the KAPA mRNA HyperPrep Kit (Roche p/n KK8580) according to manufacturer’s instructions. Briefly, mRNA was isolated from 500ng total RNA by use of paramagnetic Oligo dT beads to pull down poly-adenylated transcripts. The purified mRNA was fragmented using chemical hydrolysis (heat and divalent metal cation) and primed with random hexamers. Strand-specific first-strand cDNA was generated using reverse transcriptase in the presence of actinomycin D. The second cDNA strand was synthesised using dUTP in place of dTTP, to mark the second strand. The resultant cDNA was then “A-tailed” at the 3’ end to prevent self-ligation and adapter dimerisation. Full-length xGen adaptors (IDT), containing two unique 8-bp sample specific indexes, a unique molecular identifier (N8) and a T overhang are ligated to the A-tailed cDNA. Successfully ligated cDNA molecules were then enriched with limited cycle PCR (11 PCR cycles). The high fidelity polymerase employed in the PCR is unable to extend through uracil. This means only the first strand cDNA is amplified for sequencing, making the library strand specific (first-strand). High yield, adaptor-dimer free libraries were confirmed on the Agilent TapeStation 4200 (High Sensitivity Agilent DNA 1000 assay) and a library quantification was estimated using the Qubit dsDNA HS assay (Life Technolgies). Libraries were normalised to 4nM and then an equal volume of each were pooled together. The library pool was denatured and sequenced on the NextSeq 2000 instrument (Illumina, San Diego, US) at 750pM, using a 56bp paired-read run with corresponding 8bp unique dual sample indexes and 8bp unique molecular index.

tag: Sex

value: Female

tag: mcmv status

value: positive

tag: mtb status

tag: sample time_point_post_mtb_infection

tag: lung log10_cfu

tag: spleen log10_cfu

tag: lymph node_log10_cfu


title: L292_293/+-3

description: Library name: 68_CNC14_B6

tag: tissue

tag: cell line

tag: cell type


title: G4m4_4

description: Library name: X53

tag: strain


title: G4m3_4

description: Library name: X52


title: Standard Protein - Standard 6

description: Library name: 37


title: Spt16 Flag ChIP-seq, ChIP DNA: pob3-E154K, IAA rep 1

description: Library name: 666_93_Flag_rep1

tag: genotype

tag: treatment


title: Low Protein - Standard 5

description: Library name: 40


title: aortic cells GVHD hto

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
Library name: F3_HTO
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v4.3.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: Aorta

extract_protocol:
B6.Ldlr-/- mice underwent a BM transplantation and were fed a WD or normal chow as described above. Single cell RNA-seq was performed as described (34). After euthanasia, aortas were collected, and in some instances, 2 aortas were pooled to generate 1 replicate for single cell analysis. Aortas were minced and digested for 90 minutes at 37°C under agitation in RPMI containing 450 U/ml collagenase I (Sigma-Aldrich, #C0130), 125 U/ml Collagenase XI (Sigma-Aldrich, C7657), 60 U/ml Hyaluronidase (Sigma-Aldrich, H3506), 60 U/ml DNAse (Roche #11284932001), washed in PBS/1% FCS and passed through a 70 μm cell strainer to generate aortic cell suspensions. Cell suspensions were incubated for 5 minutes on ice with TruStain FcX™ (anti-mouse CD16/32, Biolegend #101320, 10 μg/ml), and then labelled with anti-CD45.2-Alexa488 (clone 104, 2 μg/ml, Biolegend #109816), Fixable Viability Dye e780 (ThermoFisher #65-0865-14, 1:1000) and anti-mouse TotalSeqA-Hashtag Antibodies 1 to 15 (1:250 dilution; all from BioLegend, TotalSeq™-A anti-mouse Hashtag antibodies) as follows: hashtag 1 to 4: BMT WD; hashtag 5-8: BM WD. (Hashtag 9-12 refer to samples not included in this study). After 25 minutes incubation at 4°C, cells were washed twice in PBS + 1% FCS and pooled. Viable CD45.2-APC(i.v.)neg CD45.2-Alexa488+ were sorted using a FACS Aria III (BD Biosciences) with a 100μm nozzle. In this experiment, cells were labelled post-sort with a panel of TotalSeq-A CITE-seq antibodies against surface markers, but due to technical issues with the preparation of the CITE-seq cDNA library, the CITE-seq results are not interpretable. Cells were washed twice with PBS supplemented with 0.04% ultrapure BSA (Thermofisher AM2616), counted and loaded in the 10x Genomics Chromium with the aim to recover 10,000 cells.
Single cells were encapsulated into droplets with the Chromium™ Controller (10x Genomics). Transcripts captured in all cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 12 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) following the detailed protocol provided by the manufacturer.
-CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
-HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGC-3’ TruSeq D701_s primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.

