title: Producer4_3


title: A_5

status: Public on Feb 28 2023

type: SRA

city: Dallas

first: Karthigayini

last: Sivaprakasam

state: Texas

address: Forest Road

country: USA

institute: University of Texas Southwestern Medical Center

description: SMARTer Stranded total RNA v2-pico input w/rRNA Zap

library_source: transcriptomic

data_processing:
PicardTools were used for basecalling
Files were aligned to human genome using HiSat2-2.1.0 and the duplicates were marked with picard tools
Raw counts were called with HTSEQ
Genome_build: GRCh38
Supplementary_files_format_and_content: HTSEQ file in text format

molecule: total RNA

organism: Homo sapiens

source_name: Fresh frozen laser captured Purkinje cells

extract_protocol:
A JoVE visual experiment video and protocol are available by the lead author that describes in detail how the purkinje cells were removed from post-mortem human brain. PMID: 30735198
Total RNA was extracted from approximately ~2000 Purkinje cells per patient using a Qiagen Rneasy Micro kit (Cat# 74004) with repeated loading of the spin column in step 3. Samples were eluted in 14uL of water with RNase inhibitors. RNA quality was checked using an Agilent bioanalyzer pico chip.
Library was constructed following manufacturers protocols of the SMARTer Stranded RNA-seq kit v2 Pico input (Cat# 634413), including indexing primers for 96 samples. 5ng inputs of total RNA were fragmented for 4 mins. Next, first strand synthesis and addition of illumina adapters, followed by AMpure bead cleanup. Samples underwent rRNA depletion with ZapR and R-probes. Library was amplified with 13 cycles and cleaned a second time with AMpure beads. Library cDNA was eluted in 15uL of Tris buffer.

tag: diagnosis

value: Control

tag: gender

value: Female

tag: age

tag: cell type

value: Purkinje Cells


title: Bw_KBAB6_pCER_plus_LB_biol rep 2

city: JOUY-EN-JOSAS

first: Alicia

last: Nevers

address: Domaine de Vilvert

department: Micalis

country: France

institute: Institut national de la recherche agronomique (Inrae)

data_processing:
Demultiplexing using bcl2fastq2-2.18.12
Adaptors trimming with Cutadapt 3.2
Read alignment to references genome with Bowtie2 in Galaxy. Write unaligned reads (in fastq format) to separate file(s): False; Write aligned reads (in fastq format) to separate file(s): False; Do you want to set paired-end options?: no  Will you select a reference genome from your history or use a built-in index?: indexed; Select reference genome: internal genomes uploaded from NCBI; Set read groups information?: do_not_set; Select analysis mode: simple; Do you want to use presets?: Very fast end-to-end (--very-fast); Save the bowtie2 mapping statistics to the history: True
Read counting with MulticovBed in Galaxy. Calculation based on strandedness?: Only overlaps occurring on the **same** strand.; minimum overlap required as a fraction of A: 1e-09; Require that the fraction of overlap be reciprocal for A and B: False; Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage: False; Minimum mapping quality (MAPQ) allowed:0; Include duplicate reads: True; Include failed-QC reads: False; Only count proper pairs: False
CP001179 (pCER270); CP001177 (Chromosome) and CP001178-CP001181 (plasmids) for AH187 = Bc_F4810-72; CP004069 (Chromosome) and CP004069-CP004076 (plasmids) excluding  CP004072 (pAW63) for B_th_HD73; in-house unpublished genome for B_we_KBABA6
Supplementary files format and content: raw count txt files
Supplementary files format and content: BweKBAB6_pXO16tcR_corrV170303.txt is a file with FASTA sequences corresponding to each transcriptional feature

organism: Bacillus mycoides

source_name: liquid bacterial culture

growth_protocol: For RNA preparation, LB cultures were collected two hours (early stationary phase) after the beginning of stationary phase, whereas in HCT medium the cultures were collected four hours after the onset of the stationary phase (commitment to sporulation). The onset of the stationary phase is determined as the end of the exponential growth and corresponds to an inflection of the growth curve.

extract_protocol:
RNA extraction was performed using Trizol and 1-bromo-3-chloropropane
After ribosomal RNA depletion, NextSeq 500/550 High Output Kit v2 was used to construct library
Single-read 75 sequencing run

tag: strain

tag: tissue

value: liquid bacterial culture

tag: time

value: Early stationary phase

tag: genotype

tag: medium

value: LB


title: Producer4_2

city: Heidelberg

first: Geetha

last: Venkatesh

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

library_source: genomic

data_processing:
Basecalling with: bcl2fastq 2.20.0.422
Preprocessing, read trimming: Trimmomatic 0.38
Preprocessing, quality filtering: Trimmomatic 0.38
BS-mapping: BSMAP 2.9
Computation of methylation ratios: methratio.py (part of bsmap package)
Assembly: GCA_020271785.1
Supplementary files format and content: bedGraph-format containing the genomic methylation ratios and coverage values of the respective sample

molecule: genomic DNA

organism: Penaeus vannamei

source_name: Abdominal musculature

extract_protocol:
Genomic DNA was extracted from abdominal muscle using a Tissue Ruptor (Qiagen), followed by proteinase K digestion and isopropanol precipitation
Accel-NGS Methyl-Seq DNA

value: Abdominal musculature

tag: location


title: A_4


title: Bw_KBAB6_pCER_plus_LB_biol rep 1


title: Producer4_1


title: A_2

value: Male


title: A_3


title: Bw_KBAB6_pCER_minus_LB_biol rep 3


title: A_1


title: Bw_KBAB6_pCER_minus_LB_biol rep 1


title: Bw_KBAB6_pCER_minus_LB_biol rep 2


title: SHEP MYCN-ER 4OHT 36hr rep2

status: Public on Feb 27 2023

city: Chapel Hill

first: Donghai

last: Wang

state: North Carolina

address: 125 Mason Farm Rd

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill (UNC)

description: spiked in RNA-seq

data_processing:
All RNA-seq reads were aligned to the Drosophila genome (dm6) and human genome (hg38) by HISAT2 version 2.1.0, respectively. Raw read counts were normalized to RPM (Reads per Million) per sample and then displayed in the UCSC genome browser as bigWig-formatted coverage tracks. Read counts at indicated regions were calculated by HTSeq-count (version 0.12.3) and were provided to DEseq2 (version 1.32.0) for differential gene expression analysis. Human gene expression was normalized using Drosophila spiked-in genes. An FDR threshold of 0.05 and a log2 fold change cut off of 0.5 was used to identify differentially expressed genes.
Assembly: hg38
Assembly: dm6
Supplementary files format and content: Library normalized bigWig files were provided for all samples

source_name: SHEP MYCN-ER

growth_protocol: SHEP MYCN-ER cells were cultured in RPMI-1640 (Hyclone, #SH30809.01) medium supplemented with 10% fetal bovine serum (FBS, Gibco, #10099-141) and 1% penicillin/streptomycin (Hyclone, #S110JV).

extract_protocol:
For RNA-seq, total RNA was extracted using Trizol.
For RNA-seq, Total RNA was extracted from 50 million SHEP MYCN-ER cells spiked-in with 15% Drosophila S2 cells using Trizol reagent. mRNA was purified from 1 ug total RNA with the VAHTS mRNA capture beads, and fragmented to 200-500 bp size long in 2× ProtoScript II buffer. First- and second-strand DNA synthesis and adaptor ligation were conducteded using NEB Next Ultra RNA library prep kit for Illumina. The resulting strand-specific RNA-Seq libraries were subjected to 150 bp paired-end sequencing on a NovaSeq 6000.

treatment_protocol: A total of 1 × 107 SHEP MYCN-ER cells were treated with DMSO or 4-OHT (100 nM). For TT-seq, cells were then labeled with 400 μM 4-thiouridine at 37°C for 10 minutes before total RNA extraction with Trizol reagent. To assess elongation rates, cells were pre-treated with flavopiridol for 1 hour to pause Pol II near the transcription start sites (TSS) before 4sU labeling.The extracted total RNA was spiked-in with 4sU-labeled Drosophila S2 RNA.

tag: cell line

value: SHEP MYCN-ER

tag: treatment

value: 4-OHT 36hours

tag: antibody


title: SHEP MYCN-ER 4OHT 24hr rep1

description: spiked in RNA-seq

value: 4-OHT 24hours


title: SHEP MYCN-ER 4OHT 24hr rep2

description: spiked in RNA-seq


title: SHEP MYCN-ER 4OHT 36hr rep3

description: spiked in RNA-seq


title: SHEP MYCN-ER 4OHT 36hr rep1

description: spiked in RNA-seq


title: SHEP MYCN-ER 4OHT 24hr rep3

description: spiked in RNA-seq


title: SHEP MYCN-ER 4OHT 12hr rep3

description: spiked in RNA-seq

value: 4-OHT 12hours


title: SHEP MYCN-ER 4OHT 12hr rep2

description: spiked in RNA-seq


title: SHEP MYCN-ER 4OHT 0hr rep2

description: spiked in RNA-seq

value: DMSO


title: SHEP MYCN-ER 4OHT 0hr rep1

description: spiked in RNA-seq


title: SHEP MYCN-ER 4OHT 12hr rep1

description: spiked in RNA-seq


title: SHEP MYCN-ER sgEAF1 S2P DMSO

description:
ChIP-seq
WHH-sgEAF1-4OHT-CST-S2P

data_processing:
All RNA-seq reads were aligned to the Drosophila genome (dm6) and human genome (hg38) by HISAT2 version 2.1.0, respectively. Raw read counts were normalized to RPM (Reads per Million) per sample and then displayed in the UCSC genome browser as bigWig-formatted coverage tracks. Read counts at indicated regions were calculated by HTSeq-count (version 0.12.3) and were provided to DEseq2 (version 1.32.0) for differential gene expression analysis. Human gene expression was normalized using Drosophila spiked-in genes. An FDR threshold of 0.05 and a log2 fold change cut off of 0.5 was used to identify differentially expressed genes.
TT-seq reads were aligned to the Drosophila genome (dm6) and human genome (hg38) using HISAT2 version 2.1.0. The resulting reads were normalized to total reads aligned (Reads per Million) for each strand with deepTools (version 3.3.0). The read counts across each gene were counted with HT-seq (version 0.12.3), and DESeq2 were used for differentially gene expression analysis.
ChIP-seq raw reads were aligned to the human genome (hg38) with Bowtie (version 1.1.2) using default settings. Read coverage was performed with deepTools and were visualized on the UCSC genome browser. Peaks were called using MACS2 (version 2.1.2) using default parameters and an FDR cut off at 1e10-5 prior to annotation by ChIPseeker (version 1.28.3).
Assembly: hg38
Assembly: dm6
Supplementary files format and content: Library normalized bigWig files were provided.
Supplementary files format and content: Comma-separated text files were provided.

extract_protocol:
For ChIP-seq, DNA fragments was immunoprecipitated with indicated antibodies and Protein A/G beads.
For ChIP-seq, SHEP MYCN-ER cells were crosslinked with 1% paraformaldehyde for 10 minutes and were quenched with glycine for 5 minutes. After cell lysis, fixed chromatin was fragmented to 200-600 bp DNA size using a Diagenode Bioruptor Plus. DNA fragments was immunoprecipitated with indicated antibodies and Protein A/G beads. Specific antibodies against MYCN, MAX, AFF1 and AFF4, were generated by immunization in rabbits with recombinant antigens. 1-10 ng of immunoprecipitated DNA was used for DNA library preparation.

treatment_protocol: A total of 1 × 10^7 SHEP MYCN-ER cells were treated with DMSO or 4-OHT (100 nM). For TT-seq, cells were then labeled with 400 μM 4-thiouridine at 37°C for 10 minutes before total RNA extraction with Trizol reagent. To assess elongation rates, cells were pre-treated with flavopiridol for 1 hour to pause Pol II near the transcription start sites (TSS) before 4sU labeling. The extracted total RNA was spiked-in with 4sU-labeled Drosophila S2 RNA.


