title: ET10, A549, rep3

description:
Library name: ET_10_rep_3
column name in et02b26_consensuscoverage_counts_annotations.txt: et10_3

data_processing:
The fastq files were generated and demultiplexed with the bcl-convert v4.1.7 Conversion Software (Illumina)
Adaptors were trimmed from the 3'-end of the reads
Alignment was done using Bowtie2/2.4.5 with GRCh38
Blacklisted regions (hg38-blacklist.v2.bed) were filtered out with pybedtools/0.9.0
Peaks were called using MACS2/2.2.5
.bw files were generated with bamCoverage from deepTools/3.5.2 with a binSize of 20 and normalized using CPM
The consensus coverage txt file was generated from making a consensus file with bedtools, and peaks per counted and annotated to make the consensuscoverage_countmatrix_counts.txt
Assembly: NCBI GRCh38 with Ensembl99
Supplementary files format and content: tab-delimited file containing a full count matrix for the accessible regions per cell line and replicate
Supplementary files format and content: bigWig file for peak visualization

extract_protocol:
24 hours after seeding, the A549 cells were trypsinized and collected on ice before taken to the sequencing facility. The cells were then processed using the ATACseq kit from Active Motif.
The libraries were prepared using the ATACseq kit from Active Motif. They were then pooled and sequenced on one 10B lane for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 sequencing kits

value: cell line

value: human alveolar epithelial cells


title: DLD-1 Input_NELFC-KD_R1

status: Public on Dec 13 2025

type: SRA

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

description:
Library name: Input_NELFC-KD_R1
ChIP-seq

library_source: genomic

data_processing:
Adapters were trimmed with Cutadapt with the following options: --minimum-length 10 -q 15, 10 -j 16 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA. Trimmed reads were mapped to the Drosophila melanogaster BDGP6.32 and human GRCh38.p13 reference genome with STAR and the parameters: --runThreadN 16 --readFilesCommand gunzip -c -k –alignIntronMax 1 --outFilterMultimapNmax 20 --limitBAMsortRAM 20000000000 --outSAMtype BAM SortedByCoordinate. SAMtools was used to retain the properly mapped reads and to remove PCR duplicates. Reads mapping to the human DAC Exclusion List Regions (accession: ENCSR636HFF) were removed with BEDtools. For spike-in normalization, CSTF64 and INTS3 Drosophila peaks were called against their respective Inputs with MACS379 callpeak and the options -B -f BAMPE -g 1.5e8 -q 0.01 –scale-to small –call-summits. Each peak was then defined as peak summit – 150 bp to peak summit + 150 bp. Only peaks found to overlap between the DMSO and IAA 4h conditions were kept, using the overlapping region as the peak region. BEDtools multicov was then used to quantify Input, CSTF64, and INTS3 signals across their respective peaks, normalised for the library size and the length of the peak region, and used for calculating the spike-in normalization factor for the IAA 4h condition, with the DMSO condition put to 1. After subsampling the human bam files to the smallest library with SAMtools view, spike-in normalized bigwig files were created with deepTools2 bamCoverage tool with the parameters -bs 10 -p max –scaleFactor Normalization_Factor -e.
Assembly: hg38
Supplementary files format and content: bigWig files

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cells were cultured in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS) and penicillin/streptomycin. All the cells were maintained in a humidified incubator at 5% CO2, 37oC.

extract_protocol:
Cells were cultivated on 150 mm dishes until 50% confluency, fixed by addition of 1% formaldehyde (Sigma) for 15 min at 37°C and quenched by 125mM glycine for 10 min at 37°C. The cells were collected by scraping, washed 3 times with cold PBS, resuspended in 1.5 mL L1 buffer (50 mM Tris pH 8.0; 2 mM EDTA pH 8.0; 0,1% NP40; 10% glycerol; protease inhibitors (Nacalai Tesque)) per 107 cells, and lysed on ice for 5 min. The nuclei were collected by centrifugation at 800g for 5m at 4°C and lysed in 1.5 mL of L2 buffer (0,2% SDS; 10 mM EDTA; 50 mM Tris pH 8.0; protease inhibitors (Nacalai Tesque)). The suspension was sonicated in 15 mL conical tubes in a cooled Bioruptor 2 (Diagenode) for 15 min at low settings. Sonicated chromatin was centrifuged for 10 min at 1,4000 rpm and collected the supernatant. The shared chromatin was diluted 10x in the dilution buffer.  For calibration, 4 ng of spike-in chromatin (Active Motif) was added to each IP sample. 60 µg of Protein A Dynabeads (Thermo Fisher Scientific) for each sample were pre-washed twice with dilution buffer (0,5% NP40; 200 mM NaCl; 50 mM Tris pH 8.0; protease inhibitors). The chromatin was incubated with pre-washed beads for 1h at 4°C to clear unspecific binding proteins to the beads. 3μg of the pre-cleared chromatin was incubated with 6 μg of α-CSTF64 (A301-092A, Bethyl) or α-INTS3 (16620-1-AP, Proteintech) and 4.4 μg of spike-in specific antibody (Active Motif), O/N at 4°C on rotator. Next, 60 μL pre-washed beads were added to the chromatin+antibody sample and incubated for 1-2hr at 4°C on rotator. After the incubation, the beads were washed 2 times with buffer A (0.05% SDS; 0.5% TritonX; 2 mM EDTA; 150 mM NaCl; 20 mM Tris pH 8.0), 3 times with buffer B (0.02% SDS; 0.5% NP40; 2 mM EDTA; 250 mM NaCl; 20 mM Tris pH 8.0), 2 times with buffer C (0.05% DOC; 0.5% NP40; 2 mM EDTA; 500 mM NaCl; 20 mM Tris pH 8.0) and finally once again with buffer D (1 mM EDTA; 10 mM Tris pH 8.0). The immunoprecipitated DNA fragments were eluted from the beads with 100ul elution buffer (1% SDS, 100mM NaHCO3) for 15 min at 30°C, and repeated this step twice. After elution, for de-crosslinking, the DNA fragments were incubated for 4h at 65°C in the presence of 10µg RNase A (EN0531, Thermo Fisher Scientific) on thermo mixer (eppendorf). The immunoprecipitated DNA was then purified with the DNA Clean & Concentrator Kit (ZYMO) according to manufacturer’s protocol and used for library preparation.
NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) was used to prepare libraries for sequencing, following manufacturer’s instructions.

treatment_protocol: Cells were treated with 500 µM Auxin or DMSO for 4 h to degrade the AID-tagged protein.

tag: antibody

tag: cell line

tag: cell type

value: Colorectal adenocarcinoma

tag: genotype

value: NELF-C-AID OsTIR1

tag: treatment

value: Auxin 4h


title: ET10, A549, rep2

city: Urbana

first: Elizabeth

middle: Anne

last: Thayer

state: IL

address: 407 S Goodwin Ave

department: Microbiology

country: USA

institute: University of Illinois at Urbana-Champaign

description:
Library name: ET_10_rep_2
column name in et02b26_consensuscoverage_counts_annotations.txt: et10_2

source_name: cell line

growth_protocol: A549 cells were maintained in DMEM supplemented with 8.3% fetal bovine serum in an incubator at 37℃ with 5%CO2

tag: tissue

tag: clone


title: ET10, A549, rep1

description:
Library name: ET_10_rep_1
column name in et02b26_consensuscoverage_counts_annotations.txt: et10_1


title: DLD-1 Input_DMSO_R2

description:
Library name: Input_DMSO_R2
ChIP-seq

value: DMSO 4h


title: DLD-1 Input_DMSO_R1

description:
Library name: Input_DMSO_R1
ChIP-seq


title: ET9, A549, rep3

description:
Library name: ET_9_rep_3
column name in et02b26_consensuscoverage_counts_annotations.txt: et9_3


title: ET9, A549, rep2

description:
Library name: ET_9_rep_2
column name in et02b26_consensuscoverage_counts_annotations.txt: et9_2


title: CSTF64_NELFC-KD_R2

description:
Library name: CSTF64_NELFC-KD_R2
ChIP-seq

value: A301-092A, Bethyl


title: ARK1 cells_CTX-439_2

city: Kyoto

first: Shunsuke

last: Kawahara

address: 54 Kawahara-cho, Shogoin

department: Obstetrics and Gynecology

country: Japan

institute: Kyoto University Hospital

description:
Library name: Sample 6
ARK1 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).

library_source: transcriptomic

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform (RRID: 223 SCR_016387, Illumina) to generate 100 bp paired-end reads.
Raw reads were preprocessed using fastp (version 0.23.2) and aligned to the human reference genome GRCh38 using STAR (version 2.7.10a) and RSEM (version 1.3.1).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw read counts for every gene in each sample.

molecule: total RNA

source_name: Endometrium

extract_protocol:
Total RNA was extracted from frozen tumors using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Endometrium

value: unknown


title: CSTF64_DMSO_R2

description:
Library name: CSTF64_DMSO_R2
ChIP-seq


title: ET9, A549, rep1

description:
Library name: ET_9_rep_1
column name in et02b26_consensuscoverage_counts_annotations.txt: et9_1


title: ET8, A549, rep2

description:
Library name: ET_8_rep_2
column name in et02b26_consensuscoverage_counts_annotations.txt: et8_2


title: ARK1 cells_control_2

description:
Library name: Sample 2
ARK1 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with vehicle (DMSO) as control.

value: vehicle (DMSO, same dosage as CTX-439 group)


title: ARK1 cells_CTX-439_4

description:
Library name: Sample 8
ARK1 endometrial cancer cell xenograft model. RNA was collected 6 hours after the last dose. Mice were treated with CTX-439 (15 mg/kg, oral, twice per week).


