title: HCT116-siPUS7-mRNA-seq-rp1

description:
Library name: HCT116-mRNA-seq-7
HCT116-siPUS7_VS_siCtrl-mRNA-seq.DEresults.xlsx

tag: genotype


title: 15533006, CD4+ T cells, asthma case

status: Public on Sep 09 2025

type: SRA

city: Aurora

first: Randi

middle: K

last: Johnson

state: Colorado

address: 1890 N. Revere Court

country: USA

institute: University of Colorado

description: Library name: 15533006

library_source: transcriptomic

data_processing:
CoCo was used to adjust the Ensembl annotation file for alignment and assembly.
FastQC was used to detect technical issues, then adapter trimming was performed using BBDuk.
FastQC was then run again to confirm trimming was successful. HISAT2 was used for alignment to GRCh38 using the default options.
Sorting and flagging of reads was performed using SAMtools prior to transcript assembly with StringTie and applying the CoCo correct_count function using the corrected Ensembl annotation file to account for overlapping genes and multi-mapping reads.
Raw counts were converted to transcripts per million (TPM) values for each gene and each sample.
Within-sample TPM distributions were used to detect and exclude samples where data generation was not successful. Additional sample-level metrics such as ribosomal contamination were calculated using Picard CollectRnaSeqMetrics. Transcripts with inadequate variability for detection of differential expression were filtered using the DESeq2 theta value. The DESeq2 varianceStabilizingTransformation function was used to transform the count data (normalized by division by the size factors or normalization factors), to be approximately homoscedastic and normalized with respect to library size.
Technical variability present in the cleaned and transformed TPM values due to sequencing batch was removed with the removeBatchEffect function in limma.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes transformed, batch-adjusted TPM values

molecule: total RNA

organism: Homo sapiens

source_name: CD4+ T cells

extract_protocol:
CD4+ T helper cells were isolated from PBMCs by negative selection using magnetic depletion of non-target cells (CD4 + T Cell Isolation Kit, Miltenyi Biotec Inc) and then lysed immediately. RNA and DNA were extracted at the same time (AllPrep protocol, Qiagen Inc).
Libraries were prepared using the TruSeq total RNA Ribo Zero kit (Illumina Inc) and sequenced on the HISEQ 4000 using 151bp paired-end reads.

tag: tissue

value: CD4+ T cells

tag: cell type

tag: age

tag: Sex

value: male

tag: genetic pc1

tag: asthma

value: case

tag: geo loc_name

value: Barbados


title: MCD52

city: HANGZHOU

first: junxia

last: min

state: zhejiang province

address: zhejiang university zijingang campus medcine school research building C155

department: school of medicine

country: China

institute: zhejiang university

library_source: genomic

data_processing:
RNA-seq reads were mapped to the mouse reference genome using TopHat.
For sequencing read alignment, a set of possible 17- and 18-bp tags was created from all CCGG sites in the Mus musculus genome assembly; Only uniquely aligned reads were used for gene and exon quantification.
The locations of the CCGG sites were annotated as the gene promoter (-2000 to -1 bp), coding sequence (CDS), exon, intron, 5’ UTR, 3’ UTR, or intergenic region.
The Cufflinks tool was used to quantify isoform expression. Differentially methylated sites were analyzed using a one-way ANOVA (R package) and mapped to signaling pathways using the KEGG pathway mapping tool.
Assembly: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: mice tissue

extract_protocol:
For RNA sequencing, mice livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® （NR604-01/02）following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Where indicated, 8-weeks-old male control mice and Slc7a11-LTG mice were fed MCD for 1week (Research Diets, A02082002BR) ,isolated mice liver and extracted RNA.

value: liver


title: blood, day 19, group 6 #9

city: shimogyo-ku

first: Tomohiro

last: Sensui

address: chudoji, awatacho

country: Japan

institute: Maruho

description: Library name: PR3287_119_b

data_processing:
rRNA was filtered using RiboPicker, and mapped to the mouse genome GRCm39 using the DRAGEN Bio-IT Platform (Illumina).
Assembly: GRCm39
Supplementary files format and content: txt file including raw counts for each sample
Supplementary files format and content: txt file including TPM for each sample

source_name: whole blood

extract_protocol:
Blood samples were collected from the tail vein (approximately 0.1 mL) using EDTA-2K-coated capillary tubes without anesthesia. Total RNA was isolated from blood using a NucleoSpin RNA Blood Kit (Macherey-Nagel, Easton, PA, USA), according to the manufacturer’s instructions.
Libraries were prepared using TruSeq Stranded Total RNA with RiboZero Globin (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: whole blood

tag: strain

value: NC/Nga

value: WT

tag: condition

value: conventional

tag: group

value: group 6

tag: dermatitis score

tag: time

value: day 19


title: blood, day 19, group 6 #10

description: Library name: PR3287_120_b


title: 15532001, CD4+ T cells, asthma case

description: Library name: 15532001

value: female


title: 15528001, CD4+ T cells, asthma case

description: Library name: 15528001


title: MCD50


title: MCD49


title: blood, day 19, group 6 #8

description: Library name: PR3287_118_b


title: HCT116-si7SK-mRNA-seq-rp1

city: Chicago

first: Chuan

last: He

state: IL

address: 929 E 57th St

department: Chemistry Department

institute: University of Chicago

description:
Library name: HCT116-mRNA-seq-4
HCT116-si7SK_VS_siCtrl-mRNA-seq.DEresults.xlsx

data_processing:
The code for sequencing data analysis has been publicly available on GitHub (https://github.com/YutaoZhao1224/PUS7-project). BID-seq: Only R1 reads of paired-end reads were processed for BID-seq data analysis. R1 was trimmed by cutadapt (version 4.8) with following parameters “-a ATCACGAGATCGGAAGAGCA -g TTCTACAGTCCGACGATC -e 0.1 -q 20 -m 32 -n 3 -O 8” to remove adaptors and low-quality reads. PCR duplicates were removed with BBMap tool (v.38.73.). 5-mer random barcodes at reads ends were trimmed by cutadapt (version 4.8). Remaining reads were aligned to hg38 by STAR mapping software (2.7.11b). The generated bam file was sorted by samtools (1.21) and subjected to samtools mpileup for searching deletion signature. The Ψ candidate needs to satisfy the following criteria:  1) deletion ratio above 0.05 (with deletion count above four) in bisulfite-treated library; 2) deletion ratio below 0.02 in input libraries; 3) total read coverage depth above 20 for bisulfite-treated and input libraries; 4) all deletion signatures must be from ‘U’ sites marked by hg38; 5) all deletion signatures should be identified in each biological replicates. The differentially regulated Ψ sites were identified by two-tailed Student’s t-test (p < 0.05).  PAR-CLIP:  Only R1 reads of paired-end reads were processed for PAR-CLIP data analysis. R1 was trimmed by cutadapt (version 4.8) with following parameters -a ATCACGAGATCGGAAGAGCA -g TTCTACAGTCCGACGATC -e 0.1 -q 20 -m 32 -n 3 -O 8” to remove adaptors and low-quality reads. PCR duplicates were removed with BBMap tool (v.38.73.). 5-mer random barcodes at reads ends were trimmed by cutadapt (version 4.8). Remaining reads were aligned to hg38 by bowtie2 mapping software (2.4.4). The aligned sam files were subjected to PARalyzer (v1.5) for peak identification. The parameters in the “.ini” file used as the input for PARazyler are as follows: BANDWIDTH=3 CONVERSION=T>C MINIMUM_READ_COUNT_PER_GROUP=5 MINIMUM_READ_COUNT_PER_CLUSTER=2 MINIMUM_READ_COUNT_FOR_KDE=3 MINIMUM_CLUSTER_SIZE=11 MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=2 MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=2 MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=1 MINIMUM_READ_LENGTH=20 MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=1  KAS-seq: The paired-end reads were trimmed by cutadapt (version 4.8) with following parameters “-a AGATCGGAAGAGCACACGTCTG -A AGATCGGAAGAGCGTCGTGT -n 3 --pair-filter=any -n 3 -O 8” to remove adaptors and low-quality reads. PCR duplicates were removed with BBMap tool (v.38.73). Remaining reads were aligned to hg38 by bowtie2 mapping software (2.4.4). The sorted bam files were converted to bigwig files by bamCoverage (deeptools 3.5.5). The peaks were identified by macs2 (version 2.2.6) and visualized by IGV (version 11.0.13). The read coverage on promoter (from TSS-100 to TSS+300 bp) and genebody (from TSS+300 to TSS+2000 bp) was calculated by bedtools coverage (v2.30.0). The Pol II release ratio was calculated as read coverage of genebody over promoter. Those genes with promoter read coverage less than 20 were discarded for data analysis.  mRNA-seq: The paired-end reads were trimmed by cutadapt (version 4.8) with following parameters “-a AGATCGGAAGAGCACACGTCTG -A AGATCGGAAGAGCGTCGTGT -e 0.15 -q 20 --nextseq-trim=20 -O 6 -n 3 --pair-filter=any” to remove adaptors and low-quality reads. PCR duplicates were removed with BBMap tool (v.38.73). Remaining reads were aligned to hg38 by STAR mapping software (2.7.11b). The generated bam file was sorted by samtools (version 1.21). FeatureCounts software (version 2.0.3) was used to count reads mapped to protein-coding genes from hg38, and differentially expressed gene analysis was conducted by DEseq2 software. Differentially expressed genes were identified with cutoff p < 0.01, |log2FC|≥1.
Assembly: hg38
Supplementary files format and content: "HCT116-siPUS7_VS_siCtrl_BID-seq.xlsx" shows the pseudorudine profile changes on nucleus RNA by BID-seq; "HCT116_PARclip_1.bed" and "HCT116_PARclip_2.bed" are bed files for PUS7 binding RNA peaks; "HCT116-KAS-seq-PRR.values.xlsx" shows "pol II release ratio" for each gene in PUS7 KD, 7SK KD and control groups; All bigwig files show the genomic coverage of KAS-seq in PUS7 KD, 7SK KD and control groups; "HCT116-si7SK_VS_siCtrl-mRNA-seq.DEresults.xlsx" and "HCT116-siPUS7_VS_siCtrl-mRNA-seq.DEresults.xlsx" show mRNA expression level change after 7SK KD or PUS7 KD, respectively.

molecule: polyA RNA

source_name: Colon tissue

growth_protocol: HCT116 cells were grown in RPMI-1640, with 10% FBS and 1% penicillin-streptomycin. Cells were maintained at 37°C with 5% CO2.