title: SHEP MYCN-ER sgCtrl S2P DMSO

description:
ChIP-seq
WHH-control-4OHT-CST-S2P


title: SHEP MYCN-ER sgEAF1 S2P 4-OHT

description:
ChIP-seq
WHH-sgEAF1-DMSO-CST-S2P


title: SHEP MYCN-ER sgEAF1 AFF1 DMSO

description: ChIP-seq

data_processing:
All RNA-seq reads were aligned to the Drosophila genome (dm6) and human genome (hg38) by HISAT2 version 2.1.0, respectively. Raw read counts were normalized to RPM (Reads per Million) per sample and then displayed in the UCSC genome browser as bigWig-formatted coverage tracks. Read counts at indicated regions were calculated by HTSeq-count (version 0.12.3) and were provided to DEseq2 (version 1.32.0) for differential gene expression analysis. Human gene expression was normalized using Drosophila spiked-in genes. An FDR threshold of 0.05 and a log2 fold change cut off of 0.5 was used to identify differentially expressed genes.
TT-seq reads were aligned to the Drosophila genome (dm6) and human genome (hg38) using HISAT2 version 2.1.0. The resulting reads were normalized to total reads aligned (Reads per Million) for each strand with deepTools (version 3.3.0). The read counts across each gene were counted with HT-seq (version 0.12.3), and DESeq2 were used for differentially gene expression analysis.
ChIP-seq raw reads were aligned to the human genome (hg38) with Bowtie (version 1.1.2) using default settings. Read coverage was performed with deepTools and were visualized on the UCSC genome browser. Peaks were called using MACS2 (version 2.1.2) using default parameters and an FDR cut off at 1e10-5 prior to annotation by ChIPseeker (version 1.28.3).
Assembly: hg38
Assembly: dm6
Supplementary files format and content: Library normalized bigWig files were provided for all samples

extract_protocol:
For ChIP-seq, DNA fragments was immunoprecipitated with indicated antibodies and Protein A/G beads.
For ChIP-seq, SHEP MYCN-ER cells were crosslinked with 1% paraformaldehyde for 10 minutes and were quenched with glycine for 5 minutes. After cell lysis, fixed chromatin was fragmented to 200-600 bp DNA size using a Diagenode Bruptor Plus. DNA fragments was immunoprecipitated with indicated antibodies and Protein A/G beads. Specific antibodies against MYCN, MAX, AFF1 and AFF4, were generated by immunization in rabbits with recombinant antigens. 1-10 ng of immunoprecipitated DNA was used for DNA library preparation.


title: B_2


title: SHEP MYCN-ER sgCtrl AFF1 DMSO

description: ChIP-seq


title: SHEP MYCN-ER sgEAF1 AFF1 4-OHT

description: ChIP-seq


title: SHEP MYCN-ER sgCtrl AFF1 4-OHT

description: ChIP-seq


title: SHEP MYCN-ER sgEAF1 MYCN DMSO

description: ChIP-seq

value: N-MYC


title: SHEP MYCN-ER sgCtrl S2P 4-OHT

description:
ChIP-seq
WHH-control-DMSO-CST-S2P


title: SHEP MYCN-ER sgEAF1 MYCN 4-OHT

description: ChIP-seq


title: SHEP MYCN-ER sgCtrl MYCN 4-OHT

description: ChIP-seq


title: SHEP MYCN-ER sgCtrl MYCN DMSO

description: ChIP-seq


title: SHEP MYCN-ER sgEAF1 AFF4 DMSO

description: ChIP-seq


title: SHEP MYCN-ER sgEAF1 AFF4 4-OHT

description: ChIP-seq


title: SHEP MYCN-ER sgCtrl AFF4 4-OHT

description: ChIP-seq


title: SHEP MYCN-ER sgCtrl AFF4 DMSO

description: ChIP-seq


title: SHEP MYCN-ER 4OHT 0hr rep3

description: spiked in RNA-seq


title: SHEP MYCN-ER FP-TT-Seq 4-OHT/KL-2 rep3

description: spiked in TT-seq

data_processing:
Library strategy: TT-seq
All RNA-seq reads were aligned to the Drosophila genome (dm6) and human genome (hg38) by HISAT2 version 2.1.0, respectively. Raw read counts were normalized to RPM (Reads per Million) per sample and then displayed in the UCSC genome browser as bigWig-formatted coverage tracks. Read counts at indicated regions were calculated by HTSeq-count (version 0.12.3) and were provided to DEseq2 (version 1.32.0) for differential gene expression analysis. Human gene expression was normalized using Drosophila spiked-in genes. An FDR threshold of 0.05 and a log2 fold change cut off of 0.5 was used to identify differentially expressed genes.
TT-seq reads were aligned to the Drosophila genome (dm6) and human genome (hg38) using HISAT2 version 2.1.0. The resulting reads were normalized to total reads aligned (Reads per Million) for each strand with deepTools (version 3.3.0). The read counts across each gene were counted with HT-seq (version 0.12.3), and DESeq2 were used for differentially gene expression analysis.
ChIP-seq raw reads were aligned to the human genome (hg38) with Bowtie (version 1.1.2) using default settings. Read coverage was performed with deepTools and were visualized on the UCSC genome browser. Peaks were called using MACS2 (version 2.1.2) using default parameters and an FDR cut off at 1e10-5 prior to annotation by ChIPseeker (version 1.28.3).
Assembly: hg38
Assembly: dm6
Supplementary files format and content: Library normalized bigWig files were provided for all samples

extract_protocol:
For TT-seq, total RNA extraction with Trizol reagent.
For TT-seq, the extracted total RNA was spiked-in with 4sU-labeled Drosophila S2 RNA. RNA was fragmented by 0.2 M NaOH, neutralized by 1× volume of 1 M Tris-HCl (pH 6.8) and precipitated with isopropyl alcohol. 100 μg of total RNA was subjected to biotinylation reaction in a total volume of 250 μl containing 10 mM HEPES (pH 7.5), 1 mM EDTA, and 5 ug of biotin-XX-MTSEA at room temperature for 30 minutes. The RNA was purified with Sera Mag carboxylate modified magnetic beads. The biotin-labeled RNA was further purified with the MyOne streptavidin C1 dynabeads. 4sU-RNA was eluted with DTT and subjected to strand-specific RNA-Seq library preparation prior to next generation sequencing on a NovaSeq 6000.


title: SHEP MYCN-ER FP-TT-Seq 4-OHT/KL-2 rep1

description: spiked in TT-seq


title: SHEP MYCN-ER FP-TT-Seq 4-OHT/KL-2 rep2

description: spiked in TT-seq


title: SHEP MYCN-ER FP-TT-Seq KL-2 rep2

description: spiked in TT-seq


title: SHEP MYCN-ER FP-TT-Seq KL-2 rep3

description: spiked in TT-seq


title: SHEP MYCN-ER FP-TT-Seq KL-2 rep1

description: spiked in TT-seq


title: SHEP MYCN-ER FP-TT-Seq 4-OHT rep2

description: spiked in TT-seq


title: SHEP MYCN-ER FP-TT-Seq 4-OHT rep3

description: spiked in TT-seq


title: SHEP MYCN-ER FP-TT-Seq DMSO rep3

description: spiked in TT-seq


title: SHEP MYCN-ER FP-TT-Seq 4-OHT rep1

description: spiked in TT-seq


title: SHEP MYCN-ER FP-TT-Seq DMSO rep2

description: spiked in TT-seq


title: SHEP MYCN-ER FP-TT-Seq DMSO rep1

description: spiked in TT-seq


title: SHEP MYCN-ER 4-OHT/KL-2 rep2

description: spiked in RNA-seq


title: SHEP MYCN-ER 4-OHT/KL-2 rep1

description: spiked in RNA-seq


title: SHEP MYCN-ER KL-2 rep3

description: spiked in RNA-seq


title: SHEP MYCN-ER 4-OHT rep1

description: spiked in RNA-seq


title: SHEP MYCN-ER 4-OHT rep3

description: spiked in RNA-seq


title: SHEP MYCN-ER 4-OHT rep2

description: spiked in RNA-seq


title: SHEP MYCN-ER DMSO rep3

description: spiked in RNA-seq


title: SHEP MYCN-ER KL-2 rep1

description: spiked in RNA-seq


title: SHEP MYCN-ER KL-2 rep2

description: spiked in RNA-seq


title: SHEP MYCN-ER DMSO rep2

description: spiked in RNA-seq


title: SHEP MYCN-ER DMSO rep1

description: spiked in RNA-seq


title: SHEP MYCN-ER AFF4 4-OHT

description: ChIP-seq


title: SHEP MYCN-ER AFF1 DMSO

description: ChIP-seq


title: SHEP MYCN-ER AFF4 DMSO

description: ChIP-seq


title: SHEP MYCN-ER MAX 4-OHT

description: ChIP-seq

value: MAX


title: SHEP MYCN-ER MAX DMSO

description: ChIP-seq


title: SHEP MYCN-ER MYCN DMSO

description: ChIP-seq


title: SHEP MYCN-ER MYCN 4-OHT

description: ChIP-seq


title: SHEP MYCN-ER shSEC 4-OHT rep1

description: spiked in RNA-seq

value: shSEC 4-OHT


title: SHEP MYCN-ER shSEC DMSO rep3

description: spiked in RNA-seq

value: shSEC DMSO


title: SHEP MYCN-ER shSEC DMSO rep1

description: spiked in RNA-seq


title: SHEP MYCN-ER shSEC 4-OHT rep3

description: spiked in RNA-seq


title: SHEP MYCN-ER shSEC 4-OHT rep2

description: spiked in RNA-seq


title: SHEP MYCN-ER 4-OHT/KL-2 rep3

description: spiked in RNA-seq


title: SHEP MYCN-ER shGFP 4-OHT rep3

description: spiked in RNA-seq

value: shGFP 4-OHT


title: SHEP MYCN-ER shSEC DMSO rep2

description: spiked in RNA-seq


title: SHEP MYCN-ER shGFP DMSO rep1

description: spiked in RNA-seq

value: shGFP DMSO


title: SHEP MYCN-ER shGFP 4-OHT rep2

description: spiked in RNA-seq


title: D_5

value: Essential Tremor

value: Female

value: Purkinje Cells


title: SHEP MYCN-ER AFF1 4-OHT

description: ChIP-seq


title: SHEP MYCN-ER TT-seq DMSO rep2

description: spiked in TT-seq


title: SHEP MYCN-ER TT-seq 4-OHT rep1

description: spiked in TT-seq


title: SHEP MYCN-ER TT-seq 4-OHT rep2

description: spiked in TT-seq


title: SHEP MYCN-ER TT-seq DMSO rep3

description: spiked in TT-seq


title: SHEP MYCN-ER TT-seq DMSO rep1

description: spiked in TT-seq


title: BMSCs_T8E

status: Public on Feb 24 2023

city: Taichung City

first: Chun-Te

last: Ho

address: 7F, No. 6, Xueshi Rd., North Dist.

department: Integrative Stem Cell Center

country: Taiwan

institute: China Medical University Hospital

data_processing:
Illumina RTA v1.17.21.3 software used for basecalling, and CASAVA V1.8.2 software used for demultiplex and data converstion
The low quality of sequencing bases were trimmed based on adapter sequences by Trimmomatic 0.3.
The alignment, quantification, normalization, and differential expression analysis were performed by STAR 2.7.8a, featureCounts 2.0.1, and edgeR 3.40.2, respectively.
Assembly: hg38
Supplementary files format and content: RNA seq_BMMSC_21150 gene.txt (tab-delimited text files include DEG values of 21150 genes for each Sample)
Supplementary files format and content: GSE109503_37973_gene.txt (normalized counts for 6 samples re-analyzed from Series GSE109503)
Supplementary files format and content: GSM2944707_D1D0_D3D21_S1_L005.count.txt (raw counts for 6 samples re-analyzed from Series GSE109503)

molecule: polyA RNA

source_name: bone marrow-derived mesenchymal stem cell

growth_protocol: The isolation of human BMSCs has been described previously which was originally derived from the iliac crest of donors (Tsai et al. 2011). Briefly, mononuclear cells were isolated from heparinized bone marrow by density gradient centrifugation using Ficoll- Hypaque of a density of 1.077 g/L, followed by seeding into 6-well plate with CM at 37°C under 5% CO2 atmosphere. At 9 days after seeding, BMSCs were recovered and reseeded in 10-cm plastic dishes at an initial density of 4×10^3 cells/cm2 and the culture medium was changed twice per week. BMSCs subculture are performed at 1:3 to 1:5 split every week.

extract_protocol:
Total RNA was isolated with the GeneAll Hybrid-R RNA purification kit
RNA libraries were prepared for sequencing using Illumina TruSeq RNA sample Prep kit

value: BMSC

tag: passage

value: early

tag: individual


title: BMSCs_T9L

value: late


title: BMSCs_T9E


title: BMSCs_T8L


title: BMSCs_T7E


title: SHEP MYCN-ER TT-seq 4-OHT rep3

description: spiked in TT-seq

value: SHEP MYCN-ER


title: Liver, Refed-2h-3, mRNA-seq

city: shanghai

first: NANA

last: JI

address: Dongan road 130

country: China

institute: Fudan university

data_processing:
hisat2 for sequence alignment
stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
samtools tools for related file processing
Assembly: mm10
Supplementary files format and content: Excel format representing FPKM and count values of mRNAs