title: ET8, A549, rep1

description:
Library name: ET_8_rep_1
column name in et02b26_consensuscoverage_counts_annotations.txt: et8_1


title: siDKO_1

city: Philadelphia

first: Mark

last: Kahn

state: PA

address: 3400 Civic Center Blvd

department: Cardiovascular Institute

institute: University of Pennsylvania

data_processing:
Kallisto alignment to GRCh38
Filtering, normalization and differential expressing using edgeR and limma
Assembly: GRCh38
Supplementary files format and content: Normalized expression matrix, log2 counts per million

source_name: Umbilical artery

extract_protocol: Total RNA

value: Umbilical artery

value: HUAECs

value: arterial endothelial cells

value: UNC5B and DLL4 siRNA


title: INTS3_NELFC-KD_R1

description:
Library name: INTS3_NELFC-KD_R1
ChIP-seq

value: 16620-1-AP, Proteintech


title: siDKO_2


title: ET7, A549, rep3

description:
Library name: ET_7_rep_3
column name in et02b26_consensuscoverage_counts_annotations.txt: et7_3


title: CSTF64_NELFC-KD_R1

description:
Library name: CSTF64_NELFC-KD_R1
ChIP-seq


title: ET7, A549, rep2

description:
Library name: ET_7_rep_2
column name in et02b26_consensuscoverage_counts_annotations.txt: et7_2


title: siUNC5B_3

value: UNC5B siRNA


title: ET7, A549, rep1

description:
Library name: ET_7_rep_1
column name in et02b26_consensuscoverage_counts_annotations.txtt: et7_1


title: siDKO_3


title: ET3, A549, rep2

description:
Library name: ET_3_rep_2
column name in et02b26_consensuscoverage_counts_annotations.txt: et3_2


title: ET3, A549, rep3

description:
Library name: ET_3_rep_3
column name in et02b26_consensuscoverage_counts_annotations.txt: et3_3


title: siDLL4_3

value: DLL4 siRNA


title: siUNC5B_1


title: siUNC5B_2


title: ET3, A549, rep1

description:
Library name: ET_3_rep_1
column name in et02b26_consensuscoverage_counts_annotations.txt: et3_1

value: cell line


title: ET2, A549, rep3

description:
Library name: ET_2_rep_3
column name in et02b26_consensuscoverage_counts_annotations.txt: et2_3

value: human alveolar epithelial cells


title: ET2, A549, rep2

description:
Library name: ET_2_rep_2
column name in et02b26_consensuscoverage_counts_annotations.txt: et2_2


title: CSTF64_DMSO_R1

description:
Library name: CSTF64_DMSO_R1
ChIP-seq

value: Colorectal adenocarcinoma


title: siCTRL_3

value: Control siRNA


title: ET2, A549, rep1

description:
Library name: ET_2_rep_1
column name in et02b26_consensuscoverage_counts_annotations.txt: et2_1


title: ET8, A549, rep3

description:
Library name: ET_8_rep_3
column name in et02b26_consensuscoverage_counts_annotations.txt: et8_3


title: siDLL4_1


title: siCTRL_1


title: siCTRL_2


title: TT-seq-NELFCAID-Auxin4h-NVP2_60m-Rep2

data_processing:
library strategy: Transient transcriptome sequencing (TT-seq)
The low-quality bases were removed from 3' end of raw reads using cutadapt 4.2. The reads were aligned to the human genome assembly GRCh38 release 103. The alighed reads with primary alignment and MAPQ ≥ 20 were retained. The strand-specific bigwig files with CPM were generated using deepTools bamCoverage 3.5.1.
Assembly: hg38
Supplementary files format and content: bigWig files contain the strand-specific TT-seq signal.

molecule: nuclear RNA

growth_protocol: Human DLD-1 cells that constitutively express OsTIR1 were cultured at 37°C in DMEM supplemented with 10% FBS and 1% Pen-Strep in CO2 incubators.

extract_protocol:
Nascent RNA was labeled with 500 µM 4sU for 10 min in the cell culture. Total RNA was extracted using TRIzol. RNA was fragmented at 94°C for 2 min usng NEBNext Magnesium RNA Fragmentation Module. MTSEA-biotin-XX was used for biotinylation of fragmented 4sU RNA. The labeled RNA was purified using Dynabeads MyOne Streptavidin C1 and eluted by DTT.
rRNA was depleted using NEBNext rRNA Depletion Kit. The remaining labeled RNA was used for library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: Cells were treated with 500 µM Auxin or DMSO for 4 h to degrade the AID-tagged protein. CDK9 was inhibited by 250 nM NVP-2 for the indicated time.

value: NELF-C-AID OsTIR1


title: ET1, A549, rep2

description:
Library name: ET_1_rep_2
column name in et02b26_consensuscoverage_counts_annotations.txt: et1_2


title: TT-seq-NELFCAID-DMSO4h-NVP2_60m-Rep2


title: siDLL4_2


title: TT-seq-NELFCAID-DMSO4h-NVP2_0m-Rep2


title: scRNAseq, A549, Pool2

description:
Library name: et02b04_SamplePool2
The samples are organized based the aggr_timepoints.csv file

library_source: transcriptomic single cell

data_processing:
The fastq files were generated and demultiplexed using bcl-convert v4.1.7  Conversion Software (Illumina)
The processed files were generated using the CellRanger/7.1.0 multi and aggr functions.
Assembly: NCBI GRCh38 with Ensembl99
Supplementary files format and content: CellRanger aggr output filtered_feature_bc_matrix output in HDF5 format
Supplementary files format and content: Supplementary file et02b04_feature_README.txt: additional sample characteristics and multiplexing probe barcodes
Supplementary files format and content: Supplementary file aggr_timepoints.csv: input configuration file for CellRanger aggr
Supplementary files format and content: Supplementary files pool1_input.csv, pool2_input.csv, pool3_input.csv: input configuration files for CellRanger multi
Supplementary files format and content: Supplementary file barcodes_umap_probabilities_info.csv: cell barcodes with their clusters, counts, ids, velocity score, umap positions, and probability scores for each terminal state

extract_protocol:
The A549 cells were trypsinized then collected on ice before being transported to the sequencing facility to be further prepared using the Chromium Next GEM Single Cell FixedRNA Sample Preparation Kit.
The libraries were prepared using the Chromium Next GEM Single Cell FixedRNA Sample Preparation Kit for Human Transcriptome per the manufacturer's protocol. The libraries were sequenced on two 10B lanes with 28x150nt reads. Read1 is 28nt in length, Read2 is 150nt in length, I1 and I2 are 10nt in length.

treatment_protocol: A549 cells were either untreated or transfected with 5 ng/mL pIC at varying time points in order to collect all the samples at once.

value: untreated or 5 ng/mL pIC for 4, 8, 12, or 16 hours


title: ET1, A549, rep3

description:
Library name: ET_1_rep_3
column name in et02b26_consensuscoverage_counts_annotations.txt: et1_3


title: TT-seq-NELFCAID-DMSO4h-NVP2_60m-Rep1


title: A549,  10 μM ruxolitinib + 24 μM JNK-IN-8 + pIC, rep3

description:
Library name: JAK_JNK_PIC_3
column name in et02b21.48_counts.txt:JAK_JNK_PIC_3

data_processing:
Adaptors were trimmed from the 3'-end of the reads.
The fastq files were generated and demultiplexed using bcl-convert v4.1.7  Conversion Software (Illumina)
Reads were aligned using STAR/2.7.6a
Count matrix was made for each gene in each datafile then compiled into one count matrix for the entire experiment.
Assembly: NCBI GRCh38 with Ensembl99
Supplementary files format and content: tab-delimited textfile containing a full raw count matrix for all the samples (columns) and genes (rows)

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN).
The libraries were prepared using Roche's Kapa Hyper Stranded mRNA library kit per the manufacturer's protocol. The libraries were pooled and sequencined on one 10B lane for 101 cycles from one end of the fragments on a NovaSeq X Plus with v1.0 sequencing kits.

treatment_protocol: A549 cells were treated with DMSO, JNK-IN-8, Ruxolitinib, or both inhibitors for 4 hours before being transfected with either 5 ng/mL pIC or just lipofectamine without pIC. The RNA was extracted 16 hours post pIC treatment.

value: 10 μM ruxolitinib + 24 μM JNK-IN-8 + 5 ng/mL pIC


title: A549,  10 μM ruxolitinib + 24 μM JNK-IN-8 + pIC, rep1

description:
Library name: JAK_JNK_PIC_1
column name in et02b21.48_counts.txt: JAK_JNK_PIC_1


title: POINTseq_NELFC_12h_SIRV_R2

description: SIRV spiked POINT-seq in NELFC-AID cells

data_processing:
library strategy: polymerase intact nascent transcript (POINT-Seq)
Adapters were trimmed with Cutadapt v1.18 with the following options: --minimum-length 10 -q 15, 10 -j 16 -A GATCGTCGGACTGTAGAACTCTGAAC -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC.
Trimmed reads were mapped to the human GRCh38.p13 reference sequence or the SIRV-Set 2: SIRV isoform Mix E0 sequences (See Lexogen website) with STAR v2.7.0 and the parameters: --runThreadN 16 -- readFilesCommand gunzip -c -k --limitBAMsortRAM  20000000000 --outFilterMultimapNmax 1 --outFilterScoreMin 10 --outSAMtype BAM SortedByCoordinate.
SAMtools v1.9 was used to retain the properly mapped reads.
For non-spiked POINT-seq, FPKM-normalized bigwig files were created with deepTools2 v3.4.2 bamCoverage tool with the parameters -bs 10 -p max –filterRNAstrand forward (or reverse) --normalizeUsing RPKM.
For SIRV spiked POINT-seq, SAMtools view with the –s option was used to subsample all the bam files to the bam file containing the lowest number of reads and then to create strand-specific BAM files. The normalization factor was calculated as: (number of SIRV reads) / (number of human reads + number of SIRV reads). Spiked normalized bedGraph files were created with BEDtools v2.29.2 genomecov and the options: -bg -split –scale (1 / normalization factor). Bigwig files were generated from the BedGraph files with the bedGraphToBigWig v2.10 tool.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: DLD-1 SPT4-AID

extract_protocol:
10 million cells were lysed with 4 mL ice-cold hypotonic buffer (10 mM Tris-Cl pH 7.5, 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40) on ice for 5 min. The cell lysate was carefully underlaid with 1 mL sucrose cushion buffer (hypotonic buffer with 10% (w/v) sucrose). The nuclear fraction was pelleted by centrifugation (300 g, 5 min at 4 oC), then washed with ice-cold hypotonic buffer (without NP-40) once. The purified nuclear fraction was first resuspended in 300 µL (200~500 µL, depending on the pellet size) ice-chilled NUN1 buffer (20 mM Tris-HCl pH 7.9, 75 mM NaCl, 0.5 mM EDTA pH 8.0, and 50% glycerol) and then lysed in 3 mL (at least 10-fold volume of NUN1) ice-cold NUN2 buffer (20 mM HEPES-KOH pH 7.6, 300 mM NaCl, 0.2 mM EDTA pH 8.0, 7.5 mM MgCl2, 1% NP-40, 1 M Urea, 3% Empigen BB, 1x Protease inhibitor Complete EDTA-free, and 1x PhosSTOP). Note: The cotton candy-like chromatin should appear within a few minutes. The chromatin was then pelleted and washed with ice-cold PBS once (300 g, 1 min at 4 oC). Chromatin-bound Pol II was released by DNase digestion in the reaction mixture (10 mM Tris-HCl pH 7.5, 400 mM NaCl, 100 mM MnCl2, 2 Units/ µL RiboLock, and 0.2 Units/µL Turbo DNase) at 37oC for 15 min in the ThemoMixer C (Eppendorf) at 1200rpm. EDTA pH 8.0 (final 1mM) was used to stop the DNase reaction, and the supernatant was collected by high-speed centrifugation (14,000g, 10 min at 4oC). A 5-fold volume of ice-cold NET-2E buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.05 % NP-40, and 3% Empigen BB) was used for the dilution of the supernatant.  The 10 µg of anti-Pol II antibody MABI601 were mixed with 200 µL anti-mouse IgG Dynabeads solution in 1 mL NET-2 buffer (NET-2E without Empigen) and incubated at 4 oC with mild rotation for at least 1 hour. The conjugated beads were washed with NET-2 buffer once and resuspended in 200 µL NET-2E buffer. The resuspended beads were added to the diluted supernatant of chromatin for at least 1 hours and then incubated at 4oC with mild rotation (Note: Avoid overnight incubation). After the incubation, beads were washed with 1 mL of ice-cold NET-2E buffer at least 6 times. Pol II-bound nascent RNAs (POINTs) were extracted from the beads using Tri Reagent and subsequently purified by Direct-zol kit following the manufacturer's protocol.  Equal amount of SIRV spike-in oligos were added to each POINTs.
NEBNext Ultra II Directional RNA library prep kit

treatment_protocol: AID-tagged protein degradation was induced by adding 500 µM auxin (IAA) to the culture media. For Pladienolide B treatment, a concentration of 1 μM was used.