value: Aorta

value: Immune

value: Various (see hashtag)


title: L292_293/+-1

description: Library name: 68_CNC14_B2

value: brain


title: Low Protein - Standard 7

description: Library name: 42

value: Muscle


title: isoL292_293-2

description: Library name: 68_CC3_B5

value: isogenic iPSC lines


title: Standard Protein - Standard 7

description: Library name: 38


title: Spt16 Flag ChIP-seq, ChIP DNA: spt6Δ2-238, IAA rep 2

description: Library name: 661_95_Flag_rep2

value: 3-indoleacetic acid


title: isoL292_293-1

description: Library name: 68_CC3_B2


title: aortic cells GVHD adt

description:
Library name: F3_ADT
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads


title: Low Protein - Standard + 20% Lys 4

description: Library name: 35


title: Standard Protein - Standard 5

description: Library name: 36


title: Spt16 Flag ChIP-seq, ChIP DNA: pob3-E154K, IAA rep 3

description: Library name: 666_93_Flag_rep3

value: SPT6-3xFLAG, SPT16-13xMYC, pob3-E154K, SPT6-V5-AID


title: Spt16 Flag ChIP-seq, ChIP DNA: spt6Δ2-238, IAA rep 1

description: Library name: 661_95_Flag_rep1


title: G4m1_4

description: Library name: X50

value: Lung


title: Spt16 Flag ChIP-seq, ChIP DNA: wild-type, IAA rep 3

description: Library name: 661_93_Flag_rep3

value: SPT6-3xFLAG, SPT16-13xMYC, SPT6-V5-AID


title: aortic cells GVHD gex

description:
Library name: F3
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: G3m5_4

description: Library name: X49

value: negative


title: G4m2_4

description: Library name: X51


title: Spt16 Flag ChIP-seq, ChIP DNA: wild-type, IAA rep 2

description: Library name: 661_93_Flag_rep2


title: Low Protein - Standard + 20% Lys 3

description: Library name: 34


title: Spt16 Flag ChIP-seq, ChIP DNA: wild-type, IAA rep 1

description: Library name: 661_93_Flag_rep1


title: Spt16 ChIP-seq input DNA: spt6Δ2-238 pob3-E154K, IAA rep 1

description: Library name: 666_95_input_rep1

value: spt6D2-238-3xFLAG, SPT16-13xMYC, pob3-E154K, SPT6-V5-AID


title: Low Protein - Standard + 20% Lys 1

description: Library name: 32


title: G3m1_4

description: Library name: X45


title: G3m2_4

description: Library name: X46


title: Spt16 ChIP-seq input DNA: spt6Δ2-238 pob3-E154K, IAA rep 2

description: Library name: 666_95_input_rep2


title: G3m4_4

description: Library name: X48


title: Low Protein - Standard + 10% Lys 3

description: Library name: 30


title: G2m4_4

description: Library name: X44

value: uninfected


title: P7 Ki67CreERT/+;Rosa26RtdTomato/+ cochlea, rep1

first: Alan

last: Cheng

state: CA

address: 240 Pasteur Drive

description: Library name: P7_control_rep1

data_processing:
Cell Ranger - 6.0.0
Seurat - 5.1.0
Assembly: mm10
Supplementary files format and content: Files containing the cell barcodes and detected features for each sample are provided in .tsv format. A filtered matrix file containing the number of detected UMIs for each feature and barcode is also provided in .mtx format (filtered to contain only cell-associated barcodes).

source_name: cochlea

extract_protocol:
Following microdissection, cochlear tissues were incubated in 0.5mg/mL Thermolysin at 37°C for 45 minutes, followed by incubation in Accutase for 20 minutes. The reaction was stopped by adding 300 µL of DMEM/F12 with 5% fetal bovine serum, and the tissue was titurated 60x by pipetting to dissociate into single cells. Cell clumps were removed by filtering the cells through a 40 µm pluriSelect filter mini strainer, followed by pelleting in a 4C centrifuge for 5 min at 300 rcf. Supernatant was aspirated and the cell pellet was resuspended in 60 µL DMEM/F12 with 5% FBS. After quantifying cell numbers and viability, cells were placed on ice and brought to the Stanford Functional Genomics Core for 10x Genomics scRNA-seq capture and sequencing.
10x Genomics Single Cell 3' v3