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was harvested using Trizol reagent and used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

treatment_protocol: 10-week-old male C57BL/6J mice were purchased from the Shanghai Laboratory Animal Company (SLAC, Shanghai, China). Mice were fed ad libitum or fasted for 24 hour. Then, mice were sacrificed and livers were harvested for RNA extraction.

value: Liver

tag: Sex

value: male

value: Wild-type

value: Refed 2h


title: Liver, Refed-2h-2, mRNA-seq


title: BMSCs_T7L


title: DHX15-KO

library_source: transcriptomic single cell

data_processing:
RNA-seq reads quality was evaluated using FastQC (version 0.11.9) and mapped to the human genome reference assembly (hg19) using STAR 2.4.1.7 Differential gene expression analysis was performed using DESeq2 (version 1.32.0). Differential alternative splicing (AS) events were quantified by using rMATS8 and JUM9 for five major types (SE, A5SS, A3SS, MXE, IR). AS events were considered as significant if |IncLevelDifference| or |ΔPSI |>0.1 and p-value < 0.05.
For RIP-Seq, the reads quality was evaluated using FastQC (version 0.11.9) and mapped to the human genome reference assembly (hg38) using STAR software (version 2.7.5c). The resulting P values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR). Genes with Log2[fold change (FC)] > 1 and FDR < 0.05 found by DESeq were considered to be significant enrichment..
For scRNA-seq, we demultiplexed the sequencing reads into single cells according to unique barcode sequences and aligned them to the mm10 reference using Cell Ranger (version 6.0.2). We merged the single cell expression data from Dhx15fl/fl and Dhx15 KO thymocytes and eliminated potential doublets using Scanpy (version 1.7.1). We retained cells expressing more than 500 genes and containing less than 20% of transcripts mapping to mitochondrial genes, and filtered out uninformative genes which were detected in less than 3 cells. We further excluded the cells with gene counts or unique molecule identifier (UMI) counts detected outside the interval of mean value plus or minus two-fold standard deviation. We then normalized, scaled and log-transformed gene expression for each cell, and performed principal component analysis using the highly variable genes selected by dispersion-based methods in Scanpy. Uniform Manifold Approximation and Projection (UMAP) was used to visualize the distribution of cells in the projection of the significant principal components and cells were clustered using Leiden algorithm. Trajectory analysis were performed using Monocle 3. Cell cycle states (G1, S, G2/M) of cells were annotated by scoring gene sets with Scanpy.
Assembly: hg38
Assembly: mm10
Supplementary files format and content: csv and tsv

source_name: mouse thymus

growth_protocol: T-ALL line CUTLL1 cells were grown in complete RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS, Gemini), 1% penicillin/streptomycin (Hyclone), 1% non-essential amino acids (Gibco), 2mM L-glutamine (Sigma), 1 mM sodium pyruvate (Sigma), and 100 μM β-mercaptoethanol (Sigma).

extract_protocol:
For RNA-seq, total RNA was extracted using Trizol.
For RIP-seq, total RNA extraction with Trizol.
For scRNA-seq, total RNA was extracted using Trizol.
For RNA-seq, total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and subjected to quality control for RNA integrity by Agilent Bioanalyzer 2100 system (Agilent Technologies). Total RNA was further purified by RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (QIAGEN). Poly(A)+ RNA libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme) and sequenced as 150 bp paired-end reads by Illumina NovaSeq 6000 (Annoroad Gene Technology Corporation).
For RIP-seq, ten million CUTLL1 cells were lysed in RIP lysis buffer [20 mM Tris-HCl pH 7.6, 150 mM NaCl, 1% NP-40, 1 mM EDTA, 0.1% SDS, 100 U/ml RNasin Ribonuclease Inhibitors (Promega)]. The resulting cell lysates were incubated with 5 µg of DHX15 antibody (Abcam) or control IgG at 4°C overnight. Protein A/G magnetic beads (Thermo Fisher Scientific) were then added and incubated for 2 h at 4°C to conjugate the protein-antibody complexes. After washing with RIP buffer, beads were resuspended in 80 μl PBS, followed by DNase treatment (Thermo Fisher Scientific) and proteinase K (50 μg) (Thermo Fisher Scientific) digestion at 37 °C for 15 min.  Input and co-immunoprecipitated RNAs were isolated by TRIzol reagent (Thermo Fisher Scientific), and analyzed by qPCR or RNA-seq. NEBNext rRNA Depletion Kit v2 (New England BioLabs) was used to remove rRNA, and NEBNext Ultra II RNA Library Prep Kit (New England BioLabs) was then applied for library construction. RNAs were sequenced as 150 bp paired-end reads using Illumina NovaSeq 6000 (Annoroad Gene Technology Corporation, China).
For scRNA-seq, single-cell suspensions of total thymocytes from 6-week-old Dhx15fl/fl or Dhx15 KO mice were prepared by filtering thymus tissues against a 40-μm cell strainer. Single cells were captured in droplet emulsions using a GemCode Single-Cell Instrument (10Genomics). scRNA-seq libraries were constructed according to the 10 Genomics protocol using Chromium Single-Cell 3′ Library and Gel Bead Kit V3.1 (10Genomics), and sequenced using Illumina NovaSeq 6000 (Annoroad Gene Technology Corporation).

treatment_protocol: CUTLL1 cells were infected with lentiviruses expressing DHX15 shRNA or treated with ciclopirox (MedChemExpress, HY-B0450)  for indicated hours .

value: mouse thymus


title: Liver, Fed-3, mRNA-seq

value: Fed ad libitum


title: Liver, Fed-2, mRNA-seq


title: Liver, Fast-2, mRNA-seq

value: Fasted for 24 hour


title: Liver, Fast-1, mRNA-seq


title: SHEP MYCN-ER shGFP 4-OHT rep1

description: spiked in RNA-seq


title: SHEP MYCN-ER shGFP DMSO rep3

description: spiked in RNA-seq


title: Liver, Fed-1, mRNA-seq


title: Liver, Fast-3, mRNA-seq


title: DHX15-flox


title: TGFb_sc451

status: Public on Feb 23 2023

city: Philadelphia

first: Inyoung

last: Jung

state: PA

address: SPE, 9-304, 3400 Civic Center Blvd, Bldg. 421

institute: University of Pennsylvania

data_processing:
Raw read files were processed and aligned to the human reference genome (GRCh38) using Cell Ranger 6.1.2.
Supplementary files format and content: raw_feature_bc_matrix.h5
Assembly: GRCh38

molecule: cytoplasmic RNA

source_name: blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from healthy subjects via leukapheresis. Written informed consent for leukocyte collection was provided by study subjects according to the Declaration of Helsinki and the International Conference on Harmonization Guidelines for Good Clinical Practice. PBMCs were isolated from buffy coats and cryopreserved at 4 × 107 cells per vial. Cryopreserved PBMCs were thawed, and T-cell purification was carried out using the Pan T Cell Isolation Kit according to the manufacturer’s instructions (Miltenyi Biotec). For CAR-TCONV manufacturing, T-cells were activated with Cell Therapy Systems CD3/CD28 Dynabeads™ (Thermo Fisher Scientific) at a bead to cell ratio of 3:1 for three days in T-cell OpTmizer CTS SFM media (Gibco) supplemented with 5% human AB serum and 100U/mL human IL-2 (T-cell media). At 24-hours post-T-cell activation, T-cells were transduced with the lentiviral vector (M5bbz CAR) at a multiplicity of infection (MOI) of 3. T-cell media was added to cultures every two days, and on day nine, CAR T-cells were cryopreserved in T-cell media supplemented with 20% human AB serum and 10% dimethyl sulfoxide. For CAR-TRM production, T-cell culture media was supplemented with 2ng/mL of TGFβ (R&D Systems or Cell Signaling Technology) in addition to IL-2, and the CAR T-cell engineering process was carried out.

extract_protocol: Anti-mesothelin M5 CAR-TCONV and CAR-TRM cells were harvested after nine days of in vitro expansion. Dead cells were eliminated using the Dead Cell Removal Kit (Miltenyi Biotec). Mesothelin-directed M5 CAR-TCONV and -TRM cells were magnetically isolated using anti-mesothelin-coated beads. After isolation, T-cell viability and quantity were evaluated using trypan blue exclusion and cells were resuspended in PBS containing 0.04% BSA. Approximately 20,000 cells were loaded per reaction to capture ~10,000 cells for scRNA-seq library preparation using Chromium Single Cell 5' v2 Reagent kits (10X Genomics) according to manufacturer’s protocol. Sequencing was performed on a NovaSeq 6000 instrument.

value: blood

tag: cell subtype

value: CAR-T

value: T-cell

value: TGFb

tag: biological replication

value: Normal donor 1_rep1


title: SHEP MYCN-ER shGFP DMSO rep2

description: spiked in RNA-seq

value: shGFP DMSO


title: IL2_sc451


title: Liver, Refed-2h-1, mRNA-seq


title: CnT K36M+DMOG K27me3 replicate 2

status: Public on Feb 21 2023

city: Boston

first: Michael

last: Hoetker

state: Massachusetts

address: Simches Building, Mail code CPZN 4200

department: Department of Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Sequencing reads were mapped to mm9 reference genome using bwa aligner. Peak calling was performed using Homer94. Heatmaps and average profiles of CUT&Tag read densities were generated using deepTools95. Bedtools was used to calculate read densities over given regions. Gene ontology analysis was performed with ClusterProfiler after annotation using ChipSeeker.
Assembly: mm9
Supplementary files format and content: read coverage (bigwig)
Library strategy: CUT&Tag

source_name: reprogramming intermediate

growth_protocol: Samples underwent reprogramming for four days in AGi conditions. DMOG samples were also treated with DMOG for these four days. iPSC samples are from passaged iPSCs (S/L on feeders, off dox).

extract_protocol:
CUT&Tag was performed as previously described (Kaya-Okur, Janssens, Henikoff, Ahmad, & Henikoff, 2020). In brief, 100,000 bead-bound cells per sample were permeabilized and incubated with primary antibodies targeting the desired epitopes (anti-H3K4me3 (active motif 39060), anti-H3K27ac (Millipore Sigma MABE647), H3K27me3 (Cell Signaling 9733), anti-H3.3K36M (Revmab 31-1085-00-S), Sox2 (Cell Signaling 23064)). After incubation with secondary antibody (Guinea Pig anti-Rabbit IgG, antibodies online ABIN101961) to amplify local abundance of immunoglobulins, protein A/G-tethered transposase (pAG-Tn5, Epicypher) was added and bound in situ at target loci. E. coli DNA spike-in was added for normalization purposes.
After tagmentation and DNA clean-up, libraries were prepared by PCR amplification with barcoded Illumina-compatible primers. Tapestation 2200 analysis using High Sensitivity D1000 ScreenTape (Agilent) was performed to confirm successful library preparation before sequencing.

value: reprogramming intermediate

tag: chip antibody

value: anti-H3K27me3 (Cell Signaling 9733)


title: CnT K36M+DMOG K36me2 replicate 2

value: anti-K36me2 (Active motif 39256)


title: CnT K36M+DMOG K27me3 replicate 1


title: CnT K36M+DMOG K36me2 replicate 1


title: CnT K36M+DMOG K36me3 replicate 2

value: anti-K36me3 (Thermo Fisher MA5-24687)


title: CnT K36M+DMOG K36me3 replicate 1


title: CnT K36M+DMOG K27ac replicate 2

value: anti-H3K27ac (Millipore Sigma MABE647)


title: CnT K36M+DMOG K27ac replicate 1


title: Colon_PdgfraLo_Rep1

first: Ramesh

middle: A.