value: DLD-1 SPT4-AID

value: Colorectal cancer

value: Auxin 12 hours


title: A549,  10 μM ruxolitinib + 24 μM JNK-IN-8, rep2

description:
Library name: JAK_JNK_2
column name in et02b21.48_counts.txt: JAK_JNK_2

value: 10 μM ruxolitinib + 24 μM JNK-IN-8


title: A549,  10 μM ruxolitinib + 24 μM JNK-IN-8 + pIC, rep2

description:
Library name: JAK_JNK_PIC_2
column name in et02b21.48_counts.txt: JAK_JNK_PIC_2


title: TT-seq-NELFCAID-DMSO4h-NVP2_0m-Rep1


title: POINTseq_NELFC_24h_SIRV_R1

value: Auxin 24 hours


title: A549,  10 μM ruxolitinib + 24 μM JNK-IN-8, rep3

description:
Library name: JAK_JNK_3
column name in et02b21.48_counts.txt: JAK_JNK_3


title: POINTseq_NELFC_12h_SIRV_R1


title: POINTseq_NELFC_4h_SIRV_R2

value: Auxin 4 hours


title: POINTseq_NELFC_24h_SIRV_R2


title: A549,  10 μM ruxolitinib, rep3

description:
Library name: JAK_3
column name in et02b21.48_counts.txt: JAK_3

value: 10 μM ruxolitinib


title: POINTseq_NELFC_4h_SIRV_R1


title: A549,  10 μM ruxolitinib, rep2

description:
Library name: JAK_2
column name in et02b21.48_counts.txt: JAK_2


title: A549,  10 μM ruxolitinib, rep1

description:
Library name: JAK_1
column name in et02b21.48_counts.txt: JAK_1


title: ET1, A549, rep1

description:
Library name: ET_1_rep_1
column name in et02b26_consensuscoverage_counts_annotations.txt: et1_1


title: A549,  10 μM ruxolitinib + 24 μM JNK-IN-8, rep1

description:
Library name: JAK_JNK_1
column name in et02b21.48_counts.txt: JAK_JNK_1


title: POINTseq_NELFC_0h_SIRV_R1

value: DMSO


title: POINTseq_SPT4_3h_R2

description: POINT-seq in SPT4-AID cells

value: Auxin 3 hours


title: scRNAseq, A549, Pool1

description:
Library name: et02b04_SamplePool1
The samples are organized based the aggr_timepoints.csv file


title: POINTseq_SPT4_3h_R1

description: POINT-seq in SPT4-AID cells


title: A549,  24 μM JNK-IN-8 + pIC, rep1

description:
Library name: JNK_PIC_24_1
column name in et02b21.48_counts.txt: JNK_PIC_24_1

value: 24 μM JNK-IN-8 + 5 ng/mL pIC


title: TT-seq-NELFCAID-Auxin4h-NVP2_30m-Rep2


title: A549,  24 μM JNK-IN-8 + pIC, rep3

description:
Library name: JNK_PIC_24_3
column name in et02b21.48_counts.txt: JNK_PIC_24_3

value: cell line


title: A549,  24 μM JNK-IN-8 + pIC, rep2

description:
Library name: JNK_PIC_24_2
column name in et02b21.48_counts.txt: JNK_PIC_24_2

value: human alveolar epithelial cells


title: A549,  24 μM JNK-IN-8, rep3

description:
Library name: JNK_24_3
column name in et02b21.48_counts.txt: JNK_24_3

value: 24 μM JNK-IN-8


title: POINTseq_SPT4_0h_R2

description: POINT-seq in SPT4-AID cells


title: POINTseq_SPT4_0h_R1

description: POINT-seq in SPT4-AID cells


title: A549,  24 μM JNK-IN-8, rep2

description:
Library name: JNK_24_2
column name in et02b21.48_counts.txt: JNK_24_2


title: TT-seq-NELFCAID-Auxin4h-NVP2_60m-Rep1

value: Colorectal adenocarcinoma


title: POINTseq_NELFE_4h_R2

description: POINT-seq in NELFE-AID cells

source_name: DLD-1 NELFE-AID

value: DLD-1 NELFE-AID


title: A549, DMSO + pIC, rep3

description:
Library name: DMSO_PIC_3
column name in et02b21.48_counts.txt: DMSO_PIC_3

value: DMSO + 5 ng/mL pIC


title: POINTseq_NELFC_0h_SIRV_R2


title: A549,  10 μM ruxolitinib + pIC, rep3

description:
Library name: JAK_PIC_3
column name in et02b21.48_counts.txt: JAK_PIC_3

value: 10 μM ruxolitinib + 5 ng/mL pIC


title: A549,  24 μM JNK-IN-8, rep1

description:
Library name: JNK_24_1
column name in et02b21.48_counts.txt: JNK_24_1


title: POINTseq_NELFE_4h_R1

description: POINT-seq in NELFE-AID cells


title: POINTseq_NELFE_0h_R2

description: POINT-seq in NELFE-AID cells


title: A549, DMSO + pIC, rep1

description:
Library name: DMSO_PIC_1
column name in et02b21.48_counts.txt: DMSO_PIC_1


title: A549, DMSO + pIC, rep2

description:
Library name: DMSO_PIC_2
column name in et02b21.48_counts.txt: DMSO_PIC_2


title: A549, DMSO, rep3

description:
Library name: DMSO_3
column name in et02b21.48_counts.txt: DMSO_3


title: POINTseq_NELFC_4h_PlaB_R2

description: POINT-seq in NELFC-AID cells

source_name: DLD-1 NELFC-AID

value: DLD-1 NELFC-AID

value: Auxin 4 hours & PlaB


title: A549, DMSO, rep2

description:
Library name: DMSO_2
column name in et02b21.48_counts.txt: DMSO_2


title: Parental (WT), A549, rep2

description:
Library name: WT_rep_2
column name in et02b26_consensuscoverage_counts_annotations.txt: wt_3

value: WT


title: POINTseq_NELFC_4h_PlaB_R1

description: POINT-seq in NELFC-AID cells

value: Colorectal cancer


title: POINTseq_NELFC_0h_PlaB_R2

description: POINT-seq in NELFC-AID cells

value: DMSO & PlaB


title: POINTseq_NELFC_0h_PlaB_R1

description: POINT-seq in NELFC-AID cells


title: DLD-1, NELFC-AID, replicate 2, BrdU-IP

city: Tokyo

first: Yasukazu

last: Daigaku

address: 3-8-31 Ariake Koto-ku

department: Cancer institute

institute: Japanese Foundation for Cancer Research

description: Library name: NELFC-AID, replicate 2, BrdU-IP

data_processing:
For each sample approx. 200 million PE read were obtained. Raw reads were aligned to GRCh38 using Bowtie2 (version 2.3.5). Those which aligned to multiple genomic locations with the same mismatch scores (AS and XS scores as outputted by Bowtie2) were excluded using a custom Perl script: sam-dup-align-exclude-v2.pl (available at the GitHub site: https://github.com/yasukasu/sam-dup-align-exclude). The position of center of each read was determined, and the number of reads in 1-kb bins across the genome were counted using a custom Perl script: pe-sam-to-bincount.pl (available at the GitHub site: https://github.com/yasukasu/sam-to-bincount). At the chromosome coordinate x, CB(x) is the count for the BrdU-IP sample; CI(x) is count for the input sample. After obtaining the genome-wide read count data, genomic bins where the count of the input samples are less than 5 in both strands (e.g. CI(x)<5) were excluded from further calculation for BrdU enrichment. These datasets were then normalised with the total number of reads:  NB(x) = CB(x)/ΣCB(x), NI(x) = CI(x)/ΣCI(x). Enrichments for BrdU-incorporated fragments were calculated: E(x) = NB(x)/NI(x). When these data were used for further analysis, they were smoothed using moving average of 2m+1; the data point for each bin is an average of 2m+1 bins: the central bin and the m bins either side. In this study, m was set 10.
Assembly: GRCh38
Supplementary files format and content: BigWig

growth_protocol: Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS) and penicillin/streptomycin. All the cells were maintained in a humidified incubator at 5% CO2, 37oC.

extract_protocol:
Genomic DNA was extracted using the Blood & Cell Culture DNA Midi Kit with 100/G Genomic-tips (Qiagen). After measuring DNA concentration, 10 µg of DNA was dissolved in 200 µL of TE buffer and subjected to sonication using ultrasound (30 seconds on, 30 seconds off, for 60 cycles) with the Bioruptor II (BMbio). A 15 µL aliquot of the sonicated DNA solution was set aside as the input sample, and the remaining 150 µL was heated at 96°C for 10 min and snap-cooled in ice-cold water to denature the DNA before immunoprecipitation with an anti-BrdU antibody (Clone B44, BD Biosciences).To the denatured DNA solution, an equal volume of 2× BrdU-IP buffer (200 mM sodium phosphate, pH 7.3, 280 mM NaCl, 0.1% Triton X-100) was added. Next, 20 µL of BrdU antibody (3.75 µg) pre-bound to Protein G Dynabeads (Life Technologies) was added to the solution and incubated at 37°C for 1h. The tube containing the solution was placed on a magnetic stand, and the beads were washed twice with 1×BrdU-IP buffer and once with TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA). Bead-bound DNA was eluted in 50 µL of elution buffer (50 mM Tris-HCl, pH 8.0, 1% SDS). Both the input DNA and BrdU-IP DNA were purified using AMPure beads (Beckman Coulter) following the manufacturer's instructions and dissolved in 100 µL of 1 mM Tris-HCl (pH 8.0).
A total of 4 ng of immunoprecipitated single-stranded DNA (ssDNA) fragments in 30 μl of 1 mM Tris-HCl (pH 8.0) was mixed with 5 μl of 3 mg/ml custom-synthesized 8N random primer, heated at 95°C, and immediately snap-cooled on ice. The samples were then incubated with 2.5 μl (12.5 units) of Klenow fragment (NEB) and 5 μl of 2 mM dNTPs in a total volume of 50 μl to convert single-stranded DNA (ssDNA) into double-stranded DNA (dsDNA). The resulting dsDNA was purified using AMPure XP beads (Beckman Coulter), and its concentration was determined by fluorometric quantification (PicoGreen; Life Technologies). Fragment size distribution was analyzed with an Agilent TapeStation. Subsequently, all purified dsDNA was used for Illumina library preparation with the NEBNext Ultra II DNA Library Prep Kit (NEB).