value: cochlea

tag: time


title: Spt16 ChIP-seq input DNA: pob3-E154K, IAA rep 3

description: Library name: 666_93_input_rep3


title: P7 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ cochlea, rep2

description: Library name: P7_damage_rep2


title: P7 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ cochlea, rep1

description: Library name: P7_damage_rep1


title: P6 Ki67CreERT/+;Rosa26RtdTomato/+ cochlea, rep2

description: Library name: P6_control_rep2


title: G3m3_4

description: Library name: X47


title: G2m3_4

description: Library name: X43


title: Spt16 ChIP-seq input DNA: pob3-E154K, IAA rep 2

description: Library name: 666_93_input_rep2


title: P6 Ki67CreERT/+;Rosa26RtdTomato/+ cochlea, rep1

description: Library name: P6_control_rep1


title: Spt16 ChIP-seq input DNA: spt6Δ2-238 pob3-E154K, IAA rep 3

description: Library name: 666_95_input_rep3


title: G2m2_4

description: Library name: X42


title: Spt16 ChIP-seq input DNA: pob3-E154K, IAA rep 1

description: Library name: 666_93_input_rep1


title: Low Protein - Standard + 20% Lys 2

description: Library name: 33


title: Low Protein - Standard 4

description: Library name: 27


title: P6 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ cochlea, rep2

description: Library name: P6_damage_rep2


title: P6 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ cochlea, rep1

description: Library name: P6_damage_rep1


title: P7 Ki67CreERT/+;Rosa26RtdTomato/+ cochlea, rep2

description: Library name: P7_control_rep2


title: Low Protein - Standard + 10% Lys 2

description: Library name: 29


title: Low Protein - Standard + 10% Lys 1

description: Library name: 28


title: G2m1_4

description: Library name: X41


title: G1m3_4

description: Library name: X39


title: P5 Ki67CreERT/+;Rosa26RtdTomato/+ cochlea, rep1

description: Library name: P5_control_rep1


title: Spt16 ChIP-seq input DNA: spt6Δ2-238, IAA rep 3

description: Library name: 661_95_input_rep3


title: G1m2_4

description: Library name: X38


title: Low Protein - Standard + 10% Lys 4

description: Library name: 31


title: Spt16 ChIP-seq input DNA: spt6Δ2-238, IAA rep 1

description: Library name: 661_95_input_rep1


title: Spt16 ChIP-seq input DNA: spt6Δ2-238, IAA rep 2

description: Library name: 661_95_input_rep2


title: Low Protein - Standard 3

description: Library name: 26


title: Standard Protein - Standard 4

description: Library name: 23


title: P5 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ cochlea, rep1

description: Library name: P5_damage_rep1


title: P4 Ki67CreERT/+;Rosa26RtdTomato/+ cochlea, rep2

description: Library name: P4_control_rep2


title: G1m4_4

description: Library name: X40


title: Standard Protein - Standard 2

description: Library name: 21


title: P5 Ki67CreERT/+;Rosa26RtdTomato/+ cochlea, rep2

description: Library name: P5_control_rep2


title: Low Protein - Standard 2

description: Library name: 25


title: G1m1_4

description: Library name: X37


title: P4 Ki67CreERT/+;Rosa26RtdTomato/+ cochlea, rep1

description: Library name: P4_control_rep1


title: Spt16 ChIP-seq input DNA: wild-type, IAA rep 3

description: Library name: 661_93_input_rep3


title: Low Protein - Standard 1

description: Library name: 24


title: Standard Protein - Standard 1

description: Library name: 20


title: P5 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ cochlea, rep2

description: Library name: P5_damage_rep2


title: G4m5_3

description: Library name: X36


title: G4m4_3

description: Library name: X35


title: P4 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ cochlea, rep2

description: Library name: P4_damage_rep2


title: G4m3_3

description: Library name: X34


title: DLBCL Patient_43

type: RNA

city: Madrid

first: Juana

last: Serrano López

address: Avda Reyes Católicos 2

country: Spain

institute: IIS-FJD

hyb_protocol: 100 ng of total RNA imput were prepared according to NanoString nCounter guidelines. Each sample imput was adjusted by DV300 value, measured with TapeStation 4200 and RNA ScreenTape Assay (Agilent, Santa Clara, CA, USA). Hybridization of adjusted RNA samples and NanoString IO360 panel probes was performed in a SimpliAmp Thermal Cycler (Thermo Fisher Scientific, Waltham, Massachusetts, USA) during 20 hours at 65ºC.

scan_protocol: After hybridization, samples were processed with NanoString nCounter Prep Station (NanoString Technologies, Seattle, WA, USA) Research mode protocol and scanned with NanoStringnCounter Digital Analyzer (NanoString Technologies, Seattle, WA, USA) according to manufacturer´s guidelines.

data_processing: RCC raw data was processed and analysed with NanoString nSolver version 4.0 + Advanced Analysis Data Package version 2.0. After Quality Control and data normalization, Advanced Analysis was performed with nSolver Software, as well as extracting normalized data (both with housekeeping genes and control probes included in the panel) which has been used in complementary software.

source_name: Lymph Node Biopsy

extract_protocol: On average, 5 5 um-thick sections were prepared for the extraction of total RNA from these samples with RNeasy FFPE Kit (Qiagen, Hilden, Germany). 30 uL of eluted RNA were extracted from each sample. Then, measurement of quality and quantity of this RNA was done with NanoDrop 2000c (Thermo Fisher Scientific, Waltham, Massachusetts, USA).