extract_protocol:
RNA was isolated using Trizol method and precipitated using ethanol.
BID-seq for nucleus RNA: Nucleus fraction was isolated based on cell fractionation protocol. Nucleus RNA was purified by TRIzol reagent (Invitrogen) and ethanol precipitation. rRNA was further removed from Nucleus RNA by RiboMinus™ Eukaryote System v2 (Invitrogen). 50 ng nucleus RNA from PUS7KD and control HCT116 cells were used for BID-seq. The BID-seq was performed as previously described. 3 biological replicates were used for both the PUS7 KD and control conditions. PAR-CLIP: We performed PAR-CLIP based on a previously reported protocol. Briefly, four 15 cm plates of HCT116 cells were seeded per replicate and grown to 80% confluency before adding 4 μL of 1M 4SU to each plate. After 14 hours of incubation, the media was aspirated, and the cells were washed once with 5 mL of ice-cold PBS per plate. The cells were crosslinked on ice using 0.15 J cm⁻² of 365 nm UV light, applied twice. Crosslinked cells were collected with cell lifters, and four volumes of lysis buffer (50 mM HEPES, pH 7.5; 150 mM KCl; 2 mM EDTA; 0.5% [v/v] NP-40; freshly added 1:100 protease inhibitor (Roche)) were added to the pellet. After 10 minutes of incubation on ice with periodic mixing, the lysate was centrifuged at 15,000 g for 15 minutes, and the supernatant was collected. RNase T1 (Thermo Scientific) was added to a final concentration of 0.1 U μL⁻¹, followed by a 15-minute incubation at room temperature, which was then quenched on ice. 5 µg of anti-PUS7 were added to the lysate and incubated at 4 °C for 2 hours with periodic rotation. 100 µL Protein A or G beads (Thermo Scientific) were washed twice with IP wash buffer (50 mM HEPES, pH 7.5; 300 mM KCl; 0.05% [v/v] NP-40; freshly added 1:100 protease inhibitor (Roche) and 40 U mL⁻¹ RNasin®) and resuspended in 50 μL lysis buffer before being added to the antibody-lysate mixture. Another 2-hour incubation at 4 °C with low-speed rotation followed. After incubation, the beads were washed three times with IP wash buffer, resuspended in 200 μL of IP wash buffer, and subjected to a second RNase T1 digestion (10 U μL⁻¹ final concentration) for 15 minutes at room temperature. The reaction was quenched with 10 μL SUPERase-In, followed by a 5-minute incubation on ice. Beads were washed three times with high-salt wash buffer (50 mM HEPES, pH 7.5; 500 mM KCl; 0.05% [v/v] NP-40; freshly added 1:100 protease inhibitor (Roche)) and twice with 1X PNK buffer (NEB). They were resuspended in 200 μL of 1X PNK buffer and underwent T4 PNK end repair (Thermo Fisher Scientific) at 37 °C using standard procedures. After incubation, beads were washed once with 1X PNK buffer, followed by proteinase K digestion. RNA was recovered using RNA Clean & Concentrator (Zymo Research) and prepared for library construction using the NEBNext Small RNA Library Prep Set for Illumina (NEB). Alternative adaptors were used for small RNA library preparation. 3′ SR Adapter: 5′App-NNNNNATCACGAGATCGGAAGAGCACACGTCT-3SpC3; 5′ SR Adapter: 5′-GUUCAGAGUUCUACAGUCCGACGAUC NNNNN-3′. The libraries were purified on a 3.5% low melting point agarose gel and sequenced on Illumina Nova-seq 6000 platform. KAS-seq: KAS-seq was performed following a previously reported protocol. Briefly, HCT116 cells were transfected with siPUS7, 7SK ASO, or siCtrl and harvested into 1.5 mL tubes after 3 days. Cells were suspended in 1 mL medium containing 500 mM N3-kethoxal and incubated on a shaker at 37 °C for 10 minutes to label genomic ssDNA. The medium was then discarded, and genomic DNA was extracted. The N3-kethoxal-labeled ssDNA was biotinylated, enriched, and fragmented according to the established KAS-seq protocol. Dual-index libraries were prepared for high-throughput sequencing using the Accel-NGS Methyl-seq DNA Library Kit and sequenced on Illumina Nova-seq 6000 platform. mRNA-seq: HCT116 cells were transfected with siPUS7, 7SK ASO, or siCtrl and harvested into 1.5 mL tubes after 3 days. mRNA was extracted and applied to mRNA-seq using NEBNext® Ultra™ II RNA Library Prep Kit (NEB). The libraries were sequenced on Illumina Nova-seq 6000 platform.

treatment_protocol: HCT116 cells were transfected with siPUS7, 7SK ASO or siCtr and harvested 72 h post transfection.

value: Colon tissue

tag: cell line

value: CRC

value: 7SK knockdown


title: blood, day 19, group 6 #7

description: Library name: PR3287_117_b


title: HCT116-siCtrl-mRNA-seq-rp3

description: Library name: HCT116-mRNA-seq-3


title: Bulk RNA-seq: SMA Infant #1, Post-Treatment

city: Atlanta

first: Manoj

last: Bhasin

state: GA

address: 1750 Haygood Dr NE, N320

department: Aflac Cancer and Blood Disorders Center

institute: Children's Healthcare of Atlanta

description: Library name: S13PO

data_processing:
Bulk RNA-seq: The resulting FastQ files underwent comprehensive quality control using FastQC (version 0.12.0), followed by trimming of low-quality reads and adapters using Skewer (version 0.2.2). Subsequently, Salmon (version 1.10.1) was employed to align the trimmed FastQ files to the hg38 reference genome and generate transcript counts for each sample. These were then summarized into gene-level counts using tximport.
Single-cell RNA-seq: Reads were aligned to the hg19 reference genome and quantified with CellRanger (version 3.0.2). Quality control and preprocessing were performed using the Seurat package (version 4.4.0) to ensure the inclusion of high-quality cells based on the percentage of mitochondrial genes and the number of genes/molecules. Doublets were identified and removed using DoubletFinder (version 2.0.4), and normalization and variance stabilization were performed with the SCTransform algorithm (version 0.4.1).
Assembly: GRCh38 (bulk RNA-seq), GRCh37 (single-cell RNA-seq)
Supplementary files format and content: tab-delimited text file with raw gene counts for each healthy/SMA sample in bulk RNA data
Supplementary files format and content: RDS object file with seurat object containing all healthy and SMA single-cell samples

source_name: Peripheral Blood

extract_protocol:
Bulk RNA-seq: RNA was extracted from whole blood using a Quick-RNA Whole Blood kit (Cat #R1201, Zymo Research) following the manufacturer’s protocol. The quality and integrity of the extracted RNA were assessed using an Agilent Bioanalyzer to ensure sufficient RNA quality for sequencing. Library preparation was then performed using the Illumina TruSeq RNA Sample Preparation Kit, converting the RNA into cDNA for sequencing.
Single-cell RNA-seq: All samples were collected in lavender blood collection tubes, transported to the lab on ice, and cryopreserved using the SENSE protocol. PBMCs were isolated using an EasySep human CD15 positive selection kit (Cat #18651, STEMCELL), and viability was confirmed to exceed 80% with the TC20 Automated Cell Counter (Cat #1450102, Bio-Rad).
Bulk RNA-seq: The raw sequencing libraries were sequenced on an Illumina NovaSeq 6000 platform (Novogene, Sacramento, CA), generating paired-end 150 bp reads.
Single-cell RNA-seq: Single-cell RNA sequencing (scRNA-seq) was performed on viably thawed samples using the Drop-seq approach, which encapsulates single cells and uniquely barcoded primer beads in oil droplets for high-throughput transcriptome analysis. Single-cell suspensions were processed with the 10x Genomics workflow, generating digitally barcoded droplets for cell lysis and library preparation using a 10x Chromium Controller. Libraries were prepared with the 10x Genomics Single Cell 5’ v2 and Chromium Next GEM Single Cell 5’ v2 reagent kits. Sequencing was conducted on the NovaSeq 6000 platform, achieving an average detection of ~1,000–2,000 genes per cell.

value: Peripheral Blood

value: PBMC


title: 15410002, CD4+ T cells, asthma case

description: Library name: 15410002

value: CD4+ T cells


title: CT26_CTL_R

city: Hangzhou

first: Xu

last: Kailun

state: zhejiang

address: No.88, Jiefang Road

institute: The Second Affiliated Hospital of Medical School of Zhejiang University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: CT26 cells, FOSL2-KO, Chemoradiotherapy

growth_protocol: CT26 mesenchymal cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
FOSL2-KO
Chemoradiotherapy

value: CT26 cells

value: colon adenocarcinoma cells

tag: treatment

value: Chemoradiotherapy


title: blood, day 19, group 6 #5

description: Library name: PR3287_115_b

value: male


title: blood, day 19, group 6 #6

description: Library name: PR3287_116_b

value: whole blood


title: 15376001, CD4+ T cells, asthma case

description: Library name: 15376001

value: case

value: Barbados


title: HCT116-siCtrl-mRNA-seq-rp2

description: Library name: HCT116-mRNA-seq-2

value: WT


title: HCT116-siCtrl-mRNA-seq-rp1

description: Library name: HCT116-mRNA-seq-1


title: CT26_CTL

source_name: CT26 cells, FOSL2-WT, Control

value: PBS


title: 15372001, CD4+ T cells, asthma case

description: Library name: 15372001


title: HCT116-siPUS7-KAS-seq-Treated-rp2

description:
Library name: HCT116-KAS-seq-12
HCT116-KAS-seq-PRR.values.xlsx

value: PUS7 knockdown


title: CT26_102_R


title: HCT116-si7SK-mRNA-seq-rp2

description:
Library name: HCT116-mRNA-seq-5
HCT116-si7SK_VS_siCtrl-mRNA-seq.DEresults.xlsx


title: 15369001, CD4+ T cells, asthma case

description: Library name: 15369001

value: female


title: blood, day 19, group 6 #2

description: Library name: PR3287_112_b

value: NC/Nga

value: conventional

value: group 6

value: day 19


title: blood, day 19, group 6 #3

description: Library name: PR3287_113_b


title: HCT116-siPUS7-KAS-seq-Treated-rp1

description:
Library name: HCT116-KAS-seq-11
HCT116-KAS-seq-PRR.values.xlsx

value: Colon tissue

value: CRC


title: Sorafenib_48h_2

city: Stanford

first: Dean

middle: W

last: Felsher

state: California

address: CCSR 1120 269 Campus Drive

department: Medicine/Oncology

institute: Stanford University

data_processing:
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
Quantification of gene expression level: HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: MGSCv37 (mm9)
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: HCC tissue

extract_protocol:
Hepatocellular carcinoma (HCC) tissues were flash frozen on dry ice and stored at -80⁰ C. RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions (Cat# 74136, Qiagen, MD, USA), followed by quantification using the with Nanodrop 200 Spectrometer (Thermofisher, MA, USA). RNA quality was established using the Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). A total of 1 μg of RNA per sample was used for preparation of RNA samples.
Sequencing libraries were produced using the NEBNext UltraTM RNA Library Prep Kit (Illumina, CA, USA) according to the manufacturer’s instructions and sequencing was performed by Novogene using the Illumina HiSeq 2500 sequencer.

treatment_protocol: Lap-tTA/Tet-O-MYC transgenic mice were treated with Vehicle (5/5/90 Transcutol/Solutol HS 15/Water) @ 10 mg/kg I.P. 1x/wk, doxycycline at 100 µg/ml in water, RMC-4627 @ 10 mg/kg I.P. 1x/wk, RMC-6272 @ 10 mg/kg I.P. 1x/wk, Sorafenib @ 30 mg/kg/day O.G. (oral gavage) before euthanasia

value: HCC tumor

value: Sorafenib at 30 mg/kg/day O.G. (oral gavage)

value: FVB/N

tag: trasngenic mouse model

value: Lap-tTA/Tet-O-MYC

tag: trreatment time (7 days + time below)


title: CT26_102

value: CT26 cells

value: colon adenocarcinoma cells

tag: genotype


title: 15360004, CD4+ T cells, control

description: Library name: 15360004

tag: tissue

value: CD4+ T cells

value: male

value: control

value: Barbados


title: blood, day 19, group 6 #4

description: Library name: PR3287_114_b

value: whole blood

value: WT


title: Sorafenib_48h_1


title: HCT116-si7SK-KAS-seq-Treated-rp2

description:
Library name: HCT116-KAS-seq-10
HCT116-KAS-seq-PRR.values.xlsx

tag: cell type

value: 7SK knockdown


title: Sorafenib_4h_3


title: 15479001, CD4+ T cells, asthma case

description: Library name: 15479001

tag: age

value: female

value: case


title: HCT116-si7SK-KAS-seq-Treated-rp1

description:
Library name: HCT116-KAS-seq-9
HCT116-KAS-seq-PRR.values.xlsx

value: Colon tissue


title: 15360001, CD4+ T cells, asthma case

description: Library name: 15360001

tag: Sex


title: 15354001, CD4+ T cells, asthma case

description: Library name: 15354001

tag: genetic pc1


title: blood, day 19, group 6 #1

description: Library name: PR3287_111_b

value: NC/Nga

value: conventional

value: group 6

value: day 19


title: blood, day 44, group 5 #10

description: Library name: PR3287_110_b

value: group 5

value: day 44


title: Sorafenib_4h_2

value: HCC tumor

value: Sorafenib at 30 mg/kg/day O.G. (oral gavage)