treatment_protocol: Cell cultures (0.75 × 10⁵ cells/ml) were seeded in 25 ml of medium in 15 cm dishes. After 48h of incubation, 50 ng/ml nocodazole (Noc) was added to the culture to synchronize the cells in the M phase. Following 24 h of Noc treatment, cells were released from the M phase by washing off the Noc through two media exchanges. After a 8hr release, 500  μM of IAA was added and, after a 12h release, BrdU was added to the cell cultures and incubated for 2 h.

value: colorectal adenocarcinoma cell line


title: POINTseq_NELFC_4h_DMSO_R2

description: POINT-seq in NELFC-AID cells

value: DMSO & Auxin 4 hours


title: TT-seq-NELFCAID-Auxin4h-NVP2_0m-Rep2

value: NELF-C-AID OsTIR1


title: Parental (WT), A549, rep1

description:
Library name: WT_rep_1
column name in et02b26_consensuscoverage_counts_annotations.txt.txt: wt_1


title: DLD-1, NELFC-AID, replicate 2, INPUT

description: Library name: NELFC-AID, replicate 2, INPUT


title: DLD-1, control, replicate 2, BrdU-IP

description: Library name: Control, replicate 2, BrdU-IP


title: POINTseq_NELFC_0h_DMSO_R1

description: POINT-seq in NELFC-AID cells

value: DMSO


title: POINTseq_NELFC_4h_DMSO_R1

description: POINT-seq in NELFC-AID cells


title: POINTseq_NELFE_0h_R1

description: POINT-seq in NELFE-AID cells


title: DLD-1, control, replicate 1, BrdU-IP

description: Library name: Control, replicate 1, BrdU-IP


title: DLD-1, control, replicate 2, INPUT

description: Library name: Control, replicate 2, INPUT


title: POINTseq_NELFC_0h_DMSO_R2

description: POINT-seq in NELFC-AID cells


title: DLD-1, NELFC-AID, replicate 1, INPUT

description: Library name: NELFC-AID, replicate 1, INPUT


title: POINTseq_NELFC_4h_R2

description: POINT-seq in NELFC-AID cells

value: Auxin 4 hours


title: TT-seq-NELFCAID-Auxin4h-NVP2_30m-Rep1


title: POINTseq_NELFC_4h_R1

description: POINT-seq in NELFC-AID cells


title: DLD-1, control, replicate 1, INPUT

description: Library name: Control, replicate 1, INPUT


title: POINTseq_NELFC_0h_R2

description: POINT-seq in NELFC-AID cells


title: POINTseq_NELFC_0h_R1

description: POINT-seq in NELFC-AID cells


title: RNAseq_Nuclear_pA_24h_R1

data_processing:
Adapters were trimmed with Cutadapt v1.18 with the following options: --minimum-length 10 -q 15, 10 -j 16 -A GATCGTCGGACTGTAGAACTCTGAAC -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC.
The remaining rRNA reads were removed by mapping the reads to the rRNA genes defined in the human ribosomal DNA complete repeating unit (GenBank: U13369.1) with STAR v2.7.0 and the parameters --runThreadN 16 --readFilesCommand gunzip -c -k --outReadsUnmapped Fastx --limitBAMsortRAM 20000000000--outSAMtype BAM SortedByCoordinate. The unmapped reads were mapped to the human GRCh38.p13 reference sequence with STAR and the parameters: --readFilesCommand gunzip -c -k --limitBAMsortRAM  20000000000 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate.
SAMtools v1.9 was used to retain the properly paired and mapped reads (-f 3) and to create strand-specific BAM files.
FPKM-normalized bigwig files were created with deepTools2 v3.4.2 bamCoverage tool with the parameters -bs 10 -p max –normalizeUsing RPKM.
For differential expression analysis, the outputs of STAR –quantMode GeneCounts were imported DESeq2 v1.30.1 and apeglm v1.18.0 keeping only the genes with a fold change < -2 or > 2 and an adjusted p-value below 0.05.
Assembly: hg38
Supplementary files format and content: bigwig

molecule: polyA RNA

extract_protocol:
Nuclear RNAs were extracted from DLD-1 cells using Tri Reagent and subsequently purified by Direct-zol kit following the manufacturer's protocol.
NEBNext Ultra II Directional RNA library prep kit

treatment_protocol: AID-tagged protein degradation was induced by adding 500 µM auxin (IAA) to the culture media.

value: Auxin 24 hours

tag: molecule subtype

value: Nuclear polyA RNA


title: RNAseq_Nuclear_pA_12h_R2

value: Auxin 12 hours


title: RNAseq_Nuclear_pA_24h_R2


title: DD_DMSO_CD4_S29

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

description:
Library name: DD_DMSO_CD4_S29
DA_DMSO_CD4; DC_DMSO_CD4; DD_DMSO_CD4

data_processing:
trimmed high quality reads were aligned to genome  using bowtie2
Raw count values generated with Subread
Gene expression values were nromalized to transcripts per million
Differential peak analysis determined using DESeq2 with cutoffs of 2 fold and p value<0.05
Assembly: mm10
Supplementary files format and content: csv file contains transcripts per million (TPM)

source_name: T CELLS

extract_protocol:
Rneasy miniplus kit
Illumina Truseq RNA

value: T CELLS

value: CD4 T cells

value: DMSO CONTROL


title: DD_DMSO_CD8_S30

description:
Library name: DD_DMSO_CD8_S30
DA_DMSO_CD8; DC_DMSO_CD8; DD_DMSO_CD8

value: CD8 T Cells


title: DD_991_CD4_S31

description:
Library name: DD_991_CD4_S31
DA_991_CD4; DC_991_CD4; DD_991_CD4

value: 991 TREATMENT


title: DD_991_CD8_S32

description:
Library name: DD_991_CD8_S32
DA_991_CD8; DC_991_CD8; DD_991_CD8


title: DLD-1, NELFC-AID, replicate 1, BrdU-IP

description: Library name: NELFC-AID, replicate 1, BrdU-IP


title: DC_DMSO_CD8_S26

description:
Library name: DC_DMSO_CD8_S26
DA_DMSO_CD8; DC_DMSO_CD8; DD_DMSO_CD8


title: RNAseq_Nuclear_pA_4h_R2

value: DLD-1 NELFC-AID


title: DC_DMSO_CD4_S25

description:
Library name: DC_DMSO_CD4_S25
DA_DMSO_CD4; DC_DMSO_CD4; DD_DMSO_CD4


title: RNAseq_Nuclear_pA_12h_R1


title: RNAseq_Nuclear_pA_4h_R1


title: RNAseq_Nuclear_pA_0h_R2


title: DC_991_CD4_S27

description:
Library name: DC_991_CD4_S27
DA_991_CD4; DC_991_CD4; DD_991_CD4


title: RNAseq_Nuclear_pA_0h_R1


title: DA_DMSO_CD8_S22

description:
Library name: DA_DMSO_CD8_S22
DA_DMSO_CD8; DC_DMSO_CD8; DD_DMSO_CD8


title: RNAseq_pA_4h_R2

value: Total polyA RNA


title: DA_DMSO_CD4_S21

description:
Library name: DA_DMSO_CD4_S21
DA_DMSO_CD4; DC_DMSO_CD4; DD_DMSO_CD4


title: RNAseq_pA_4h_R1

value: Colorectal cancer


title: DA_991_CD8_S24

description:
Library name: DA_991_CD8_S24
DA_991_CD8; DC_991_CD8; DD_991_CD8


title: Sorted Memory B and T cells from Patient 8 and 10 week 36 – Gene Expression

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

country: Germany

description: Library name: SLE_Patient_25_26_T_B_PB_GEX

data_processing:
CellRanger v7.0.0 functions count and aggr were used in default settings
Assembly: hg38
Supplementary files format and content: *.h5 files containing the information needed to evaluate date in R using Seurat (e.g.)
Supplementary files format and content: *.csv files containing the repertoir information of the cells.

source_name: Sorted Memory B and T Lymphocytes

extract_protocol:
At week 0, 9 and 36, PBMCs were isolated from fresh heparin-anticoagulated blood using Ficoll-Paque PLUS gradient (GE Healthcare), washed and incubated with fluorescent antibodies against CD3, CD19, CD45RA, CCR7 and CD27. In case more than one patient sample was analysed at the same day, TotalSeq™-C anti-human Hashtag antibodies (BioLegend) were used. Using a BD AriaII™ cell sorter, we sorted both CD19+CD27+ memory B cells/plasmablasts and CD3+ non-naïve (i.e. not positive for both CCR7 and CD45RA) T cells, and adjusted cell numbers to sequence 10.000 cells per patient and time point. Due to organisational/technical problems, data from patients #6 and #8, as well as the week 36 time point of patient #4 had to be excluded.
Single-cell RNA library construction and sequencing was done as previously described.5,55 Briefly, Chromium Next GEM Single Cell 5’ reagent kits v2 (dual index) with feature barcode technology for cell surface protein (CITE) mapping (10X Genomics) were used according to the manufacturer’s protocol. Final CITE-Seq libraries were generated after index PCR with dual Index Kit TN Set A (10X Genomics) while final GEX and TCR/BCR libraries were generated after fragmentation, adapter ligation and final index PCR with a dual Index Kit TT Set A (10X Genomics). Libraries were quantified using a Qubit HS DNA assay kit (Life Technologies) and fragment sizes were determined using a HS NGS Fragment (1-6000 bp) kit (Agilent). All libraries were sequenced on a NextSeq2000 sequencer (Illumina). GEX and CITE libraries were sequenced using a P3 reagent cartridge (100 cycles) (Illumina) with the following recommended sequencing conditions: read1: 26 nt, index1: 10 nt, read2: 90 nt, index2: 10 nt. The BCR and TCR libraries spiked-in with 10% 2nM PhiX were sequenced using a P3 reagent cartridge (300 cycles) (Illumina) with the following recommended sequencing conditions: read1: 151 nt, index1: 10 nt, read2: 151 nt, index2: 10 nt.
The sequencing was performed on a NextSeq2000 (or NextSeq500) device (Illumina) using NextSeq 1000/2000 P3 reagent kits (200 Cycles, Illumina) with the recommended sequencing conditions for 5’ GEX and Cite-Seq libraries (read1: 26nt, read2: 90nt, index1: 10nt, index2: 10nt) and NextSeq 1000/2000 P3 reagent kits.

treatment_protocol: Patients were treated accodring to standard of care. For dataset before and after Methylprednisolone puls children were treated with methylprednisolon 20-30 mg/kg(bodyweight)/day for 3 consecutive days. B07 (MIS-C patient Berlin 07), B09 and B 10 were captured before treatment with methylprednisolone, B08 was treated with 1-2mg/kg methylprednisolone for 2 days, B06 was treated with 1-2 mg/kg methylprednisolone for 3 days. Patients B01, B02 B04, B05 and B11 were treated with 20-30 mg/kg methylprednisolone for 1 day and B03 was treated with 20-30 mg/kg methylprednisolone for 4 days before capturing.