last: Shivdasani

state: MA

address: 450 Brookline Ave. SM1060

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
ATAC-seq reads were trimmed using trim_galore v0.4.5, using a stringency of 3 for adapter trimming and a minimum trimmed read length of 30.
Alignment to the mm10 genome was done using bowtie2 v2.3.4.3 with default parameters. Samtools v1.9 was used for file processing, including the removal of duplicate reads. Sample quality was assessed using the RSeqQC v4.0.0 suite.
Samtools v1.9 was used for file processing, including the removal of duplicate reads. Sample quality was assessed using the RSeqQC v4.0.0 suite.
MACS2 v2.1.1 was used for peak calling, with a q-value cut-off of 0.001, lower Mfold=5, upper Mfold=50.
Bigwigs were produced using bamCoverage from the DeepTools v3.0.2 package, with bin size of 10 bp, smoothing of 30 bp, and normalizing using reads per genomic content
RNA-Seq
RNA-seq samples were aligned to the mm10 genome and processed using the Viper pipeline (Cornwell et al.(2018). BMC Bioinformatics, 19. https://doi.org/10.1186/S12859-018-2139-9) with default parameters.
scRNA-Seq
Samples were aligned to the mm10 genome using 10x Genomics Cell Ranger 3.0.2 using default parameters
Assembly: mm10
Supplementary files format and content: bigwig files
Supplementary files format and content: mtx

source_name: Colon

extract_protocol:
Mice were sacrificed and intracardially perfused with PBS, tissue was harvested, washed and the outer muscle layer was carefully removed with tweezers under a stereomicroscope. Tissue pieces were incubated twice in 10mM EDTA in HBSS +10mM HEPES + 5%FBS for 30min under 300rpm shaking at 37°C, washed and digested with 3mg/ml collagenase2 for 20min at 37°C. Filtered cell suspension was  washed  before staining procedures and sorting. For colonic whole mesenchyme sc-RNA-seq, cells were stained for EpCAM (eBioscience, 12-5791-83, 1:100) and CD45 (Invitrogen, 17045182, 1:100) by incubation for 25min at 4C; and cells were sorted for EpCAM- CD45-.  Single cell (sc)-RNAseq of PdgfraH2BeGFP cells proceeded on unstained cells sorted for GFP-level. 8,000 live (DAPI-negative) cells were loaded to a 10X Chromium controller proceeding with the Single Cell 3′ V3.1 assay (10X Genomics).
Single Cell 3′ V3.1 assay (10X Genomics).

treatment_protocol: PdgfraH2BeGFP (JAX strain 007669) mice were obtained from Jackson Laboratories. Adult mice of both sexes were used in this study.

value: Colon

value: Mesenchymal cells

value: mesenchymal cells

value: PdgfraH2BeGFP (JAX strain 007669)


title: Colon_PdgfraLo_Rep2


title: PdgfraLo_CD81-_Jejunum_Rep1

source_name: Small Intestine

extract_protocol:
Adult murine tissue was harvested by dividing the small intestine into 5 segments of equal length using the first one as Duodenum, the third as Jejunum and the fifth one as Ileum, intermediate regions discarded. For colonic cells, the proximal half of the colon (approximal 3cm) was used. TIssue was washed and the outer muscle layer was removed with tweezers under a stereomicroscope. Tissue pieces were incubated twice in 10mM EDTA in HBSS  +10mM HEPES + 5%FBS for 30min at 37°C, washed and digested with 3mg/ml collagenase2 for 20min at 37°C. The filtered cell suspension was stained with biotinylated anti-CD81 (eBiosciences 13-0811-81) or control biotinylated IgG for 25min at 4°C, washed and incubated with streptavidin-APC (eBiosciences, 17431782) for 25min at 4°C. Cells were sorted three-way for Pdgfra_eGFP high; Pdgfra_eGFP low CD81+ and Pdgfra_eGFP low CD81-  at the Dana-Farber Flow cytometry core facility using a BD FACS M Aria II instrument. Freshly sorted mesenchymal cells from different regions were used immediately for RNA extraction with RNAeasy Plus micro kit (Qiagen).
Samples with RNA-integrity number of >8.5 were processed with SMART-Seq v4 Ultra Low Input RNA library construction kit per manufacturer's recommendation; and sequenced on Illumina Novaseq platform by the molecular biology core facility at Dana-Farber.

value: Small Intestine

tag: tissue subtype

value: Jejunum

value: Pdgfra_low_CD81- mesenchymal cells


title: PdgfraHi_Jejunum_Rep1

tag: cell type

value: Pdgfra_high mesenchymal cells


title: PdgfraLo_CD81-_Ileum_Rep1

value: Ileum


title: PdgfraHi_Duodenum_Rep2

value: Duodenum


title: PdgfraLo_CD81-_Colon_Rep2


title: PdgfraHi_Jejunum_Rep2


title: PdgfraHi_Colon_Rep2


title: PdgfraLo_CD81+_Jejunum_Rep1

value: Pdgfra_low_CD81+ mesenchymal cells


title: Colon_whole_Mesenchyme

value: control


title: PdgfraLo_CD81-_Duodenum_Rep2


title: PdgfraLo_CD81-_Duodenum_Rep1


title: PdgfraHi_Duodenum_Rep1


title: PdgfraLo_CD81-_Ileum_Rep2


title: PdgfraLo_CD81+_Jejunum_Rep2


title: PdgfraLo_CD81-_Jejunum_Rep2


title: PdgfraHi_Ileum_Rep2


title: PdgfraLo_CD81-_Colon_Rep1


title: PdgfraHi_Colon_Rep1


title: PdgfraLo_CD81+_Ileum_Rep1


title: PdgfraLo_CD81+_Duodenum_Rep2


title: PdgfraLo_CD81+_Ileum_Rep2


title: PdgfraLo_CD81+_Duodenum_Rep1


title: Pdgfra_lo_CD81-rep2

source_name: Small intestine

extract_protocol:
Adult murine small intestinal tissue was harvested, washed and the outer muscle layer was removed with tweezers under a stereomicroscope. Tissue pieces were incubated twice in 10mM EDTA in HBSS  +10mM + 5%FBS for 30min under 300rpm shaking at 37°C, washed and digested with 3mg/ml collagenase2 for 20min at 37°C. The filtered cell suspension was stained with biotinylated anti-CD81 (eBiosciences 13-0811-81, 1:50) or control biotinylated IgG for 25min at 4°C, washed and incubated with streptavidin-APC (eBiosciences, 17431782, 1:100) for 25min at 4°C. Cells were sorted three-way for Pdgfra_eGFP high; Pdgfra_eGFP low CD81+ and Pdgfra_eGFP low CD81-  at the Dana-Farber Flow cytometry core facility using a BD FACS M Aria II instrument.
ATAC-seq was performed on 50,000 freshly sorted live mesenchymal cells using the “Omni-ATAC” protocol as described in Buenrostro, J. D., Wu, B., Chang, H. Y., & Greenleaf, W. J. (2015). Protocols in Molecular Biology, 109, 21.29.1-9. https://doi.org/10.1002/0471142727.mb2129s109 and library preparation as described in. Library quantification was performed by Qubit dsDNA high-sensitivity assay and library quality was assessed on a High Sensitivity DNA Kit on a Bioanalyzer 2100. Libraries were size-selected to exclude primer via AMPure beads

value: Small intestine


title: Pdgfra_lo_CD81-rep1


title: PdgfraLo_CD81+_Colon_Rep1


title: PdgfraLo_CD81+_Colon_Rep2


title: Pdgfra_lo_CD81+rep2


title: PdgfraHi_Ileum_Rep1


title: Pdgfra_hi_rep2


title: Pdgfra_lo_CD81+rep1


title: Pdgfra_hi_rep1


title: RNA-Seq_dRPB3_Untreated_rep1

status: Public on Feb 16 2023

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

description: Transcriptomic

data_processing:
Cutadapt V1.18 (Martin, 2011) was used to remove the adaptors (TELP libraries adaptor) and low-quality reads from the paired-end sequencing reads, then the filtered reads were mapped to the mm10 genome with bowtie2 (--very-sensitive-local) (Langmead and Salzberg, 2012).
In order to obtain the more reliable nascent RNA signals, the duplicate, discordant and multi-mapping reads were removed, rRNA reads were also removed with split_bam.py from RseQC V 2.6.6 (Wang et al., 2012).
The remaining reads were adapter trimmed and aligned against the concatenated genome of mm10 and dm6 using the STAR aligner (Dobin et al., 2013) with default parameters, and then subsequently separated into the mouse and fly bins. Finally, non-redundant reads were determined by samtools.
To display the information of the plus and minus chains at the same time, bamCoverage (Ramirez et al., 2014) was used to make the tracks for plus and minus chains separately with parameters –filterRNAstrand forward/reverse and –scaleFactor.
The uniquely aligned reads were counted over the Gencode annotated genes (M23) using featureCounts, and the output files from two replicates of each group were subsequently analyzed with a custom R script utilizing the DESeq2 package (Love et al., 2014), which incorporates spike-in calibration for data normalization and differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: dRPB3_RNA-Seq_DEseq2_results.txt: Tab-delimited text file includes raw read counts per sample per replicate and DESeq2 results.

source_name: mouse embryonic stem cells (V6.5)

growth_protocol: For RNA-seq, dRPB3 degron cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 1 × nucleoside (Millipore, Cat#ES-008-D), 3 μM CHIR99021 (Selleck, Cat#S1263), 0.5 μM PD0325901 (Selleck, Cat#S1036), 143 uM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) and maintained at 37℃ cell incubator with 5% CO2. The Schneider 2 (S2) cells were cultured in complete Schneider’s Drosophila Medium (Invitrogen, Cat#21720024) supplemented with 10% FBS (CellMax, Cat#SA311.02) at room temperature.

extract_protocol:
Total RNA were extracted according to the manufacturer’s instructions.
RNA samples were delivered to Novogene Company. The total RNA's concentration, purity, and integrity were examined and followed by PolyA RNA library generation.

treatment_protocol: Cells were treated with 1 μg/ml Doxycycline for 12 h to induce TIR1 expression, then treated with or without 500 μM IAA for 12 h to induce target protein degradation. To evaluate the potential secondary effects of Pol II subunit depletion, we performed poly(A) RNA-Seq after depleting RPB1, RPB3, RPB6 for 1 h, with dox treatment as the control.

value: dRPB3-mAID-GFP degron mESCs treated with 1ug/ml Dox for 12 h


title: RNA-Seq_dRPB3_Untreated_rep2

description: Transcriptomic


title: RNA-Seq_dRPB3_IAA_rep2

description: Transcriptomic

value: dRPB3-mAID-GFP degron mESCs treated with 1ug/ml Dox for 12 h, then treated with 500 uM IAA for 12 h


title: RNA-Seq_dRPB3_IAA_rep1

description: Transcriptomic


title: DC TcdA t8 sample 2

status: Public on Feb 13 2023

city: Durham

first: Jarrett

last: Bliton

address: 6 Davis Drive

institute: Altis Biosystems

description:
GEO_CDiff_tx_TMM_data.csv
GEO_CDiff_tx_adata.h5ad
GEO_CDiff_tx_raw_gene_counts.csv

data_processing:
Transcript quantification and pseudoalignment: The Kallisto package was used to quantify transcript abundance which were pseudoaligned to human genome GRCh38.
Normalization: raw gene matrices underwent TMM normalization as part of matrix assembly
Log Transformation: TMM normalized data were normalized to the dataset median and log transformed
Assembly: GRCh38
Supplementary files format and content: csv - raw or TMM normalized gene expression values per sample
Supplementary files format and content: h5ad - annotated matrix with read counts per gene x sample

source_name: Healthy human descending colon epithelium

growth_protocol: Biobanked human intestinal stem cells derived from transplant-grade descending colon tissue were expanded as monolayers on collagen hydrogels and then plated on 12-well Transwells pre-coated with 1% Matrigel, incubated at 37 ºC and 5% CO2.

extract_protocol:
To examine the changes in gene expression as colon stem cells differentiate into late absorptive colonocytes (ACCs) in vitro, RNAseq was performed on human colonic epithelial monolayers that were harvested the day after seeding onto Transwells (Expansion Media, EM Day 1), immediately prior to switching to Differentiation Media, DM (Day 0), and on Days 2 and 4 of differentiation on Transwells. Differentiated cells were also collected after apical exposure to 300 pM C. difficile TcdA or TcdB for 20h. For Caco-2, RNAseq was performed using cells harvested on Day 22 of differentiation.
Three technical replicates were collected from 12-well Transwells at each time point of differentiation or C. difficile toxin exposure, and RNA was extracted via the RNAqueous-Micro Total RNA Isolation Kit (AM1931; ThermoFisher, Waltham, MA) according to the manufacturer’s protocol. Before cDNA library preparation, RNA quality was determined by quantifying RNA integrity number (RIN), the ratio of 28s/18s RNA present, and RNA concentration in each sample. All samples used in library preparation had a RIN of at least 7. RIN was determined with the RNA 6000 Pico Kit for the Agilent 2100 Bioanalyzer. The Advanta RNA-Seq NGS Library Prep Kit for the Standard BioTools (formerly Fluidigm) Juno was used to prepare cDNA libraries for sequencing. Bulk sequencing was run on a NovaSeq 6000 instrument using one lane of an S4 v1.5 flow cell (Illumina).