value: FVB/N

value: Lap-tTA/Tet-O-MYC


title: HCT116-siCtrl-KAS-seq-Treated-rp2

description:
Library name: HCT116-KAS-seq-8
HCT116-KAS-seq-PRR.values.xlsx

value: CRC


title: Sorafenib_4h_1


title: blood, day 44, group 5 #8

description: Library name: PR3287_108_b

value: whole blood

value: male


title: 15349001, CD4+ T cells, asthma case

description: Library name: 15349001

value: CD4+ T cells

tag: asthma

value: Barbados


title: RMC-6272_72h_3

value: RMC-6272 at 10 mg/kg I.P. 1x/wk + one more dose for 72h


title: HCT116-siCtrl-KAS-seq-Treated-rp1

description:
Library name: HCT116-KAS-seq-7
HCT116-KAS-seq-PRR.values.xlsx

value: Colon tissue

value: WT


title: 15537004, CD4+ T cells, control

description: Library name: 15537004

value: female

value: control

tag: geo loc_name


title: blood, day 44, group 5 #7

description: Library name: PR3287_107_b

tag: strain

value: NC/Nga

value: conventional


title: HCT116-siPUS7-KAS-seq-Input-rp1

description:
Library name: HCT116-KAS-seq-5
HCT116-KAS-seq-PRR.values.xlsx

value: PUS7 knockdown


title: RMC-6272_72h_2

value: HCC tumor


title: 15280002, CD4+ T cells, asthma case

description: Library name: 15280002

value: case


title: blood, day 44, group 5 #6

description: Library name: PR3287_106_b

tag: condition

value: group 5

value: day 44


title: 15252001, CD4+ T cells, asthma case

description: Library name: 15252001


title: HCT116-si7SK-KAS-seq-Input-rp2

description:
Library name: HCT116-KAS-seq-4
HCT116-KAS-seq-PRR.values.xlsx

value: CRC

value: 7SK knockdown


title: RMC-6272_72h_1

value: FVB/N

value: Lap-tTA/Tet-O-MYC


title: blood, day 44, group 5 #4

description: Library name: PR3287_104_b

value: whole blood

value: male

tag: group


title: blood, day 44, group 5 #5

description: Library name: PR3287_105_b

tag: dermatitis score


title: HCT116-si7SK-KAS-seq-Input-rp1

description:
Library name: HCT116-KAS-seq-3
HCT116-KAS-seq-PRR.values.xlsx

value: Colon tissue


title: 15238001, CD4+ T cells, asthma case

description: Library name: 15238001

value: CD4+ T cells

value: Barbados


title: RMC-6272_48h_2

value: RMC-6272 at 10 mg/kg I.P. 1x/wk + one more dose for 48h


title: HCT116-siCtrl-KAS-seq-Input-rp1

description:
Library name: HCT116-KAS-seq-1
HCT116-KAS-seq-PRR.values.xlsx

value: WT


title: HCT116-siCtrl-KAS-seq-Input-rp2

description:
Library name: HCT116-KAS-seq-2
HCT116-KAS-seq-PRR.values.xlsx


title: RMC-6272_48h_1


title: blood, day 44, group 5 #3

description: Library name: PR3287_103_b

value: NC/Nga

value: conventional

tag: time


title: 15351001, CD4+ T cells, asthma case

description: Library name: 15351001

value: female


title: blood, day 44, group 5 #9

description: Library name: PR3287_109_b


title: HCT116-siPUS7-KAS-seq-Input-rp2

description:
Library name: HCT116-KAS-seq-6
HCT116-KAS-seq-PRR.values.xlsx

tag: cell line

value: PUS7 knockdown


title: blood, day 44, group 5 #2

description: Library name: PR3287_102_b

value: group 5


title: 15225002, CD4+ T cells, control

description: Library name: 15225002

value: control


title: RMC-6272_12h_1

value: HCC tumor

tag: treatment

value: RMC-6272 at 10 mg/kg I.P. 1x/wk + one more dose for 12h


title: HCT116-PUS7-PARclip-rp2

description: Library name: HCT116-PARclip-2

value: CRC


title: blood, day 44, group 5 #1

description: Library name: PR3287_101_b

value: day 44


title: 15209001, CD4+ T cells, asthma case

description: Library name: 15209001

value: case


title: HCT116-PUS7-PARclip-rp1

description: Library name: HCT116-PARclip-1


title: Sorafenib_24h_2

value: Sorafenib at 30 mg/kg/day O.G. (oral gavage)

value: FVB/N

tag: trasngenic mouse model

value: Lap-tTA/Tet-O-MYC


title: blood, day 16, group 5 #10

description: Library name: PR3287_100_b

value: whole blood

value: male

value: day 16


title: 15208003, CD4+ T cells, asthma case

description: Library name: 15208003

value: CD4+ T cells

value: Barbados


title: Sorafenib_24h_1

tag: trreatment time (7 days + time below)


title: RMC-6272_48h_3

value: RMC-6272 at 10 mg/kg I.P. 1x/wk + one more dose for 48h


title: 15208001, CD4+ T cells, asthma case

description: Library name: 15208001


title: blood, day 16, group 5 #9

description: Library name: PR3287_099_b

value: NC/Nga

tag: genotype

value: WT

value: conventional


title: 15231001, CD4+ T cells, asthma case

description: Library name: 15231001

tag: tissue


title: RMC-6272_24h_3

value: HCC tumor

value: RMC-6272 at 10 mg/kg I.P. 1x/wk + one more dose for 24h


title: HCT116-siPUS7-BID-seq-BS-Treated-rp2

description:
Library name: HCT116-BID-seq-11
HCT116-siPUS7_VS_siCtrl_BID-seq.xlsx

molecule: nuclear RNA

value: Colon tissue

tag: cell type

value: CRC

value: PUS7 knockdown


title: blood, day 16, group 5 #8

description: Library name: PR3287_098_b

value: group 5


title: RMC-6272_24h_2

value: FVB/N


title: 15196004, CD4+ T cells, control

description: Library name: 15196004

tag: age

value: control


title: blood, day 16, group 5 #7

description: Library name: PR3287_097_b

value: whole blood

tag: Sex


title: 15194001, CD4+ T cells, asthma case

description: Library name: 15194001

value: male

tag: genetic pc1

value: case


title: HCT116-siPUS7-BID-seq-Input-rp3

description:
Library name: HCT116-BID-seq-9
HCT116-siPUS7_VS_siCtrl_BID-seq.xlsx


title: blood, day 16, group 5 #6

description: Library name: PR3287_096_b

value: day 16


title: 15192008, CD4+ T cells, asthma case

description: Library name: 15192008

value: CD4+ T cells

value: female

tag: asthma

value: Barbados


title: HCT116-siPUS7-BID-seq-Input-rp2

description:
Library name: HCT116-BID-seq-8
HCT116-siPUS7_VS_siCtrl_BID-seq.xlsx


title: HCT116-siPUS7-BID-seq-BS-Treated-rp3

description:
Library name: HCT116-BID-seq-12
HCT116-siPUS7_VS_siCtrl_BID-seq.xlsx


title: RMC-4627_24h_2

value: RMC-4627 at 10 mg/kg I.P. 1x/wk + one more dose for 24h

value: Lap-tTA/Tet-O-MYC


title: HCT116-siPUS7-BID-seq-Input-rp1

description:
Library name: HCT116-BID-seq-7
HCT116-siPUS7_VS_siCtrl_BID-seq.xlsx


title: HCT116-siPUS7-BID-seq-BS-Treated-rp1

description:
Library name: HCT116-BID-seq-10
HCT116-siPUS7_VS_siCtrl_BID-seq.xlsx


title: 15183002, CD4+ T cells, asthma case

description: Library name: 15183002

tag: geo loc_name


title: blood, day 16, group 5 #4

description: Library name: PR3287_094_b

tag: strain

value: NC/Nga

value: WT

value: conventional


title: HCT116-siCtrl-BID-seq-BS-Treated-rp3

description:
Library name: HCT116-BID-seq-6
HCT116-siPUS7_VS_siCtrl_BID-seq.xlsx

value: Colon tissue

value: CRC


title: blood, day 16, group 5 #3

description: Library name: PR3287_093_b

tag: condition

value: group 5


title: 15177001, CD4+ T cells, asthma case

description: Library name: 15177001


title: DOX_24h_2

value: HCC tumor

value: doxycycline at 100 ug/ml in water

value: FVB/N


title: 15186003, CD4+ T cells, control

description: Library name: 15186003

value: control


title: DOX_24h_1


title: HCT116-siCtrl-BID-seq-BS-Treated-rp2

description:
Library name: HCT116-BID-seq-5
HCT116-siPUS7_VS_siCtrl_BID-seq.xlsx


title: 15176001, CD4+ T cells, asthma case

description: Library name: 15176001

value: case


title: 15174001, CD4+ T cells, asthma case

description: Library name: 15174001

value: male


title: HCT116-siCtrl-BID-seq-BS-Treated-rp1

description:
Library name: HCT116-BID-seq-4
HCT116-siPUS7_VS_siCtrl_BID-seq.xlsx


title: blood, day 16, group 5 #1

description: Library name: PR3287_091_b

value: whole blood

tag: group

value: day 16


title: Veh_24h_2

value: Vehicle (5/5/90 Transcutol/Solutol HS 15/Water) at 10 mg/kg I.P. 1x/wk


title: HCT116-siCtrl-BID-seq-Input-rp3

description:
Library name: HCT116-BID-seq-3
HCT116-siPUS7_VS_siCtrl_BID-seq.xlsx


title: RMC-6272_24h_1

value: RMC-6272 at 10 mg/kg I.P. 1x/wk + one more dose for 24h


title: HCT116-siCtrl-BID-seq-Input-rp2

description:
Library name: HCT116-BID-seq-2
HCT116-siPUS7_VS_siCtrl_BID-seq.xlsx


title: blood, day 16, group 5 #5

description: Library name: PR3287_095_b

tag: dermatitis score


title: blood, day 40, group 4 #10

description: Library name: PR3287_090_b

value: group 4

tag: time

value: day 40


title: 15166005, CD4+ T cells, asthma case

description: Library name: 15166005

value: CD4+ T cells

value: Barbados


title: 15165004, CD4+ T cells, control

description: Library name: 15165004


title: HCT116-siCtrl-BID-seq-Input-rp1

description:
Library name: HCT116-BID-seq-1
HCT116-siPUS7_VS_siCtrl_BID-seq.xlsx

value: Colon tissue

tag: cell line

value: WT


title: RMC-4627_24h_1

tag: treatment

value: RMC-4627 at 10 mg/kg I.P. 1x/wk + one more dose for 24h

value: Lap-tTA/Tet-O-MYC


title: blood, day 40, group 4 #9

description: Library name: PR3287_089_b

value: NC/Nga

value: conventional


title: inCAGE scRNA-seq of fresh and fixed K562 cells for comparing to PFA fixed cells (Fresh_Fixed)

city: Boston

first: Ignas

last: Mazelis

state: MA

address: 210 Longwood Avenue

department: System Biology

institute: Harvard Medical School

description:
Library name: K562_fresh and K562_fixed
inCAGE scRNA-seq of fresh K562 cells for comparing to PFA fixed cells
inCAGE scRNA-seq of PFA fixed K562 cells for comparing to PFA fixed cells

library_source: transcriptomic single cell

data_processing:
BCL sequencing files received from Illumina BaseSpace portal were converted to raw FASTQ files for each of the 4 (R1, R2, R3, R4) sequencing reads without read trimming or masking by using bcl2fastq software (Illumina, v2.20.0.422). Raw FASTQ files were processed using a custom pipeline (available at https://github.com/AllonKleinLab/paper-data/tree/master/Mazelis2025_CAGEs). In brief, sequencing reads were demultiplexed based on Read1 index sequence (stored as read3) (index used: TATGCAGT, TACTCCTT), and were filtered based on expected structure (all barcodes matching a barcode whitelist with hamming distance of 1). The demultiplexed reads were then processed using Trimmomatic (1) (with parameters: LEADING 28; SLIDINGWINDOW 4:20; MINLEN 20), followed by Poly-A length trim to 4 nt and selecting reads that are longer than MINLEN. For surviving reads, the fraction of length composed out of same base repeats (only considering > 5) was determined, rejecting reads whose fraction is greater than 0.5.
Count matrices were generated using STARsolo pipeline (2) (STAR 2.7.9a) with the with parameters (--soloFeatures Gene, GeneFull, --genomeSAsparseD 3, --outSAMtype BAM SortedByCoordinate, --outSAMattributes CB CR UR UB UY GN GX, --outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3, --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts, --soloUMIfiltering MultiGeneUMI_CR, --soloUMIdedup 1MM_CR, --soloMultiMappers EM, --soloCellFilter EmptyDrops_CR, --quantMode TranscriptomeSAM GeneCounts) Human GRCh38.101 genome assembly was used.
Count matrices were filtered by selecting barcodes with >1000 UMIs and fraction of mitochondrial counts being below 0.4.  Different conditions were demultiplexed based on RT barcode
Assembly: Human GRCh38.101genome assembly
Supplementary files format and content: h5ad cell x genes expression matrix for different conditions