value: Sorted Memory B and T Lymphocytes

value: After 8 x weekly 1800mg Daratumumab sc


title: DA_991_CD4_S23

description:
Library name: DA_991_CD4_S23
DA_991_CD4; DC_991_CD4; DD_991_CD4


title: RNAseq_pA_0h_R2


title: Sorted Memory B and T cells from Patient 9 week 36 – TCR

description: Library name: SLE_Patient_24_T_B_PB_hTCR

library_source: other

molecule: other


title: ATAC_24h_R1

description: ATAC-seq IAA 24 hours Rep1

data_processing:
Adapters were trimmed with Cutadapt v1.18 with the following options: --minimum-length 10 -q 15, 10 -j 16 -A GATCGTCGGACTGTAGAACTCTGAAC -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC.
Trimmed reads were mapped to the human GRCh38.p13 reference sequence with STAR v2.7.0 and the parameters: --runThreadN 16 --readFilesCommand gunzip -c -k –alignIntronMax 1 --limitBAMsortRAM 20000000000 --outSAMtype BAM SortedByCoordinate.
SAMtools v1.9 was used to retain the properly mapped reads and to remove PCR duplicates.
Reads mapping to the DAC Exclusion List Regions (accession: ENCSR636HFF) and to the mitochondrial genome were removed with BEDtools v2.29.2.
FPKM-normalized bigwig files were created with deepTools2 v3.4.2 bamCoverage tool with the parameters -bs 10 -p max –normalizeUsing RPKM -e.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Extraction was perfromed with the ATAC-seq kit (Active Motif, cat. 53510)
Illumina Nextera XT DNA Library Preparation Kit


title: ATAC_24h_R2

description: ATAC-seq IAA 24 hours Rep2


title: RNAseq_pA_0h_R1


title: TT-seq-NELFCAID-Auxin4h-NVP2_0m-Rep1

value: Colorectal adenocarcinoma


title: cGAS-KO; HD A3 (25172XR-01-12)

city: Jupiter

first: Srini

last: Subramaniam

state: FL

address: 5353 parkside drive,, MC19, 213,

department: Neuroscience

institute: Florida Atlantic University

description: Library name: cGAS-KO; HD A3 (25172XR-01-12)

data_processing:
Libraries were pooled equimolarly and sequenced on an Illumina® NovaSeq X Plus with a read configuration of 150-bp paired-end, generating 40M PE reads per sample (20M each direction).
Supplementary files format and content: count_raw.txt files are included for each sample

organism: Mus musculus

source_name: Striatal tissue

extract_protocol:
Three mice per group were used to generate biological triplicates (total n = 12). Striatal tissue was preserved in TRIzol reagent. RNA quality was assessed using High Sensitivity RNA TapeStation (Agilent Technologies Inc., CA, USA) and quantified using Infinite F Nano+ 200 Pro Tecan® (Tecan, Switzerland). Poly(A)+ RNA was isolated using paramagnetic beads coupled with oligo d(T)25 following the NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Samples were randomly primed (5´d(N6)3´ [N = A, C, G, T]) and fragmented before first-strand synthesis using Protoscript II Reverse Transcriptase (30 min at 42°C). All further steps followed the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®.
Library concentrations were assessed using Qubit 2.0 (ThermoFisher), and quality was assessed with TapeStation HSD1000 ScreenTape (Agilent). Average final library size was ~400 bp, with ~250 bp insert size. Illumina® 8-nt dual indices were used.

value: Striatal tissue


title: Sorted Memory B and T cells from Patient 9 week 36 – BCR

description: Library name: SLE_Patient_24_T_B_PB_hBCR


title: DC_991_CD8_S28

description:
Library name: DC_991_CD8_S28
DA_991_CD8; DC_991_CD8; DD_991_CD8


title: Sorted Memory B and T cells from Patient 9 week 36 – Gene Expression

description: Library name: SLE_Patient_24_T_B_PB_GEX


title: ATAC_4h_R2

description: ATAC-seq IAA 4 hours Rep2


title: A549, DMSO, rep1

description:
Library name: DMSO_1
column name in et02b21.48_counts.txt: DMSO_1

value: cell line

value: human alveolar epithelial cells

value: DMSO


title: cGAS-KO; HD A2 (25172XR-01-11)

description: Library name: cGAS-KO; HD A2 (25172XR-01-11)


title: Sorted Memory B and T cells from Patient 10 week 9 – TCR

description: Library name: SLE_Patient_23_T_B_PB_hTCR


title: Sorted Memory B and T cells from Patient 10 week 9 – Gene Expression

description: Library name: SLE_Patient_23_T_B_PB_GEX


title: Sorted Memory B and T cells from Patient 9 week 9 – TCR

description: Library name: SLE_Patient_22_T_B_PB_hTCR


title: Sorted Memory B and T cells from Patient 10 week 9 – BCR

description: Library name: SLE_Patient_23_T_B_PB_hBCR


title: cGAS-KO A3 (25172XR-01-09)

description: Library name: cGAS-KO A3 (25172XR-01-09)


title: cGAS-KO; HD A1 (25172XR-01-10)

description: Library name: cGAS-KO; HD A1 (25172XR-01-10)


title: ATAC_0h_R2

description: ATAC-seq DMSO Rep2


title: Sorted Memory B and T cells from Patient 8 and 10 week 36 – BCR

description: Library name: SLE_Patient_25_26_T_B_PB_hBCR


title: cGAS-KO A2 (25172XR-01-08)

description: Library name: cGAS-KO A2 (25172XR-01-08)


title: Sorted Memory B and T cells from Patient 9 week 9 – BCR

description: Library name: SLE_Patient_22_T_B_PB_hBCR


title: bHSCt  6

city: Changchun

first: Yutong

last: Dong

state: Jilin

address: NO.1 Xinmin Street

department: Hepatology Department, Center of Infectious Diseases and Pathogen Biology

country: China

institute: First Hospital of Jilin University

data_processing:
Filtration: The adaptor sequences were removed, and the poor quality reads (lower than Q20) were trimmed using Cutadapt
Comparative analysis: RNA-Seq sequencing data were compared and analyzed using HTSeq, DESeq software.
Transcript analysis: Mapped reads were assembled and the novel transcripts were predicted by StringTie (http://ccb.jhu.edu/software/stringtie/)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: hepatic tissue

extract_protocol:
Total RNA was extracted from primary human HSCs with the RNeasy Mini kit .RNA concentration was measured by Nanodrop 2000 spectrophotometer . The Epicentre Ribo-Zero™ rRNA Removal Kit was used to remove the ribosomal RNA from the total RNA. Complementary DNA (cDNA) was generated using TaqMan reverse transcription reagents. Agilent 2100 Bioanalyzer and Agilent High Sensitivity DNA Kit was used to determine RNA purity, RNA integrity, and library integrity.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

tag: Sex

value: M

tag: disease state

value: HBV liver cirrhosis


title: Sorted Memory B and T cells from Patient 7 week 36 and Patient 9 week 9 – BCR

description: Library name: SLE_Patient_20_21_T_B_PB_hBCR


title: Sorted Memory B and T cells from Patient 7 week 36 and Patient 9 week 9 – TCR

description: Library name: SLE_Patient_20_21_T_B_PB_hTCR


title: ATAC_0h_R1

description: ATAC-seq DMSO Rep1


title: Sorted Memory B and T cells from Patient 9 week 9 – Gene Expression

description: Library name: SLE_Patient_22_T_B_PB_GEX


title: TT-seq-NELFCAID-DMSO4h-NVP2_30m-Rep2

value: NELF-C-AID OsTIR1


title: TT-seq-NELFCAID-DMSO4h-NVP2_30m-Rep1


title: cGAS-KO A1 (25172XR-01-07)

description: Library name: cGAS-KO A1 (25172XR-01-07)


title: A549,  10 μM ruxolitinib + pIC, rep1

description:
Library name: JAK_PIC_1
column name in et02b21.48_counts.txt: JAK_PIC_1

value: 10 μM ruxolitinib + 5 ng/mL pIC


title: HD A3 (25172XR-01-06)

description: Library name: HD A3 (25172XR-01-06)


title: ATAC_4h_R1

description: ATAC-seq IAA 4 hours Rep1

value: Auxin 4 hours


title: scRNAseq, A549, Pool3

description:
Library name: et02b04_SamplePool3
The samples are organized based the aggr_timepoints.csv file

value: untreated or 5 ng/mL pIC for 4, 8, 12, or 16 hours


title: Sorted Memory B and T cells from Patient 7 week 36 and Patient 9 week 9 – Gene Expression

description: Library name: SLE_Patient_20_21_T_B_PB_GEX


title: bHSCt  5

value: F


title: Sorted Memory B and T cells from Patient 5 week 36 and Patient 10 week 0 – TCR

description: Library name: SLE_Patient_18_19_T_B_PB_hTCR


title: A549,  10 μM ruxolitinib + pIC, rep2

description:
Library name: JAK_PIC_2
column name in et02b21.48_counts.txt: JAK_PIC_2


title: Sorted Memory B and T cells from Patient 5 week 36 and Patient 10 week 0  – BCR

description: Library name: SLE_Patient_18_19_T_B_PB_hBCR


title: bHSCt  4


title: HD A1 (25172XR-01-04)

description: Library name: HD A1 (25172XR-01-04)


title: Sorted Memory B and T cells from Patient 9 week 0 – BCR

description: Library name: SLE_Patient_17_T_B_PB_hBCR

value: pre-treatment


title: Sorted Memory B and T cells from Patient 9 week 0 – TCR

description: Library name: SLE_Patient_17_T_B_PB_hTCR


title: bHSCt  2


title: Sorted Memory B and T cells from Patient 5 week 36 and Patient 10 week 0 – Gene Expression

description: Library name: SLE_Patient_18_19_T_B_PB_GEX


title: Sorted Memory B and T cells from Patient 3 week 36 – TCR

description: Library name: SLE_Patient_16_T_B_PB_hTCR


title: bHSCt  3


title: Sorted Memory B and T cells from Patient 3 week 36 – Gene Expression

description: Library name: SLE_Patient16_T_B_PB_GEX


title: WT A3 (25172XR-01-03)

description: Library name: WT A3 (25172XR-01-03)


title: bHSCt  1


title: WT A2 (25172XR-01-02)

description: Library name: WT A2 (25172XR-01-02)


title: nHSCt_5

value: Hepatic hemangioma


title: Sorted Memory B and T cells from Patient 5 week 9  and Patient 7 week 9 – TCR

description: Library name: SLE_Patient_14_15_T_B_PB_hTCR


title: Sorted Memory B and T cells from Patient 5 week 9  and Patient 7 week 9 – BCR

description: Library name: SLE_Patient_14_15_T_B_PB_hBCR


title: Sorted Memory B and T cells from Patient 5 week 9  and Patient 7 week 9 – Gene Expression

