title: 15700033, CD4+ T cells, asthma case

description: Library name: 15700033

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.


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_B5_S128

status: Public on Sep 09 2025

type: SRA

city: Houston

first: Katayoun

last: Rezvani

address: 1515 Holcombe Blvd

department: Department of Stem Cell Transplantation and Cellular Therapy

country: USA

institute: The University of Texas MD Anderson Cancer Center

description: non-responder

library_source: transcriptomic single cell

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.

molecule: total RNA

organism: Homo sapiens

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).

tag: tissue

value: peripheral blood

tag: cell type

value: Bcells

tag: genotype

value: Female

tag: treatment


title: 15700041, CD4+ T cells, asthma case

city: Aurora

first: Randi

middle: K

last: Johnson

state: Colorado

address: 1890 N. Revere Court

institute: University of Colorado

description: Library name: 15700041

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

source_name: CD4+ T cells

value: CD4+ T cells

tag: age

tag: Sex

value: female

tag: genetic pc1

tag: asthma

value: case

tag: geo loc_name

value: Barbados


title: blood, day 16, control #4

city: shimogyo-ku

first: Tomohiro

last: Sensui

address: chudoji, awatacho

country: Japan

institute: Maruho

description: Library name: PR3287_004_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

organism: Mus musculus

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: male

value: WT

tag: condition

value: specific-pathogen-free

tag: group

value: control

tag: dermatitis score

tag: time

value: day 16


title: ATAC_seq_tumour_056_MM

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: ATACseq of CD138+ MM plasma cells

library_source: genomic

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.

molecule: genomic DNA

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.
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: bone marrow

tag: cell line

value: primary MM plasma cells

value: CD138+ plasma cells

value: Multiple Myeloma


title: E10-5-MLF1_WT-2-1

city: Nanjing

first: Jimiao

last: Gao

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

country: China

institute: Nanjing Medical University

description: Library name: Sample 36

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


title: ATAC_seq_tumour_055_MM

description: ATACseq of CD138+ MM plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_B4_S124

description: non-responder

value: peripheral blood

value: Bcells

value: Female


title: 15700029, CD4+ T cells, asthma case

description: Library name: 15700029

value: CD4+ T cells

value: female

value: case

value: Barbados


title: E10-5-MLF1-3

description: Library name: Sample 35

value: Mlf1 KO


title: 15700028, CD4+ T cells, asthma case

description: Library name: 15700028


title: ATAC_seq_tumour_054_MM

description: ATACseq of CD138+ MM plasma cells


title: blood, day 16, control #2

description: Library name: PR3287_002_b

value: whole blood

value: NC/Nga

value: male

value: WT

value: specific-pathogen-free


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_B3_S120

description: non-responder


title: E10-5-MLF1-2

description: Library name: Sample 34


title: ATAC_seq_tumour_051_MM

description: ATACseq of CD138+ MM plasma cells

value: bone marrow

value: primary MM plasma cells

value: CD138+ plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_B8_S140

description: non-responder


title: 15700026, CD4+ T cells, asthma case

description: Library name: 15700026


title: E10-5-MLF1-1

description: Library name: Sample 33

value: heart


title: E10-5-MLF1_WT-2-3

description: Library name: Sample 38

value: wild-type


title: ATAC_seq_tumour_048_MM

description: ATACseq of CD138+ MM plasma cells

value: Multiple Myeloma


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_B1_S112

description: non-responder

value: peripheral blood

value: Bcells

value: Female


title: ATAC_seq_tumour_047_MM

description: ATACseq of CD138+ MM plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_B12_S156

description: non-responder


title: 15700024, CD4+ T cells, asthma case

description: Library name: 15700024

value: CD4+ T cells

value: female

value: case


title: E10-5_Tekt3-WT-6-2

description: Library name: Sample 31


title: ATAC_seq_tumour_046_MM

description: ATACseq of CD138+ MM plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_B11_S152

description: non-responder


title: 15600022, CD4+ T cells, control

description: Library name: 15600022

value: control

value: Barbados


title: E10-5_Tekt3-WT-6-1

description: Library name: Sample 30


title: ATAC_seq_tumour_045_MM

description: ATACseq of CD138+ MM plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_B10_S148

description: non-responder


title: E10-5-Tekt3-3

description: Library name: Sample 29

value: Tekt3 KO


title: 15700022, CD4+ T cells, asthma case

description: Library name: 15700022


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_A9_S143

description: non-responder


title: 15700027, CD4+ T cells, asthma case

description: Library name: 15700027


title: 15700021, CD4+ T cells, asthma case

description: Library name: 15700021

value: male


title: ATAC_seq_tumour_043_MM

description: ATACseq of CD138+ MM plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_A8_S139

description: non-responder


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_B2_S116

description: non-responder


title: 15600016, CD4+ T cells, control

description: Library name: 15600016


title: ATAC_seq_tumour_042_MM

description: ATACseq of CD138+ MM plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_A7_S135

description: non-responder


title: E10-5_Tekt3-WT-6-3

description: Library name: Sample 32


title: 15700025, CD4+ T cells, asthma case

description: Library name: 15700025


title: 15600010, CD4+ T cells, control

description: Library name: 15600010


title: E10-5_Sptbn5-WT-5-3

description: Library name: Sample 26


title: ATAC_seq_tumour_041_MM

description: ATACseq of CD138+ MM plasma cells


title: E10-5_Sptbn5-WT-5-2

description: Library name: Sample 25


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_A6_S131

description: non-responder


title: 15600011, CD4+ T cells, control

description: Library name: 15600011


title: ATAC_seq_tumour_040_MM

description: ATACseq of CD138+ MM plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_A5_S127

description: non-responder


title: 15222002, CD4+ T cells, control

description: Library name: 15222002


title: E10-5_Sptbn5-WT-5-1

description: Library name: Sample 24


title: ATAC_seq_tumour_039_MM

description: ATACseq of CD138+ MM plasma cells


title: E10-5-Sptbn5-3

description: Library name: Sample 23

value: Sptbn5 KO


title: 15260001, CD4+ T cells, asthma case

description: Library name: 15260001


title: ATAC_seq_tumour_044_MM

description: ATACseq of CD138+ MM plasma cells

value: bone marrow


title: E10-5-Tekt3-2

description: Library name: Sample 28


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_A4_S123

description: non-responder


title: ATAC_seq_tumour_038_MM

description: ATACseq of CD138+ MM plasma cells

value: primary MM plasma cells


title: E10-5-Tekt3-1

description: Library name: Sample 27


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_A3_S119

description: non-responder


title: 15383001, CD4+ T cells, asthma case

description: Library name: 15383001


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_A2_S115

description: non-responder


title: 15700019, CD4+ T cells, asthma case

description: Library name: 15700019


title: ATAC_seq_tumour_036_MM

description: ATACseq of CD138+ MM plasma cells

value: CD138+ plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_A1_S111

description: non-responder


title: E10-5-Sptbn5-1

description: Library name: Sample 21

value: heart


title: 15423001, CD4+ T cells, asthma case

description: Library name: 15423001


title: E10-5_Ppef2-WT-7-2

description: Library name: Sample 19

value: wild-type


title: ATAC_seq_tumour_035_MM

description: ATACseq of CD138+ MM plasma cells

value: Multiple Myeloma


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_A12_S155

description: non-responder

value: peripheral blood


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_A11_S151

description: non-responder

value: Bcells


title: ATAC_seq_tumour_037_MM

description: ATACseq of CD138+ MM plasma cells


title: E10-5_Ppef2-WT-7-3

description: Library name: Sample 20


title: 15475001, CD4+ T cells, asthma case

description: Library name: 15475001


title: ATAC_seq_tumour_033_MM

description: ATACseq of CD138+ MM plasma cells


title: MDanderson_Bcells_patient10_timepoint3d28_sc_smartseq_pl3_A10_S147

description: non-responder

value: Female


title: E10-5-Ppef2-3

description: Library name: Sample 17

value: Ppef2 KO


title: 15345001, CD4+ T cells, asthma case

description: Library name: 15345001

value: CD4+ T cells

value: female


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_F9_S86

description: non-responder


title: ATAC_seq_tumour_031_MM

description: ATACseq of CD138+ MM plasma cells


title: 15600028, CD4+ T cells, control

description: Library name: 15600028

value: control


title: 15317001, CD4+ T cells, asthma case

description: Library name: 15317001

value: case

value: Barbados


title: E10-5-Ppef2-2

description: Library name: Sample 16


title: E10-5-Sptbn5-2

description: Library name: Sample 22


title: ATAC_seq_tumour_030_MM

description: ATACseq of CD138+ MM plasma cells


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_F8_S78

description: non-responder


title: E10-5-Ppef2-1

description: Library name: Sample 15


title: ATAC_seq_tumour_029_MM

description: ATACseq of CD138+ MM plasma cells


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_F7_S70

description: non-responder


title: 15298001, CD4+ T cells, asthma case

description: Library name: 15298001


title: 15700016, CD4+ T cells, asthma case

description: Library name: 15700016


title: E10-5_PKHD1L1-WT-3-3

description: Library name: Sample 14


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_F6_S62

description: non-responder


title: ATAC_seq_tumour_028_MM

description: ATACseq of CD138+ MM plasma cells


title: E10-5_PKHD1L1-WT-3-2

description: Library name: Sample 13


title: 15305001, CD4+ T cells, asthma case

description: Library name: 15305001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_F5_S54

description: non-responder


title: ATAC_seq_tumour_027_MM

description: ATACseq of CD138+ MM plasma cells


title: E10-5_Ppef2-WT-7-1

description: Library name: Sample 18


title: ATAC_seq_tumour_032_MM

description: ATACseq of CD138+ MM plasma cells


title: 15365001, CD4+ T cells, asthma case

description: Library name: 15365001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_F4_S46