treatment_protocol: Formalin-Fixed Paraffin-Embedded (FFPE) samples from selected tumoral sections were identified by specialized pathologists after diagnose with both routine and additional stainings.

tag: age

tag: survival

value: Dead

tag: subtype

value: ABC


title: G4m2_3

description: Library name: X33

tag: Sex

value: Female

value: positive


title: Low Protein 6

description: Library name: 19


title: Spt16 ChIP-seq input DNA: wild-type, IAA rep 1

description: Library name: 661_93_input_rep1

tag: plasmid

tag: chip antibody


title: Standard Protein - Standard 3

description: Library name: 22


title: P4 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ cochlea, rep1

description: Library name: P4_damage_rep1


title: Low Protein 3

description: Library name: 16


title: Low Protein 5

description: Library name: 18


title: C57BL/6 mice liver, AAV-GFP

city: Seoul

first: Haena

last: Choi

address: , Gwanak_1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: Library name: Control

data_processing:
Paired-end sequencing reads were generated on the Illumina sequencing NovaSeq platform. Before starting analysis, Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality. The cleaned reads were aligned to the Mus musculus(mm10) using HISAT v2.1.0 (KIM et al, 2015). The reference genome sequence and gene annotation data were downloaded from NCBI Genome assembly and NCBI RefSeq database respectively. Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b (Pertea, Mihaela, et al., 2015, 2016). Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes count, FPKM and TPM for each sample

source_name: liver

extract_protocol:
RNA was harvested using Rneasy Rneasy mini kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
Total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen, #R11490). To assess the integrity of the total RNA, samples are run on the TapeStation RNA screentape (Agilent, #5067-5576). Only high-quality RNA preparations, with RIN greater than 7.0, were used for RNA library construction. A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #20020595). The first step in the workflow involves purifying the poly‐A containing mRNA molecules using poly‐T‐attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase (Invitrogen, #18064014) and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I, RNase H and dUTP. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. The libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, # 5067-5582). Indexed libraries were then submitted to an Illumina NovaSeq (Illumina, Inc., San Diego, CA, USA), and the paired-end (2×100 bp) sequencing was performed by the Macrogen Incorporated.

value: liver

value: GFP overexpression

value: High-fat diet fed


title: C57BL/6 mice liver, AAV-Wee1-AS

description: Library name: U10

value: Wee1-AS overexpression


title: Spt16 ChIP-seq input DNA: wild-type, IAA rep 2

city: Boston

description: Library name: 661_93_input_rep2


title: DLBCL Patient_40

value: Male

value: Alive


title: G3m4_3

description: Library name: X30

tag: mcmv status

tag: mtb status

tag: sample time_point_post_mtb_infection


title: Standard Protein 6

description: Library name: 15

value: Muscle


title: G3m5_3

description: Library name: X31

value: Lung

tag: lung log10_cfu

tag: spleen log10_cfu

tag: lymph node_log10_cfu


title: G4m1_3

description: Library name: X32

tag: tissue


title: Standard Protein 4

description: Library name: 13


title: DLBCL Patient_42


title: G3m1_3

description: Library name: X27

tag: strain


title: DLBCL Patient_41


title: DLBCL Patient_37


title: DLBCL Patient_38


title: Lep(ob/ob) pancreas, CCKR-I (proglumide), 12-week age, male, 72

city: New Haven

first: Mandar

middle: Deepak

last: Muzumdar

state: CT

address: 333 Cedar Street

institute: Yale University

description:
Library name: PG.6_72
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: PG.6_72
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 72_PG-6_188_005_S9

data_processing:
Low-quality bases and adapter sequences were trimmed using Trim Galore (version 0.6.7) and CutAdapt (version 3.5).
Cleaned reads were aligned to the University of California Santa Cruz mouse genome (mm10) using the STAR aligner (version 2.7.9). Gene-level quantification was performed using the -quantMode GeneCounts option in STAR, which generates a matrix of raw read counts for each gene.
Assembly: mm10
Supplementary files format and content: Raw counts processed from sequence-aligned read counts (mm10, gene level) as output from STAR. First row is sample name header, in .txt tab-delimited format. Gene_name is only row descriptor, unsorted by gene, and sample column names are directly from FASTQ file names
Supplementary files format and content: Normalized counts processed from raw counts (mm10, gene level) via DESeq2 in R, in .txt tab-delimited format, absolute normalized counts (linear, not log counts), with UCSC Gene_symbol, ENTREZ_ID as first two columns, first row header contains sample names with simplified name corresponding to GEO sample library name. Genes without any reads are excluded

source_name: pancreas

growth_protocol: WT C57BL6/J originally from Jackson Laboratories (Farmington, CT) were bred in house. Leptin-deficient Lep(ob/ob) mice were purchased (also Jackson Laboratories).