description: Library name: SLE_14_15_GEX


title: nHSCt_4


title: Sorted Memory B and T cells from Patient 1 week 36 and Patient 2 week 36 – BCR

description: Library name: SLE_Patient_12_13_T_B_PB_hBCR


title: WT A1 (25172XR-01-01)

description: Library name: WT A1 (25172XR-01-01)


title: nHSCt_3


title: Neuro-2a cells, inputA

city: Hangzhou

first: Shuaishuai

last: Wang

address: 866 Yuhangtang Road

institute: Zhejiang University

description: Library name: sample1

data_processing:
The purified input and immunoprecipitated DNA samples were submitted to Novogene for ChIP-seq high-throughput sequencing
Assembly: mm10
Supplementary files format and content: bigWig

source_name: mouse brain

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min and neutralized with 0.125 M glycine for 5 min. The lysates were sonicated on ice using a SCIENTZ-IID ultrasonic homogenizer
A 10 µl aliquot of the sonicated lysate was used for analyzing DNA size distribution. This aliquot was incubated with 110 µl of water containing 0.2 M NaCl at 65°C for 3-6 h to reverse crosslinking, followed by treatment with 0.2 mg/ml RNase A (Transgenic Biotechnology #GE101-01) for 1 h at 37°C, then with 0.5 mg/ml proteinase K (Transgenic Biotechnology #GE201-01) for 1 h at 55°C. DNA was purified using a HiPure Gel DNA Mini Kit (Magen #D2111-03). DNA size distribution was analyzed by agarose gel electrophoresis. This DNA sample also served as an input control. After an optimal DNA fragment size range of 100-500 bp was achieved, immunoprecipitation reaction was carried out by incubating 40 µl of FLAG affinity gel (Merck Millipore #F2426) and 280 µl of the sonicated cell lysate in 1 ml of ChIP dilution buffer [20 mM Tris-HCl (pH 8), 150 mM NaCl, 2 mM EDTA (pH 8), 1% Nonidet P-40, 0.1% sodium deoxycholate, and 0.01% SDS], supplemented with protease inhibitors (1 tablet per 50 ml, Roche #K562) with rotation for 3 h at 4°C.

value: mouse brain

value: Neuro-2a cells

value: mouse brain neuroblastoma cells

value: HSV-1 infection

tag: sample type

value: input


title: Sorted Memory B and T cells from Patient 1 week 36 and Patient 2 week 36 – TCR

description: Library name: SLE_Patient_12_13_T_B_PB_hTCR

value: Sorted Memory B and T Lymphocytes

value: After 8 x weekly 1800mg Daratumumab sc


title: Neuro-2a cells, IPA

description: Library name: sample2

value: IPA


title: HD A2 (25172XR-01-05)

description: Library name: HD A2 (25172XR-01-05)

value: Striatal tissue


title: Sorted Memory B and T cells from Patient 4 week 9 – Gene Expression

description: Library name: SLE_Patient11_T_B_PB_GEX


title: Obese mouse, High-fat diet (HFD) + 60 mg/kg/day UB-NPs, 8 weeks, rep5

city: 北京

first: 尚年

last: 刘

state: 北京

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: Uro5
Column name is Uro5

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome (Mus musculus GRCm39) with orientation mode using HISAT2 software. The mapped read so feach sample were assembled by StringTie in a reference-based approach.
Assembly: Mus musculus GRCm39
Supplementary files format and content: "gene.count.matrix.annot.xls" includes the counts for each sample and gene annotation, "tpm.xls" includes the TPM (transcripts per million) for each sample, "diff_summary_deseq2.xls" includes the results for each comparison between groups.

source_name: Liver

extract_protocol:
Total RNA was extracted from the tissue using TRIzol®Reagent according the manufacturer’s  instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co.,Ltd. (Shanghai,China) according to the manufacturer’s instructions. The XXRNA-seq transcriptome librariy was prepared following Illumina®Stranded mRNAPrep, Ligation (SanDiego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNAwas synthesized using a SuperScript double-stranded cDNAsynthesis kit (Invitrogen, CA)with random hexamer primers.Then the synthesized cDNA was subjected to end-repair, phosphory lation and adapter addition according to library construction protocol. Libraries were sizeselected for cDNA target fragments of 300bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit4.0, these quencing library was performed on NovaSeq X Plus platform (PE150) using NovaSeq Reagent Kit.

value: Liver


title: Sorted Memory B and T cells from Patient 9 week 0 – Gene Expression

description: Library name: SLE_Patient17_T_B_PB_GEX


title: nHSCt_1


title: Sorted Memory B and T cells from Patient 4 week 9 – TCR

description: Library name: SLE_Patient_11_T_B_PB_hTCR


title: Parental (WT), A549, rep3

description:
Library name: WT_rep_3
column name in et02b26_consensuscoverage_counts_annotations.txt: wt_3

data_processing:
The fastq files were generated and demultiplexed with the bcl-convert v4.1.7 Conversion Software (Illumina)
Adaptors were trimmed from the 3'-end of the reads
Alignment was done using Bowtie2/2.4.5 with GRCh38
Blacklisted regions (hg38-blacklist.v2.bed) were filtered out with pybedtools/0.9.0
Peaks were called using MACS2/2.2.5
.bw files were generated with bamCoverage from deepTools/3.5.2 with a binSize of 20 and normalized using CPM
The consensus coverage txt file was generated from making a consensus file with bedtools, and peaks per counted and annotated to make the consensuscoverage_countmatrix_counts.txt
Assembly: NCBI GRCh38 with Ensembl99
Supplementary files format and content: tab-delimited file containing a full count matrix for the accessible regions per cell line and replicate
Supplementary files format and content: bigWig file for peak visualization

extract_protocol:
24 hours after seeding, the A549 cells were trypsinized and collected on ice before taken to the sequencing facility. The cells were then processed using the ATACseq kit from Active Motif.
The libraries were prepared using the ATACseq kit from Active Motif. They were then pooled and sequenced on one 10B lane for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 sequencing kits

value: cell line

value: human alveolar epithelial cells

value: WT


title: Sorted Memory B and T cells from Patient 1 week 36 and Patient 2 week 36 – Gene Expression

description: Library name: SLE_12_13_GEX


title: Obese mouse, High-fat diet (HFD) + 60 mg/kg/day UB-NPs, 8 weeks, rep4

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: Uro4
Column name is Uro4


title: Sorted Memory B and T cells from Patient 5 week 0  and Patient 7 week 0 – BCR

description: Library name: SLE_Patient_9_10_T_B_PB_hBCR


title: Sorted Memory B and T cells from Patient 5 week 0  and Patient 7 week 0 – TCR

description: Library name: SLE_Patient_9_10_T_B_PB_hTCR


title: Sorted Memory B and T cells from Patient 3 week 36 – BCR

description: Library name: SLE_Patient_16_T_B_PB_hBCR


title: nHSCt_2


title: Sorted Memory B and T cells from Patient 4 week 0 – TCR

description: Library name: SLE_Patient7_T_B_PB_mix_TCR


title: Sorted Memory B and T cells from Patient 5 week 0  and Patient 7 week 0 – Gene Expression

description: Library name: SLE_Patient9_10_T_B_PB_GEX


title: Obese mouse, High-fat diet (HFD) + 60 mg/kg/day UB-NPs, 8 weeks, rep3

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: Uro3
Column name is Uro3


title: Obese mouse, High-fat diet (HFD) + 60 mg/kg/day UB-NPs, 8 weeks, rep2

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: Uro2
Column name is Uro2


title: Sorted Memory B and T cells from Patient 4 week 0 – Gene Expression

description: Library name: SLE_Patient7_T_B_PB_GEX


title: Obese mouse, High-fat diet (HFD) + 60 mg/kg/day UB-NPs, 8 weeks, rep1

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: Uro1
Column name is Uro1


title: Sorted Memory B and T cells from Patient 4 week 9 – BCR

description: Library name: SLE_Patient_11_T_B_PB_hBCR


title: Pa01c BVD-523-ATI-450 Rep3

city: Saint Louis

first: Iftikhar Ali

last: Khawar

state: Missouri

address: McDonnell Medical Sciences Building, Room 502 4566 Scott Ave

department: Internal Medicine

institute: Washington University in Saint Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Ensembl Release 76 GRCm38.76
Supplementary files format and content: Gene counts in tab-delimitted text format

source_name: Pancreatic cancer

growth_protocol: All cells were cultured in DMEM/10% FBS, 1% Pen/Strep.

extract_protocol:
RNA was harvested using Trizol reagent. mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pancreatic cancer

value: Cancer cells

value: Kras12D mutant cells

value: BVD-523+AA Rep3


title: Pa01c BVD-523-ATI-450 Rep2

value: BVD-523+AA Rep2


title: Sorted Memory B and T cells from Patient 3 week 9 – BCR

description: Library name: SLE_Patient6_T_B_PB_mix_BCR


title: Sorted Memory B and T cells from Patient 3 week 9 – Gene Expression

description: Library name: SLE_Patient6_T_B_PB_GEX


title: Obese mouse, High-fat diet (HFD)  + water, 8 weeks, rep5

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: HFD5
Column name is HFD5


title: Pa01c BVD-523-ATI-450 Rep1

value: BVD-523+AA Rep1


title: Obese mouse, High-fat diet (HFD)  + water, 8 weeks, rep4

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: HFD4
Column name is HFD4


title: Obese mouse, High-fat diet (HFD)  + water, 8 weeks, rep3

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: HFD3
Column name is HFD3


title: NPC cell line replicate 1

type: genomic

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

country: France

institute: CNRS/ Université de Paris

hyb_protocol: The hybridization was performed according to the manufacturer instructions on 4× 180K mouse microarray

scan_protocol: Microarrays were scanned with an Agilent's High-Resolution C Scanner using a resolution of 3 µm and the autofocus option.

data_processing: Feature extraction was performed with the Feature Extraction 9.1 software (Agilent technologies). For each experiment, the raw data sets were automatically normalized by the Feature extraction software with a lowess normalization of the log2 of Cy3/Cy5. Analysis was performed with the START-R software.

source_name: nascent DNA from early S-phase

label_protocol: Microarray hybridization requires a minimum of 1000 ng of DNA and to obtain sufficient specific immunoprecipited DNA, whole genome amplification (WGA) was conducted (Seq-plex, Sigma). To be sure that this step does not introduce bias, an after WGA qPCR was performed to confirm the specific enrichment in each fractions S1 and S2. After amplification, early and late neo-synthesized DNA were labeled with Cy3 and Cy5 ULS molecules (Genomic DNA labeling Kit, Agilent) as recommended by the manufacturer.