description: non-responder


title: ATAC_seq_tumour_026_MM

description: ATACseq of CD138+ MM plasma cells


title: ATAC_seq_tumour_025_MM

description: ATACseq of CD138+ MM plasma cells


title: 15412001, CD4+ T cells, asthma case

description: Library name: 15412001

value: male


title: 15888009, CD4+ T cells, control

description: Library name: 15888009


title: E10-5-PKHD1L1-1

description: Library name: Sample 9

value: Pkhd1l1 KO


title: E10-5-PKHD1L1-2

description: Library name: Sample 10


title: ATAC_seq_tumour_024_MM

description: ATACseq of CD138+ MM plasma cells

value: bone marrow


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_F2_S30

description: non-responder


title: ATAC_seq_tumour_023_MM

description: ATACseq of CD138+ MM plasma cells

value: primary MM plasma cells


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_F1_S22

description: non-responder


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_F12_S110

description: non-responder


title: ATAC_seq_tumour_022_MM

description: ATACseq of CD138+ MM plasma cells

value: CD138+ plasma cells


title: E10-5_Agbl2_WT_4

description: Library name: Sample 8

value: heart


title: 15294001, CD4+ T cells, asthma case

description: Library name: 15294001


title: 15600003, CD4+ T cells, control

description: Library name: 15600003


title: E10-5_Agbl2_WT_3

description: Library name: Sample 7

value: wild-type


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_F11_S102

description: non-responder


title: ATAC_seq_tumour_020_MM

description: ATACseq of CD138+ MM plasma cells

value: Multiple Myeloma


title: E10-5_Agbl2_WT_2

description: Library name: Sample 6


title: E10-5_PKHD1L1-WT-3-1

description: Library name: Sample 12


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_F10_S94

description: non-responder

value: peripheral blood


title: ATAC_seq_tumour_021_MM

description: ATACseq of CD138+ MM plasma cells


title: 15178002, CD4+ T cells, asthma case

description: Library name: 15178002


title: E10-5_Agbl2_WT_1

description: Library name: Sample 5


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_E9_S85

description: non-responder

value: Bcells


title: ATAC_seq_tumour_019_MM

description: ATACseq of CD138+ MM plasma cells


title: E10-5_Agbl2_4

description: Library name: Sample 4

value: Agbl2 KO


title: E10-5-PKHD1L1-3

description: Library name: Sample 11


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_F3_S38

description: non-responder

value: Female


title: 15335001, CD4+ T cells, asthma case

description: Library name: 15335001

value: CD4+ T cells


title: 15381001, CD4+ T cells, asthma case

description: Library name: 15381001

value: female


title: ATAC_seq_tumour_018_MM

description: ATACseq of CD138+ MM plasma cells


title: 15358001, CD4+ T cells, asthma case

description: Library name: 15358001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_E8_S77

description: non-responder


title: 15487001, CD4+ T cells, control

description: Library name: 15487001

value: control


title: E10-5_Agbl2_3

description: Library name: Sample 3


title: ATAC_seq_tumour_016_MM

description: ATACseq of CD138+ MM plasma cells


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_E7_S69

description: non-responder


title: E10-5_Agbl2_2

description: Library name: Sample 2


title: 15500001, CD4+ T cells, control

description: Library name: 15500001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_E6_S61

description: non-responder


title: E10-5_Agbl2_1

description: Library name: Sample 1


title: 15424001, CD4+ T cells, asthma case

description: Library name: 15424001

value: case


title: ATAC_seq_tumour_012_MM

description: ATACseq of CD138+ MM plasma cells


title: Zfp_MB037 ChIP-seq (batch5)

city: Bethesda

first: Melania

last: Bruno

state: Maryland

address: 6 Center Drive

institute: National Institutes of Health

description: Library name: Zfp_MB037_ChIP_batch5

data_processing:
Reads were aligned to the Mus musculus GRCm39 reference genome assembly (GCF_000001635.27) for all the KZFP ChIP-seq experiments, using the Burrows-Wheeler Alignment (BWA) tool v0.7.17 .
Sam files were then converted into bam files with SAMtools v1.19, while removing eventually unmapped and duplicated reads, and retaining only primary alignments (samtools view -F 0x4,0x400,0x100,0x800 -b -h file.sam > file.bam).
Bam files were sorted and indexed with SAMtools and converted to bigwig normalized to 1x genome coverage (RPGC normalization) for each sample with deepTools v3.5.4 (bamCoverage --bam file.bam -o file.bw -of bigwig --binSize 10 --effectiveGenomeSize 2521902382 --normalizeUsing RPGC --extendReads 200)
ChIP bigwigs were further normalized by the input of the respective batch using deepTools (bigwigCompare -b1 ChIP.bw -b2 input.bw -o ChIP_input_ratio.bw -of bigwig --operation ratio –skipZeroOverZero --binSize 10)
Peaks from the KZFP ChIP-seq experiments were called using MACS2 v2.2.7.1 (macs2 callpeak -t ChIP.bam -c input.bam -f BAMPE -g 2521902382). Peaks with even 1bp overlap with peaks called in any of the negative control replicate samples were removed. Peaks were further filtered to only retain the ones with qValue =< 0.01 and fold enrichment over input of 10 (10xFE). For the samples that retained less than 20 peaks, fold enrichment over input of 5 was used as cutoff (5xFE).
Assembly: GRCm39
Supplementary files format and content: bigwig files of ChIP/input ratio after 1x genome coverage normalization (RPGC)
Supplementary files format and content: final peak files after filtering (only for KZFP ChIP)

extract_protocol:
Cells were counted and fixed in 1% formaldehyde for 10min at room temperature with gentle mixing. Fixation was quenched with 0.4M glycine for 5min at room temperature with gentle mixing. Cells were washed twice with cold PBS and cell pellet was frozen on dry ice and stored at -80ºC. Cells were lysed in cell lysis buffer (5mM PIPES pH8.0, 85mM KCl, 0.5% NP-40, 1X EDTA-free protease inhibitor cocktail (Roche, 5056489001)) for 10min on ice and homogenized using type-B dounce homogenizer. Released nuclei were pelleted and lysed in nuclei lysis buffer (50mM Tris-HCl pH8.0, 150mM NaCl, 2mM EDTA pH8.0, 1% NP-40, 0.5% Sodium Deoxycholate, 0.1% SDS, 1X EDTA-free protease inhibitor cocktail) to release chromatin. Chromatin was sonicated with a Bioruptor 300 (Diogenode), nuclear debris were then pelleted at 14000rpm for 15min at 4ºC and supernatant was used for chromatin immunoprecipitation. Sonicated chromatin from 30million cells was used for each ChIP.
DNA was purified with the DNA Clean & Concentrator-5 kit (Zymo Research, D4004). DNA libraries for NGS were obtained with the ThruPLEX DNA-Seq Kit (Takara, R400676) with DNA Single Index Kit -12S Set A and B (Takara, R400695 and R400695), following manufacturer instructions. Input samples for each experimental batch were mixed in equal amounts at the library preparation step to generate batch specific input samples.

value: embryo carcinoma


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_E5_S53

description: non-responder


title: Zfp_MB036 ChIP-seq (batch5)

description: Library name: Zfp_MB036_ChIP_batch5


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_E4_S45

description: non-responder


title: ATAC_seq_tumour_011_MM

description: ATACseq of CD138+ MM plasma cells


title: 15700012, CD4+ T cells, asthma case

description: Library name: 15700012

value: Barbados


title: 15243001, CD4+ T cells, asthma case

description: Library name: 15243001


title: ATAC_seq_tumour_010_MM

description: ATACseq of CD138+ MM plasma cells


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_E3_S37

description: non-responder


title: Mixed input from KZFP ChIP (batch5)

description: Library name: input_KZFP_ChIP_batch5


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_E2_S29

description: non-responder


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_E1_S21

description: non-responder


title: 15300001, CD4+ T cells, asthma case

description: Library name: 15300001


title: ATAC_seq_tumour_009_MM

description: ATACseq of CD138+ MM plasma cells


title: Zfp_MB035 ChIP-seq (batch5)

description: Library name: Zfp_MB035_ChIP_batch5


title: ATAC_seq_tumour_013_MM

description: ATACseq of CD138+ MM plasma cells


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_E12_S109

description: non-responder


title: Zfp_MB029 ChIP-seq (batch4)

description: Library name: Zfp_MB029_ChIP_batch4


title: ATAC_seq_tumour_002_MM

description: ATACseq of CD138+ MM plasma cells


title: 15227002, CD4+ T cells, asthma case

description: Library name: 15227002

value: male


title: ATAC_seq_tumour_003_MM

description: ATACseq of CD138+ MM plasma cells

value: bone marrow


title: 15303001, CD4+ T cells, asthma case

description: Library name: 15303001


title: Zfp_MB031 ChIP-seq (batch4)

description: Library name: Zfp_MB031_ChIP_batch4


title: 15227001, CD4+ T cells, asthma case

description: Library name: 15227001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_E11_S101

description: non-responder


title: 15319001, CD4+ T cells, asthma case

description: Library name: 15319001


title: ATAC_seq_tumour_001_MM

description: ATACseq of CD138+ MM plasma cells

value: primary MM plasma cells


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_E10_S93

description: non-responder


title: 15314001, CD4+ T cells, asthma case

description: Library name: 15314001


title: Zfp_MB028 ChIP-seq (batch4)

description: Library name: Zfp_MB028_ChIP_batch4


title: 15700010, CD4+ T cells, asthma case

description: Library name: 15700010


title: Zfp_MB027 ChIP-seq (batch4)

description: Library name: Zfp_MB027_ChIP_batch4


title: Zfp_MB026 ChIP-seq (batch4)

description: Library name: Zfp_MB026_ChIP_batch4


title: ATAC_seq_U266_MM_CELL_LINES

description: ATACseq of U266 cell lines

extract_protocol:
Cell lines were maintained in RPMI 1640 medium supplemented with 10% FBS and 1% glutamine. Subsequently, the cell lines were washed twice with 1x PBS.
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: B lymphocyte