extract_protocol:
Mouse pancreata were snap frozen in liquid nitrogen and manually pulverized using the BioPulverizer (BioSpec Products 59012MS). Total RNA was extracted from pulverized tissue (20-40 mg), homogenized via QIAshredder column, and purified using the RNeasy Mini Kit (Qiagen) with on column DNAse I digestion, per the manufacturer's protocol.
RNA quality and quantity was assessed using an Agilent Bioanalyzer, and only high-quality RNA samples (RIN>7) were used in downstream analysis. RNA-seq libraries were prepared from mRNA purified from approximately 200ng total RNA with oligo-dT bead polyA selection (Illumina)  and sheared by incubation at 94C in the presence of Mg (Roche Kapa mRNA Hyper Prep Cat# KR1352). Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs are ligated to library insert fragments.  Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends.  Strands marked with dUTP are not amplified. Indexed libraries are quantified by qRT-PCR using a commercially available kit (Roch KAPA Biosystems Cat# KK4854) and insert size distribution determined by either the Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/ul and a size distribution of 150-300bp are used for sequencing.
Sequenced (>25M 100-bp paired-end (2x100) reads on NovaSeq 6000 (Illumina)) with the Yale Center for Genome Analysis (YCGA)

treatment_protocol: Animals from WT and Lep(ob/ob) of 6 weeks of age were treated with control or CCKR-inhibitor drinking water (proglumide 0.1mg/ml, or lorglumide 0.05mg/ml) for 6 weeks, changed weekly, and euthanized at 12 weeks of age.

value: pancreas

tag: genotype

value: Lep(ob/ob)

value: 12 weeks

value: CCKR-I, proglumide (0.1mg/ml) water, 6 weeks

tag: weight g_final

tag: batch


title: G3m2_3

description: Library name: X28

value: negative


title: Low Protein 4

description: Library name: 17


title: Lep(ob/ob) pancreas, control, 12-week age, male, 464

description:
Library name: OB.6_64
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: OB.6_64
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 64_OB-6_129_064_S6

tag: age

tag: treatment

value: Control water, 6 weeks


title: DLBCL Patient_34

tag: survival

tag: subtype

value: ABC


title: DLBCL Patient_39

tag: Sex


title: Lep(ob/ob) pancreas, CCKR-I (lorglumide), 12-week age, male, 76

description:
Library name: LG.6_76
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: LG.6_76
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 76_LG-6_164_029_S11

value: CCKR-I, lorglumide water (0.05mg/ml), 6 weeks


title: Lep(ob/ob) pancreas, CCKR-I (lorglumide), 12-week age, male, 74

description:
Library name: LG.6_74
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: LG.6_74
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 74_LG-6_176_017_S10


title: G3m3_3

description: Library name: X29

value: Female

value: positive


title: Low Protein 2

description: Library name: 9


title: Lep(ob/ob) pancreas, control, 12-week age, male, 461

description:
Library name: OB.6_61
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: OB.6_61
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 61_OB-6_153_040_S4


title: G2m4_3

description: Library name: X26

value: uninfected


title: Standard Protein 3

description: Library name: 12


title: DLBCL Patient_36

value: Dead


title: Lep(ob/ob) pancreas, CCKR-I (proglumide), 12-week age, male, 69

description:
Library name: PG.6_69
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: PG.6_69
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 69_PG-6_105_088_S8


title: G1m4_3

description: Library name: X22


title: Lep(ob/ob) pancreas, control, 12-week age, male, 463

description:
Library name: OB.6_63
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: OB.6_63
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 63_OB-6_141_052_S5


title: Low Protein 1

description: Library name: 8


title: G2m3_3

description: Library name: X25


title: DLBCL Patient_35


title: DLBCL Patient_33


title: Lep(ob/ob) pancreas, control, 12-week age, male, 417

description:
Library name: OB.6_417
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: OB.6_417
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 9_OB_417_257_320_S40


title: G2m2_3

description: Library name: X24


title: DLBCL Patient_31


title: Standard Protein 1

description: Library name: 10


title: Lep(ob/ob) pancreas, control, 12-week age, male, 447

description:
Library name: OB.6_447
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: OB.6_447
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 10OB_447_245_332_S41


title: Standard Protein 2

description: Library name: 11


title: G2m1_3

description: Library name: X23


title: Lep(ob/ob) pancreas, control, 12-week age, male, 472

description:
Library name: OB.6_472
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: OB.6_472
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 8_OB_472_269_308_S39


title: G1m3_3

description: Library name: X21


title: Standard Protein 5

description: Library name: 14


title: BL6

description: Library name: 6


title: DLBCL Patient_30


title: DLBCL Patient_32


title: BL7

description: Library name: 7


title: Lep(ob/ob) pancreas, control, 12-week age, male, 441

description:
Library name: OB.6_441
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: OB.6_441
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 7_OB_441_281_296_S38