value: 300 pM TcdA apical

tag: subject/individual

value: :Hispanic male


title: DM Day 2 sample 3

description:
GEO_differentiation_TMM_data.csv
GEO_differentiation_processed_v3.h5ad
GEO_differentiation_invivo-vs-invitro.h5ad
GEO_differentiation_raw_gene_counts.csv

tag: tissue

value: Healthy human descending colon epithelium

tag: time point

value: DM Day 2


title: DM Day 4 (aka DC Control t0) sample 1

description:
GEO_CDiff_tx_TMM_data.csv
GEO_CDiff_tx_adata.h5ad
GEO_differentiation_TMM_data.csv
GEO_differentiation_processed_v3.h5ad
GEO_differentiation_invivo-vs-invitro.h5ad
GEO_CDiff_tx_raw_gene_counts.csv
DC_differentiation_raw_gene_counts.csv

value: DM Day 4


title: DM Day 4 (aka DC Control t0) sample 3


title: DC TcdA t20 sample 2


title: Caco-2 Day 22 sample 1

source_name: Human colon cancer

value: Human colon cancer

value: ATCC Caco-2

value: Day 22

value: :White male


title: DC TcdA t8 sample 3


title: DC TcdA t20 sample 1


title: DC TcdA t8 sample 1


title: DM Day 0 (aka EM Day 4) sample 3

value: DM Day 0


title: DM Day 2 sample 2


title: DM Day 0 (aka EM Day 4) sample 2


title: DM Day 0 (aka EM Day 4) sample 1


title: DC TcdA t20 sample 3


title: Caco-2 Day 22 sample 2


title: EM Day 1 sample 3

value: EM Day 1


title: PDX2_ChIP_TET1_WT_IP

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
Raw reads from ChIP-seq were firstly quality controlled by FastQC and then mapped to human genome (hg38) by use of bowtie2 (version 2.3.2).
After alignments, the PCR duplicates were marked and removed by using Picard software (version 2.21.1, https://broadinstitute.github.io/picard/).
To analyze binding regions of TET1 and STAT5B, we used MACS2 (version 2.2.7.1) to call the enriched peaks with narrow peak mode and fragment sizes of ChIP-seq libraries estimated by phantompeakqualtools.
Finally, the peaks with p-values less than 0.01 were recognized as significantly enriched binding regions and kept for downstream analysis. The STAT5B-ChIP sequencing tag densities around TET1 peaks were calculated by HOMER (version v3.13), while the TET1 and STAT5B-ChIP sequencing tag densities along gene bodies and ±5.0 kb TSS/TTS were calculated by deeptools (version 3.5.1).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files and narrowPeak files

growth_protocol: PDX2 with or without overexpression of TET1 (WT and MUT) cells are regular cultured in full MEM alpha medium with 20% FBS.

extract_protocol:
Active Motif ChIP kit
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (Kapa Biosystems, Wilmington, NC) following manufacturer’s protocol. ChIP DNA was subjected to end repair with subsequent 3’ adenylation to create 3’ dA overhang suitable for adaptor ligation. Illumina adaptors were ligated to both ends of the DNA and amplified using 10 cycles of PCR with primers specific to the adaptor sequences to generate amplicons of approximately 200–500 bp in size. Libraries were purified using KAPA Pure Beads (Kapa Biosystems). Each library was quantified by Qubit fluorometer (Thermo Fisher Scientific) and evaluated by the 2100 Bioanalyzer (Agilent Technologies).
The libraries were amplified using the cBot (Illumina) and single end reads with 50-nt length were obtained using Illumina HiSeq2500 instrument.

treatment_protocol: Cells were treated with 1% formaldehyde for 10 minutes at 37 °C and subject to lysis and chromatin shearing with Qsonica Q800R

value: TET1 WT

value: Flag (F3165, MilliporeSigma)


title: Caco-2 Day 22 sample 3


title: DM Day 2 sample 1


title: DM Day 4 (aka DC Control t0) sample 2


title: PDX2_ChIP_WT_input


title: PDX2_ChIP_TET1_MUT_input

value: TET1 mutant (CD domain)


title: PDX2_ChIP_TET1_MUT_IP


title: PDX2_ChIP_STAT5B_sgTET1_IP

value: STAT5B (Ab178941, Abcam)


title: PDX2_RNA_sgNS_rep2

description: RNA-seq

data_processing:
The human genome indexes were built with gene annotations (gencode v32) and the human GRCh38 reference genome sequences by using STAR (version 2.7.2b) and RSEM (version 1.2.31) software.
Then raw reads from RNA-seq were quality controlled through FastQC (version 0.11.5, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and mapped to the reference genome with built index by use of STAR.
After alignments, RSEM was used to estimate the read counts of genes. To analyze the differentially expressed genes, we kept the genes with read counts >= 1 in at least 50% samples and passed them to DESeq2 using shrinkage estimators for dispersion and fold change. The gene enrichment and GSEA analyses were performed by clusterProfiler R package.
Genome_build: hg38
Supplementary_files_format_and_content: gene counts from RSEM and DEG outputs from DESeq2

growth_protocol: Culture the PDX2 cells with full medium and check the Cas9 induction and TET1 knock out by western blot.

extract_protocol:
Qiagen miRNeasy Mini Kit
Each RNA sample was spiked in with an appropriate amount of either Mix1 or Mix2 according to Life Technologies’ guidelines which would lead to about 1% of the total number of RNA-Seq reads mapping to the 92 ERCC control sequences. 300 ng total RNA of each sample was used for library preparation according to the manufacture’s protocol of KAPA mRNA HyperPrep Kit (Illumina Platforms). 10 cycles of PCR amplification were performed. KAPA Pure Beads (Kapa Biosystems) were used for library purification. The quality of each library was verified using a Qubit fluorometer (Thermo Fisher Scientific) and further evaluated by the 2100 Bioanalyzer (Agilent Technologies).
Sequencing was performed on an Illumina® Hiseq 2500 (Illumina, San Diego, CA) instrument using the TruSeq SR Cluster Kit V4-cBot-HS (Illumina®) to generate 51-nt single-end reads sequencing with v4 chemistry. Quality control of RNA-Seq reads was performed using FastQC.

treatment_protocol: Treat with doxycylcine with 1 µg/ml each other day, 3 times in total.

value: sgNS


title: PDX2_RNA_sgTET1_rep1

description: RNA-seq


title: PDX2_ChIP_STAT5B_sgNS_IP


title: PDX2_RNA_sgTET1_rep2

description: RNA-seq


title: EM Day 1 sample 1


title: EM Day 1 sample 2


title: PDX2_RNA_sgNS_rep1

description: RNA-seq


title: spt-2 KO A, 20C, replicate 3

status: Public on Feb 09 2023

city: Cambridge

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

country: United Kingdom

institute: University of Cambridge

description: Batch 1

data_processing:
C. elegans RNA-seq reads were aligned to the WS285 C. elegans genome assembly using STAR (2.7.5a) with the TwoPass mode and the WS285 gene annotation as a guide. Strand-specific wiggle output was converted to BigWig.
Assembly: WS285
Supplementary files format and content: BigWig tracks of multiple and unique reads, strand specific, RPM normalised, 1bp resolution

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Worms were grown on 1xNGM plates with HB101 bacteria.

extract_protocol:
RNA was harvested using Trizol and treated with Turbo DNA-free kit (Invitrogen).
RNA libraries for RNA-seq were prepared using the NEB Next Poly(A) mRNA Magnetic Isolation kit according to the manufacturer's protocols. 1ug of total RNA was used to make the libraries. Libraries were indexed with NEBNext Multiplex Oligos for Illumina.

treatment_protocol: Synchronised worms growing at 20C were harvested at the gravid adult stage.

tag: developmental stage

value: synchronised adults

value: whole worms

tag: genotype

value: spt-2 KO-A

value: growth at 20C


title: WT, 20C, replicate 1

description: Batch 1

value: WT N2


title: spt-2 KO B, 20C, replicate 1

description: Batch 1

value: spt-2 KO-B


title: spt-2 KO B, 20C, replicate 2

description: Batch 1


title: spt-2 KO A, 20C, replicate 1

description: Batch 1


title: spt-2 M627A, 20C, replicate 1

description: Batch 2

value: spt-2 M627A


title: WT, 20C, replicate 4

description: Batch 2


title: WT, 20C, replicate 5

description: Batch 2


title: spt-2 KO C, 20C, replicate 3

description: Batch 1


title: spt-2 M627A, 20C, replicate 2

description: Batch 2


title: WT, 20C, replicate 6

description: Batch 2


title: +aTc TetR-PfGCN::GFP L-Glu rep3

status: Public on Feb 08 2023

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

description: RNA-seq

data_processing:
Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Only reads that had a minimum length of 50 base pairs were retained.
Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2
Differentially expressed genes are determined by DESeq2  with Padj < 0.05 and absolute fold change higher than 1.5.
The transcriptional profiles are normalized by TPM for multi-time points or condition comparisons.
Assembly: pf3D7_V3.0.fasta
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Plasmodium falciparum

source_name: Plasmodium parasite

growth_protocol: 3D7 strains of P. falciparum were cultured in type O+ human RBCs at 5% hematocrit in RPMI 1640 medium supplemented with 25 mM HEPES, 50mg/L hypoxanthine, 25 mM NaHCO3, 0.5% Albumax II and 40 mg/ml gentamicin sulfate. The culture was maintained at 37°C in a gas mixture of 5% CO2, 3% O2 and 92% N2.

extract_protocol:
Parasites of designated developmental stages were harvested after lysis of the RBC membrane with 0.1% (v/v) saponin in PBS. Total RNA was isolated from the purified parasites using Quick-RNA MiniPrep kit (Zymo Research). The RNA was treated with the ezDNaseTM Enzyme (Invitrogen) to remove contaminating genomic DNA. RNA pellets were dissolved in 50 µL RNase-free water, and the RNA integrity was checked using the Agilent Bioanalyzer.
RNA sequencing libraries were prepared using the KAPA stranded RNA-seq library preparation kit (Roche) with 500 ng RNA from each sample. RNA was fragmented by heating at 94 °C for 8 min, and cDNA was synthesized using reverse transcriptase with random primers. Afterward, 3’ dTMP adapters were ligated to the 3’ dAMP library fragments. The quality of the barcoded libraries was validated using the Agilent Bioanalyzer. The DNA 1000 Reagents were used to quantify the library sizes and confirm the absence of primer dimers. Libraries were quantified using a KAPA Universal Library Quantification Kit (Roche), and library concentrations were adjusted for library size. Libraries were sequenced on an Illumina NextSeq 550 in the Rapid Run mode using 150 nt paired end read sequencing .

value: wildtype

tag: Stage

value: Ring stage

value: low-glucose (L-Glu)


title: -aTc TetR-PfGCN::GFP HS rep1

description: RNA-seq

value: PfGCN5 KD

value: Heat shock (HS)


title: +aTc TetR-PfGCN::GFP L-Glu rep2

description: RNA-seq


title: +aTc TetR-PfGCN::GFP DHA rep3

description: RNA-seq

value: Dihydroartemisinin (DHA)


title: -aTc TetR-PfGCN::GFP L-Glu rep3

description: RNA-seq


title: -aTc TetR-PfGCN::GFP L-Glu rep1

description: RNA-seq


title: -aTc TetR-PfGCN::GFP DHA rep2

description: RNA-seq


title: -aTc TetR-PfGCN::GFP L-Glu rep2

description: RNA-seq


title: +aTc TetR-PfGCN::GFP DHA rep1

description: RNA-seq


title: +aTc TetR-PfGCN::GFP DHA rep2

description: RNA-seq


title: +aTc TetR-PfGCN::GFP HS rep2

description: RNA-seq


title: +aTc TetR-PfGCN::GFP HS rep3

description: RNA-seq


title: +aTc TetR-PfGCN::GFP HS rep1

description: RNA-seq


title: -aTc TetR-PfGCN::GFP rep3

description: RNA-seq

value: no treatment


title: -aTc TetR-PfGCN::GFP rep2

description: RNA-seq


title: -aTc TetR-PfGCN::GFP DHA rep1

description: RNA-seq


title: +aTc TetR-PfGCN::GFP rep2

description: RNA-seq


title: PRAISE-WT-rRNA_rep1

status: Public on Feb 06 2023

first: Jiang

last: Zhe

state: Beijing

address: No. 5 Yiheyuan Road, Haidian District

data_processing:
trimiming using cutadapt
mapping using HISAT2 and then tailored alignment
remove multiple mapping
converting bam into bw using bamCoverage
Assembly: hg38
Supplementary files format and content: bw files including mapping result data