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_D8_S76

description: non-responder


title: ATAC_seq_RPMI_MM_CELL_LINES

description: ATACseq of RPMI8226 cell lines


title: ATAC_seq_tumour_008_MM

description: ATACseq of CD138+ MM plasma cells

value: CD138+ plasma cells


title: ATAC_seq_KMS27_MM_CELL_LINES

description: ATACseq of KMS27 cell lines


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_D9_S84

description: non-responder


title: 15239001, CD4+ T cells, asthma case

description: Library name: 15239001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_D7_S68

description: non-responder


title: Zfp_MB025 ChIP-seq (batch4)

description: Library name: Zfp_MB025_ChIP_batch4


title: 15405001, CD4+ T cells, asthma case

description: Library name: 15405001


title: ATAC_seq_MM196_MM_CELL_LINES

description: ATACseq of CD138+ plasma cells


title: Zfp_MB024 ChIP-seq (batch4)

description: Library name: Zfp_MB024_ChIP_batch4


title: Zfp_MB023 ChIP-seq (batch4)

description: Library name: Zfp_MB023_ChIP_batch4


title: 15367001, CD4+ T cells, asthma case

description: Library name: 15367001


title: 15700009, CD4+ T cells, asthma case

description: Library name: 15700009


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_D6_S60

description: non-responder


title: Insoluble_fraction_Dox_RNA_Ins5

city: Leiden

first: Vered

last: Raz

address: Einthovenweg

department: Human genetics

country: Netherlands

institute: LUMC

data_processing:
RNAseq reads in FASTQ format are first filtered using Cutadapt (version 2.10) to remove all of the remaining adapter sequences. Then, the reads were aligned to the human reference transcriptome based on ENSEMBL gene annotation version 106 using STAR (version 2.7.5a). UMI-based deduplication was performed using UMI-Tools (version 1.1.1). featureCounts (version 2.0.1) was used to estimate abundance at different regions of interest on the all human transcripts.
Assembly: human reference genome GRCh38
Supplementary files format and content: tab-delimited text files include transcripts LCPM values for each sample after filtering low counts

source_name: Muscle Cell

extract_protocol:
RNA was extracted from cytosolic, nuclear, and insoluble fractions using the PureLink™ RNA Mini Kit (Invitrogen™ 12183018A), according to the manufacturer protocol, continue with on-column DNase treatment PureLink™ DNase Set (Invitrogen™ 12185010). RNAs were stored at -80. RNA integrity was quantified using Qubit and checked on an RNA 6000 Nano Agilent Lab-on-a-Chip kit with Bioanalyzer Systems before cDNA library preparation. The generation of cDNA for the RNA sequencing data was carried out as detailed in (Shademan et al., 2024), using the 1C library preparation protocol.
The generation of cDNA for the RNA-seq data was carried out with the mcSCRB-seq protocol, with the following modifications to the workflow: instead of single cells, we used 1–100 ng isolated total RNA, 7.5% PEG8000 was replaced with 0.5% polyvinylpyrrolidone, and the oligo-dT primer was replaced with the SCIFI_LIG384_001 primer. All samples were barcoded during reverse transcription using a well barcode. Illumina paired-end sequencing of the library was done on a NovaSeq 6000 using paired-end 150-bp sequencing and v1.5 chemistry. After sequencing followed by filtering en clipping the reads on used adapter sequences, the first 8 bases with the qvalues of read2 were pasted at the beginning of read 1.
1C RNA-seq

tag: fraction

value: Insoluble

value: Muscle Cell

value: Ala16-Expanded PABPN1

value: Dox


title: Insoluble_fraction_Dox_RNA_Ins6


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_D4_S44

description: non-responder

value: peripheral blood

value: Bcells


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_D5_S52

description: non-responder

value: Female


title: Zfp_MB021 ChIP-seq (batch4)

description: Library name: Zfp_MB021_ChIP_batch4


title: Insoluble_fraction_Dox_RNA_Ins4


title: 15700008, CD4+ T cells, asthma case

description: Library name: 15700008

value: CD4+ T cells

value: female


title: Zfp_MB020 ChIP-seq (batch4)

description: Library name: Zfp_MB020_ChIP_batch4


title: 15106002, CD4+ T cells, asthma case

description: Library name: 15106002

value: case


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_D3_S36

description: non-responder


title: 15391001, CD4+ T cells, asthma case

description: Library name: 15391001


title: Insoluble_fraction_vehicle_RNA_Ins3

value: Vehicle


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_D2_S28

description: non-responder


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_D1_S20

description: non-responder


title: Insoluble_fraction_vehicle_RNA_Ins2


title: Zfp_MB018 ChIP-seq (batch4)

description: Library name: Zfp_MB018_ChIP_batch4

value: embryo carcinoma


title: 15253003, CD4+ T cells, asthma case

description: Library name: 15253003

value: Barbados


title: Zfp_MB016 ChIP-seq (batch4)

description: Library name: Zfp_MB016_ChIP_batch4


title: Insoluble_fraction_vehicle_RNA_Ins1


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_D12_S108

description: non-responder


title: Nuclear_fraction_Dox_RNA_N6

value: Nuclear


title: 15347001, CD4+ T cells, asthma case

description: Library name: 15347001

value: male


title: Zfp_MB001 ChIP-seq (batch4)

description: Library name: Zfp_MB001_ChIP_batch4


title: Zfp_MB015 ChIP-seq (batch4)

description: Library name: Zfp_MB015_ChIP_batch4


title: Zfp_MB022 ChIP-seq (batch4)

description: Library name: Zfp_MB022_ChIP_batch4


title: 15287001, CD4+ T cells, asthma case

description: Library name: 15287001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_D10_S92

description: non-responder


title: Nuclear_fraction_Dox_RNA_N5


title: 15006003, CD4+ T cells, asthma case

description: Library name: 15006003


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_C9_S83

description: non-responder


title: Nuclear_fraction_Dox_RNA_N4


title: Zfp600 ChIP-seq (batch4)

description: Library name: Zfp600_ChIP_batch4


title: Zfp980 ChIP-seq (batch4)

description: Library name: Zfp980_ChIP_batch4


title: Nuclear_fraction_vehicle_RNA_N3


title: Rex2 ChIP-seq (batch4)

description: Library name: Rex2_ChIP_batch4


title: Nuclear_fraction_vehicle_RNA_N2


title: 15230001, CD4+ T cells, asthma case

description: Library name: 15230001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_C7_S67

description: non-responder


title: 15346001, CD4+ T cells, asthma case

description: Library name: 15346001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_C6_S59

description: non-responder


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_C5_S51

description: non-responder


title: 15277001, CD4+ T cells, asthma case

description: Library name: 15277001


title: Cytosolic_fraction_Dox_RNA_C6

value: Cytosolic


title: Empty vector control replicate 4 ChIP-seq (batch4)

description: Library name: EV_control_rep4_KZFP_ChIP_batch4


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_D11_S100

description: non-responder


title: Cytosolic_fraction_Dox_RNA_C5


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_C4_S43

description: non-responder


title: Gm21411 ChIP-seq (batch4)

description: Library name: Gm21411_ChIP_batch4


title: 15374001, CD4+ T cells, asthma case

description: Library name: 15374001


title: 15290001, CD4+ T cells, asthma case

description: Library name: 15290001


title: Empty vector control replicate 3 ChIP-seq (batch4)

description: Library name: EV_control_rep3_KZFP_ChIP_batch4


title: 15486001, CD4+ T cells, asthma case

description: Library name: 15486001


title: Nuclear_fraction_vehicle_RNA_N1


title: Mixed input from KZFP ChIP (batch4)

description: Library name: input_KZFP_ChIP_batch4


title: 15499001, CD4+ T cells, asthma case

description: Library name: 15499001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_C3_S35

description: non-responder


title: Cytosolic_fraction_vehicle_RNA_C3


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_C2_S27

description: non-responder


title: Zfp_MB014 ChIP-seq (batch3)

description: Library name: Zfp_MB014_ChIP_batch3


title: 15353001, CD4+ T cells, asthma case

description: Library name: 15353001


title: Cytosolic_fraction_vehicle_RNA_C2


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_C8_S75

description: non-responder


title: Zfp268 ChIP-seq (batch4)

description: Library name: Zfp268_ChIP_batch4


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_C1_S19

description: non-responder


title: Cytosolic_fraction_vehicle_RNA_C1


title: 15282001, CD4+ T cells, asthma case

description: Library name: 15282001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_C12_S107

description: non-responder


title: Zfp_MB012 ChIP-seq (batch3)

description: Library name: Zfp_MB012_ChIP_batch3


title: Zfp_MB013 ChIP-seq (batch3)

description: Library name: Zfp_MB013_ChIP_batch3


title: 15288001, CD4+ T cells, asthma case

description: Library name: 15288001


title: Healthy control sample 14

city: El Paso

first: Enrique

middle: Ivan

last: Ramos

state: Texas

address: 5001 El Paso Dr.

department: Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center El Paso

data_processing:
Reads were aligned to GRCh38.p13 using the hisat2 aligner
Read counts were generated using feature counts with Ensembl version 101 and GENCODE v35 as reference with "-t exon, -g gene_id or -g exon_id, and -a annotation.gtf" as options.
Differential gene expression was determined using the DeSeq2 package in R
Assembly: GRCh38.p13
Supplementary files format and content: tab delimited txt file with raw read counts for each sample
Supplementary files format and content: FPKM    TPM

source_name: Brain

extract_protocol:
Total RNA including miRNA was extracted from the synaptosomes of AD and control postmortem brain samples using the TriZol reagent.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system. All extracted RNA was used in the library preparation following Illumina’s TruSeq -small-RNA-sample preparation protocols (Illumina, San Diego, CA, USA). Quality control analysis and quantification of the DNA library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Single-end sequencing 50bp was performed on Illumina’s Hiseq 2500 sequencing system following the manufacture’s recommended protocols

value: Brain

tag: disease

value: Healthy control


title: Zfp_MB011 ChIP-seq (batch3)

description: Library name: Zfp_MB011_ChIP_batch3


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_C10_S91

description: non-responder

tag: tissue


title: Healthy control sample 13


title: 15420001, CD4+ T cells, asthma case

description: Library name: 15420001

tag: cell type


title: Zfp_MB010 ChIP-seq (batch3)

description: Library name: Zfp_MB010_ChIP_batch3


title: 15234001, CD4+ T cells, asthma case

description: Library name: 15234001


title: 15390001, CD4+ T cells, asthma case

description: Library name: 15390001


title: Cytosolic_fraction_Dox_RNA_C4

value: Muscle Cell

tag: genotype


title: Zfp_MB004 ChIP-seq (batch3)

description: Library name: Zfp_MB004_ChIP_batch3


title: Zfp_MB005 ChIP-seq (batch3)

description: Library name: Zfp_MB005_ChIP_batch3


title: 15425001, CD4+ T cells, asthma case

description: Library name: 15425001


title: Healthy control sample 10


title: Healthy control sample 11


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_B8_S74

description: non-responder

tag: treatment


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_B7_S66

description: non-responder


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_C11_S99

description: non-responder


title: Zfp_MB003 ChIP-seq (batch3)

description: Library name: Zfp_MB003_ChIP_batch3


title: Healthy control sample 9


title: 15382001, CD4+ T cells, asthma case

description: Library name: 15382001

tag: age


title: Zfp993 ChIP-seq (batch3)