title: BL5

description: Library name: 5


title: DLBCL Patient_29


title: WT pancreas, control, 12-week age, male, 59

description:
Library name: WT.6_59
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: WT.6_59
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 59_WT_165_028_S3

value: WT


title: BL4

description: Library name: 4


title: G1m2_3

description: Library name: X20


title: G1m1_3

description: Library name: X19


title: G4m4_1

description: Library name: X17

value: not detected


title: G4m5_1

description: Library name: X18


title: DLBCL Patient_28

value: Alive


title: BL3

description: Library name: 3

value: Muscle


title: WT pancreas, control, 12-week age, male, 5492

description:
Library name: WT.6_5492
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: WT.6_5492
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 4_WT5492_210_367_S36


title: G4m3_1

description: Library name: X16

value: Lung


title: BL2

description: Library name: 2


title: BL1

description: Library name: 1


title: WT pancreas, control, 12-week age, male, 58

description:
Library name: WT.6_58
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: WT.6_58
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 58_WT_177_016_S2

value: pancreas


title: WT pancreas, control, 12-week age, male, 5494

description:
Library name: WT.6_5494
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: WT.6_5494
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 5_WT5494_198_379_S37


title: DLBCL Patient_27


title: DLBCL Patient_26

value: Male


title: DLBCL Patient_25


title: WT pancreas, control, 12-week age, male, 5489

description:
Library name: WT.6_5489
Column name in Garcia-Venkat_pancreas_RNAseq_normalized_counts.txt file: WT.6_5489
Column name in Garcia-Venkat_pancreas_RNAseq_raw_counts.txt file: 2_WT5489_222_355_S35

value: 12 weeks


title: diff_GATA1s_1KI9_2, Gata1s, replica 2

first: Te

last: Ling

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

description:
Library name: diff_GATA1s_1KI9_2
diffHUDEP1G1sKI9_2

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline. The raw reads were firs trimmed (Trim-Galore version 0.60) and mapped to hg38 (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation Human Release 31(GRCh38.p12).
Assembly: GRCh38(hg38)
Supplementary files format and content: gene-level TPM tsv file

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:
Total RNA 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 (day 4) conditions, respectively. The purification process was conducted using TaKaRa RNA Plus XS (REF#740990.50).
RNA-seq

tag: cell line

tag: cell type

value: erythroid progenitor cell line

value: differentiation


title: diff_GATA1s_1KI9_3, Gata1s, replica 3

description:
Library name: diff_GATA1s_1KI9_3
diffHUDEP1G1sKI9_3


title: G4m2_1

description: Library name: X15

tag: mcmv status

tag: mtb status


title: DLBCL Patient_24


title: Renal cortex, I/R-AKI, biol rep 3 IP

city: guangzhou

first: peng

last: wang

address: 1838 North Guangzhou Avenue

institute: Southern Medical University

description: Library name: Sample12

data_processing:
For acRIP-seq, paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of input libraries were aligned to reference genome (UCSC HG19) by STAR software. Then circRNAs were identified by DCC software using the STAR alignment results. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). acetylated sites on RNAs (peaks) were identified by MACS software. Differentially acetylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and chosen by home-made scripts.  For RNA-seq,paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.circRNA: The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. LncRNA & mRNA: The high quality reads were aligned to the reference genome with hisat2 software (v2.0.4). Then, HTSeq software (v0.9.1) was used to get the gene level (mRNA) and transcript level (lncRNA) raw count as the expression profiling, and edgeR (v3.16.5) was used to perform normalization and differentially expressed mRNAs were identified by p-value and fold change.
Assembly: GRCm38/mm10
Supplementary files format and content: EXCEL file iclude peak information for each sample
Supplementary files format and content: EXCEL file include FPKM or CPM values for each sample

source_name: Renal cortex

extract_protocol:
For acRIP-seq, total RNA was subjected to immunoprecipitation with the GenSeq® ac4C RIP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified.  For RNA-seq, total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions.
For acRIP-seq, RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer (Agilent) and then sequenced in a NovaSeq platform (Illumina).  For RNA-seq,  libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina Novaseq instrument with 150bp paired end reads.