source_name: Human and mouse Blood

growth_protocol: K562 and L1210 cells were cultured in IMDM (Thermo Fisher, 10566016) + 10% FBS (ATCC, 30-2020) + 1x penicillin/streptomycin (Thermo Fisher, 10378016) in T25 flasks (Corning). Cell lines were cultured until they reached ~80-90% confluency. For passaging, suspension cells (K562, L1210) were resuspended gently and collected into a 15 mL tube. 5 mL of 37ºC pre-warmed complete media was used to wash the flask and was added into the same 15 mL tube. Cells were centrifuged at 300g for 4 min, followed by media aspiration and resuspension in 5 mL of fresh pre-warmed complete media. Cells were counted using an automatic cell counter and 500,000 cells were seeded into 5 mL of 37ºC pre-warmed complete media in a 25cm2 flask. For encapsulation experiments, cells were washed twice with ice cold DPBS with 0.1% BSA

extract_protocol:
Cells were washed twice with DPBS with 0.1% BSA, mixed at 1:1 ration and were encapsulated into CAGEs at a final concentration of 1.2e6 cells/mL in core mix. Next, the CAGE core dextran was removed using dextranase enzyme. Following this, all steps were performed on ice. First, capsules were washed three times with an ice-cold 3X SSCI buffer with 800g spins for 1 min. Fresh cells were lysed by washing with ice-cold 7.5pH TEIS with 5 min incubations on ice. Fixed cells were reverse cross-linked in CAGEs by washing the CAGEs twice with 3x SSCI + 0.01U/μL RiboLock RNAse Inhibitor (ThermoFisher, EO0381). Next, CAGEs were washed three times with 100mM Tris (pH 7.5) with 10mM EDTA, 0.1% Igepal CA-630 (Millipore Sigma, I8896-50ML), 0.1% SDS. Finally, CAGEs were resuspended in the same solution to a volume of 1 mL and 50 μL of proteinase K (NEB, P8107S) was added followed by incubation at 56ºC for 30 min. After the reverse crosslinking, CAGEs were washed three times with 3X SSCI, three times. CAGEs were imaged and washed three times with 3X SSCI and three times with HI10, packed at 800g for 1 min and stored on ice. Reverse-transcription reaction was set on ice and performed in PCR strip tubes. A standard 100μL reaction was composed out of 60.5μL of packed capsules, 2.5μL of 10μM RT poly(T) primer housing a 10nt UMI and 6nt barcode (Table S3, RT), 3μL of 10% Igepal CA-630 (Millipore Sigma, I8896-50ML), 20μL of 5X SMARTseq3 RT buffer (100mM Tris pH 8.3, 150mM NaCl, 12.5mM MgCl2, 5mM GTP, 40mM DTT), 0.5μL of 10mM dNTPs (NEB, N0447L), 2.5μL of 40U/μL Recombinant RNase Inhibitor (Takara Bio, 2313A), 1.5μL of 50μM TSO, 5μL of Maxima H- reverse transcriptase (ThermoFisher, EP0753). Reaction volumes were scaled according to the amount of capsules used and number of reactions performed. To set up the reaction, capsules, RT primer and Igepal CA-630 (Millipore Sigma, I8896-50ML) were mixed on ice in a PCR tube, with each housing a different RT barcode. Capsules were incubated on ice for 10 min to allow the RT primer to diffuse in, followed by heating at 70ºC for 5 min and cooling down on ice. Next, RT master mix, composed out of the remaining reagents was added to each tube, ensuring a thought mixing of capsules with pipetting. Tubes were incubated on ice for 5 min and the reaction was carried out at 42ºC for 90 min, followed by cycling between 50ºC and 42ºC incubation of 2 mins for 15 cycles. Reactions were left at room temperature overnight and processed the next day. After the RT reaction, capsules were washed three times with TI100 (pH 8.0), twice with TIbS (pH 8.0), three times with ice-cold TI100 (pH 8.0) with 2 min incubations on ice. Finally capsules were washed twice with TI10 (pH 8.0). Next, Capsule dU PCR was performed to carry out cDNA amplification. After the cDNA amplification, capsules were washed three times with TI100 (pH 8.0), twice with TIbS (pH 8.0), three times with TI100 (pH 8.0), twice with TI10 (pH 8.0). Washed capsules were subjected to tree rounds of split-and-pool barcoding. Following split-and-pool barcoding, capsules were split into 8 tubes and were dissolved  using 10M NaOH. DNA was purified using MinElute PCR purification kit and barcoded cDNA was eluted into 20μL of the elution buffer. Barcoded and purified DNA was amplified using PCR. After the reaction, amplified barcoded cDNA was purified using 0.8X AMPure XP beads (Beckman Coulter, A63881) and was eluted into a 15μL Elution Buffer.
To construct Illumina sequencing libraries, 50 ng of barcoded and amplified cDNA was fragmented, blunted and dA-tailed by mixing it with 3.5 μL of NEBNext Ultra II FS Reaction buffer (NEB), 1 μL of fully mixed NEBNext Ultra II FS Enzyme mix (NEB) and nuclease free water to a final volume of 17.5 μL. The reaction mix was vortexed for 10 s, spanned down and placed into a preheated PCR machine for incubation at 37°C for 10 min; 65°C for 30 min; hold 4°C (lid at 75ºC). Fragmented DNA was purified using 0.8X AMPure XP beads (Beckman Coulter, A63881) and eluted into 16μL of water. Single-stranded DNA adapter, containing Illumina’s TruSeq read 1 (Adp. TruSeq R1 FW and RV) sequences were annealed together at the final concentration of 1.5 μM by mixing 1.5 μL of forward ligation primer and reverse ligation primer (each at 100 μM) with 97 μL of nuclease-free water and heating the solution to 95°C for 2 min and cooling it at room temperature for 5 min. 16 μL of the purified fragmented DNA was mixed with 1.25 μL of 1.5 μM annealed adapters, 1.5μL of 10X T4 DNA ligase buffer, 15 μL of NEBNext Ultra II Ligation Master Mix (NEB, E7805S kit) and 0.5 μL of NEBNext Ultra II Ligation Master Enhancer (NEB, E7805S kit). The ligation reaction was carried out by incubating in the thermocycler for 15 min at 20°C (lid at 30ºC). After ligation, the reaction mix was diluted to 100 μL and was purified using AMPure XP beads (Beckman Coulter, A63881) with 0.8X volume ratio and eluted into 40 μL nuclease-free water. Indexing PCR was carried out by mixing purified DNA with 25 μL of 2x NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0543L) and 2.5 μL of 20μM P7 binding primer, 8 sets of 2.5μL of 20μM indexing primer that houses an 8bp library index and water to 50μL. PCR cycling program: 98 °C, 2 min; 3 cycles of 98 °C, 20 s; 55 °C, 30 s; 72 °C, 20 s and 9 cycles 98 °C, 20 s; 65 °C, 30 s; 72 °C, 20 s; with a 1 min final extension at 72 °C, and 4 °C, hold at the end. Following final library indexing, DNA was double-side purified using 0.6x-0.8x SPRIselect (Beckman Coulter, B23318) magnetic beads and eluted into 15μL.

value: Human and mouse Blood

value: Lymphoblast


title: blood, day 40, group 4 #8

description: Library name: PR3287_088_b

value: male


title: Veh_24h_3

value: HCC tumor

value: FVB/N

tag: trasngenic mouse model


title: Veh_24h_1

value: Vehicle (5/5/90 Transcutol/Solutol HS 15/Water) at 10 mg/kg I.P. 1x/wk

tag: trreatment time (7 days + time below)


title: RNA_seq_Multiple_Myeloma_MM298

city: Rome

first: Maurizio

last: Fanciulli

address: Via Elio Chianesi 53

department: Department of Research, Advanced Diagnostic, and Technological Innovation

country: Italy

institute: IRCCS Regina Elena National Cancer Institute

description:
Library name: Sample_21
RNAseq of CD138+ plasma cells from MM298 sample

data_processing:
Read quantification was performed using the quant function of the Kallisto v.0.46.0 tool with the parameter -b 100.
Assembly: hg19
Supplementary files format and content: A tab-delimited text file containing the transcript ID, transcript length, effective transcript length used for abundance estimation, estimated number of reads mapped to the transcript, and transcripts per million count.

source_name: bone marrow

extract_protocol:
Plasma cells from bone marrow were isolated using the Miltenyi CD138 Multiple Myeloma MACS kit, following the manufacturer's standard protocol. Total RNA was extracted from an equal number of viable cells using QIAzol Lysis Reagent (Qiagen) and purified from DNA contamination through a digestion step with the RNase-Free DNase Set (Qiagen).
RNA libraries were generated using an equal amount of RNA from each sample, following the protocol of the Illumina Stranded Total RNA Prep kit, with an initial ribosomial depletion step using Ribo-Zero Plus from Illumina.

value: bone marrow

value: primary MM plasma cells

value: CD138+ plasma cells

tag: genotype

value: Multiple Myeloma


title: inCAGE scRNA-seq of HEK293t cells encapsulated in DPBS buffers and cryopreserved for a week

description: Library name: HEK293t_frozen

data_processing:
BCL sequencing files received from Illumina BaseSpace portal were converted to raw FASTQ files for each of the 4 (R1, R2, R3, R4) sequencing reads without read trimming or masking by using bcl2fastq software (Illumina, v2.20.0.422). Raw FASTQ files were processed using a custom pipeline (available at https://github.com/AllonKleinLab/paper-data/tree/master/Mazelis2025_CAGEs). In brief, sequencing reads were demultiplexed based on Read1 index sequence (stored as read3) (index used: GAGAATTG, GTGGATGG), and were filtered based on expected structure (all barcodes matching a barcode whitelist with hamming distance of 1). The demultiplexed reads were then processed using Trimmomatic (1) (with parameters: LEADING 28; SLIDINGWINDOW 4:20; MINLEN 20), followed by Poly-A length trim to 4 nt and selecting reads that are longer than MINLEN. For surviving reads, the fraction of length composed out of same base repeats (only considering > 5) was determined, rejecting reads whose fraction is greater than 0.5.
Count matrices were generated using STARsolo pipeline (2) (STAR 2.7.9a) with the with parameters (--soloFeatures Gene, GeneFull, --genomeSAsparseD 3, --outSAMtype BAM SortedByCoordinate, --outSAMattributes CB CR UR UB UY GN GX, --outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3, --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts, --soloUMIfiltering MultiGeneUMI_CR, --soloUMIdedup 1MM_CR, --soloMultiMappers EM, --soloCellFilter EmptyDrops_CR, --quantMode TranscriptomeSAM GeneCounts) Mixed Human GRCh38.101 and mouse GRCm.101 genome assembly was used.
Count matrices were filtered by selecting barcodes with >1000 UMIs and fraction of mitochondrial counts being below 0.4. Mouse and human cells were filered based on gene expression and different conditions were demultiplexed based on RT barcode
Assembly: Mixed Human GRCh38.101 and mouse GRCm.101 genome assembly
Supplementary files format and content: h5ad cell x genes expression matrix for different conditions

source_name: Embryonic kidney

growth_protocol: HEK293t and NIH/3t3 cells were cultured in RPMI1640 (Thermo Fisher, 61870036) + 10% FBS (ATCC, 30-2020) + 1x penicillin/streptomycin (Thermo Fisher, 10378016) in T25 flasks (Corning). Cell lines were cultured until they reached ~80-90% confluency. For passaging cells were passaged by aspirating the used media and washing 2 times with 2 mL of 37ºC pre-warmed 1x DPBS buffer. Cells were detached by adding 1 mL of TrypLE reagent (Thermofisher Scientific, 12605010), waiting 10s and quickly aspirating all of the TrypLE. Cells were incubated in 37ºC for 2 minutes and were resuspended in 5 mL of 37ºC pre-warmed complete media. Cells were centrifuged at 300g for 4 min, followed by media aspiration and resuspension in 5 mL of fresh pre-warmed complete media. Cells were counted using an automatic cell counter and 500,000 cells were seeded into 5 mL of 37ºC pre-warmed complete media in a 25cm2 flask.