description: Library name: Zfp993_ChIP_batch3


title: Healthy control sample 8


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_B5_S50

description: non-responder


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_B4_S42

description: non-responder


title: Zfp988 ChIP-seq (batch3)

description: Library name: Zfp988_ChIP_batch3


title: 15191001, CD4+ T cells, asthma case

description: Library name: 15191001

tag: Sex


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_B9_S82

description: non-responder


title: 15404001, CD4+ T cells, asthma case

description: Library name: 15404001

tag: genetic pc1


title: Healthy control sample 7


title: Healthy control sample 12


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_B3_S34

description: non-responder


title: Zfp986 ChIP-seq (batch3)

description: Library name: Zfp986_ChIP_batch3


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_B2_S26

description: non-responder


title: Healthy control sample 6


title: 15240001, CD4+ T cells, asthma case

description: Library name: 15240001

tag: asthma


title: 15265001, CD4+ T cells, asthma case

description: Library name: 15265001

tag: geo loc_name


title: Healthy control sample 4


title: Zfp981 ChIP-seq (batch3)

description: Library name: Zfp981_ChIP_batch3


title: 15379001, CD4+ T cells, asthma case

description: Library name: 15379001


title: Mixed input from KZFP ChIP (batch3)

description: Library name: input_KZFP_ChIP_batch3


title: 15232001, CD4+ T cells, asthma case

description: Library name: 15232001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_B12_S106

description: non-responder


title: Zfp600_3 ChIP-seq (batch2)

description: Library name: Zfp6003_ChIP_batch2


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_B6_S58

description: non-responder


title: Healthy control sample 2


title: Zfp992 ChIP-seq (batch3)

description: Library name: Zfp992_ChIP_batch3


title: Healthy control sample 1


title: Zfp600_1 ChIP-seq (batch2)

description: Library name: Zfp6001_ChIP_batch2


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_A9_S81

description: non-responder


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_B10_S90

description: non-responder


title: Healthy control sample 5


title: Empty vector control replicate 2 ChIP-seq (batch2)

description: Library name: EV_control_rep2_KZFP_ChIP_batch2


title: 15470001, CD4+ T cells, asthma case

description: Library name: 15470001


title: 15419001, CD4+ T cells, asthma case

description: Library name: 15419001


title: Alzheimer's disease sample 27

value: Alzheimer's disease


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_A8_S73

description: non-responder


title: Alzheimer's disease sample 26


title: Healthy control sample 3


title: 15554001, CD4+ T cells, asthma case

description: Library name: 15554001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_A7_S65

description: non-responder


title: Alzheimer's disease sample 25


title: Mixed input from KZFP ChIP (batch2)

description: Library name: input_KZFP_ChIP_batch2


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_B1_S18

description: non-responder


title: Zfp982 ChIP-seq (batch 1)

description: Library name: Zfp982_ChIP_batch1


title: 15450001, CD4+ T cells, asthma case

description: Library name: 15450001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_B11_S98

description: non-responder


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_A6_S57

description: non-responder


title: Zfp979 ChIP-seq (batch 1)

description: Library name: Zfp979_ChIP_batch1


title: Zfp600_2 ChIP-seq (batch2)

description: Library name: Zfp6002_ChIP_batch2


title: 15455001, CD4+ T cells, asthma case

description: Library name: 15455001


title: Alzheimer's disease sample 24


title: Alzheimer's disease sample 23


title: 15284001, CD4+ T cells, asthma case

description: Library name: 15284001


title: Zfp978 ChIP-seq (batch 1)

description: Library name: Zfp978_ChIP_batch1


title: 15430001, CD4+ T cells, asthma case

description: Library name: 15430001


title: Empty vector control replicate 1 for KZFP ChIP-seq (batch 1)

description: Library name: EV_control_rep1_KZFP_ChIP_batch1


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_A4_S41

description: non-responder


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_A3_S33

description: non-responder


title: Alzheimer's disease sample 21


title: 15422001, CD4+ T cells, asthma case

description: Library name: 15422001


title: 15145002, CD4+ T cells, asthma case

description: Library name: 15145002


title: Mixed input from KZFP ChIP-seq (batch 1)

description: Library name: input_KZFP_ChIP_batch1


title: Alzheimer's disease sample 20


title: Input from HGTC8 mESCs

description: Library name: HGTC8_input

value: mESCs


title: 15459001, CD4+ T cells, asthma case

description: Library name: 15459001


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_A1_S17

description: non-responder

value: peripheral blood


title: H3K9me3 ChIP-seq in HGTC8 mESCs

description: Library name: HGTC8_H3K9me3_ChIP


title: 15433001, CD4+ T cells, asthma case

description: Library name: 15433001


title: 15452001, CD4+ T cells, control

description: Library name: 15452001

value: control


title: H3K4me3 ChIP-seq in HGTC8 mESCs

description: Library name: HGTC8_H3K4me3_ChIP


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_A12_S105

description: non-responder

value: Bcells

value: Female


title: Alzheimer's disease sample 18


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_A5_S49

description: non-responder


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_A11_S97

description: non-responder


title: HSC_RBC_2

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

description: Library name: GA21114

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Bone marrow

extract_protocol:
Total RNA was extracted from cells with QIAzol reagent and a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan). According to the SMART-Seq kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: Bone marrow

value: Primary cell

value: Lin- Sca-1+ c-Kit+ CD48- CD150+ cells

value: WT

value: co-culture

value: LT-HSC with red blood cell


title: Alzheimer's disease sample 17


title: Alzheimer's disease sample 16


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_A10_S89

description: non-responder


title: HSC_RBC_1

description: Library name: GA21113


title: Alzheimer's disease sample 22


title: 15462001, CD4+ T cells, asthma case

description: Library name: 15462001

value: CD4+ T cells

value: male

value: case

value: Barbados


title: HSC_Ctrl_2

description: Library name: GA21112

value: single culture

value: LT-HSC


title: Alzheimer's disease sample 15

value: Brain

value: Alzheimer's disease


title: MDanderson_Bcells_patient10_timepoint1d7_sc_smartseq_pl1_B5_S48

description: non-responder

value: peripheral blood


title: MDanderson_Bcells_patient10_timepoint2d14_sc_smartseq_pl2_A2_S25

description: non-responder

value: Bcells


title: MDanderson_Bcells_patient10_timepoint1d7_sc_smartseq_pl1_B6_S56

description: non-responder

value: Female


title: Alzheimer's disease sample 19


title: Alzheimer's disease sample 14


title: 15490001, CD4+ T cells, asthma case

description: Library name: 15490001

value: female


title: HSC_Ctrl_1

description: Library name: GA21111

value: Bone marrow

value: Primary cell


title: LSK_RBC_2

description: Library name: GA21110

value: Lin-/Sca-1+/cKit+ cells

value: WT

value: LSK with red blood cell


title: MDanderson_Bcells_patient10_timepoint1d7_sc_smartseq_pl1_B4_S40

description: non-responder


title: Alzheimer's disease sample 12


title: Alzheimer's disease sample 13


title: MDanderson_Bcells_patient10_timepoint1d7_sc_smartseq_pl1_B3_S32

description: non-responder


title: MDanderson_Bcells_patient10_timepoint1d7_sc_smartseq_pl1_B2_S24

description: non-responder


title: 15429001, CD4+ T cells, asthma case

description: Library name: 15429001

value: CD4+ T cells


title: LSK_RBC_1

description: Library name: GA21109

value: co-culture


title: 15463001, CD4+ T cells, asthma case

description: Library name: 15463001

value: male

value: case


title: 15515001, CD4+ T cells, asthma case

description: Library name: 15515001

value: Barbados


title: 15254003, CD4+ T cells, asthma case

description: Library name: 15254003


title: Alzheimer's disease sample 10


title: LSK_Ctrl_2

description: Library name: GA21108

value: single culture

value: LSK only


title: LSK_Ctrl_1

description: Library name: GA21107


title: 15483001, CD4+ T cells, asthma case

description: Library name: 15483001


title: Alzheimer's disease sample 9

value: Brain

value: Alzheimer's disease


title: MDanderson_Bcells_patient10_timepoint1d7_sc_smartseq_pl1_B1_S16

description: non-responder

value: peripheral blood

value: Bcells


title: MDanderson_Bcells_patient10_timepoint1d7_sc_smartseq_pl1_A9_S79

description: non-responder

value: Female


title: 15494001, CD4+ T cells, asthma case

description: Library name: 15494001


title: 15476001, CD4+ T cells, asthma case

description: Library name: 15476001

value: female


title: MDanderson_Bcells_patient10_timepoint1d7_sc_smartseq_pl1_A8_S71

description: non-responder


title: Alzheimer's disease sample 8


title: 15371001, CD4+ T cells, asthma case

description: Library name: 15371001


title: Thap6h_48h_RNAseq_rep3

city: Shanghai

first: Peipei

last: Jiang

state: Shanghai

address: No. 115 Jinzun Road, Pudong New Area, Shanghai

institute: Shanghai Jiao Tong University

data_processing:
Sequenced reads were trimmed for adaptor sequence using trim_galore with the default parameters
Trimmed sequence reads were mapped to mm10 genome using STAR (v2.5.3a ) with default parameters
All mapped bam files were converted to bigwig using bedtools (v2.31.0) (ref) for visualization in IGV
Diferentially expressed genes were analyzed by DEseq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for some samples

growth_protocol: C2C12 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% C02 at 37℃

extract_protocol:
RNA was harvested using MolPure Cell RNA Kit (YEASEN, 19231ES50)
RNA library for RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

treatment_protocol:
C2C12 cells were treated with 100nM DMSO and 100nM thapsigargin respectively for 2h, 6h, 12h.
C2C12 cells were treated with 100nM thapsigargin for 6h and then followed by incubation in thapsigargin-free medium for 48h