value: Renal cortex

value: IRI


title: G4m1_1

description: Library name: X14

tag: sample time_point_post_mtb_infection

tag: lung log10_cfu


title: DLBCL Patient_23

value: GCB


title: Renal cortex, I/R-AKI, biol rep 3 input

description: Library name: Sample11


title: G3m4_1

description: Library name: X12

value: Female

value: negative

tag: spleen log10_cfu

tag: lymph node_log10_cfu


title: diff_GATA1s_1D5_2, Gata1s, replica 2

city: Memphis

description:
Library name: diff_GATA1s_1D5_2
diffHUDEP1G1s1D5_2


title: Renal cortex, I/R-AKI, biol rep 2 IP

description: Library name: Sample10

tag: tissue


title: G3m2_1

description: Library name: X10

tag: strain

value: positive


title: Renal cortex, I/R-AKI, biol rep 2 input

description: Library name: Sample9

tag: genotype


title: Renal cortex, I/R-AKI, biol rep 1 input

description: Library name: Sample7


title: G3m5_1

description: Library name: X13


title: G3m3_1

description: Library name: X11


title: diff_GATA1s_1KI9_1, Gata1s, replica 1

description:
Library name: diff_GATA1s_1KI9_1
diffHUDEP1G1sKI9_1


title: DLBCL Patient_22


title: DLBCL Patient_19

value: Dead


title: diff_GATA1s_1D5_3, Gata1s, replica 3

description:
Library name: diff_GATA1s_1D5_3
diffHUDEP1G1s1D5_3


title: DLBCL Patient_21


title: DLBCL Patient_20


title: G2m4_1

description: Library name: X8

value: uninfected


title: diff_GATA1FL_3, FL , replica 3

description:
Library name: diff_GATA1FL_3
diffHUDEP1FL1_3


title: Renal cortex, I/R-AKI, biol rep 1 IP

description: Library name: Sample8

value: WT


title: G3m1_1

description: Library name: X9

value: not detected


title: DLBCL Patient_18

value: Alive


title: DLBCL Patient_17


title: diff_GATA1FL_2, FL , replica 2

description:
Library name: diff_GATA1FL_2
diffHUDEP1FL1_2


title: Renal cortex, Sham-operated, biol rep 3 IP

description: Library name: Sample6

value: Sham


title: diff_GATA1FL_1, FL , replica 1

description:
Library name: diff_GATA1FL_1
diffHUDEP1FL1_1


title: G2m3_1

description: Library name: X7

value: Lung


title: Renal cortex, Sham-operated, biol rep 3 input

description: Library name: Sample5


title: DLBCL Patient_16

value: Male


title: Renal cortex, Sham-operated, biol rep 2 IP

description: Library name: Sample4


title: G2m2_1

description: Library name: X6


title: DLBCL Patient_15


title: Renal cortex, Sham-operated, biol rep 2 input

description: Library name: Sample3


title: DLBCL Patient_14


title: G2m1_1

description: Library name: X5


title: GATA1s_1KI9_2, Gata1s, replica 2

description:
Library name: GATA1s_1KI9_2
HUDEP1G1sKI9_2

value: expansion


title: GATA1s_1KI9_3, Gata1s, replica 3

description:
Library name: GATA1s_1KI9_3
HUDEP1G1sKI9_3

value: erythroid progenitor cell line


title: GATA1s_1KI9_1, Gata1s, replica 1

description:
Library name: GATA1s_1KI9_1
HUDEP1G1sKI9_1


title: DLBCL Patient_13


title: GATA1s_1D5_3, Gata1s, replica 3

description:
Library name: GATA1s_1D5_3
HUDEP1G1s1D5_3


title: G1m2_1

description: Library name: X2


title: DP3

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

description: Library name: DP3

data_processing:
Raw paired-end sequenced reads were first cut for adapter sequences and trimmed using trim_galore (v.0.6.6).
Cleaned fastq data were mapped to the mm10 reference genome for sample from mouse using STAR (v.2.7.10a).
Reads from specific chromosome regions with annotation were counted using htseq-count (0.13.5).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: spleen

extract_protocol:
Briefly, single-cell suspensions were obatined by mincing and filtering mouse spleens and bone marrows through 70-μm cell strainers.  Cells were incubated in phosphate-buffered saline (PBS) containing 2% (w/v) FCS with indicated antibodies for 25min at 4°C. Cell sorting were performed with BD Aria II or Aria Fusion.
2 ug total RNAs were used for stranded RNA sequencing library preparation using KC-Digital(TM) Stranded mRNA Library Prep Kit for Illumina(R) (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer's instruction.

treatment_protocol: To obatin enough GC center B cells, mice were immunized with 2×107 SRBCs (i.p.) and challenged with 2×108 SRBCs (i.p.) 5days later. At day 12, mice were euthanized for analysis.

value: spleen

value: Spleen germinal center B cells

value: SRBC (i.p.)