extract_protocol:
Cells were washed twice with IMDM or DPBS with 0.1% BSA, mixed at 1:1 ration and were encapsulated into CAGEs at a final concentration of 1.4e6 cells/mL in core mix. Next, for some samples the CAGE core dextran was removed using dextranase enzyme. Following this, all steps were performed on ice. First, capsules were washed three times with an ice-cold 3X SSCI buffer with 800g spins for 1 min. Cells were lysed by washing with ice-cold 7.5pH TEIS with 5 min incubations on ice. After lysis, capsules were imaged, washed three times with 3X SSCI and three times with HI10, packed at 800g for 1 min and stored on ice. Part of the sample was frozen at -80ºC in 10% DMSO. Reverse-transcription reaction was set on ice and performed in PCR strip tubes. A standard 100μL reaction was composed out of 60.5μL of packed capsules, 2.5μL of 10μM RT poly(T) primer housing a 10nt UMI and 6nt barcode (Table S3, RT), 3μL of 10% Igepal CA-630 (Millipore Sigma, I8896-50ML), 20μL of 5X SMARTseq3 RT buffer (100mM Tris pH 8.3, 150mM NaCl, 12.5mM MgCl2, 5mM GTP, 40mM DTT), 0.5μL of 10mM dNTPs (NEB, N0447L), 2.5μL of 40U/μL Recombinant RNase Inhibitor (Takara Bio, 2313A), 1.5μL of 50μM TSO, 5μL of Maxima H- reverse transcriptase (ThermoFisher, EP0753). Reaction volumes were scaled according to the amount of capsules used and number of reactions performed. To set up the reaction, capsules, RT primer and Igepal CA-630 (Millipore Sigma, I8896-50ML) were mixed on ice in a PCR tube, with each housing a different RT barcode. Capsules were incubated on ice for 10 min to allow the RT primer to diffuse in, followed by heating at 70ºC for 5 min and cooling down on ice. Next, RT master mix, composed out of the remaining reagents was added to each tube, ensuring a thought mixing of capsules with pipetting. Tubes were incubated on ice for 5 min and the reaction was carried out at 42ºC for 90 min, followed by cycling between 50ºC and 42ºC incubation of 2 mins for 15 cycles. Reactions were left at room temperature overnight and processed the next day. After the RT reaction, capsules were washed three times with TI100 (pH 8.0), twice with TIbS (pH 8.0), three times with ice-cold TI100 (pH 8.0) with 2 min incubations on ice. Finally capsules were washed twice with TI10 (pH 8.0). Next, Capsule dU PCR was performed to carry out cDNA amplification. After the cDNA amplification, capsules were washed three times with TI100 (pH 8.0), twice with TIbS (pH 8.0), three times with TI100 (pH 8.0), twice with TI10 (pH 8.0). Washed capsules were subjected to tree rounds of split-and-pool barcoding. Following split-and-pool barcoding, capsules were split into 8 tubes and were dissolved  using 10M NaOH. DNA was purified using MinElute PCR purification kit and barcoded cDNA was eluted into 20μL of the elution buffer. Barcoded and purified DNA was amplified using PCR. After the reaction, amplified barcoded cDNA was purified using 0.8X AMPure XP beads (Beckman Coulter, A63881) and was eluted into a 15μL Elution Buffer.
To construct Illumina sequencing libraries, 50 ng of barcoded and amplified cDNA was fragmented, blunted and dA-tailed by mixing it with 3.5 μL of NEBNext Ultra II FS Reaction buffer (NEB), 1 μL of fully mixed NEBNext Ultra II FS Enzyme mix (NEB) and nuclease free water to a final volume of 17.5 μL. The reaction mix was vortexed for 10 s, spanned down and placed into a preheated PCR machine for incubation at 37°C for 10 min; 65°C for 30 min; hold 4°C (lid at 75ºC). Fragmented DNA was purified using 0.8X AMPure XP beads (Beckman Coulter, A63881) and eluted into 16μL of water. Single-stranded DNA adapter, containing Illumina’s TruSeq read 1 (Adp. TruSeq R1 FW and RV) sequences were annealed together at the final concentration of 1.5 μM by mixing 1.5 μL of forward ligation primer and reverse ligation primer (each at 100 μM) with 97 μL of nuclease-free water and heating the solution to 95°C for 2 min and cooling it at room temperature for 5 min. 16 μL of the purified fragmented DNA was mixed with 1.25 μL of 1.5 μM annealed adapters, 1.5μL of 10X T4 DNA ligase buffer, 15 μL of NEBNext Ultra II Ligation Master Mix (NEB, E7805S kit) and 0.5 μL of NEBNext Ultra II Ligation Master Enhancer (NEB, E7805S kit). The ligation reaction was carried out by incubating in the thermocycler for 15 min at 20°C (lid at 30ºC). After ligation, the reaction mix was diluted to 100 μL and was purified using AMPure XP beads (Beckman Coulter, A63881) with 0.8X volume ratio and eluted into 40 μL nuclease-free water. Indexing PCR was carried out by mixing purified DNA with 25 μL of 2x NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0543L) and 2.5 μL of 20μM P7 binding primer, 8 sets of 2.5μL of 20μM indexing primer that houses an 8bp library index and water to 50μL. PCR cycling program: 98 °C, 2 min; 3 cycles of 98 °C, 20 s; 55 °C, 30 s; 72 °C, 20 s and 9 cycles 98 °C, 20 s; 65 °C, 30 s; 72 °C, 20 s; with a 1 min final extension at 72 °C, and 4 °C, hold at the end. Following final library indexing, DNA was double-side purified using 0.6x-0.8x SPRIselect (Beckman Coulter, B23318) magnetic beads and eluted into 15μL.

tag: tissue

value: Embryonic kidney

value: Embryonic kindey cells


title: blood, day 40, group 4 #6

description: Library name: PR3287_086_b

value: whole blood

value: WT

value: group 4

value: day 40


title: 15151001, CD4+ T cells, asthma case

description: Library name: 15151001

value: CD4+ T cells

tag: cell type

value: female

value: case

value: Barbados


title: blood, day 16, group 5 #2

description: Library name: PR3287_092_b

value: NC/Nga

value: male

value: conventional

value: group 5

value: day 16


title: RNA_seq_Multiple_Myeloma_MM288

description:
Library name: Sample_20
RNAseq of CD138+ plasma cells from MM288 sample

value: bone marrow

value: primary MM plasma cells

value: CD138+ plasma cells


title: blood, day 40, group 4 #7

description: Library name: PR3287_087_b


title: inCAGE scRNA-seq of HEK293t cells encapsulated in IMDM media with dextranase trated CAGEs, replicate

description: Library name: HEK293t_Media_dextranase_rep

value: Embryonic kidney

value: Embryonic kindey cells


title: RNA_seq_Multiple_Myeloma_MM283

description:
Library name: Sample_19
RNAseq of CD138+ plasma cells from MM283 sample

value: Multiple Myeloma


title: 15150002, CD4+ T cells, asthma case

description: Library name: 15150002

tag: age


title: blood, day 40, group 4 #5

description: Library name: PR3287_085_b

value: whole blood

tag: Sex

value: WT

value: group 4


title: 15146001, CD4+ T cells, asthma case

description: Library name: 15146001

value: CD4+ T cells

tag: genetic pc1


title: inCAGE scRNA-seq of HEK293t cells encapsulated in DPBS buffers with dextranase trated CAGEs

description: Library name: HEK293t_DBPS_dextranase


title: inCAGE scRNA-seq of HEK293t cells encapsulated in IMDM media with dextranase trated CAGEs

description: Library name: HEK293t_Media_dextranase


title: blood, day 40, group 4 #2

description: Library name: PR3287_082_b

value: day 40


title: 15144001, CD4+ T cells, asthma case

description: Library name: 15144001

value: female

tag: asthma

value: case

value: Barbados


title: 15140003, CD4+ T cells, control

description: Library name: 15140003

value: control

tag: geo loc_name


title: RNA_seq_Multiple_Myeloma_MM214

description:
Library name: Sample_14
RNAseq of CD138+ plasma cells from MM214 sample


title: RNA_seq_Multiple_Myeloma_MM266

description:
Library name: Sample_17
RNAseq of CD138+ plasma cells from MM266 sample


title: 15143003, CD4+ T cells, asthma case

description: Library name: 15143003


title: MDanderson_NKcells_patient6_timepoint3_sc_smartseq_pl1_C6_S273

city: Houston

first: Katayoun

last: Rezvani

address: 1515 Holcombe Blvd

department: Department of Stem Cell Transplantation and Cellular Therapy

institute: The University of Texas MD Anderson Cancer Center

description: responder

data_processing:
HISAT2 to align reads and htseq-count for counting reads.
Supplementary files format and content: Processed data is in avaliable in count matrix format after removing low quality cells. Meta data information including response, cell type and time points.

source_name: peripheral blood

extract_protocol:
PBMCs from the recipients of CAR19/IL-15 NK cell therapy were enriched by Ficoll-hypaquse density gradient centrifugation, kept frozen in the vapor phase of liquid nitrogen, and thawed from the time points as indicated. Thawed cells were rested for 20 min in a humidified incubator at 37 degree Celsius in the presence of 5% CO2, washed in PBS with 1% BSA, and stained for a viability dye (Tonbo BioScience), CD19 (Clone HIB19: BD Bioscience), CD33 (Clone P67.6: BD Bioscience), CD14 (Clone M5E2: BD Bioscience), CD3 (Clone SK7: BD Bioscience),CD20 (Clone 2H7: BD Bioscience), CD56 (Clone N901: BeckMan Coulter), CD45 (Clone J33: BeckMan Coulter). CAR was detected on donor HLA positive, CD3- , CD16+ and CD56+ cells by using the fluorophore-tagged F(ab)2 fragment against Human IgG (Jackson Immunoresearch) as described previously . Single cells from the donor NK cell population, or from B cells of the patients were sorted into each well of a 96 well plate with lysis buffer (10 X l of TCL buffer, Qiagen and 1% 2-mercaptoethanol: Sigma). The plates were spun down at 400xg for 5 minutes at 4 degree Celsius and immediately stored at -80°C until library preparation.
cDNA was synthesized as described by the Smart-Seq2 protocol from Picelli et al.. Briefly, RNA was purified using RNAClean XP beads (Beckman Coulter) and reverse transcribed to cDNA using Maxima RNAse H-minus (ThermoFisher) in the presence of biotinylated oligo-dT30VN, biotinylated template-switching oligonucleotides, and betaine. Next, a PCR pre-amplification step was done with KAPA HiFi HotStart Ready Mix (Roche Diagnostics) and biotinylated ISPCR primers. DNA products were further purified with Agencourt XP DNA beads, and the concentration of each sample was quantified by Qubit dsDNA HS Assay kits (Invitrogen). Quality of samples was analyzed on a 2100 Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). 0.15 ng of each sample was tagmented and Nextera index adapters were used for barcoding according to the Illumina Nextera XT DNA sample preparation kit (Illumina).

value: peripheral blood

value: NKcells

value: Female


title: MDanderson_NKcells_patient6_timepoint3_sc_smartseq_pl1_C8_S275

description: responder


title: 15152001, CD4+ T cells, asthma case

description: Library name: 15152001

value: male


title: inCAGE scRNA-seq of HEK293t cells encapsulated in DPBS buffers

description: Library name: HEK293t_DBPS


title: blood, day 40, group 4 #3

description: Library name: PR3287_083_b

tag: strain

value: NC/Nga

value: conventional


title: RNA_seq_Multiple_Myeloma_MM234

description:
Library name: Sample_15
RNAseq of CD138+ plasma cells from MM234 sample

value: bone marrow

value: primary MM plasma cells

value: CD138+ plasma cells


title: MDanderson_NKcells_patient6_timepoint3_sc_smartseq_pl1_C12_S279

description: responder


title: RNA_seq_Multiple_Myeloma_MM251

description:
Library name: Sample_16
RNAseq of CD138+ plasma cells from MM251 sample

value: Multiple Myeloma


title: blood, day 40, group 4 #1

description: Library name: PR3287_081_b

value: whole blood

value: WT

tag: condition

value: group 4


title: 15119001, CD4+ T cells, asthma case

description: Library name: 15119001

value: CD4+ T cells


title: blood, day 12, group 4 #9

description: Library name: PR3287_079_b

tag: group

value: day 12


title: blood, day 12, group 4 #8

description: Library name: PR3287_078_b

tag: dermatitis score


title: RNA_seq_Multiple_Myeloma_MM196

description:
Library name: Sample_13
RNAseq of CD138+ plasma cells from MM196 sample


title: MDanderson_NKcells_patient6_timepoint3_sc_smartseq_pl1_A5_S248

description: responder


title: MDanderson_NKcells_patient6_timepoint3_sc_smartseq_pl1_A12_S255

description: responder


title: MDanderson_NKcells_patient6_timepoint3_sc_smartseq_pl1_A3_S246

description: responder


title: RNA_seq_Multiple_Myeloma_MM267

description:
Library name: Sample_18
RNAseq of CD138+ plasma cells from MM267 sample