value: Mouse myoblasts

value: Thapsigargin 6h and then Thapsigargin-free 48h


title: Thap6h_48h_RNAseq_rep2

value: WT


title: 15120005, CD4+ T cells, asthma case

description: Library name: 15120005


title: MDanderson_Bcells_patient10_timepoint1d7_sc_smartseq_pl1_A7_S63

description: non-responder


title: Alzheimer's disease sample 7


title: 15044013, CD4+ T cells, control

description: Library name: 15044013

value: control


title: Alzheimer's disease sample 11


title: MDanderson_Bcells_patient10_timepoint1d7_sc_smartseq_pl1_A12_S103

description: non-responder


title: Thap6h_48h_RNAseq_rep1


title: Alzheimer's disease sample 6


title: 15258002, CD4+ T cells, control

description: Library name: 15258002

value: CD4+ T cells


title: Thap12h_RNAseq_rep2

value: Thapsigargin 12h


title: MDanderson_Bcells_patient10_timepoint1d7_sc_smartseq_pl1_A11_S95

description: non-responder


title: Alzheimer's disease sample 5


title: MDanderson_Bcells_patient10_timepoint1d7_sc_smartseq_pl1_A10_S87

description: non-responder


title: DMSO12h_RNAseq_rep2

value: DMSO 12h


title: Thap12h_RNAseq_rep1


title: Alzheimer's disease sample 3


title: 15313002, CD4+ T cells, control

description: Library name: 15313002

value: male


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowE_H9_S285

description: responder


title: DMSO12h_RNAseq_rep1


title: 15003006, CD4+ T cells, control

description: Library name: 15003006

value: Barbados


title: Thap6h_RNAseq_rep3

value: Thapsigargin 6h


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowE_H7_S283

description: responder


title: Alzheimer's disease sample 1


title: 15133004, CD4+ T cells, control

description: Library name: 15133004


title: U1 rep2

city: Suzhou

first: Fan

last: Zhang

address: 100 Chongwen Road

institute: Suzhou Institute of Systems Medicine

data_processing:
Reads were treated using fastp software with parameter '-n 10 -q 5 -u 50' to discard reads which are short or in poor quality
The treated reads then mapped to hg38 reference genome using CLC Genomic Workbench 12 to get expression of genes
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts, RPKM values and TPM values for each sample

extract_protocol:
The cell samples were lysed in TRlzol and extract total RNA for RNA-seq
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adenocarcinomic human alveolar basal epithelial cells

value: U1 transfection


title: Thap6h_RNAseq_rep2


title: Thap6h_RNAseq_rep1


title: 15332001, CD4+ T cells, asthma case

description: Library name: 15332001

value: case


title: 15431003, CD4+ T cells, asthma case

description: Library name: 15431003


title: RFP rep2

value: RFP transfection


title: U1 rep1


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowE_H5_S281

description: responder

value: peripheral blood

value: Bcells


title: Alzheimer's disease sample 4

value: Brain

value: Alzheimer's disease


title: RFP rep1


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowE_H3_S279

description: responder

value: Female


title: DMSO6h_RNAseq_rep3

value: Mouse myoblasts

value: WT

value: DMSO 6h


title: 15188001, CD4+ T cells, asthma case

description: Library name: 15188001

value: CD4+ T cells

value: female


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowE_H4_S280

description: responder


title: Alzheimer's disease sample 2


title: DMSO6h_RNAseq_rep1


title: 15306002, CD4+ T cells, control

description: Library name: 15306002

value: male

value: control


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowE_H2_S278

description: responder


title: Thap2h_RNAseq_rep3

value: Thapsigargin 2h


title: bone marrow cells from patients with multiple myeloma, patient 30

city: Xuzhou

first: Guihua

address: Xuzhou

department: Hematology

institute: Xuzhou Cancer Hospital

data_processing:
Genomics Workbench v11.0.1
Assembly: hg18
Supplementary files format and content: tab-delimited text files include raw count for each Sample

source_name: bone marrow cells

extract_protocol:
RNA extract Kits(Qiagen)
Pool libraries if necessary and load them onto the sequencing platform (e.g., Illumina NovaSeq). Perform high-throughput sequencing according to the manufacturer’s instructions.

value: bone marrow cells

value: multiple myeloma


title: 15297050, CD4+ T cells, control

description: Library name: 15297050

value: Barbados


title: 15142002, CD4+ T cells, asthma case

description: Library name: 15142002

value: case


title: DMSO6h_RNAseq_rep2


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowE_H8_S284

description: responder

value: peripheral blood


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowE_H6_S282

description: responder

value: Bcells


title: 15170001, CD4+ T cells, asthma case

description: Library name: 15170001


title: Thap2h_RNAseq_rep2


title: bone marrow cells from patients with multiple myeloma, patient 29


title: 15139050, CD4+ T cells, control

description: Library name: 15139050


title: bone marrow cells from patients with multiple myeloma, patient 28


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowE_H12_S288

description: responder


title: 15160002, CD4+ T cells, asthma case

description: Library name: 15160002


title: Thap2h_RNAseq_rep1


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowE_H11_S287

description: responder


title: bone marrow cells from patients with multiple myeloma, patient 26


title: bone marrow cells from patients with multiple myeloma, patient 27


title: 15185002, CD4+ T cells, asthma case

description: Library name: 15185002


title: DMSO2h_RNAseq_rep3

value: DMSO 2h


title: DMSO2h_RNAseq_rep2


title: 15549001, CD4+ T cells, asthma case

description: Library name: 15549001


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowD_H9_S381

description: responder


title: bone marrow cells from patients with multiple myeloma, patient 25


title: 15198002, CD4+ T cells, asthma case

description: Library name: 15198002


title: DMSO2h_RNAseq_rep1


title: 15254001, CD4+ T cells, asthma case

description: Library name: 15254001


title: bone marrow cells from patients with multiple myeloma, patient 24


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowD_H8_S380

description: responder


title: Thap6h_HiC

data_processing:
Raw reads were firstly trimmed using TrimGalore (v0.6.10) with default settings. The data were then processed using a standard Hi-C processing pipeline recommended by the 4D Nucleome Data Portal(https://data.4dnucleome.org/resources/data-analysis/hic-processing-pipeline). Briefly, the trimmed reads were first mapped to the mouse genome (mm10) using BWA MEM (v0.7.17-r1188) with the -SP5M option. The mapped reads were then parsed using pairtools (v0.3.0). After data aggregation and normalization, contact matrices in the.cool file format were generated using the cooler package (ref) (v0.8.11)
Assembly: mm10
Supplementary files format and content: cool

extract_protocol:
Hi-C 3.0 was performed performed as previously described with some modifications. Briefly, 5 million cells were washed once with ice-cold PBS and then crosslinked with 1% formaldehyde for 10 min at room tempreture. Crosslinking was quenched with 0.2 M glycine for 5 min. Cells were further crosslinked with 3 mM DSG for 40 min and quenched again with 0.4 M glycine for 5 min. Crosslinked cell pellets were washed with cold PBS and then resuspended in 0.5 ml of ice-cold Hi-C lysis buffer and rotated at 4 °C for 30 min. After washing with 0.5 ml of ice-cold Hi-C lysis buffer, nuclei were resuspend in 0.5% SDS to open up the chromatin at 65°C for 10 min and quenched with Triton X-100 at the final concentration of 1%. Subsequently, enzyme digestion of chromatin was performed at 37 °C overnight by adding 50 μl of 10X NEB buffer 2, 400 U of DpnⅡ(NEB #R0543M) and 400 U of DdeI (NEB#R0175L). After overnight incubation, the restriction enzymes were inactivated at 62 °C for 20 min. To fill in the DNA overhangs and add biotin tags, 35 U of DNA polymerase I (Klenow, NEB# M0210L), 10 μl of 1 mM biotin-14-dATP (Thermo fisher #19524016) and 1 μl of 10 mM dCTP/dGTP/dTTP were added and incubated at 37 °C for 4 h with interval shaking (shaked at 950 rpm for 10 s with 5-min intervals). Chromatin were then ligated with T4 DNA ligase ((NEB #M0202M) ) at 16°C for 4 hours, and de-crosslinked by proteinase K treatment, followed by phenol/chloroform extraction coupled with isopropanol precipitation using glycogen as a carrier. Then DNAs were sonicated using a Covaris S220 to approximately 300-500 bp, and biotin-labelled DNAs were purified by Dynabeads MyOne streptavidin C1 beads (Thermo Fisher #65002). The DNA libearies were further prepared for sequencing using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme # ND607) and barcoded adaptors were ligated using TruePrep Index Kit V2 for Illumina (Vazyme #TD202). Size selection was carried out using the VAHTS DNA Clean Beads (Vazyme #N411). Library quantity was assessed Qubit double-stranded DNA (dsDNA) High-Sensitivity Assay.
Hi-C 3.0 was performed performed as previously described with some modifications. Briefly, 5 million cells were washed once with ice-cold PBS and then crosslinked with 1% formaldehyde for 10 min at room tempreture. Crosslinking was quenched with 0.2 M glycine for 5 min. Cells were further crosslinked with 3 mM DSG for 40 min and quenched again with 0.4 M glycine for 5 min. Crosslinked cell pellets were washed with cold PBS and then resuspended in 0.5 ml of ice-cold Hi-C lysis buffer and rotated at 4 °C for 30 min. After washing with 0.5 ml of ice-cold Hi-C lysis buffer, nuclei were resuspend in 0.5% SDS to open up the chromatin at 65°C for 10 min and quenched with Triton X-100 at the final concentration of 1%. Subsequently, enzyme digestion of chromatin was performed at 37 °C overnight by adding 50 μl of 10X NEB buffer 2, 400 U of DpnⅡ(NEB #R0543M) and 400 U of DdeI (NEB#R0175L). After overnight incubation, the restriction enzymes were inactivated at 62 °C for 20 min. To fill in the DNA overhangs and add biotin tags, 35 U of DNA polymerase I (Klenow, NEB# M0210L), 10 μl of 1 mM biotin-14-dATP (Thermo fisher #19524016) and 1 μl of 10 mM dCTP/dGTP/dTTP were added and incubated at 37 °C for 4 h with interval shaking (shaked at 950 rpm for 10 s with 5-min intervals). Chromatin were then ligated with T4 DNA ligase ((NEB #M0202M) ) at 16°C for 4 hours, and de-crosslinked by proteinase K treatment, followed by phenol/chloroform extraction coupled with isopropanol precipitation using glycogen as a carrier. Then DNAs were sonicated using a Covaris S220 to approximately 300-500 bp, and biotin-labelled DNAs were purified by Dynabeads MyOne streptavidin C1 beads (Thermo Fisher #65002). The DNA libearies were further prepared for sequencing using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme # ND607) and barcoded adaptors were ligated using TruePrep Index Kit V2 for Illumina (Vazyme #TD202). Size selection was carried out using the VAHTS DNA Clean Beads (Vazyme #N411). Library quantity was assessed Qubit double-stranded DNA (dsDNA) High-Sensitivity Assay.
HiC3.0

treatment_protocol: C2C12 cells were treated with 100nM DMSO and 100nM thapsigargin respectively for 6h.