growth_protocol: Each cells grown in culture condition defined by ATCC

extract_protocol: cells were incubated with BrdU (50µM) for two hours, then collected, washed three times in PBS, fixed in 75% ethanol, and stored at −20°C. Fixed cells were re-suspended in PBS first with RNAse (0.5 mg/ml) and then with propidium iodide (PI) (50 µg/ml) following by an incubation of 30 min at room temperature. 150,000 cells were sorted in two fractions S1 and S2 using INFLUX 500 (Cytopeia purchased by BD Biosciences) corresponding to Early and Late fractions respectively. Neo-synthesized DNA was immunoprecipited by BrdU antibodies (Anti BrdU Pure, BD Biosciences, # 347580) . To control the quality of enrichment of early and late fractions in S1 and S2, qPCR was performed with BMP1 oligonucleotides (early control) and with Dppa2 oligonucleotides (late control).

value: NPC

tag: phase

value: early S-phase

value: nascent DNA

source_name: nascent DNA from late S-phase

value: late S-phase


title: Pa01c-ATI-450  Rep3

value: ATI-450 Rep3


title: Pa01c-ATI-450  Rep2

value: ATI-450 Rep2


title: Sorted Memory B and T cells from Patient 3 week 0 – TCR

description: Library name: SLE_Patient5_T_B_PB_mix_TCR

value: Sorted Memory B and T Lymphocytes

value: pre-treatment


title: Obese mouse, High-fat diet (HFD)  + water, 8 weeks, rep2

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: HFD2
Column name is HFD2

value: Liver


title: Sorted Memory B and T cells from Patient 3 week 0 – Gene Expression

description: Library name: SLE_Patient5_T_B_PB_GEX


title: Sorted Memory B and T cells from Patient 3 week 0 – BCR

description: Library name: SLE_Patient5_T_B_PB_mix_BCR


title: Obese mouse, High-fat diet (HFD)  + water, 8 weeks, rep1

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: HFD1
Column name is HFD1


title: Sorted Memory B and T cells from Patient 3 week 9 – TCR

description: Library name: SLE_Patient6_T_B_PB_mix_TCR

value: After 8 x weekly 1800mg Daratumumab sc


title: Pa01c-ATI-450  Rep1

value: ATI-450 Rep1


title: Sorted Memory B and T cells from Patient 2 week 9 – TCR

description: Library name: SLE_Patient4_T_B_PB_mix_TCR


title: Normal mouse, Standard diet + water, 18 weeks, rep5

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: NFD5
Column name is NFD5


title: Sorted Memory B and T cells from Patient 4 week 0 – BCR

description: Library name: SLE_Patient7_T_B_PB_mix_BCR


title: Normal mouse, Standard diet + water, 18 weeks, rep4

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: NFD4
Column name is NFD4


title: Sorted Memory B and T cells from Patient 2 week 9 – BCR

description: Library name: SLE_Patient4_T_B_PB_mix_BCR


title: Pa01c-BVD-523 Rep3

value: Pancreatic cancer

value: BVD-523 Rep3


title: Normal mouse, Standard diet + water, 18 weeks, rep3

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: NFD3
Column name is NFD3


title: Pa01c-BVD-523 Rep1

value: Cancer cells

value: Kras12D mutant cells

value: BVD-523 Rep1


title: Normal mouse, Standard diet + water, 18 weeks, rep2

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: NFD2
Column name is NFD2


title: Pa01c-DMSO Rep3


title: Sorted Memory B and T cells from Patient 1 week 9 – TCR

description: Library name: SLE_Patient3_T_B_PB_mix_TCR


title: Zfp57KO cell line replicate 2

data_processing: Feature extraction was performed with the Feature Extraction 9.1 software (Agilent technologies). For each experiment, the raw data sets were automatically normalized he Feature extraction software with a lowess normalization of the log2 of Cy3/Cy5. Analysis was performed with the START-R software.

value: JB


title: ini Meg3 -/- cell line replicate 1

description: In-Meg3-:- 1

value: BJ


title: ini Meg3 -/- cell line replicate 2

description: In-Meg3-:- 2

value: early S-phase


title: Pa01c-DMSO Rep2


title: Normal mouse, Standard diet + water, 18 weeks, rep1

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: NFD1
Column name is NFD1


title: Sorted Memory B and T cells from Patient 1 week 9 – BCR

description: Library name: SLE_Patient3_T_B_PB_mix_BCR


title: Sorted Memory B and T cells from Patient 1 week 9 – Gene Expression

description: Library name: SLE_Patient3_T_B_PB_GEX


title: Sorted Memory B and T cells from Patient 2 week 9 – Gene Expression

description: Library name: SLE_Patient4_T_B_PB_GEX


title: Ak2 cell line replicate 2

value: nascent DNA


title: omicron_37C_rep1

city: Gothenburg

first: Roshan

last: Vaid

state: Västra Götalands län [SE-14]

address: Bruna Stråket 16,

department: Department of Laboratory Medicine

country: Sweden

institute: GOTEBORGS UNIVERSITET

description:
Library name: omicron_37C_rep1
Infected cells (SARS-CoV-2 Omicron variant) at 37 ºC, omicron_37C_rep1

data_processing:
Raw paired-end RNA-sequencing data obtained from BGI was analyzed using FastQC v0.11.9 for quality control (Andrews, 2010) and trimmed with fastp v0.23.2 (S. Chen et al., 2018). Trimmed reads were mapped using HISAT2 v2.2.1 (Kim et al., 2019) to the following reference genomes: concatenated GRh38 (human) genome and wuhCor1 (SARS-CoV-2) reference genomes obtained from the UCSC Genome Browser (http://hgdownload.soe.ucsc.edu/goldenPath). Duplicate alignments were labeled with the markDuplicates from Picard v2.23.4 (http://broadinstitute.github.io/picard/). Marked alignment files were further processed using Sambamba 0.7.1 (Tarasov et al., 2015) after duplicate removal. Read counts were obtained using featureCounts v2.0.0 (Liao, Y et al., 2014).
Assembly: GRCh38
Assembly: wuhCor1
Supplementary files format and content: featureCounts matrix for RNA-seq counts

source_name: Primary human nasal epithelial cells

extract_protocol:
For RNA extraction of primary epithelial cultures, reconstructed epithelia were infected for 2 days, then washed in cold PBS and then lyzed in TRIzol reagent (Thermo Fisher Scientific) added to the apical side of the insert. RNA was purified using the Direct-zol miniprep kit (ZR2080, Zymo Research), according to the manufacturer's specifications.
RNAseq ibraries were prepared at BGI (Poland) for strand specific mRNA sequencing on a DNBSEQ platform with a PE100 sequencing read length.

value: Primary human nasal epithelial cells

tag: temperature


title: PR3 cell line replicate 1

value: late S-phase


title: Pa01c-DMSO Rep1


title: delta_37C_rep2

description:
Library name: delta_37C_rep2
Infected cells (SARS-CoV-2 Delta variant) at 37 ºC, delta_37C_rep2


title: Normal mouse, High-fat diet (HFD) + 60 mg/kg/day UB-NPs, 10 weeks, rep5

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: UB5
Column name is UB5


title: PR3 cell line replicate 2


title: Zfp57KO cell line replicate 1


title: Pa01c-BVD-523 Rep2

value: BVD-523 Rep2


title: BJ cell line replicate 1


title: BJ cell line replicate 2


title: Sorted Memory B and T cells from Patient 2 week 0 – TCR

description: Library name: SLE_Patient2_T_B_PB_mix_TCR

value: Sorted Memory B and T Lymphocytes


title: JB cell line replicate 1

description: JB


title: Ak2 cell line replicate 1


title: MDA Pca 2b Prostate Carcinoma

city: Elizabeth City

first: Hirendranath

last: Banerjee

state: North Carolina

address: 1704 Weeksville Rd,

department: Department of Natural, Pharmacy and Health sciences

institute: Elizabeth City State University

description: Library name: MDAPCa2b_AmpliSeq_Tx

data_processing:
Torrent Suite Software v. 5.12.1
Adapters were trimmed and low quality reads filtered by the Torrent Suite Software v. 5.12.1
StrandNGS software v. 3.4
Raw reads were mapped to Hg19 human reference genome using a proprietary algorithm named computationally-optimized Burrows Wheeler Transformed (COBWeb) by the Strand.
Read count extraction and Normalization was performed by StrandNGS using Deseq algorithm.
Assembly: Hg19
Supplementary files format and content: Excel file containing raw counts for each sample.

source_name: MDA Pca 2b

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 10 ng of total RNA was used for the construction of sequencing libraries.
Ampliseq Transcriptome libraries were constructed using the Ampliseq Transcriptome kit (Thermofisher) and manufacturers recommended protocol.

value: MDA Pca 2b

value: Prostate

value: WT

value: Total RNA

tag: batch

value: single


title: Normal mouse, High-fat diet (HFD) + 60 mg/kg/day UB-NPs, 10 weeks, rep4

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: UB4
Column name is UB4

value: Liver


title: d614g_37C_rep2

description:
Library name: d614g_37C_rep2
Infected cells (SARS-CoV-2 D614G variant) at 37ºC, d614g_37C_rep2


title: Metastatic Prostate Carcinoma

description: Library name: LNCaP_AmpliSeq_Tx

source_name: LNCaP

value: LNCaP


title: Sorted Memory B and T cells from Patient 2 week 0 – Gene Expression

description: Library name: SLE_Patient2_T_B_PB_GEX

value: pre-treatment


title: Sorted Memory B and T cells from Patient 2 week 0 – BCR

description: Library name: SLE_Patient2_T_B_PB_mix_BCR


title: mock_37C_rep2

description:
Library name: mock_37C_rep2
Non-infected cells at 37 ºC, mock_37C_rep2

value: Non-infected cells at 37 ºC


title: omicron_37C_rep2

description:
Library name: omicron_37C_rep2
Infected cells (SARS-CoV-2 Omicron variant) at 37 ºC, omicron_37C_rep2


title: Neuro-2a cells( knockout EGR1),e1human2,3hpi

description:
Library name: sample11
core_table_gene - 3hpi.txt

data_processing:
1. The raw data was filtered with SOAPnuke (v1.6.5)by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 1%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 40%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome by HISAT (v2.2.1)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5). The expression level of genes was calculated by RSEM (v1.3.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
RNA extraction using a LS1040 Eastep Super total RNA extraction kit (Promega). 1.5μg of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard DNBSEQ-T7 protocols

value: mouse brain

value: Neuro-2a cells

value: mouse brain neuroblastoma cells

value: EGR1 knock out

value: HSV-1 infection


title: Normal mouse, High-fat diet (HFD) + 60 mg/kg/day UB-NPs, 10 weeks, rep1

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: UB1
Column name is UB1


title: Normal mouse, High-fat diet (HFD) + 60 mg/kg/day UB-NPs, 10 weeks, rep3

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: UB3
Column name is UB3


title: Normal mouse, High-fat diet (HFD) + 60 mg/kg/day UB-NPs, 10 weeks, rep2

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: UB2
Column name is UB2


title: Neuro-2a cells( knockout EGR1),e1human3,3hpi

description:
Library name: sample12
core_table_gene - 3hpi.txt


title: delta_37C_rep1

description:
Library name: delta_37C_rep1
Infected cells (SARS-CoV-2 Delta variant) at 37 ºC, delta_37C_rep1