title: RNA_seq_Multiple_Myeloma_MM158

description:
Library name: Sample_11
RNAseq of CD138+ plasma cells from MM158 sample


title: blood, day 40, group 4 #4

description: Library name: PR3287_084_b

tag: time

value: day 40


title: 15123002, CD4+ T cells, asthma case

description: Library name: 15123002

value: case

value: Barbados


title: blood, day 12, group 4 #7

description: Library name: PR3287_077_b


title: RNA_seq_Multiple_Myeloma_MM128

description:
Library name: Sample_10
RNAseq of CD138+ plasma cells from MM128 sample

tag: cell line


title: MDanderson_NKcells_patient6_timepoint2_sc_smartseq_pl1_B2_S209

description: responder

value: peripheral blood

value: NKcells

tag: treatment


title: blood, day 12, group 4 #6

description: Library name: PR3287_076_b

value: male


title: blood, day 12, group 4 #10

description: Library name: PR3287_080_b

value: NC/Nga


title: RNA_seq_Multiple_Myeloma_MM170

description:
Library name: Sample_12
RNAseq of CD138+ plasma cells from MM170 sample


title: MDanderson_NKcells_patient6_timepoint2_sc_smartseq_pl1_D12_S243

description: responder

value: Female


title: 15051003, CD4+ T cells, asthma case

description: Library name: 15051003

value: female


title: 15112003, CD4+ T cells, asthma case

description: Library name: 15112003


title: 15046017, CD4+ T cells, asthma case

description: Library name: 15046017


title: 15116002, CD4+ T cells, asthma case

description: Library name: 15116002


title: MDanderson_NKcells_patient6_timepoint2_sc_smartseq_pl1_D3_S234

description: responder


title: RNA_seq_MGUS_CB47

description:
Library name: Sample_8
RNAseq of CD138+ plasma cells from CB47 sample

value: bone marrow

value: primary MGUS plasma cells

value: Monoclonal gammopathy of undetermined significance


title: 15115002, CD4+ T cells, asthma case

description: Library name: 15115002


title: MDanderson_NKcells_patient6_timepoint2_sc_smartseq_pl1_C7_S226

description: responder


title: MDanderson_NKcells_patient6_timepoint2_sc_smartseq_pl1_C6_S225

description: responder


title: RNA_seq_MGUS_CB51

description:
Library name: Sample_9
RNAseq of CD138+ plasma cells from CB51 sample

value: CD138+ plasma cells


title: blood, day 12, group 4 #2

description: Library name: PR3287_072_b

value: whole blood

value: WT

value: conventional


title: blood, day 12, group 4 #5

description: Library name: PR3287_075_b

value: group 4

value: day 12


title: 15041003, CD4+ T cells, control

description: Library name: 15041003

value: CD4+ T cells

value: control


title: RNA_seq_MGUS_CB45

description:
Library name: Sample_6
RNAseq of CD138+ plasma cells from CB45 sample


title: 15022026, CD4+ T cells, control

description: Library name: 15022026

value: Barbados


title: RNA_seq_MGUS_CB43

description:
Library name: Sample_5
RNAseq of CD138+ plasma cells from CB43 sample


title: MDanderson_NKcells_patient6_timepoint2_sc_smartseq_pl1_A8_S203

description: responder

value: peripheral blood

value: NKcells


title: blood, day 12, group 4 #1

description: Library name: PR3287_071_b

value: NC/Nga

value: male


title: RNA_seq_MGUS_CB41

description:
Library name: Sample_4
RNAseq of CD138+ plasma cells from CB41 sample


title: 15018005, CD4+ T cells, control

description: Library name: 15018005

value: female


title: RNA_seq_MGUS_CB31

description:
Library name: Sample_3
RNAseq of CD138+ plasma cells from CB31 sample

value: bone marrow


title: MDanderson_NKcells_patient6_timepoint2_sc_smartseq_pl1_A6_S201

description: responder

value: Female


title: 15022003, CD4+ T cells, control

description: Library name: 15022003


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_D7_S142

description: responder


title: 15012059, CD4+ T cells, asthma case

description: Library name: 15012059

value: case


title: RNA_seq_MGUS_CB28

description:
Library name: Sample_2
RNAseq of CD138+ plasma cells from CB28 sample

value: primary MGUS plasma cells

value: CD138+ plasma cells

value: Monoclonal gammopathy of undetermined significance


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_H12_S195

description: responder


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_H11_S194

description: responder


title: RNA_seq_MGUS_CB46

description:
Library name: Sample_7
RNAseq of CD138+ plasma cells from CB46 sample


title: blood, day 44, group 3 #9

description: Library name: PR3287_069_b

value: whole blood

value: WT

value: conventional

value: group 3

value: day 44


title: 15011016, CD4+ T cells, asthma case

description: Library name: 15011016

value: CD4+ T cells

value: Barbados


title: blood, day 44, group 3 #8

description: Library name: PR3287_068_b


title: blood, day 12, group 4 #3

description: Library name: PR3287_073_b

value: group 4

value: day 12


title: blood, day 44, group 3 #6

description: Library name: PR3287_066_b

value: NC/Nga

value: male


title: RNA_seq_MGUS_CB19

description:
Library name: Sample_1
RNAseq of CD138+ plasma cells from CB19 sample

value: bone marrow


title: blood, day 12, group 4 #4

description: Library name: PR3287_074_b


title: RNA_seq_KMS27-002_siNRF1

description: RNAseq siNRF1 on KMS27-002 cell line

extract_protocol:
KMS27 and KMS18 cell lines were maintained in RPMI1640 medium supplemented with 10% FBS and 1% glutamine. Total RNA was extracted from an equal number of viable cells using QIAzol Lysis Reagent (Qiagen) and purified from DNA contamination through a digestion step with the RNase-Free DNase Set (Qiagen).
RNA libraries were generated using an equal amount of RNA from each cell line sample, following the protocol of the Illumina Stranded Total RNA Prep kit, with an initial ribosomial depletion step using Ribo-Zero Plus from Illumina.

value: primary MM plasma cells

value: Multiple Myeloma


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_H10_S193

description: responder

value: peripheral blood

value: NKcells

value: Female


title: 15004024, CD4+ T cells, control

description: Library name: 15004024

value: control


title: blood, day 44, group 3 #5

description: Library name: PR3287_065_b

value: whole blood

value: WT


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_H8_S191

description: responder


title: blood, day 44, group 3 #10

description: Library name: PR3287_070_b

value: conventional

value: group 3


title: 15002012, CD4+ T cells, control

description: Library name: 15002012

value: CD4+ T cells

value: female


title: 15009003, CD4+ T cells, asthma case

description: Library name: 15009003

value: case

value: Barbados


title: RNA_seq_KMS27-001_siNRF1

description: RNAseq siNRF1 on KMS27-001 cell line

value: CD138+ plasma cells


title: 15001008, CD4+ T cells, asthma case

description: Library name: 15001008

value: male


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_H7_S190

description: responder


title: RNA_seq_KMS27-003_CN

description: RNAseq CN on KMS27-003 cell line

value: bone marrow


title: blood, day 44, group 3 #7

description: Library name: PR3287_067_b

value: NC/Nga

value: day 44


title: blood, day 44, group 3 #3

description: Library name: PR3287_063_b


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_H5_S188

description: responder

value: peripheral blood


title: RNA_seq_KMS27-002_CN

description: RNAseq CN on KMS27-002 cell line

value: primary MM plasma cells

value: Multiple Myeloma


title: RNA_seq_KMS27-001_CN

description: RNAseq CN on KMS27-001 cell line


title: 15035001, CD4+ T cells, control

description: Library name: 15035001

value: control


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_H3_S186

description: responder

value: NKcells

value: Female


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_H4_S187

description: responder


title: blood, day 44, group 3 #2

description: Library name: PR3287_062_b

value: whole blood

value: WT

value: conventional


title: 15600187, CD4+ T cells, control

description: Library name: 15600187

value: CD4+ T cells


title: blood, day 44, group 3 #4

description: Library name: PR3287_064_b

value: group 3


title: 15600141, CD4+ T cells, control

description: Library name: 15600141

value: Barbados


title: 15600204, CD4+ T cells, control

description: Library name: 15600204


title: RNA_seq_KMS18-002_siNRF1

description: RNAseq siNRF1 on KMS18-002 cell line

value: CD138+ plasma cells


title: blood, day 44, group 3 #1

description: Library name: PR3287_061_b

value: male


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_H1_S184

description: responder


title: blood, day 9, group 3 #10

description: Library name: PR3287_060_b

value: day 9


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_H2_S185

description: responder


title: RNA_seq_KMS18-003_siNRF1

description: RNAseq siNRF1 on KMS18-003 cell line

value: bone marrow


title: blood, day 9, group 3 #9

description: Library name: PR3287_059_b

value: NC/Nga


title: RNA_seq_KMS27-003_siNRF1

description: RNAseq siNRF1 on KMS27-003 cell line


title: 15600207, CD4+ T cells, control

description: Library name: 15600207


title: 15600209, CD4+ T cells, control

description: Library name: 15600209


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_G12_S183

description: responder

value: peripheral blood


title: blood, day 9, group 3 #8

description: Library name: PR3287_058_b


title: 15600178, CD4+ T cells, control

description: Library name: 15600178


title: blood, day 9, group 3 #7

description: Library name: PR3287_057_b


title: 15600166, CD4+ T cells, control

description: Library name: 15600166

value: female


title: RNA_seq_KMS18-002_CN

description: RNAseq CN on KMS18-002 cell line

value: primary MM plasma cells

value: Multiple Myeloma


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_G10_S181

description: responder

value: NKcells


title: blood, day 9, group 3 #6

description: Library name: PR3287_056_b


title: blood, day 9, group 3 #4

description: Library name: PR3287_054_b


title: blood, day 9, group 3 #5

description: Library name: PR3287_055_b


title: RNA_seq_KMS18-001_siNRF1

description: RNAseq siNRF1 on KMS18-001 cell line


title: Cut&Tag_MM196-H3k9me3_MM_rep2

description: Cut&Tag anti-H3k9me3 on MM196 plasma cells (replicate 2)

data_processing:
Sequence reads were mapped to hg19 reference genome by using bwa v.0.7.17 with default parameters.
The alignment in sam format were converted into binary format, sorted and indexed by utilizing respectively view, sort and index functions of samtools v.1.2.
Peaks were called with MACS2 v.2.2.6 with parameters -B --broad --fromat AUTO -q 0.1 -g hs.
Peaks overlapping blacklisted regions of hg19 were filtered out with the intersect function of bedtools v.2.29.2.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing the chromosome, start, end information of each detected peak for each sample.
Library strategy: CUT&TAG

extract_protocol:
MM196 and MM217 cell lines were maintained in OPTI-MEM supplemented with 15% FBS and 1% glutamine. Subsequently, both cell lines were washed twice with 1x PBS.
The libraries were constructed from nuclei extracted from 100,000 cells and processed according to the CUT&Tag protocol from Epicypher.