tag: batch


title: Renal cortex, Sham-operated, biol rep 1 input

description: Library name: Sample1

value: Renal cortex


title: GATA1s_1D5_1, Gata1s, replica 1

description:
Library name: GATA1s_1D5_1
HUDEP1G1s1D5_1


title: diff_GATA1s_1D5_1, Gata1s, replica 1

description:
Library name: diff_GATA1s_1D5_1
diffHUDEP1G1s1D5_1

value: differentiation


title: DP2

description: Library name: DP2


title: DP1

description: Library name: DP1


title: DLBCL Patient_12

tag: age

value: GCB


title: G1m3_1

description: Library name: X3

value: Female

value: negative


title: DLBCL Patient_10


title: DLBCL Patient_11


title: Renal cortex, Sham-operated, biol rep 1 IP

description: Library name: Sample2

tag: treatment


title: G1m4_1

description: Library name: X4

value: uninfected


title: GATA1FL_2, FL , replica 2

description:
Library name: GATA1FL_2
HUDEP1FL1_2


title: Monoclonal murine gastruloids – 10x lane 3

city: Seattle

first: Samuel

last: Regalado

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

institute: University of Washington

description:
Library name: Monoclonal_gastruloid_lane3_10x
Two independently generated monoclonal mouse gastruloids pooled for 10x Genomics single-cell RNA-seq library preparation (lane 3)

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline to perform sample demultiplexing, read alignment, filtering, barcode counting, and generation of gene expression count matrices for each library. Default parameters were used unless otherwise specified.
Processed data include (i) single-cell gene expression count matrices, and (ii) lineage barcode tables derived from DNA Tape capture with columns including CellBC, TapeBC, and 6xInsertBC sequences used for lineage tree reconstruction
Additional processed outputs may include filtered cell sets used for analysis (e.g., cells retaining frequent tapes) and summaries of insertion character sets used in downstream phylogenetic inference
Downstream quality control and filtering were performed prior to analysis to remove low-quality cells and genes.
Assembly: mm10
Supplementary files format and content: Processed data include (i) single-cell gene expression count matrices, and (ii) lineage barcode tables derived from DNA Tape capture with columns including CellBC, TapeBC, and 6xInsertBC sequences used for lineage tree reconstruction.

source_name: gastruloid

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured on 0.2% gelatin-coated plates at 37 °C, 5% CO₂ in serum-based medium (GMEM supplemented with 8% FBS, 8% KSR, 1× GlutaMAX, 1× MEM non-essential amino acids, 1 mM sodium pyruvate, 0.1 mM β-mercaptoethanol). To enable DNA Typewriter recording, mESCs were engineered by piggyBac transposition to integrate PB-TAPE (DNA Tape in GFP 3′UTR with 10x Capture Sequence 1 and epegRNAs), PB-PEmax (prime editor with puromycin resistance), and PB-mCherry; plasmids were transfected using Lipofectamine 2000 (4 µg DNA per 1 million cells). Cells were selected with 2 µg/mL puromycin and flow-sorted by mCherry, then plated at low density on MEFs to form monoclonal colonies. On Day 4, colonies were detached with Collagenase IV and transferred into non-adherent culture in NDiff227 to form 3D spheroids; after 24 h, spheroids were manually picked into non-adherent round-bottom 96-well plates for gastruloid induction.

extract_protocol:
Gastruloids were harvested and dissociated for single-cell profiling and processed following 10x Genomics standard protocols (Cell Preparation Guide CG00053 Rev C)
Single-cell 3′ RNA-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3′ HT Reagent Kits v3.1 (User Guide Rev D). DNA Typewriter “DNA Tape” sequences were designed for recovery during scRNA-seq via inclusion of 10x Genomics Capture Sequence 1 (CS1). Libraries were sequenced on an Illumina NextSeq 2000.

treatment_protocol: Gastruloid induction included a 24-hour pulse with 3 µM CHIR-99021 (“CHIR pulse”), followed by 3 additional days of culture in NDiff227 medium prior to harvesting for single-cell profiling.

value: gastruloid

value: mouse embryonic stem cell

value: mouse embryonic stem cell derived gastruloid cells

value: wild type


title: DLBCL Patient_9

tag: survival

value: Alive


title: DN3

description: Library name: DN3

value: WT


title: GATA1FL_3, FL , replica 3

description:
Library name: GATA1FL_3
HUDEP1FL1_3

value: expansion


title: Monoclonal murine gastruloids – 10x lane 2

description:
Library name: Monoclonal_gastruloid_lane2_10x
Two independently generated monoclonal mouse gastruloids pooled for 10x Genomics single-cell RNA-seq library preparation (lane 2)


title: GATA1FL_1, FL , replica 1

description:
Library name: GATA1FL_1
HUDEP1FL1_1

value: erythroid progenitor cell line


title: DLBCL Patient_7

value: Male

value: Dead

tag: subtype


title: GATA1s_1D5_2, Gata1s, replica 2

description:
Library name: GATA1s_1D5_2
HUDEP1G1s1D5_2


title: Monoclonal murine gastruloids – 10x lane 1

description:
Library name: Monoclonal_gastruloid_lane1_10x
Two independently generated monoclonal mouse gastruloids pooled for 10x Genomics single-cell RNA-seq library preparation (lane 1)


title: DN2

description: Library name: DN2

value: spleen

value: Spleen germinal center B cells

value: SRBC (i.p.)