value: Thapsigargin 6h


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowE_H1_S277

description: responder

value: Female


title: DMSO6h_HiC

value: Mouse myoblasts


title: bone marrow cells from patients with multiple myeloma, patient 23


title: 15195001, CD4+ T cells, asthma case

description: Library name: 15195001


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowD_H7_S379

description: responder


title: bone marrow cells from patients with multiple myeloma, patient 22


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowD_H6_S378

description: responder


title: Thap6h_CEBPγ_CUT&Tag_rep2

data_processing:
The raw reads were trimmed by Trim Galore (v0.6.10)
Trimmed reads were mapped to the mouse transcriptome (mm10) by Bowtie2
CUT&Tag peaks were identified using MACS2 (v2.2.7.1, -f BAMPE) with p<0.05.  Pronounced ATF4 peaks were then filter with the summit>100
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: bed
Library strategy: CUT&Tag

extract_protocol:
The CUT&Tag assay was performed as previously described (ref) with modifications using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme #TD903)
The CUT&Tag assay was performed as previously described (ref) with modifications using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme #TD903)

value: WT

tag: antibody

value: Thermo #PA5-80468


title: 15189001, CD4+ T cells, asthma case

description: Library name: 15189001

value: CD4+ T cells


title: bone marrow cells from patients with multiple myeloma, patient 21


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowD_H5_S377

description: responder


title: Thap6h_CEBPγ_CUT&Tag_rep1


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowE_H10_S286

description: responder


title: 15550001, CD4+ T cells, asthma case

description: Library name: 15550001

value: female


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowD_H4_S376

description: responder


title: bone marrow cells from patients with multiple myeloma, patient 20


title: DMSO6h_CEBPγ_CUT&Tag_rep2

value: DMSO 6h


title: 15105001, CD4+ T cells, asthma case

description: Library name: 15105001


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowD_H3_S375

description: responder


title: bone marrow cells from patients with multiple myeloma, patient 19


title: 15134003, CD4+ T cells, asthma case

description: Library name: 15134003


title: Thap6h_CEBPβ_CUT&Tag_rep2

value: Thermo #MA1-827


title: 15133005, CD4+ T cells, asthma case

description: Library name: 15133005

value: male


title: bone marrow cells from patients with multiple myeloma, patient 18

value: bone marrow cells


title: bone marrow cells from patients with multiple myeloma, patient 17

value: multiple myeloma


title: 15114002, CD4+ T cells, asthma case

description: Library name: 15114002

value: Barbados


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowD_H1_S373

description: responder


title: Thap6h_CEBPβ_CUT&Tag_rep1


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowD_H2_S374

description: responder


title: bone marrow cells from patients with multiple myeloma, patient 16


title: DMSO6h_CEBPβ_CUT&Tag_rep2


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowD_H12_S384

description: responder


title: bone marrow cells from patients with multiple myeloma, patient 15


title: YZHA-479

city: Chicago

first: Thomas

last: Gajewski

state: IL

address: 929 E 57th St

institute: University of Chicago

description: Library name: YZHA-479

data_processing:
Kallisto and tximport were used to align to gencode primary assembly sequence (release 39) and export sequencing data while Limma and edgeR R packages were used to process the count matrices. Samples were filtered by a minimum of 5,100,000 reads and genes were filtered using the following cutoffs: a minimum of 30 samples were required to express a given gene and with a minimum counts per million (CPM) of 1. Normalization was done using the “calcNormFactors” function, using the TMM method. Count data was transformed using “limmavoom” and data was centered using the scale function in R.
Assembly: gencode primary assembly sequence (release 39)
Supplementary files format and content: tab-delimited count matrix with samples in columns and transcripts in rows

source_name: skin

extract_protocol:
Patients donated a single 18g core biopsy which was either formalin-fixed paraffin-embedded (FFPE) or fresh frozen (FF). RNA was isolated using Qiagen RNeasy FFPE kit (Qiagen, 73504) for FFPE samples, or Qiagen RNeasy kit (Qiagen, 74104) for FF samples.
RNA QC (quality and quantity) was performed using an Agilent 2100 Bio-analyzer using Agilent reagents and protocols. RNA-SEQ libraries were generated using Illumina TruSEQ TotalRNA stranded library making kits using Illumina protocols. Library QC (quality and quantity) was performed using an Agilent 2100 Bio-analyzer using Agilent reagents and protocols. RNA-SEQ libraries were sequenced with paired-end 100 bp reads using an Illumina HiSEQ40000 with Illumina reagents and protocols.

value: skin


title: DMSO6h_CEBPβ_CUT&Tag_rep1


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowD_H11_S383

description: responder

value: peripheral blood


title: bone marrow cells from patients with multiple myeloma, patient 14


title: YZHA-403

description: Library name: YZHA-403


title: Thap6h_CHOP_CUT&Tag_rep2

value: Cell Signaling Technology #2895T


title: MDanderson_Bcells_patient6_timepoint3_sc_smartseq_pl2rowD_H10_S382

description: responder

value: Bcells


title: bone marrow cells from patients with multiple myeloma, patient 13


title: DMSO6h_CEBPγ_CUT&Tag_rep1


title: MDanderson_Bcells_patient6_timepoint2_sc_smartseq_pl2_D9_S333

description: responder


title: Thap6h_CHOP_CUT&Tag_rep1

value: Thapsigargin 6h


title: bone marrow cells from patients with multiple myeloma, patient 12


title: MDanderson_Bcells_patient6_timepoint2_sc_smartseq_pl2_D8_S332

description: responder

value: Female


title: YZHA-402

description: Library name: YZHA-402


title: DMSO6h_CHOP_CUT&Tag_rep2

value: Mouse myoblasts


title: YZHA-399

description: Library name: YZHA-399


title: bone marrow cells from patients with multiple myeloma, patient 11


title: YZHA-397

description: Library name: YZHA-397


title: bone marrow cells from patients with multiple myeloma, patient 10


title: DMSO6h_CHOP_CUT&Tag_rep1

value: WT


title: YZHA-395

description: Library name: YZHA-395


title: Thap6h_ATF4_CUT&Tag_rep1

value: Cell Signaling Technology #11815


title: MDanderson_Bcells_patient6_timepoint2_sc_smartseq_pl2_D6_S330

description: responder


title: bone marrow cells from patients with multiple myeloma, patient 9


title: Thap6h_ATF4_CUT&Tag_rep2


title: bone marrow cells from patients with multiple myeloma, patient 8


title: MDanderson_Bcells_patient6_timepoint2_sc_smartseq_pl2_D5_S329

description: responder


title: MDanderson_Bcells_patient6_timepoint2_sc_smartseq_pl2_D7_S331

description: responder


title: MDanderson_Bcells_patient6_timepoint2_sc_smartseq_pl2_D4_S328

description: responder


title: DMSO6h_ATF4_CUT&Tag_rep2


title: YZHA-387

description: Library name: YZHA-387


title: YZHA-478

description: Library name: YZHA-478


title: YZHA-389

description: Library name: YZHA-389


title: bone marrow cells from patients with multiple myeloma, patient 7


title: DMSO6h_ATF4_CUT&Tag_rep1


title: MDanderson_Bcells_patient6_timepoint2_sc_smartseq_pl2_D2_S326

description: responder


title: bone marrow cells from patients with multiple myeloma, patient 6


title: YZHA-386

description: Library name: YZHA-386


title: YZHA-385

description: Library name: YZHA-385


title: Thap6h_H3K27Ac_CUT&Tag_rep2

value: abcam #ab4729


title: bone marrow cells from patients with multiple myeloma, patient 5


title: Thap6h_H3K27Ac_CUT&Tag_rep1


title: bone marrow cells from patients with multiple myeloma, patient 4


title: MDanderson_Bcells_patient6_timepoint2_sc_smartseq_pl2_D12_S336

description: responder


title: YZHA-383

description: Library name: YZHA-383


title: DMSO6h_H3K27Ac_CUT&Tag_rep2


title: bone marrow cells from patients with multiple myeloma, patient 3


title: MDanderson_Bcells_patient6_timepoint2_sc_smartseq_pl2_D11_S335

description: responder


title: DMSO6h_H3K27Ac_CUT&Tag_rep1


title: YZHA-382

description: Library name: YZHA-382


title: YZHA-380

description: Library name: YZHA-380


title: bone marrow cells from patients with multiple myeloma, patient 2


title: MDanderson_Bcells_patient6_timepoint2_sc_smartseq_pl2_D3_S327

description: responder


title: Thap6h_ATACseq_rep2

data_processing:
The raw reads were trimmed by Trim Galore (v0.6.10)
Trimmed reads were mapped to the mouse transcriptome (mm10) by Bowtie2
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
ATAC-seq libraries were generated from approximately 1×106 cell nuclei with the TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme #TD501)
ATAC-seq libraries were generated from approximately 1×106 cell nuclei with the TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme #TD501)


title: Thap6h_ATACseq_rep1


title: MDanderson_Bcells_patient6_timepoint2_sc_smartseq_pl2_D10_S334

description: responder


title: bone marrow cells from patients with multiple myeloma, patient 1


title: MDanderson_Bcells_patient6_timepoint1_sc_smartseq_pl2_G8_S272

description: responder


title: YZHA-379

description: Library name: YZHA-379


title: 8226 cell line_OE3

value: KO


title: DMSO6h_ATACseq_rep2

value: DMSO 6h


title: YZHA-377

description: Library name: YZHA-377


title: MDanderson_Bcells_patient6_timepoint1_sc_smartseq_pl2_G9_S273

description: responder


title: MDanderson_Bcells_patient6_timepoint2_sc_smartseq_pl2_D1_S325

description: responder


title: YZHA-384

description: Library name: YZHA-384


title: MDanderson_Bcells_patient6_timepoint1_sc_smartseq_pl2_G7_S271

description: responder


title: DMSO6h_ATACseq_rep1


title: YZHA-374

description: Library name: YZHA-374


title: 8226 cell line_OE1


title: 8226 cell line_OE2


title: YZHA-373

description: Library name: YZHA-373


title: 8226 cell line_vector6

value: vector


title: MDanderson_Bcells_patient6_timepoint1_sc_smartseq_pl2_G5_S269

description: responder


title: YZHA-372

description: Library name: YZHA-372


title: WT2

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

data_processing:
Rna-seq reads were aligned with STAR-aligner using the genome build GENCODE Mus musculus GRCm39 M26
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: GENCODE Mus musculus GRCm39 M26
Supplementary files format and content: tab-delimited .txt files include 2 columns: ensemble feature identifier and count number.

source_name: Liver

extract_protocol:
RNA was extracted following the manual of the Qiagen RNeasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver


title: 8226 cell line_vector5


title: WT3


title: MDanderson_Bcells_patient6_timepoint1_sc_smartseq_pl2_G6_S270

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.