growth_protocol: HEK293T were cultured in DMEM medium (Corning) supplemented with 10% (v/v) FBS (Gibco), 1% GlutaMAX (Gibco) and 0.5% penicillin/streptomycin (Gibco) at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted with TRIzol (Life technologies) followed by isopropanol precipitation, according to the manufacturer’s instructions (Invitrogen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line


title: WT, 20C, replicate 3

description: Batch 1

tag: treatment


title: -aTc TetR-PfGCN::GFP rep1

description: RNA-seq


title: -aTc TetR-PfGCN::GFP HS rep2

description: RNA-seq


title: +aTc TetR-PfGCN::GFP rep3

description: RNA-seq


title: Cp BHI replicate 2

first: Adam

last: Rosenthal

state: NC

address: 125 Mason Farm Marsico Hall rm6201

department: Microbiology and Immunology

institute: UNC

description:
RNA hybridizing probes
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software V7.1  and using custom scripts available from the Sahand Hormoz lab (https://gitlab.com/hormozlab/bacteria_scrnaseq)
Assembly: Probe-based genome builds for B subtilis, E coli and C perfringens are deposited alongside GTF files in the Hormoz lab github: https://gitlab.com/hormozlab/bacteria_scrnaseq
Supplementary files format and content: H5 files

organism: Clostridium perfringens

source_name: Bacterial cells in suspension

extract_protocol:
Freshly collected bacterial cells were fixed in 1% paraformaldehyde for 1 hour. Cells from 2 mL of cell culture were fixed using a 30-minute incubation in 1% paraformaldehyde (final concentration) at room temperature. Formaldehyde-fixed samples were washed with 0.02 % SSC (Saline Sodium Citrate - Invitrogen) by gentle centrifugation (6,000 x G) for 2.5 minutes. After the wash, cell pellets were resuspended in 1 mL MAAM (4:1 V:V dilution of methanol to glacial acetic acid). Samples were kept at -20oC for up to 2 days before further processing. For in-situ probe hybridization, 150 µL of fixed sample was centrifuged and washed once in PBS to remove methanol and acetic acid. After the wash step, cells were incubated in 200 µL PBS with 350 u/µL of lysozyme solution (Epicentre ready-lyse) for 30 minutes at room temperature. Lysozyme concentration was optimized and other enzyme combinations were tested to achieve a protocol with maximal probe signal and minimal cell lysis (see Supplementary Figure S12) After 30 minutes cells were pelleted and washed with 500 µL PBS-tween (PBS with 0.1 % Tween 20). Cells were then re-suspended with 100 µL of probe binding buffer consisting of 5x SSC, 30% formamide, 9mM citric acid (pH 6.0). 0.1% Tween 20, 50 ug/ml heparin, and 10% low MW dextran sulfate42. Cell suspensions were placed in a 50oC shaker-incubator and allowed to pre-equilibrate for 1 hour. After 1 hour 50 µL of probes, (600 ng/µL) were added to each cell suspension, and samples were left to incubate overnight.  Following the overnight incubation samples were washed 5 times in pre-warmed (50oC) probe-wash solution (5 x SSC, 30% formamide, 9 mM citric acid pH 6.0, 0.1% Tween 20, and 50 ug/mL heparin).
Library was performed according to specifications of McNulty et al bacterial scRNAseq protocols (single cell 3’ v2 protocol, 10x Genomics). Briefly, Single cell partitioning, barcoding, and cDNA library generation was achieved using the 10X Genomics Chromium Controller with the Chromium Single Cell 3’ Reagents Kit (v2 chemistry) as described by 10X Genomics (https://support.10Xgenomics.com/single cell-gene-expression/index/doc/user-guide-chromium-single cell-3-reagent-kits-user-guide-v2-chemistry). The protocol was modified to achieve bacterial scRNA-seq. For GEM generation (10X microfluidic encapsulation), a master mix containing the following reagents (per rxn, not accounting for excess volume) was prepared: 33 µL of 4X ddPCR Multiplex Supermix (BioRad), 4 µL of custom primer (10 µM), 2.4 µL additive A (10X Genomics), 26.8 µL dH2O. All other reagents specified by 10X Genomics were omitted. Prepared cell samples were washed 3X in PBS and diluted to 1000 cells/µL before loading on the microfluidic chip (“Chip A Single Cell”) with a targeted cell recovery of 10,000 cells.

value: Bacterial cells in suspension

tag: strain

tag: age

value: Late log phase


title: Cp BHI replicate 3

description:
RNA hybridizing probes
10x Genomics


title: Cp BHI with acetate sample

description:
RNA hybridizing probes
10x Genomics


title: T3, Tail, WT; rep2

status: Public on Feb 03 2023

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
Raw read sequence were trimmed with cutadapt 3.2 to remove adapter sequence.
Trimmed reads were mapped to genome with STAR 2.7.7a.
Mapped reads were counted with featureCounts from subread 2.0.1.
Assembly: Xenopus_tropicalis (Xenbase v10.0)
Supplementary files format and content: featurecounts_by_gene_name.txt: Tab-delimited text file with read counts for each gene.

organism: Xenopus tropicalis

source_name: Tail

extract_protocol:
RNA was harvested using RNeasy® Mini Kit 250 (QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Wild-type and TRDKO tadpoles at stage 54 treated with or without 5 nM T3 at 25°C for 18 hours.

value: Tail

value: tadpoles at stage 54

value: WT

value: T3 treatment


title: T3, Tail, WT; rep3


title: Control, Tail, WT; rep2


title: T3, Tail, WT; rep1


title: Control, Tail, WT; rep3


title: T3, Tail, TRDKO; rep3

value: TRDKO


title: Control, Tail, WT; rep1


title: Control, Tail, TRDKO; rep1


title: Control, Tail, TRDKO; rep3


title: T3, Tail, TRDKO; rep1


title: +aTc TetR-PfGCN::GFP rep1

description: RNA-seq


title: Control, Intestine, WT; rep3

source_name: Intestine

value: Intestine


title: T3, Intestine, WT; rep3


title: T3, Intestine, TRDKO; rep3


title: T3, Intestine, WT; rep1


title: Control, Intestine, TRDKO; rep2


title: T3, Intestine, TRDKO; rep1


title: Control, Intestine, WT; rep2


title: Cp BHI replicate 1

description:
RNA hybridizing probes
10x Genomics


title: T3, Intestine, WT; rep2


title: Control, Intestine, WT; rep1


title: Control, Intestine, TRDKO; rep3


title: T3+_Liver_rep2

status: Public on Jan 31 2023

data_processing:
Adapter removal (cutadapt 3.4)
Short reads mapping (STAR 2.7.8a)
Assembly: Xenopus_tropicalis (Xenbase v10.0)
Supplementary files format and content: Tab-delimited text file for reads counts of each gene.

growth_protocol: Hepatic samples were collected from WT tadpoles which born from same parents.

extract_protocol:
Hepatic RNA was harvested by using RNeasy. One ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When tadpoles reached to stage 54, tadpoles were treated with 10nM T3 for 18 hours.

value: Liver

value: wild type

value: T3 treatment for 18 hours

tag: time

value: Stage 54


title: T3, Intestine, TRDKO; rep2


title: T3, Tail, TRDKO; rep2


title: Control, Tail, TRDKO; rep2


title: T3+_Liver_rep1


title: st66_Liver_rep3

value: Stage 66


title: st66_Liver_rep2


title: st66_Liver_rep1


title: st61_Liver_rep3

value: Stage 61


title: Control, Intestine, TRDKO; rep1


title: st61_Liver_rep2


title: st61_Liver_rep1


title: st54_Liver_rep3


title: st54_Liver_rep1


title: RNA-Seq HumanBrain_50um

status: Public on Jan 29 2023

city: New Haven

first: Di

last: Zhang

state: CT

address: 55 Prospect St

department: Biomedical Engineering

institute: Yale University

data_processing:
Two constant linker sequences (linker 1 and linker 2)  were used to filter Read 2, the Read 2 was refined to extract the Barcode A, Barcode B, and UMI. ST pipeline v1.7.2 was used to map the processed read 1 against the mouse genome (GRCm38), which created the gene matrix for downstream analysis. The gene expression matrix contains information of genes and spatial locations (barcode A x barcode B).
Assembly: Grch38
Supplementary files format and content: *tsv: Tab-delimited text files include counts for each pixels for each Sample.

source_name: Human hippocampus

extract_protocol: The fresh frozen tissue section was fixed with formaldehyde. The adapters loaded Tn5/pA-Tn5 transposition containing a ligation linker was inserted into transposase accessible genomic DNA loci. The biotin decorated poly-T primer with a ligation linker was added to capture the mRNA for reverse transcription. In situ ligation was conducted by introducing distinct spatial barcode Ai (i = 1-50/100) to the adapters through an array of lateral microchannels. Then, distinct spatial barcode Bj (j = 1-50/100) were introduced through the longitudinal microchannels. Barcodes A and B with linkers were ligated to the 5’ end of the Tn5//pA-Tn5 oligo separately during each ligation. The tissue can be spatially barcoded with a distinct combination of barcodes Ai and Bj (i = 1-50/100, j = 1-50/100, n of barcoded pixels = 2,500/10,000). To correlate the spatially chromatin accessibility, transcriptome, and tissue morphology, the tissue was imaged after each ligation. Reverse crosslinking was then performed to collect barcoded cDNA and DNA fragments. The streptavidin beads were used to separate DNA and cDNA fragments. The cDNA fragments can be enriched with streptavidin beads and the DNA fragment was left in the supernatant. After separation, the DNA and cDNA libraries were constructed separately during PCR amplification. NGS sequencing was then performed using a NovaSeq 6000 sequencer with pair-end 150 bp mode.

value: Human hippocampus

tag: spatial resolution

value: 50 um


title: ATAC-Seq HumanBrain_50um

data_processing:
Two constant linker sequences (linker 1 and linker 2) were used to filter Read 2, and the sequences were converted to Cell Ranger ATAC format (10x Genomics). The genome sequences were in the newly formed Read 1, barcodes A and barcodes B were included in newly formed Read 2. Human reference (GRCh38) or mouse reference (mm10) were used to align the fastq files. The achieved BED like fragments were used to conduct downstream analysis. The fragments file includes fragments information on spatial locations (barcode A x barcode B) and genome.
Assembly: Grch38
Supplementary files format and content: BED like fragments file for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).

extract_protocol: The fresh frozen tissue section was fixed with formaldehyde. The adapters loaded Tn5 transposition containing a ligation linker was inserted into transposase accessible genomic DNA loci. The biotin decorated poly-T primer with a ligation linker was added to capture the mRNA for reverse transcription. In situ ligation was conducted by introducing distinct spatial barcode Ai (i = 1-50/100) to the adapters through an array of lateral microchannels. Then, distinct spatial barcode Bj (j = 1-50/100) were introduced through the longitudinal microchannels. Barcodes A and B with linkers were ligated to the 5’ end of the Tn5 oligo separately during each ligation. The tissue can be spatially barcoded with a distinct combination of barcodes Ai and Bj (i = 1-50/100, j = 1-50/100, n of barcoded pixels = 2,500/10,000). To correlate the spatially chromatin accessibility, transcriptome, and tissue morphology, the tissue was imaged after each ligation. Reverse crosslinking was then performed to collect barcoded cDNA and DNA fragments. The streptavidin beads were used to separate DNA and cDNA fragments. The cDNA fragments can be enriched with streptavidin beads and the DNA fragment was left in the supernatant. After separation, the DNA and cDNA libraries were constructed separately during PCR amplification. NGS sequencing was then performed using a NovaSeq 6000 sequencer with pair-end 150 bp mode.