tag: antibody


title: blood, day 9, group 3 #2

description: Library name: PR3287_052_b


title: RNA_seq_KMS18-003_CN

description: RNAseq CN on KMS18-003 cell line


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_G8_S179

description: responder

value: Female


title: 15600183, CD4+ T cells, control

description: Library name: 15600183

value: control


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_G9_S180

description: responder


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_G11_S182

description: responder


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_G7_S178

description: responder


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_G6_S177

description: responder


title: blood, day 9, group 3 #3

description: Library name: PR3287_053_b

value: whole blood

value: WT


title: Cut&Tag_MM196-H3k9me3_MM_rep1

description: Cut&Tag anti-H3k9me3 on MM196 plasma cells (replicate 1)


title: 15600161, CD4+ T cells, control

description: Library name: 15600161

value: CD4+ T cells


title: 15600159, CD4+ T cells, control

description: Library name: 15600159


title: 15600160, CD4+ T cells, control

description: Library name: 15600160


title: blood, day 9, group 3 #1

description: Library name: PR3287_051_b

value: conventional

value: group 3


title: 15600167, CD4+ T cells, control

description: Library name: 15600167

value: Barbados


title: Cut&Tag_MM196-H3k4mono_MM_rep1

description: Cut&Tag anti-H3k4mono on MM196 plasma cells (replicate 1)

value: CD138+ plasma cells


title: RNA_seq_KMS18-001_CN

description: RNAseq CN on KMS18-001 cell line


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_G4_S175

description: responder


title: blood, day 40, group 2 #10

description: Library name: PR3287_050_b

value: male

value: group 2

value: day 40


title: 15600129, CD4+ T cells, control

description: Library name: 15600129


title: Cut&Tag_MM196-H3k4me3_MM_rep1

description: Cut&Tag anti-H3k4me3 on MM196 plasma cells (replicate 1)

value: bone marrow


title: Cut&Tag_MM196-H3k4me3_MM_rep2

description: Cut&Tag anti-H3k4me3 on MM196 plasma cells (replicate 2)


title: 15600177, CD4+ T cells, control

description: Library name: 15600177

value: female


title: Cut&Tag_MM196-H3k4mono_MM_rep2

description: Cut&Tag anti-H3k4mono on MM196 plasma cells (replicate 2)

value: primary MM plasma cells


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_G2_S173

description: responder

value: peripheral blood


title: blood, day 40, group 2 #9

description: Library name: PR3287_049_b

value: NC/Nga


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_G5_S176

description: responder

value: NKcells

value: Female


title: Cut&Tag_MM196-H3k27me3_MM_rep2

description: Cut&Tag anti-H3k27me3 on MM196 plasma cells (replicate 2)

value: Multiple Myeloma


title: 15600152, CD4+ T cells, control

description: Library name: 15600152

value: control


title: Cut&Tag_MM196-H3k27me3_MM_rep1

description: Cut&Tag anti-H3k27me3 on MM196 plasma cells (replicate 1)


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_C4_S127

description: responder


title: 15600153, CD4+ T cells, control

description: Library name: 15600153

value: CD4+ T cells


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_G1_S172

description: responder


title: blood, day 40, group 2 #8

description: Library name: PR3287_048_b

value: whole blood

value: WT

value: conventional


title: 15600158, CD4+ T cells, control

description: Library name: 15600158

value: Barbados


title: Cut&Tag_MM196-H3k27Ac_MM_rep1

description: Cut&Tag anti-H3k27Ac on MM196 plasma cells (replicate 1)

value: CD138+ plasma cells


title: blood, day 40, group 2 #7

description: Library name: PR3287_047_b

value: male

value: group 2


title: blood, day 40, group 2 #6

description: Library name: PR3287_046_b

value: day 40


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_C11_S134

description: responder


title: 15600137, CD4+ T cells, control

description: Library name: 15600137

value: female


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_C2_S125

description: responder


title: Cut&Tag_MM196-H3k27Ac_MM_rep2

description: Cut&Tag anti-H3k27Ac on MM196 plasma cells (replicate 2)

value: bone marrow

value: primary MM plasma cells


title: Cut&Tag_MM217-H3k9me3_MM_rep2

description: Cut&Tag anti-H3k9me3 on MM217 plasma cells (replicate 2)


title: blood, day 40, group 2 #5

description: Library name: PR3287_045_b

value: NC/Nga


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_B10_S121

description: responder

value: peripheral blood

value: NKcells


title: blood, day 40, group 2 #4

description: Library name: PR3287_044_b


title: 15600133, CD4+ T cells, control

description: Library name: 15600133


title: Cut&Tag_MM217-H3k9me3_MM_rep1

description: Cut&Tag anti-H3k9me3 on MM217 plasma cells (replicate 1)

value: Multiple Myeloma


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_B6_S117

description: responder

value: Female


title: blood, day 40, group 2 #3

description: Library name: PR3287_043_b


title: 15600150, CD4+ T cells, control

description: Library name: 15600150

value: CD4+ T cells

value: control


title: blood, day 40, group 2 #2

description: Library name: PR3287_042_b

value: whole blood

value: WT


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_B3_S114

description: responder


title: Cut&Tag_MM217-H3k4mono_MM_rep2

description: Cut&Tag anti-H3k4mono on MM217 plasma cells (replicate 2)


title: 15600131, CD4+ T cells, control

description: Library name: 15600131

value: Barbados


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_B2_S113

description: responder


title: Cut&Tag_MM217-H3k4mono_MM_rep1

description: Cut&Tag anti-H3k4mono on MM217 plasma cells (replicate 1)

value: CD138+ plasma cells


title: 15600146, CD4+ T cells, control

description: Library name: 15600146

value: male


title: 15600149, CD4+ T cells, control

description: Library name: 15600149


title: blood, day 5, group 2 #9

description: Library name: PR3287_039_b

value: conventional

value: group 2

value: day 5


title: 15600155, CD4+ T cells, control

description: Library name: 15600155

value: female


title: blood, day 40, group 2 #1

description: Library name: PR3287_041_b

value: day 40


title: blood, day 5, group 2 #10

description: Library name: PR3287_040_b

value: NC/Nga


title: Cut&Tag_MM217-H3k4me3_MM_rep1

description: Cut&Tag anti-H3k4me3 on MM217 plasma cells (replicate 1)

value: bone marrow

value: primary MM plasma cells


title: Cut&Tag_MM217-H3k27me3_MM_rep2

description: Cut&Tag anti-H3k27me3 on MM217 plasma cells (replicate 2)

value: Multiple Myeloma


title: Cut&Tag_MM217-H3k4me3_MM_rep2

description: Cut&Tag anti-H3k4me3 on MM217 plasma cells (replicate 2)


title: blood, day 5, group 2 #8

description: Library name: PR3287_038_b


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_A7_S106

description: responder

value: peripheral blood

value: NKcells

value: Female


title: 15600127, CD4+ T cells, control

description: Library name: 15600127

value: CD4+ T cells

value: control


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_A5_S104

description: responder


title: 15600143, CD4+ T cells, control

description: Library name: 15600143

value: Barbados


title: blood, day 5, group 2 #7

description: Library name: PR3287_037_b

value: whole blood

value: WT


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_A6_S105

description: responder


title: Cut&Tag_MM217-H3k27me3_MM_rep1

description: Cut&Tag anti-H3k27me3 on MM217 plasma cells (replicate 1)

value: CD138+ plasma cells


title: Cut&Tag_MM217-H3k27Ac_MM_rep2

description: Cut&Tag anti-H3k27Ac on MM217 plasma cells (replicate 2)


title: 15600124, CD4+ T cells, control

description: Library name: 15600124

value: male


title: blood, day 5, group 2 #6

description: Library name: PR3287_036_b

value: conventional

value: group 2

value: day 5


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_A4_S103

description: responder


title: 15600066, CD4+ T cells, control

description: Library name: 15600066


title: Cut&Tag_MM217-H3k27Ac_MM_rep1

description: Cut&Tag anti-H3k27Ac on MM217 plasma cells (replicate 1)


title: blood, day 5, group 2 #5

description: Library name: PR3287_035_b

value: NC/Nga


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_A3_S102

description: responder


title: 15600094, CD4+ T cells, control

description: Library name: 15600094

value: female


title: ChIP_seq_CB254_NRF1

description: ChIPseq anti-NRF1 on CD138+ Monoclonal gammopathy of undetermined significance plasma cells

data_processing:
Sequence reads were mapped to hg19 reference genome by using bwa v.0.7.17 with default parameters.
The alignment in sam format were converted into binary format, sorted and indexed by utilizing respectively view, sort and index functions of samtools v.1.2.
Peaks were called with MACS2 v.2.2.6 with parameters -B --broad --format AUTO -q 0.1 -g hs.
Peaks overlapping blacklisted regions of hg19 were filtered out with the intersect function of bedtools v.2.29.2.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing the chromosome, start, end information of each detected peak for each sample.

extract_protocol:
Plasma cells from bone marrow were isolated using the Miltenyi CD138 Multiple Myeloma MACS kit, following the manufacturer's standard protocol.
ChIP-seq libraries for NRF1 were prepared according to the ChIPmentation protocol (Christian Schmidl et al., Nature Methods, 2015) using Tn5 transposase.

value: bone marrow

value: primary plasma cells


title: MDanderson_NKcells_patient6_timepoint1_sc_smartseq_pl1_A11_S110

description: responder

value: peripheral blood


title: MDanderson_DNKcells_patient10_timepoint1d7_sc_smartseq_pl1_B12_S104

description: non-responder

value: DNKcells


title: blood, day 5, group 2 #4

description: Library name: PR3287_034_b


title: 15600074, CD4+ T cells, control

description: Library name: 15600074


title: MDanderson_DNKcells_patient10_timepoint1d7_sc_smartseq_pl1_A6_S55

description: non-responder

value: Female


title: 15600126, CD4+ T cells, control

description: Library name: 15600126

value: CD4+ T cells


title: ChIP_seq_CB21_NRF1

value: Monoclonal gammopathy of undetermined significance


title: MDanderson_DNKcells_patient10_timepoint1d7_sc_smartseq_pl1_B11_S96

description: non-responder


title: blood, day 5, group 2 #2

description: Library name: PR3287_032_b


title: blood, day 5, group 2 #3

description: Library name: PR3287_033_b


title: ChIP_seq_CB43_NRF1


title: 15600115, CD4+ T cells, control

description: Library name: 15600115

value: control

value: Barbados


title: ChIP_seq_MM57_NRF1

description: ChIPseq anti-NRF1 on CD138+ Multiple Myeloma plasma cells

value: Multiple Myeloma


title: blood, day 44, group 1 #10

description: Library name: PR3287_030_b

value: whole blood

value: WT

value: group 1

value: day 44


title: MDanderson_DNKcells_patient10_timepoint1d7_sc_smartseq_pl1_A5_S47

description: non-responder


title: MDanderson_DNKcells_patient10_timepoint1d7_sc_smartseq_pl1_A3_S31

description: non-responder


title: blood, day 5, group 2 #1

description: Library name: PR3287_031_b

value: male

value: conventional

value: group 2

value: day 5


title: 15446001, CD4+ T cells, control

description: Library name: 15446001


title: 15600114, CD4+ T cells, control

description: Library name: 15600114


title: MDanderson_DNKcells_patient10_timepoint1d7_sc_smartseq_pl1_A4_S39

description: non-responder


title: 15600057, CD4+ T cells, control

description: Library name: 15600057

value: female


title: ChIP_seq_MM52_NRF1

value: bone marrow

value: primary plasma cells

value: CD138+ plasma cells


title: MDanderson_DNKcells_patient10_timepoint1d7_sc_smartseq_pl1_A2_S23

description: non-responder

value: peripheral blood

value: DNKcells

value: Female


title: blood, day 44, group 1 #9

description: Library name: PR3287_029_b

value: NC/Nga


title: blood, day 44, group 1 #8

description: Library name: PR3287_028_b


title: MDanderson_DNKcells_patient10_timepoint1d7_sc_smartseq_pl1_A1_S15

description: non-responder


title: ChIP_seq_MM267_NRF1

value: Multiple Myeloma


title: 15600122, CD4+ T cells, control

description: Library name: 15600122

value: CD4+ T cells

value: control

value: Barbados


title: 15600063, CD4+ T cells, control

description: Library name: 15600063


title: blood, day 44, group 1 #7

description: Library name: PR3287_027_b

value: whole blood

value: WT

value: group 1

value: day 44


title: ChIP_seq_MM266_NRF1


title: ChIP_seq_CB45_NRF1

value: Monoclonal gammopathy of undetermined significance


title: 15600033, CD4+ T cells, control

description: Library name: 15600033

value: female


title: ChIP_seq_KMS18-NRF1

description: ChIPseq anti-NRF1 on KMS18

data_processing:
Sequence reads were mapped to hg19 reference genome by using bwa v.0.7.17 with default parameters.
The alignment in sam format were converted into binary format, sorted and indexed by utilizing respectively view, sort and index functions of samtools v.1.2.
Peaks were called with MACS2 v.2.2.6 with parameters -B --broad --format AUTO -q 0.1 -g hs.
Peaks overlapping blacklisted regions of hg19 were filtered out with the intersect function of bedtools v.2.29.2.
Peaks from KMS27 cell line were combined and sorted by chromosome, start, and end positions using the cat and sort functions from bash. Moreover, the cumulative list of peaks was merged using the merge function from bedtools v.2.29.2 to treat genomic regions that are close together as unique peaks.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing the chromosome, start, end information of each detected peak for each sample.