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).


title: YZHA-371

description: Library name: YZHA-371


title: WT1


title: MDanderson_Bcells_patient6_timepoint1_sc_smartseq_pl2_G3_S267

description: responder


title: ST2

value: Sting1 KO


title: YZHA-370

description: Library name: YZHA-370


title: MDanderson_Bcells_patient6_timepoint1_sc_smartseq_pl2_G2_S266

description: responder


title: 8226 cell line_KO3


title: 8226 cell line_KO2


title: YZHA-369

description: Library name: YZHA-369


title: MDanderson_Bcells_patient6_timepoint1_sc_smartseq_pl2_G1_S265

description: responder


title: YZHA-368

description: Library name: YZHA-368


title: ST3


title: ST1


title: MDanderson_Bcells_patient6_timepoint1_sc_smartseq_pl2_G12_S276

description: responder


title: MST3

value: Mcl1 Sting1 DKO


title: 8226 cell line_KO1


title: 8226 cell line_vector3


title: YZHA-367

description: Library name: YZHA-367


title: MDanderson_Bcells_patient6_timepoint1_sc_smartseq_pl2_G11_S275

description: responder


title: YZHA-364

description: Library name: YZHA-364


title: MST2


title: MDanderson_Bcells_patient6_timepoint1_sc_smartseq_pl2_G10_S274

description: responder


title: MDanderson_Bcells_patient6_timepoint1_sc_smartseq_pl2_G4_S268

description: responder


title: MST1


title: YZHA-362

description: Library name: YZHA-362


title: MCL3

value: Mcl1 KO


title: Human, replicate 3, scRNAseq

city: Vienna

first: Sergey

last: Isaev

address: Spitalgasse, 4

department: Department of Neuroimmunology

country: Austria

institute: Medical University of Vienna

description: 10x 3’ (v2)

data_processing:
Single-cell RNA sequencing data was processed using the CellRanger suite (v. 6.1.2). For human samples, the GRCh38 reference (GENCODE v32/Ensembl 98) was used. Mouse samples were aligned to mm10 (GENCODE vM23/Ensembl 98) reference. Standard CellRanger filtration strategy was used for empty droplet identification. Additionally, cells with more than 10% mitochondrial UMI counts and 15,000 total UMIs (25,000 for samples that were obtained using 10x v3 chemistry) were also removed (fig. S1C). Doublet detection was performed with Scrublet (v. 0.2.2) [PMID: 30954476].
Assembly: Mouse: mm10 / Human: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Thymus

extract_protocol:
All human tissue specimens were collected with institutional review board (IRB) approval. The tissue was processed immediately upon isolation to ensure highest possible cell quality. Murine samples were cut into fine pieces and digested in Medium 199 (M199, Gibco) with 2% (v/v) fetal bovine serum (FBS, Gibco), Liberase (0.5WU/ml, Roche) and DNAse I (0.1 KU, ThermoFisher) 3 x 15 minutes at 37°C under constant agitation. Human samples were processed by digestion with M199 with 2% FBS, DNAse I (0.1 KU) and 2 mg/ml Stemxyme 1 (Worthington) for 2 x 30 minutes at 37°C under constant agitation. For the last 30 minutes the samples were digested with the Stemxyme/DNAse I cocktail in combination with 0.125% Trypsin (Gibco). All samples were digested in the presence of RNase inhibitors (RNasin (Promega) and RNase OUT (Invitrogen). Sorted thymus stromal cells were encapsulated into emulsion droplets using the Chromium Controller (10X Genomics). scRNA sequencing libraries were subsequently prepared using Chromium Single Cell 3 v2 and v3 Reagent kits (10X Genomics).
Sorted thymus stromal cells were encapsulated into emulsion droplets using the Chromium Controller (10X Genomics). scRNA sequencing libraries were subsequently prepared using Chromium Single Cell 3 v2 and v3 Reagent kits (10X Genomics).

value: Thymus

tag: strain

value: 2 months


title: YZHA-361

description: Library name: YZHA-361

value: skin


title: 8226 cell line_vector4


title: Scar14

city: Seoul

first: Eun-jin

last: Jeong

address: 81 Ilwon-ro, Gangnam-gu

country: South Korea

institute: Samsung Advanced Institute for Health Sciences & Technolohy, Sungkyunkwan University

description:
S14
192211_4)Expression_Profile.GRCh37.gene.txt
192211_4)Expression_Profile.GRCh37.transcript.txt

data_processing:
Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality.
The cleaned reads were aligned to the Homo sapiens (GRCh37) using HISAT v2.1.0 (KIM et al, 2015), based on the HISAT and Bowtie2 implementations.
Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b (Pertea, Mihaela, et al., 2015, 2016).
Assembly: GRCh37
Supplementary files format and content: Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million).

source_name: inguinal

extract_protocol:
Total RNA was extracted from the samples using an RNeasy FFPE Kit (Qiagen, 73504) according to the manufacturer’s instructions.
A total of 100 ng of total RNA was subjected to a sequencing library construction using the Agilent SureSelectXT RNA Direct kit according to the manufacturer’s protocol.

value: inguinal


title: Human, replicate 2, scRNAseq

description: 10x 3’ (v2)

value: 4 months

value: Male


title: MCL2


title: YZHA-353

description: Library name: YZHA-353


title: Human, replicate 1, scRNAseq

description: 10x 3’ (v2)

value: 2.5 months

value: Female


title: Scar12

description:
S12
192211_4)Expression_Profile.GRCh37.gene.txt
192211_4)Expression_Profile.GRCh37.transcript.txt


title: hippocampal, 1M_1, 4mps

city: Guangzhou

first: Yi

last: Zou

address: West Huangpu Avenue

institute: Jinan University

data_processing:
Raw reads were trimmed using Seqtk (https://github.com/lh3/seqtk) to remove barcodes, adaptors and poor-quality bases before mapping to mm10 reference genome (GRCm38.p4) using Hisat2 (v2.0.4). Genes not expressed or expressed at very low level (count-per-million 454 less than 10 in two or more samples) were filtered using filterByExpr in R (v4.2.1) and among the 24558 mapped genes, 16885 genes were retained for downstream analysis, representing 48.58% of the reference genome. Gene counts were normalized to trimmed mean of M values (TMM) and the artifacts of batch effects were removed with the SAVseq in R (v4.2.1). The corrected gene counts were imported into R (v4.2.1) and differential expression analysis between two different time points was performed using edgeR, a p-value < 0.05 of unpaired t-test (2-tailed) was used as a threshold for statistical significance. The principal component analysis (PCA) of the normalized gene expression data was performed using the ‘prcomp’ function and visualized by plot3d in R (v4.2.1). The sample groups were annotated and the samples within each group were clustered together. The distribution of DEGs and their relative change of expression over time course were visualized with violin plots using ‘ggplot’. A gene expression correlation matrice was generated using the top 40 DEGs with the greatest fold changes and selected parameters of behavioral assessments (ratios of post-surgery to pre- surgery alternations in Y maze and ratios of post-surgery to pre-surgery travel distances in the center of open field tests). The results were visualized using corrplot library in R (v4.2.1).
Assembly: GRCm38.p4
Supplementary files format and content: csv file include count values for all samples

source_name: hippocampal

growth_protocol: C57BL/6J mice housed at a maximum number of 5 per cage under a standard condition of 22±2℃ in a 12/12 h light/dark cycle with free access to food and water.

extract_protocol:
Total RNA from mouse hippocampus was isolated using the TruSeq RNA Sample Prep V2 Kit (Cat.No.RS-122-2001, Illumina, San Diego, CA, USA)
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit following manufacturer’s protocols.

value: hippocampal

value: WT

value: One month after surgery


title: YZHA-351

description: Library name: YZHA-351


title: Scar10

description:
S10
192211_8)Expression_Profile.GRCh37.gene.txt
192211_8)Expression_Profile.GRCh37.transcript.txt


title: Day 5 Monocultured FB rep10

city: Kowloon

first: Sin Yen

last: Tan

address: Clear Water Bay

country: Hong Kong

institute: HKUST

data_processing:
Quality of all raw FASTQ files was checked using Fastqc.
Reads were aligned to the human reference genome GRCh38 using STAR with default parameters.
Gene counts were made using featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for each sample.

source_name: Fibroblasts (FB)

extract_protocol:
RNA were isolated using TRIzol reagent along with DNase application to purify the samples.
RNA libraries were prepared for sequencing using Smart-seq2 protocol and Illumina Nextera XT DNA Library Prep Kit.

value: Normal Human Lung Fibroblasts

value: day 5

tag: condition

value: Monocultured


title: Scar13

description:
S13
192211_4)Expression_Profile.GRCh37.gene.txt
192211_4)Expression_Profile.GRCh37.transcript.txt


title: YZHA-347

description: Library name: YZHA-347


title: Scar11

description:
S11
192211_4)Expression_Profile.GRCh37.gene.txt
192211_4)Expression_Profile.GRCh37.transcript.txt


title: MCL1

value: Liver


title: Day 5 Monocultured FB rep12


title: YZHA-349

description: Library name: YZHA-349


title: Day 5 Monocultured FB rep11


title: hippocampal, 1M_1, 3mps


title: 8226 cell line_vector2

value: vector


title: 8226 cell line_vector1


title: hippocampal, 1M_1, 1mps


title: Day 5 Monocultured FB rep9


title: Scar8

description:
S8
190109_13)Expression_Profile.GRCh38.gene.txt
190109_13)Expression_Profile.GRCh38.transcript.txt

source_name: peritoneum

value: peritoneum


title: hippocampal, 7D_3, 7dps

value: Seven days after surgery


title: YZHA-344

description: Library name: YZHA-344


title: YZHA-352

description: Library name: YZHA-352


title: Scar7

description:
S7
190109_13)Expression_Profile.GRCh38.gene.txt
190109_13)Expression_Profile.GRCh38.transcript.txt