title: Wildtype #3 E13.5 Anterior Palate

status: Public on Jan 24 2023

city: Aurora

first: Emily

middle: Anne

last: Bates

state: CO

institute: University of Colorado Anschutz Medical Campus

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Data was normalized using Single Cell Transform v0.3.2 (https://github.com/satijalab/sctransform) and analyzed with Seurat v4.0.4 (https://satijalab.org/seurat/)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Anterior Palate

extract_protocol:
In ice-cold PBS, heads were removed from embryos. The top of the head was cut flat, and the head was laid ventral. The secondary palate was exposed by removing the mandible and tongue. The anterior 1/3 of the palate was dissected away from the remainder of the head using forceps. Paired anterior palatal shelves were washed twice in PBS and transferred to 750 uL 0.25% Trypsin-EDTA for 10 minutes at 37C with frequent trituration. Trypsinization was stopped with addition of 750uL DMEM + 10% FBS . Cells were pipetted up and down 20 times to assist in cell dispersion, pelleted at 300 g for 3 min, and resuspended in PBS with 0.1% BSA before being filtered through a Flowmi 40uM cell strainer. Single cell suspensions were confirmed by microscopy and cells were counted on a hemocytometer with trypan blue staining.
Chromium single cell 3’ NextGen V3.1 chemistry (10X Genomics)

value: Anterior Palate

value: Wildtype


title: +aTc TetR-PfGCN::GFP L-Glu rep1

description: RNA-seq

value: wildtype

value: Ring stage

value: low-glucose (L-Glu)


title: Wildtype #1 E13.5 Anterior Palate

description: 10X Genomics


title: Purified Cardiomyocyte-P42_rep2

status: Public on Jan 19 2023

first: Pingzhu

last: Zhou

address: 320 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

data_processing:
Raw sequencing reads were mapped to mm10 by hichip pipleline.
Interactions were extracted from bam files by hichipper.
Loop differential analysis and filtering were implemented by diffloop.
Assembly: mm10

source_name: Heart

extract_protocol:
About 2 M cardiomyocytes were crosslinked with 2% formaldehyde for 10 min at room temperature. Crosslinked chromatin was digested using a proprietary restriction enzyme cocktail. The fragmented chromatin ends were then filled in with a biotinylated nucleotide. Spatially proximal fragmented ends were ligated. Subsequently, chromatin was fragmented using a QSonica Q800R3 sonicator and incubated with H3K27ac antibody (Catalog No: 39133, Active Motif) at 4 °C overnight. The antibody-bound chromatin was immunoprecipitated using Protein A magnetic beads (Invitrogen) and reverse crosslinked using Arima-HiC+ kit reagents.
H3K27ac HiChIP libraries were prepared using the Arima HiC+ kit (Arima Genomics). Sequencing adapters and indexing primers were added using the Swift Biosciences Accel-NGS 2S Plus DNA Library Kit. The libraries were quantified to determine the appropriate number of PCR cycles needed for library amplification using the KAPA Library Quantification Kit (Roche) and then amplified using the KAPA Library Amplification Kit (Roche).

treatment_protocol: For E12.5 and P0 CMs, ventricular apexes were dissociated using the Neonatal mouse cardiomyocyte isolation kit (Cellutron Life Technologies) and purified using the mouse neonatal cardiomyocyte isolation kit (Miltenyi). P42 CMs were dissociated and purified from ventricular apexes by Langendorf collagenase perfusion followed by differential sedimentation.


title: Purified Cardiomyocyte-E12.5_rep2


title: Purified Cardiomyocyte-P42_rep1


title: 197771: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+)

status: Public on Jan 15 2023

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
VDJ-Seq: The bioinformatic analysis of the VDJ-seq data was performed as described in detail in Chovanec et al., Nat. Protoc. 13, 2018. using the BabrahamLinkON pipeline: (1) preclean.py (default parameters), Includes trimming and alignment steps (BabrahamLinkOn pipeline) deduplicate.py (default parameters), based on UMI  (BabrahamLinkOn pipeline) (2) assemble_clones.py (default parameters)  (BabrahamLinkOn pipeline) (3) The resulting counts were summarized using customized scripts based on the statistical language R version 3.3.3. The relative usage of each VH gene is shown as percentage of all VDJH recombination events determined.
Hi-C Seq:  The HiCUP pipeline version 0.5.10 with the scorediff parameter set to "10" was used to truncate, align and filter the reads by applying the following software versions: R 3.4.1, Bowtie 2.2.9 (26) and SAMtools 1.4 (37). Contact matrix files have been produced with Juicer tools 1.8.9.
MicroC-Seq: The open2c distiller-nf pipeline [https://github.com/open2c/distiller-nf] was used to process Micro-C datasets.  The underlying methods are all based on the pairtools (https://github.com/open2c/pairtools) and cooler (Abdennur and Mirny, 2020).
ChIP-Seq: Sequence reads were uniquely aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 1.0. Peaks were called using Macs version 2.2.5 using GSE210289 as control track, and filtered for fold change > 5.
Assembly: mm9 , mm10.
Supplementary files format and content: txt: VDJ-Seq counts. Hic: HiC-Seq normalized interaction matrix, cool: MicroC-Seq normalized interaction matrix, bedGraph: ChIP-Seq read density, bed: Browser Extensible Data format
Library strategy: VDJ-Seq

source_name: bone marrow

extract_protocol:
Ex-vivo FACS sorted from bone marrow
VDJ-Seq: Comparison of VDJ arrangements in the Igk and Igh loci. The comparison is done between wildtype (Wapl(+/+)) and mutant (Wapl(deltaP1,2/deltaP1,2) for pro-B and pre-B samples, Immature B cells (Igh locus) samples are not used for a direct comparis
HiC-Seq: Hi-C libraries were prepared as described in Rao et al., 2014
MicroC-Seq: Micro-C libraries were prepared as described in Hsieh et al., 2020, from 1 × 106 cells using the Dovetail Micro-C Kit (# 21006) according to the manufacturer’s user manual.
ChIP-Seq: ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

value: Immature B cells

tag: cell preparation

value: Ex-vivo FACS sorted from bone marrow


title: 197769: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+)


title: 197774: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+)


title: st54_Liver_rep2

source_name: Liver


title: 70490: Igk VDJ-Seq Pre-B cell Wapl(∆P1,2/∆P1,2)

value: Pre-B cell


title: 197772: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+)


title: 197770: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+)


title: 161420: Igk VDJ-Seq Pre-B cell Wapl(∆P1,2/∆P1,2)


title: 197768: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+)


title: Wildtype #2 E13.5 Anterior Palate

description: 10X Genomics


title: 197767: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+)


title: 161418: Igk VDJ-Seq Pre-B cell Wapl(+/+)


title: T3+_Liver_rep3

value: Liver


title: 161417: Igk VDJ-Seq Pre-B cell Wapl(+/+)


title: 161416: Igk VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2)

value: Pro-B cell


title: 70488: Igk VDJ-Seq Pre-B cell Wapl(+/+)


title: 161419: Igk VDJ-Seq Pre-B cell Wapl(∆P1,2/∆P1,2)


title: Purified Cardiomyocyte-E12.5_rep1


title: 82657: Igk VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2)


title: 82656: Igk VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2)


title: 161415: Igk VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2)


title: 161414: Igk VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2)


title: 82658: Igk VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2)


title: 197773: Igh VDJ-Seq Immature B cells Igh(B1.8hi/+)


title: 70489: Igk VDJ-Seq Pre-B cell Wapl(∆P1,2/∆P1,2)


title: 161413: Igk VDJ-Seq Pro-B cell Wapl(+/+)


title: 161412: Igk VDJ-Seq Pro-B cell Wapl(+/+)


title: 21476: H3K27ac ChIP-Seq Pro-B cell Rag1(Cre/Cre)

data_processing:
VDJ-Seq: The bioinformatic analysis of the VDJ-seq data was performed as described in detail in Chovanec et al., Nat. Protoc. 13, 2018. using the BabrahamLinkON pipeline: (1) preclean.py (default parameters), Includes trimming and alignment steps (BabrahamLinkOn pipeline) deduplicate.py (default parameters), based on UMI  (BabrahamLinkOn pipeline) (2) assemble_clones.py (default parameters)  (BabrahamLinkOn pipeline) (3) The resulting counts were summarized using customized scripts based on the statistical language R version 3.3.3. The relative usage of each VH gene is shown as percentage of all VDJH recombination events determined.
Hi-C Seq:  The HiCUP pipeline version 0.5.10 with the scorediff parameter set to "10" was used to truncate, align and filter the reads by applying the following software versions: R 3.4.1, Bowtie 2.2.9 (26) and SAMtools 1.4 (37). Contact matrix files have been produced with Juicer tools 1.8.9.
MicroC-Seq: The open2c distiller-nf pipeline [https://github.com/open2c/distiller-nf] was used to process Micro-C datasets.  The underlying methods are all based on the pairtools (https://github.com/open2c/pairtools) and cooler (Abdennur and Mirny, 2020).
ChIP-Seq: Sequence reads were uniquely aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 1.0. Peaks were called using Macs version 2.2.5 using GSE210289 as control track, and filtered for fold change > 5.
Assembly: mm9 , mm10.
Supplementary files format and content: txt: VDJ-Seq counts. Hic: HiC-Seq normalized interaction matrix, cool: MicroC-Seq normalized interaction matrix, bedGraph: ChIP-Seq read density, bed: Browser Extensible Data format

value: Abcam H3K27ac Ab


title: 161411: Igk VDJ-Seq Pro-B cell Wapl(+/+)


title: 82654: Igk VDJ-Seq Pro-B cell Wapl(+/+)


title: 70487: Igk VDJ-Seq Pre-B cell Wapl(+/+)


title: 82655: Igk VDJ-Seq Pro-B cell Wapl(+/+)


title: 180000: HiC-Seq Pre-B cell Igh(B1.8hi/+) Rag2(-/-)


title: 131385: HiC-Seq Pre-B cell Wapl(∆P1,2/∆P1,2)


title: 163564: HiC-Seq Pre-B cell Wapl(∆P1,2/∆P1,2)


title: 180017: Micro-C Seq Pro-B cell Rag2(-/-)

data_processing:
VDJ-Seq: The bioinformatic analysis of the VDJ-seq data was performed as described in detail in Chovanec et al., Nat. Protoc. 13, 2018. using the BabrahamLinkON pipeline: (1) preclean.py (default parameters), Includes trimming and alignment steps (BabrahamLinkOn pipeline) deduplicate.py (default parameters), based on UMI  (BabrahamLinkOn pipeline) (2) assemble_clones.py (default parameters)  (BabrahamLinkOn pipeline) (3) The resulting counts were summarized using customized scripts based on the statistical language R version 3.3.3. The relative usage of each VH gene is shown as percentage of all VDJH recombination events determined.
Hi-C Seq:  The HiCUP pipeline version 0.5.10 with the scorediff parameter set to "10" was used to truncate, align and filter the reads by applying the following software versions: R 3.4.1, Bowtie 2.2.9 (26) and SAMtools 1.4 (37). Contact matrix files have been produced with Juicer tools 1.8.9.
MicroC-Seq: The open2c distiller-nf pipeline [https://github.com/open2c/distiller-nf] was used to process Micro-C datasets.  The underlying methods are all based on the pairtools (https://github.com/open2c/pairtools) and cooler (Abdennur and Mirny, 2020).
ChIP-Seq: Sequence reads were uniquely aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 1.0. Peaks were called using Macs version 2.2.5 using GSE210289 as control track, and filtered for fold change > 5.
Assembly: mm9 , mm10.
Supplementary files format and content: txt: VDJ-Seq counts. Hic: HiC-Seq normalized interaction matrix, cool: MicroC-Seq normalized interaction matrix, bedGraph: ChIP-Seq read density, bed: Browser Extensible Data format
Library strategy: MicroC-Seq


title: 180018: Micro-C Seq Pre-B cell Igh(B1.8hi/+) Rag2(-/-)


title: FR_3

status: Public on Jan 12 2023

city: Berkeley

first: Iain

middle: Christopher

last: Clark

address: 374 Stanley Hall

institute: University of California, Berkeley

description: Patient 35, replicate 1

data_processing:
The sample is aligned to human GRCh38.p13 with Salmon and quantified with alevin v1.2.0
Assembly: GRCh38.p13
Supplementary files format and content: Filtered gene expression matrices for Patients A & B, samples 1 & 2 were generated following alignment of paired-end fastqs using Salmon alevin. Background barcodes were excluded from the gene expression matrices.

source_name: Human breast tissue

extract_protocol:
Fresh reduction mammoplasty tissue was processed according to Murrow et al (2020) doi: https://doi.org/10.1101/430611
Libraries were prepared using Fluent BioSciences' PIPseq single-cell RNA-sequencing kit.

value: Breast tissue


title: 82653: Igk VDJ-Seq Pro-B cell Wapl(+/+)


title: FR_2

description: Patient 34, replicate 2


title: FR_4

description: Patient 35, replicate 2


title: 163563: HiC-Seq Pre-B cell Wapl(+/+)


title: CROP-seq RNA + sgRNA

description: immortalized myelogenous leukemia cel line

data_processing:
The sample is aligned to human GRCh38.p13 with Salmon and quantified with alevin v1.2.0 using an index modified to include the guide RNAs. sgRNA calling was performed according to Datinger et al. Nature Biotechnology
Assembly: GRCh38.p13
Supplementary files format and content: The filtered matrix consists of a zipped folder with 3 files: (1) sparse matrix, (2) barcodes file, (3) genes file. sgRNA counts have been pre-merged with the gene expression (GEX) counts. sgRNA counts can be isolated from using the GEX counts by subsetting feature names containing the following distinct patterns: "_-_", "_+_", or "neg_ctrl".  Raw data are gzipped fastqs, with 1 file per read for both the original gene expression sample and the derived sgRNA library for a total of 4 files.