extract_protocol:
KMS27 and KMS18 cell lines were maintained in RPMI 1640 medium supplemented with 10% FBS and 1% glutamine. MM196 and MM217 cell lines were maintained in OPTI-MEM supplemented with 15% FBS and 1% glutamine. Subsequently, all cell lines were washed twice with 1x PBS.
ChIP-seq libraries for NRF1 were prepared according to the ChIPmentation protocol (Christian Schmidl et al., Nature Methods, 2015) using Tn5 transposase.

value: plsma cell mulitple myeloma


title: blood, day 44, group 1 #6

description: Library name: PR3287_026_b

value: male

value: conventional


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_D9_S146

description: non-responder

value: peripheral blood

value: Bcells


title: 15600030, CD4+ T cells, control

description: Library name: 15600030


title: ChIP_seq_MM54_NRF1

value: bone marrow

value: primary plasma cells

value: CD138+ plasma cells


title: ChIP_seq_MM217-NRF1

description: ChIPseq anti-NRF1 on MM217

value: primary MM plasma cells

value: Multiple Myeloma


title: blood, day 44, group 1 #5

description: Library name: PR3287_025_b

value: NC/Nga


title: 15600090, CD4+ T cells, control

description: Library name: 15600090

value: CD4+ T cells

value: control

value: Barbados


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_D6_S134

description: non-responder

value: Female


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_D5_S130

description: non-responder


title: blood, day 44, group 1 #3

description: Library name: PR3287_023_b

value: whole blood

value: WT

value: group 1

value: day 44


title: blood, day 44, group 1 #2

description: Library name: PR3287_022_b

value: male

value: conventional


title: 15700050, CD4+ T cells, asthma case

description: Library name: 15700050

value: case


title: 15600079, CD4+ T cells, control

description: Library name: 15600079


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_D7_S138

description: non-responder

value: peripheral blood

value: Bcells


title: ChIP_seq_MM196-NRF1

description: ChIPseq anti-NRF1 on MM196

value: bone marrow

value: CD138+ plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_D4_S126

description: non-responder


title: 15600113, CD4+ T cells, control

description: Library name: 15600113


title: blood, day 44, group 1 #1

description: Library name: PR3287_021_b


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_D3_S122

description: non-responder


title: ATAC_seq_CB23_MGUS

description: ATACseq of CD138+ MGUS plasma cells

data_processing:
Sequence reads were mapped to hg19 reference genome by using bwa v.0.7.17 with default parameters.
The alignment in sam format were converted into binary format, sorted and indexed by utilizing respectively view, sort and index functions of samtools v.1.2.
Peaks were called with MACS2 v.2.2.6 with parameters -B --SPMR --broad --broad-cutoff 0.1.
Peaks overlapping blacklisted regions of hg19 were filtered out with the intersect function of bedtools v.2.29.2.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing the chromosome, start, end information of each detected peak for each sample.

extract_protocol:
Plasma cells from bone marrow were isolated using the Miltenyi CD138 Multiple Myeloma MACS kit, following the manufacturer's standard protocol.
ATAC-seq was performed in accordance with the Buenrostro protocol (Curr Protoc Mol Biol. 2015). Starting with 50.000 CD138+ plasma cells, library construction was performed using the hyperactive transposase Tn5. NGS adapters were pre-loaded onto the transposase, allowing simultaneous chromatin fragmentation and adapter integration into open chromatin regions.

value: primary MGUS plasma cells

value: Monoclonal gammopathy of undetermined significance


title: blood, day 2, group 1 #10

description: Library name: PR3287_020_b

value: NC/Nga

value: day 2


title: ChIP_seq_Kms27-NRF1_rep1

description: ChIPseq anti-NRF1 on Kms27 rep1

value: B lymphocyte

value: Multiple Myeloma


title: 15600059, CD4+ T cells, control

description: Library name: 15600059

value: CD4+ T cells

value: female

value: control

value: Barbados


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_D8_S142

description: non-responder

value: Female


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_D2_S118

description: non-responder


title: ATAC_seq_CB22_MGUS

description: ATACseq of CD138+ MGUS plasma cells


title: blood, day 2, group 1 #9

description: Library name: PR3287_019_b

value: whole blood

value: male

value: WT

value: conventional

value: group 1


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_D1_S114

description: non-responder

value: peripheral blood

value: Bcells


title: ATAC_seq_CB21_MGUS

description: ATACseq of CD138+ MGUS plasma cells

value: bone marrow

value: primary MGUS plasma cells

value: CD138+ plasma cells

value: Monoclonal gammopathy of undetermined significance


title: blood, day 44, group 1 #4

description: Library name: PR3287_024_b

value: NC/Nga

value: day 44


title: 15600049, CD4+ T cells, control

description: Library name: 15600049

value: CD4+ T cells

value: female


title: blood, day 2, group 1 #8

description: Library name: PR3287_018_b

value: day 2


title: ATAC_seq_CB20_MGUS

description: ATACseq of CD138+ MGUS plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_D12_S158

description: non-responder

value: Female


title: 15600046, CD4+ T cells, control

description: Library name: 15600046

value: control

value: Barbados


title: blood, day 2, group 1 #7

description: Library name: PR3287_017_b

value: whole blood

value: male

value: WT


title: ChIP_seq_Kms27-NRF1_rep2

description: ChIPseq anti-NRF1 on Kms27 rep2

value: peripheral blood

value: B lymphocyte

value: Multiple Myeloma


title: 15600100, CD4+ T cells, control

description: Library name: 15600100


title: blood, day 2, group 1 #6

description: Library name: PR3287_016_b

value: conventional

value: group 1


title: ATAC_seq_CB19_MGUS

description: ATACseq of CD138+ MGUS plasma cells

value: bone marrow

value: primary MGUS plasma cells

value: CD138+ plasma cells

value: Monoclonal gammopathy of undetermined significance


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_D11_S154

description: non-responder

value: Bcells


title: 15600056, CD4+ T cells, control

description: Library name: 15600056

value: CD4+ T cells

value: female


title: ATAC_seq_CB18_MGUS

description: ATACseq of CD138+ MGUS plasma cells


title: blood, day 2, group 1 #5

description: Library name: PR3287_015_b

value: NC/Nga

value: day 2


title: ATAC_seq_CB16_MGUS

description: ATACseq of CD138+ MGUS plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_C9_S145

description: non-responder

value: Female


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_D10_S150

description: non-responder


title: blood, day 2, group 1 #3

description: Library name: PR3287_013_b

value: whole blood

value: male


title: 15700049, CD4+ T cells, asthma case

description: Library name: 15700049

value: case

value: Barbados


title: 15600112, CD4+ T cells, control

description: Library name: 15600112

value: control


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_C8_S141

description: non-responder

value: peripheral blood


title: ATAC_seq_CB14_MGUS

description: ATACseq of CD138+ MGUS plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_C7_S137

description: non-responder


title: ATAC_seq_CB09_MGUS

description: ATACseq of CD138+ MGUS plasma cells


title: 15600051, CD4+ T cells, control

description: Library name: 15600051


title: blood, day 2, group 1 #1

description: Library name: PR3287_011_b

value: WT

value: conventional

value: group 1


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_C6_S133

description: non-responder


title: 15600035, CD4+ T cells, control

description: Library name: 15600035


title: blood, day 2, group 1 #2

description: Library name: PR3287_012_b


title: 15357002, CD4+ T cells, control

description: Library name: 15357002


title: ATAC_seq_CB01_MGUS

description: ATACseq of CD138+ MGUS plasma cells

value: bone marrow

value: primary MGUS plasma cells

value: CD138+ plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_C5_S129

description: non-responder

value: Bcells


title: blood, day 44, control #5

description: Library name: PR3287_010_b

value: specific-pathogen-free

value: day 44


title: blood, day 44, control #4

description: Library name: PR3287_009_b

value: NC/Nga


title: 15600014, CD4+ T cells, control

description: Library name: 15600014

value: CD4+ T cells

value: female


title: ATAC_seq_tumour_074_MM

description: ATACseq of CD138+ MM plasma cells

value: primary MM plasma cells

value: Multiple Myeloma


title: blood, day 44, control #3

description: Library name: PR3287_008_b

value: whole blood

value: male


title: ATAC_seq_tumour_073_MM

description: ATACseq of CD138+ MM plasma cells


title: blood, day 2, group 1 #4

description: Library name: PR3287_014_b

value: day 2


title: 15700048, CD4+ T cells, asthma case

description: Library name: 15700048

value: case

value: Barbados


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_C2_S117

description: non-responder

value: peripheral blood

value: Female


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_C4_S125

description: non-responder


title: ATAC_seq_tumour_072_MM

description: ATACseq of CD138+ MM plasma cells

value: bone marrow


title: 15700047, CD4+ T cells, asthma case

description: Library name: 15700047


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_C1_S113

description: non-responder


title: ATAC_seq_tumour_071_MM

description: ATACseq of CD138+ MM plasma cells

value: CD138+ plasma cells


title: blood, day 44, control #1

description: Library name: PR3287_006_b

value: WT

value: control


title: 15700045, CD4+ T cells, asthma case

description: Library name: 15700045


title: blood, day 16, control #5

description: Library name: PR3287_005_b

value: specific-pathogen-free

value: day 16


title: 15700046, CD4+ T cells, asthma case

description: Library name: 15700046

value: CD4+ T cells


title: ATAC_seq_tumour_070_MM

description: ATACseq of CD138+ MM plasma cells


title: ATAC_seq_CB02_MGUS

description: ATACseq of CD138+ MGUS plasma cells

value: primary MGUS plasma cells

value: Monoclonal gammopathy of undetermined significance


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_C12_S157

description: non-responder

value: Bcells


title: 15600020, CD4+ T cells, control

description: Library name: 15600020

value: female


title: ATAC_seq_tumour_069_MM

description: ATACseq of CD138+ MM plasma cells

value: primary MM plasma cells

value: Multiple Myeloma


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_C11_S153

description: non-responder


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_C10_S149

description: non-responder


title: ATAC_seq_tumour_068_MM

description: ATACseq of CD138+ MM plasma cells


title: blood, day 16, control #3

description: Library name: PR3287_003_b

value: whole blood

value: NC/Nga

value: male


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_C3_S121

description: non-responder

value: peripheral blood

value: Female


title: 15700039, CD4+ T cells, asthma case

description: Library name: 15700039

value: case

value: Barbados


title: ATAC_seq_tumour_067_MM

description: ATACseq of CD138+ MM plasma cells

value: bone marrow

value: CD138+ plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_B9_S144

description: non-responder


title: 15484001, CD4+ T cells, control

description: Library name: 15484001

value: control


title: blood, day 44, control #2

description: Library name: PR3287_007_b

value: WT

value: specific-pathogen-free

value: day 44


title: ATAC_seq_tumour_060_MM

description: ATACseq of CD138+ MM plasma cells


title: 15700036, CD4+ T cells, asthma case

description: Library name: 15700036

value: CD4+ T cells


title: blood, day 16, control #1

description: Library name: PR3287_001_b

value: day 16


title: ATAC_seq_tumour_059_MM

description: ATACseq of CD138+ MM plasma cells

value: primary MM plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_B7_S136

description: non-responder

value: Bcells


title: 15700035, CD4+ T cells, asthma case

description: Library name: 15700035

value: female


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_B6_S132

description: non-responder


title: ATAC_seq_tumour_057_MM

description: ATACseq of CD138+ MM plasma cells

value: Multiple Myeloma


title: E10-5-MLF1_WT-2-2

city: Nanjing

first: Jimiao

last: Gao

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

description: Library name: Sample 37

data_processing:
Raw data were filtered and processed to obtain clean data with high quality and aligned to the mouse reference genome GRCm38/mm10 with STAR software (v2.5.3a).
Assembly and quantification of the transcripts were accomplished with RESM software (v1.3.3) guided by the Ensembl gtf gene annotation file.
Read counts were used for the measurements of the relative abundance of the transcripts.
Assembly: GRCm38/mm10
Supplementary files format and content: RESULTS files include read count, FPKM, TPM for each sample

source_name: heart

extract_protocol:
Total RNA from the heart tissues of ciliary gene knockout/mutant mice and wild-type littermate mice at E10.5 was extracted with TRIzolTM X-100 (Thermo, 15596018) and a total amount of 2 µg RNA per sample was used for RNA library construction.
RNA libraries were then generated using the NEBNext® Ultra™ RNA Library Prep Kit (Illumina, E7530) following manufacturer’s protocols.

value: heart

value: wild-type