title: YZHA-343

description: Library name: YZHA-343


title: Day 5 Monocultured FB rep7


title: hippocampal, 7D_2, 7dps


title: Day 5 Monocultured FB rep6


title: hippocampal, 7D_1, 7dps


title: hippocampal, 1M_1, 2mps


title: YZHA-342

description: Library name: YZHA-342


title: Scar5

description:
S5
190109_13)Expression_Profile.GRCh38.gene.txt
190109_13)Expression_Profile.GRCh38.transcript.txt

source_name: mesentery

value: mesentery


title: Day 5 Monocultured FB rep5


title: YZHA-341

description: Library name: YZHA-341

value: skin


title: hippocampal, 3D_3, 3dps

value: Three days after surgery


title: YZHA-346

description: Library name: YZHA-346


title: Day 5 Monocultured FB rep4


title: Scar9

description:
S9
192211_8)Expression_Profile.GRCh37.gene.txt
192211_8)Expression_Profile.GRCh37.transcript.txt

value: inguinal


title: YZ-98

description: Library name: YZ-98


title: Day 5 Monocultured FB rep8


title: Scar4

description:
S4
187416_13)Expression_Profile.GRCh37.gene.txt
187416_13)Expression_Profile.GRCh37.transcript.txt


title: hippocampal, 3D_1, 3dps


title: YZ-91

description: Library name: YZ-91


title: Day 5 Monocultured FB rep3


title: Scar3

description:
S3
187416_13)Expression_Profile.GRCh37.gene.txt
187416_13)Expression_Profile.GRCh37.transcript.txt


title: Day 5 Monocultured FB rep2


title: YZ-8

description: Library name: YZ-8


title: Scar6

description:
S6
190109_13)Expression_Profile.GRCh38.gene.txt
190109_13)Expression_Profile.GRCh38.transcript.txt


title: Scar2

description:
S2
187416_13)Expression_Profile.GRCh37.gene.txt
187416_13)Expression_Profile.GRCh37.transcript.txt


title: hippocampal, 24H_4, 24hps

value: 24 hours after surgery


title: Day 5 Monocultured FB rep1


title: Scar1

description:
S1
187416_13)Expression_Profile.GRCh37.gene.txt
187416_13)Expression_Profile.GRCh37.transcript.txt


title: YZ-7

description: Library name: YZ-7


title: Desmoid type fibromatosis29

description:
D29
190109_5)Expression_Profile.GRCh38.gene.txt
190109_5)Expression_Profile.GRCh38.transcript.txt

source_name: Thigh

value: Thigh


title: Day 5 Cocultured FB rep8

value: Cocultured with EC


title: hippocampal, 24H_2, 24hps

value: hippocampal


title: YZ-6

description: Library name: YZ-6


title: hippocampal, 3D_4, 3dps

value: WT


title: Desmoid type fibromatosis28

description:
D28
190109_5)Expression_Profile.GRCh38.gene.txt
190109_5)Expression_Profile.GRCh38.transcript.txt

source_name: colon

value: colon


title: hippocampal, CON_4, con

value: con

value: Non-surgery


title: Desmoid type fibromatosis26

description:
D26
190109_5)Expression_Profile.GRCh38.gene.txt
190109_5)Expression_Profile.GRCh38.transcript.txt


title: Desmoid type fibromatosis27

description:
D27
190109_5)Expression_Profile.GRCh38.gene.txt
190109_5)Expression_Profile.GRCh38.transcript.txt

source_name: rectal muscle fascia

value: rectal muscle fascia


title: YZ-4

description: Library name: YZ-4


title: Day 5 Cocultured FB rep6

value: Normal Human Lung Fibroblasts

value: day 5


title: YZ-3

description: Library name: YZ-3


title: hippocampal, CON_2, con


title: Day 5 Cocultured FB rep5


title: Desmoid type fibromatosis25

description:
D25
190109_5)Expression_Profile.GRCh38.gene.txt
190109_5)Expression_Profile.GRCh38.transcript.txt

source_name: abdominal wall

value: abdominal wall


title: Day 5 Cocultured FB rep4


title: YZ-22

description: Library name: YZ-22


title: hippocampal, 24H_3, 24hps


title: Day 5 Cocultured FB rep3


title: Desmoid type fibromatosis24

description:
D24
192211_8)Expression_Profile.GRCh37.gene.txt
192211_8)Expression_Profile.GRCh37.transcript.txt


title: hippocampal, CON_1, con


title: YZ-24

description: Library name: YZ-24


title: YZ-217

description: Library name: YZ-217


title: Desmoid type fibromatosis22

description:
D22
192211_8)Expression_Profile.GRCh37.gene.txt
192211_8)Expression_Profile.GRCh37.transcript.txt


title: YZ-215

description: Library name: YZ-215


title: Day 5 Cocultured FB rep2


title: Day 5 Cocultured FB rep7


title: SLR14-5

city: Nashville

first: Shristi

last: Shrestha

address: 2213 Garland Ave

institute: Vanderbilt University

data_processing:
RNA sequencing reads were adapter-trimmed and quality-filtered using Trimgalore v0.6.7 (Krueger et al., 2023).
An alignment reference was generated from the mm39 mouse genome and GENCODE comprehensive gene annotations (vM31), to which trimmed reads were aligned and counted using Spliced Transcripts Alignment to a Reference (STAR) v2.7.9a (Dobin et al., 2013) with the –quantMode GeneCounts parameter.
About 27-48 million uniquely mapped reads were acquired per sample. DESeq2 package v1.36.0 (Love et al. 2014) was used to perform sample-level quality control, low count filtering, normalization and downstream differential gene expression analysis.
Assembly: mm39
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file containing normalized counts for each sample

molecule: polyA RNA

source_name: mouse kidney cancer cell line (RENCA)

growth_protocol: 5×105Renca cells were injected subcutaneously into female Balb/c (Jackson Labs) Mice.

extract_protocol:
Total RNA was extracted from tumors using the Qiagen RNeasy kit
Library preparation was completed using the NEBNext® rRNA Depletion kit andprotocol(P/N: E7850X, NEB, Ipswich, MA) per manufacturer recommendations. The kit employs an RNaseH-based method to deplete both cytoplasmic and mitochondrial rRNA. After ribosomal depletion, the RNA samples underwent mRNA enrichment using oligo(dT) beads, followed by thermal fragmentation using divalent cations under elevated temperature. First-strand cDNA synthesis was performed using random hexamer primers, while second-strand cDNA synthesis was carried out using DNA Polymerase I and RNase H. End repair, A-tailing, and adapter ligation was performed to generate the final cDNA library. The library quality was assessed using a Bioanalyzer and quantified using a qPCR-based method with the KAPA Library Quantification Kit (P/N: KK4873) and the QuantStudio 12K instrument.
NEBNext® rRNA Depletion

treatment_protocol: Intratumoral injection of lipid nanoparticles containing 3pRNA RIG-I ligand (SLR14) in 50μL of PBS was performed at 48-hour intervals for a total of 3 treatments

value: mouse kidney cancer cell line (RENCA)

value: F


title: Desmoid type fibromatosis23

description:
D23
192211_8)Expression_Profile.GRCh37.gene.txt
192211_8)Expression_Profile.GRCh37.transcript.txt


title: hippocampal, CON_5, con


title: YZ-208

description: Library name: YZ-208

value: skin


title: Day 3 Monocultured FB rep6

value: day 3

value: Monocultured


title: Desmoid type fibromatosis21

description:
D21
192211_8)Expression_Profile.GRCh37.gene.txt
192211_8)Expression_Profile.GRCh37.transcript.txt

source_name: small bowel

value: small bowel


title: Day 3 Monocultured FB rep5


title: YZ-2

description: Library name: YZ-2


title: YZ-16

description: Library name: YZ-16


title: SLR14-1


title: Desmoid type fibromatosis19

description:
D19
192211_8)Expression_Profile.GRCh37.gene.txt
192211_8)Expression_Profile.GRCh37.transcript.txt


title: PBS-5

value: PBS


title: SLR14-2


title: Desmoid type fibromatosis20

description:
D20
192211_8)Expression_Profile.GRCh37.gene.txt
192211_8)Expression_Profile.GRCh37.transcript.txt

source_name: chest wall

value: chest wall


title: Desmoid type fibromatosis18

description:
D18
190109_13)Expression_Profile.GRCh38.gene.txt
190109_13)Expression_Profile.GRCh38.transcript.txt

value: mesentery


title: YZ-15

description: Library name: YZ-15


title: YZ-14

description: Library name: YZ-14


title: SLR14-4


title: PBS-4


title: Day 3 Monocultured FB rep2


title: Desmoid type fibromatosis17

description:
D17
190109_13)Expression_Profile.GRCh38.gene.txt
190109_13)Expression_Profile.GRCh38.transcript.txt


title: Day 3 Monocultured FB rep3


title: PBS-3


title: Day 5 Cocultured FB rep1

value: Cocultured with EC


title: SLR14-3


title: Day 3 Monocultured FB rep1


title: YZ-13

description: Library name: YZ-13


title: PBS-2


title: YZ-12

description: Library name: YZ-12


title: Desmoid type fibromatosis15

description:
D15
190109_13)Expression_Profile.GRCh38.gene.txt
190109_13)Expression_Profile.GRCh38.transcript.txt


title: Desmoid type fibromatosis16

description:
D16
190109_13)Expression_Profile.GRCh38.gene.txt
190109_13)Expression_Profile.GRCh38.transcript.txt

value: colon


title: Day 3 Cocultured FB rep6


title: PBS-1


title: YZ-114

description: Library name: YZ-114


title: Desmoid type fibromatosis14

description:
D14
190109_13)Expression_Profile.GRCh38.gene.txt
190109_13)Expression_Profile.GRCh38.transcript.txt


title: Day 3 Monocultured FB rep4


title: Day 3 Cocultured FB rep4


title: U1 HSV-1 rep3

data_processing:
Reads were treated using fastp software with parameter '-n 10 -q 5 -u 50' to discard reads which are short or in poor quality
The treated reads then mapped to mm10 reference genome using CLC Genomic Workbench 12 to get expression of genes
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: BMDM

extract_protocol:
The cell samples were lysed in TRIzol and extract total RNA for RNA-seq
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BMDM

value: Bone-marrow-derived macrophage

value: U1 snRNA knock-in

value: HSV-1 infection


title: YZ-11

description: Library name: YZ-11


title: U1 HSV-1 rep2


title: Desmoid type fibromatosis13

description:
D13
190109_13)Expression_Profile.GRCh38.gene.txt
190109_13)Expression_Profile.GRCh38.transcript.txt