source_name: lymphoblasts

growth_protocol: RPMI-1640 (Gibco #11875093) with 10% FBS (Thermo Fisher Scientific, #10438026) and 1% penicillin/streptomycin (Thermo Fisher Scientific, #15140148) in an incubator at 37C with 5% CO2

extract_protocol:
PIP-seq
PIP-seq + sgRNA recovery
PIP-seq + separate sgRNA library preparation

treatment_protocol: K562 CRISPRi cells were transduced with a lentivirus library containing 138 sgRNA32 at a multiplicity of infection of 0.1.

value: K-562 cells

tag: Sex

value: Female


title: FR_1

description: Patient 34, replicate 1


title: HEK P2R 3

status: Public on Jan 01 2023

city: Riverside

first: Fedor

last: Karginov

state: California

address: 900 University Ave

department: MCSB

institute: UC Riverside

data_processing:
reads were aligned to the GRCh38 genome assembly using HISAT2 and annotated with Gencode v40 annotations. Differentially expressed genes were identified using DESeq2
Assembly: GRCh38
Supplementary files format and content: comma-separated value files with per-gene results of DESeq2 analysis of PDKO vs WT comparisons, and rescue vs PDKO comparisons for T-Rex-293 cells
Supplementary files format and content: comma-separated value file with raw read counts per gene for every sample

growth_protocol: T-REx-293 cells were grown in DMEM (Corning) with 10% fetal bovine serum (Corning) and 10 units/mL of penicillin/streptomycin (Gibco) at 37°C with 5% CO2. HCT116 cells were grown in McCoy's 5A (Iwakata & Grace Modification) media (Corning) with 10% fetal bovine serum (Corning) and 10 units/mL of penicillin/streptomycin (Gibco) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted with Ribozol
libraries were prepared using the NEB mRNA magnetic isolation module (E7490S), NEBNext Ultra RNA Library prep kit (E7420L), and NEB Multiplex Oligos for Illumina Index Primer Sets 1 (E7335S) and 2 (E75500S)


title: HEK P1R 3


title: HCT WT 3

value: WT


title: HCT PDKO 3

value: PDKO


title: HCT PDKO 2


title: HEK WT 3


title: HEK PDKO 3


title: HEK GFP 3

value: GFPR


title: HCT WT 2


title: 131384: HiC-Seq Pre-B cell Wapl(+/+)


title: HEK PDKO 2


title: HEK GFP 2


title: HEK P1R 2


title: HEK P2R 2


title: HEK P2R 1


title: HCT WT 1


title: HEK GFP 1


title: HEK PDKO 1


title: HCT PDKO 1


title: HEK P1R 1


title: Hp10 biol rep 3

city: chongqing

first: ruoyi

last: xue

address: GaoTanYan street

institute: unknown

data_processing:
The original image data file obtained by Illumina HiseqTM was analyzed and converted into the original sequencing sequence by CASAVA Base Calling
Trimmomatic was used for data processing
HISAT2 was used to compare the sequencing sequence after quality control with the reference genome
RSeQC was used to calculate the comparison results.
StringTie and known gene models were used to evaluate gene expression.
Assembly: 10000 sequences were randomly selected from Clean data for blastn comparison with NCBI NT database
Supplementary files format and content: TPM values for each Sample

extract_protocol:
BMDCs were co-incubated with PBS, Hp4 or Hp10 for 48 hours, and 1ml Trizol was added to each well for re-suspension before collection.
RNA-seq library was generated and sequenced by Shanghai Sangon.

value: BMDC

value: Bone marrow-derived dendritic cells

value: Hp10 treatment


title: Hp4 biol rep 3

value: Hp4 treatment


title: Hp4 biol rep 1

value: bone marrow


title: HEK WT 1


title: Hp10 biol rep 1


title: PBS biol rep 1

value: PBS treatment


title: PBS biol rep 3


title: Hp4 biol rep 2


title: C4-2B-Abi_S12

city: Cleveland

first: Shiv

last: Verma

state: Ohio

address: 10900 Euclid Avenue, 2

department: Urology

institute: Case Western Reserve University

description: THIS SUBMISSION IS LACKING RAW DATA BECAUSE SUBMITTER FAILED TO COMPLY WITH GEO REQUIREMENTS

data_processing: Sequencing reads generated were assessed for quality using FastQC. The library preps and sequencing were performed in the Genomics Core Facility at Case Western Reserve University. Differential expression was determined using Cufflinks v2.2.1. Differentially expressed genes (DEGs) were identified using a multiple testing corrected q-value < 0.05.

source_name: bone metastasis

growth_protocol: The C42-B parent cell lines and C42-B-Abi (resistance) cell lines were cultured in RPMI-1640 media, containing 10%FBS. The cell lines were maintained in a 5% CO2 atmosphere at 37 °C.

extract_protocol:
Total RNA was extracted from C42-B parental and C42-B-Abi (resistance) cells treated with Abiraterone (10uM), using RNA RNeasy kit (Qiagen).
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.
The quality of total RNA integrity (RIN) was assessed using an RNA 6000 nanochip (Agilent technologies, Lexington, MA) on a Bioanalyzer 2100 (Agilent Technologies). Libraries were prepared using the Illumina TruSeq Stranded Total RNA sample preparation kit according to the manufacturer’s protocol. 50 bp single-end sequencing was performed on pooled libraries using an Illumina HiSeq 2500 platform.

treatment_protocol: C42-B  cells were recurrently exposed to increasing concentrations of Abiraterone (1-20μM) by a passage in a complete cell culture medium containing Abiraterone. In each concentration of Abiraterone, the cells were grown in RPMI 1640 (GE Healthcare) for a week allowing them to acclimatize and propagate for a minimum of six months. The resistant cells generated from 20 µM Abiraterone were maintained in media containing 5 µM Abiraterone, defined here as  C42BP Abiraterone-resistant cells.

value: Human prostate cancer cell line derived from subcutaneous LNCaP xenografts in castrated nude mice

tag: passages

tag: cell subtype

value: Derivative subline of human prostate cancer LNCaP-derived C4-2 cells.


title: C4-2B-V1-4_S10

tag: cell type


title: C4-2B-Abi_S11


title: PBS biol rep 2


title: BT549 cells, GATA 2

city: Nanjing

first: Zhen

last: Zhu

address: 101Longmian Avenue

institute: Nanjing medical university

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp)[1] with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)[2] software.
The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/) in a reference-based approach
Supplementary files format and content: Text files include FPKM values for each Sample

source_name: mammary epithelial cells

growth_protocol: HCC1806 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol (Thermo Fisher). 1 ug of total RNA was used for the construction of sequencing libraries.
The ranscriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.

value: mammary epithelial cells

value: breast cancer cell line

value: GATA3 overexpression


title: C4-2B-Abi-4_S10


title: C4-2B-V2_S11


title: BT549 cells, GATA 1


title: C4-2B-V3_S12


title: BT549 cells, GATA 3


title: BT549 cells, CTL 3

value: control vector  overexpression


title: Hp10 biol rep 2


title: BT549 cells, CTL 2


title: BT549 cells, CTL 1


title: BALB/c, mouse lung, MA10 infected, vehicle, DPI4, rep4

status: Public on Dec 27 2022

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

data_processing:
CLC Genomics Workbench v12.0.3
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to either Mus_musculus.GRCm38.100 or Mus_musculus_balbcj.BALB_cJ_v1.100 using standard parameters.
Read counts extraction was performed using CLC Genomics Workbench.
Assembly: Mus_musculus.GRCm38.100 or Mus_musculus_balbcj.BALB_cJ_v1.100
Supplementary files format and content: tab-delimited text files include raw counts for each strain

source_name: lung

extract_protocol:
RNA was extracted from inferior lung lobes using TRIzol Reagent (ThermoFisher Scientific), precipitated overnight at -20 C overnight, and quantified using a NanoDrop (ThermoFisher Scientific). NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (New England Biolabs Inc.) was used to remove ribosomal RNA from 1000 ng total extracted RNA.RNA was harvested using Trizol (Illumina). 1 ug of total RNA was used in library construction.
RNA libraries were prepared using NEBNext Ultra II Directional Library Prep Kits following manufacturers protocol.

treatment_protocol:
Mice were lightly sedated with 50 mg/kg ketamine and 15 mg/kg xylazine and intranasally inoculated with 10E4 pfu of SARS-CoV-2-MA10.
Starting 1 day post infection (DPI) mice were administered vehicle (0.5% methylcellulose + 0.025% Tween + 2.5% DMSO) twice a day by oral gavage. Mice were euthanized by isoflurane overdose and lung tissues were collected.

value: BALB/c

value: lung

tag: virus

value: 10E4 pfu SARS-CoV-2-MA10

tag: dpi (day)


title: C57BL/6, mouse lung, uninfected, vehicle, rep3

tag: tissue

value: WT

value: no

value: vehicle (0.5% methylcellulose + 0.025% Tween + 2.5% DMSO)


title: BALB/c, mouse lung, MA10 infected, vehicle, DPI4, rep2


title: BALB/c, mouse lung, MA10 infected, vehicle, DPI4, rep1


title: C57BL/6, mouse lung, MA10 infected, vehicle, DPI4, rep4


title: C57BL/6, mouse lung, MA10 infected, vehicle, DPI4, rep3


title: C57BL/6, mouse lung, uninfected, vehicle, rep2


title: BALB/c, mouse lung, uninfected, vehicle, rep2


title: BALB/c, mouse lung, uninfected, vehicle, rep3


title: C57BL/6, mouse lung, MA10 infected, vehicle, DPI4, rep2


title: C57BL/6, mouse lung, uninfected, vehicle, rep4


title: HEK WT 2


title: C57BL/6, mouse lung, MA10 infected, vehicle, DPI4, rep1


title: JY10772

status: Public on Dec 05 2022

city: Houston

first: Maria

last: Szwarc

address: One Baylor Plaza

institute: Baylor College of MEdicine

data_processing:
The pair-ended reads were mapped to the mouse genome using STAR (Dobin et al., 2013) with NCBI RefSeq genes as the reference. STAR generated read count for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: columns with counts for each sample (JY10337; JY10516; JY10772; JY10338; JY10767; JY10769) and with gene descriptors (EntrezGene; symbol; Description; Description2)

source_name: thymus

extract_protocol:
Total RNA was extracted from thymus tissues using TRIzol reagent (ThermoFisher Scientific) and further purified with the RNeasy Plus Mini Kit (Qiagen). RNA purity was evaluated with a NanoDrop spectrophotometer (ThermoFisher Scientific) and RNA integrity was determined using a 2100 Bioanalyzer with RNA chips (Agilent Technologies).
Libraries for mRNA sequencing were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina) from 250 ng of RNA. Quality analysis of libraries was performed using Agilent 4200 TapeStation with D1000 ScreenTape assays (Agilent Technologies). Libraries were pooled and then quantified by two methods: 1) on a 2100 Bioanalyzer with DNA chips using High Sensitivity DNA Kit (Agilent Technologies); and 2) with KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems).

treatment_protocol: Control and K5-rtTA:TetO-RANKL mice were administered doxycycline (in food and water) at 9-weeks of age for two weeks to induce transgenic RANKL expression.

value: thymus

value: control


title: NGS02466

status: Public on Dec 01 2022

first: Julie

middle: E

last: Niemela

address: 10 Center Dr.

department: Dept. of Lab. Medicine

institute: NIH Clinical center

data_processing:
Demultiplexed reads were mapped to the hg19 genome using the splice-aware aligner Tophat (Trapnell et al., 2009)
Read counts were variance stabilized (normalized) using DeSeq2
Assembly: Homo sapiens (human) genome assembly GRCh37 (hg19)
Supplementary files format and content: File with raw counts for every gene and every sample

source_name: Blood

extract_protocol:
AmpliSeq for Illumina Transcriptome Human Gene Expression panel
Targeted Sequencing Library (>20,000 human RefSeq genes)

value: CD4+ T-cell blasts

value: TCF3 wild-type / TCF3 G486Lfs*4 (Null)

tag: disease state

value: affected


title: C57BL/6, mouse lung, uninfected, vehicle, rep1

tag: genotype


title: NGS02469

value: TCF3 wild-type / TCF3 S514X (HI)


title: BALB/c, mouse lung, MA10 infected, vehicle, DPI4, rep3


title: JY10769