value: Primary human nasal epithelial cells


title: Sorted Memory B and T cells from Patient 1 week 0 – BCR

description: Library name: SLE_Patient1_T_B_PB_mix_BCR


title: Sorted Memory B and T cells from Patient 1 week 0 – TCR

description: Library name: SLE_Patient1_T_B_PB_mix_TCR


title: Normal mouse, High-fat diet (HFD) + water, 10 weeks, rep5

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: MC5
Column name is MC5


title: Sorted Memory B and T cells from Patient 1 week 0 – Gene Expression

description: Library name: SLE_Patient1_T_B_PB_mix_GEX


title: d614g_37C_rep1

description:
Library name: d614g_37C_rep1
Infected cells (SARS-CoV-2 D614G variant) at 37ºC, d614g_37C_rep1


title: mock_37C_rep1

description:
Library name: mock_37C_rep1
Non-infected cells at 37 ºC, mock_37C_rep1


title: omicron_33C_rep2

description:
Library name: omicron_33C_rep2
Infected cells (SARS-CoV-2 Omicron variant) at 33 ºC, omicron_33C_rep2


title: omicron_33C_rep1

description:
Library name: omicron_33C_rep1
Infected cells (SARS-CoV-2 Omicron variant) at 33 ºC, omicron_33C_rep1


title: Neuro-2a cells( knockout EGR1),pc2,3hpi

description:
Library name: sample8
core_table_gene - 3hpi.txt


title: Neuro-2a cells( knockout EGR1),pc1,3hpi

description:
Library name: sample7
core_table_gene - 3hpi.txt


title: Normal mouse, High-fat diet (HFD) + water, 10 weeks, rep4

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: MC4
Column name is MC4


title: Normal mouse, High-fat diet (HFD) + water, 10 weeks, rep3

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: MC3
Column name is MC3


title: S6_BAL

city: Warsaw

first: Katarzyna

last: Mleczko-Sanecka

address: 4 Ksiecia Trojdena

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

description: Library name: Sample 6

data_processing:
Sequencing was done on an Illumina NextSEq 500 platform (75 bp single-end reads)
Raw reads were trimmed with Trimmomatic v.0.36 and aligned to the Mus musculus GRCm38 reference genome available on ENSEMBL using STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Normalization and differential expression analysis were performed using DESeq2
Assembly: Mouse genome assembly GRCm38 (mm10)
Supplementary files format and content: tab-delimited text file including raw gene counts for each sample (featureCounts output).

source_name: spleenic red pulp macrophages

growth_protocol: Female C57BL/6J mice were used for all the experiments and were maintained in pathogen-free conditions at the Experimental Medicine Centre (Bialystok, Poland).

extract_protocol:
Samples represent total RNA from red pulp macrophages (RPMs;  approx. 100 000 cells) sorted using F4/80 and TREML4 markers. Sorting was performed to TRIzol, and RNA was isolated using Direct-zol columns.
mRNA sequencing libraries were prepared using poly(A) selection followed by Illumina-compatible cDNA library construction.

tag: strain

value: spleenic red pulp macrophages

value: female

value: control


title: Normal mouse, High-fat diet (HFD) + water, 10 weeks, rep2

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: MC2
Column name is MC2


title: S8_BAL

description: Library name: Sample 8


title: Neuro-2a cells( knockout EGR1),pc3,3hpi

description:
Library name: sample9
core_table_gene - 3hpi.txt


title: delta_33C_rep1

description:
Library name: delta_33C_rep1
Infected cells (SARS-CoV-2 Delta variant) at 33 ºC, delta_33C_rep1


title: Neuro-2a cells( knockout EGR1), EGR1human2,10hpi

description:
Library name: sample5
core_table_gene - 10hpi.txt


title: Normal mouse, Standard diet + water, 10 weeks, rep5

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: NC5
Column name is NC5


title: Neuro-2a cells( knockout EGR1), EGR1human3,10hpi

description:
Library name: sample6
core_table_gene - 10hpi.txt


title: S5_BAL

description: Library name: Sample 5


title: delta_33C_rep2

description:
Library name: delta_33C_rep2
Infected cells (SARS-CoV-2 Delta variant) at 33 ºC, delta_33C_rep2


title: S7_BAL

description: Library name: Sample 7


title: S4_DEF

description: Library name: Sample 4

value: iron-deficient


title: Neuro-2a cells( knockout EGR1), EGR1human1,10hpi

description:
Library name: sample4
core_table_gene - 10hpi.txt


title: Normal mouse, Standard diet + water, 10 weeks, rep3

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: NC3
Column name is NC3


title: d614g_33C_rep1

description:
Library name: d614g_33C_rep1
Infected cells (SARS-CoV-2 D614G variant) at 33ºC, d614g_33C_rep1


title: Neuro-2a cells( knockout EGR1),e1human1,3hpi

description:
Library name: sample10
core_table_gene - 3hpi.txt


title: Neuro-2a cells( knockout EGR1), pcDNA3,10hpi

description:
Library name: sample3
core_table_gene - 10hpi.txt


title: mock_33C_rep2

description:
Library name: mock_33C_rep2
Non-infected cells at 33 ºC, mock_33C_rep2

value: Non-infected cells at 33 ºC


title: S2_DEF

description: Library name: Sample 2


title: Normal mouse, Standard diet + water, 10 weeks, rep2

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: NC2
Column name is NC2


title: Normal mouse, High-fat diet (HFD) + water, 10 weeks, rep1

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: MC1
Column name is MC1


title: mock_33C_rep1

description:
Library name: mock_33C_rep1
Non-infected cells at 33 ºC, mock_33C_rep1


title: Normal mouse, Standard diet + water, 10 weeks, rep1

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: NC1
Column name is NC1


title: Neuro-2a cells( knockout EGR1), pcDNA1,10hpi

description:
Library name: sample1
core_table_gene - 10hpi.txt


title: Neuro-2a cells( knockout EGR1), pcDNA2,10hpi

description:
Library name: sample2
core_table_gene - 10hpi.txt


title: d614g_33C_rep2

description:
Library name: d614g_33C_rep2
Infected cells (SARS-CoV-2 D614G variant) at 33ºC, d614g_33C_rep2


title: Wild-type hepatocyte, replicate 4

status: Public on Dec 12 2025

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

description: Library name: WT4_set2_S78

data_processing:
The data was processed using the Nextflow rnaseq v.23.04.3 pipeline using the mm10 genome assembly and star_rsem gene quantification method.
Assembly: mm10
Supplementary files format and content: text, tab-separated

source_name: liver

extract_protocol:
Total RNA was extracted using the QIAGEN miRNAeasy Mini Kit (QIAGEN, Valencia, CA). cDNA preparation was done using ABI cDNA synthesis kit (Applied Biosystems, Foster City, CA). Real-time polymerase chain reaction (RT-PCR) was performed using an ABI ViiA7 fast real-time PCR system and Taqman gene expression assays according to the manufacturer’s protocol (Applied Biosystems, Foster City, CA)
RNA-Seq library was prepared using Illumina TruSeq RNA sample preparation kit and subject to two rounds of sequencing on Illumina HiSeq3000 platform.
RNA-Seq libraries were pooled together to aim about 25-40M read passed filtered reads per sample.

value: liver

value: hepatocytes

value: WT


title: Wild-type hepatocyte, replicate 2

description: Library name: WT2_set2_S76


title: hepatocyte-specific Taf2 conditional knockout mice, replicate 3

description: Library name: CKO3_set2_S81

value: TAF2 KO


title: hepatocyte-specific Taf2 conditional knockout mice, replicate 2

description: Library name: CKO2_set2_S80


title: Normal mouse, Standard diet + water, 10 weeks, rep4

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

description:
Library name: NC4
Column name is NC4

value: Liver


title: hepatocyte-specific Taf2 conditional knockout mice, replicate 1

description: Library name: CKO1_set2_S79


title: S3_DEF

description: Library name: Sample 3


title: Wild-type hepatocyte, replicate 1

description: Library name: WT1_set2_S75


title: hepatocyte-specific Taf2 conditional knockout mice, replicate 4

description: Library name: CKO4_set2_S82


title: T replicate 2

data_processing:
All sequencing reads were quality controlled using FastQC v0.11.2. Illumina adapters were trimmed using trimmomatic v.0.33 [PMID: 24695404], replicates were merged and aligned with their reference genome (UCSC mouse genome build mm10 using STAR v. 2.5.2b [PMID: 23104886]).
The BAM files from alignment were processed using featureCounts v1.4.6-p4 with GRCm38 v.100 gene annotations for mouse cells to obtain the counts per gene in all samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count values for each Sample

extract_protocol:
Total RNA was extracted using the QIAGEN miRNAeasy Mini Kit (QIAGEN, Valencia, CA). cDNA preparation was done using ABI cDNA synthesis kit (Applied Biosystems, Foster City, CA). Q-RT-PCR was performed using an ABI ViiA7 fast real-time PCR system and Taqman gene expression assays according to the manufacturer’s protocol (Applied Biosystems, Foster City, CA).
RNA-Seq library was prepared using Illumina TruSeq RNA sample preparation kit and subjected to sequencing on Illumina HiSeq3000 platform.

value: TAF2 overexpression

value: plasmids expressing human TAF2


title: T replicate 1


title: S replicate 4

value: Control

value: empty plasmids


title: S replicate 3


title: TM replicate 3

value: c-MYC and TAF2 overexpression

value: plasmids expressing human c-MYC and TAF2


title: TM replicate 2


title: T replicate 3


title: S replicate 2


title: Wild-type hepatocyte, replicate 3

description: Library name: WT3_set2_S77


title: S1_DEF

description: Library name: Sample 1


title: M replicate 3

value: c-MYC overexpression

value: plasmids expressing human c-MYC


title: M replicate 2


title: PBMC healthy donor CITE-seq replicate 3-10

city: San Francisco

first: Bridget

middle: P

last: Keenan

state: CA

address: 505 PARNASSUS AVE

institute: University of California San Francisco

description: Library name: HC3-10_FB

data_processing:
Cell Ranger version 7.0.0 (10x Genomics, Genome Build: GRCh38 3.0.0) was used to align the raw sequencing data. The feature barcoding library sequences were aligned to a customized reference genome provided by Biolegend containing the oligonucleotide sequences corresponding to each antibody. Cell Ranger generated a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
Assembly: GRCm38
Supplementary files format and content: Cell Ranger output filtered matrix files for both scRNA-seq libraries and CITE-seq (feature barcoding) libraries: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.
Library strategy: CITE-seq

source_name: Hepatocellular Carcinoma (HCC)

extract_protocol:
Blood samples were processed using Ficoll (Cytiva); after centrifugation, the PBMC layer was isolated and cryopreserved in cell media with human serum and DMSO. Previously frozen PBMCs were thawed using media containing RPMI, heat-inactivated sterile filtered fetal bovine serum, penicillin-streptomycin, non-essential amino acids, sodium pyruvate, and L-glutamine. 1.1x105 cells from each sample were combined into staining buffer (1 mmol/L EDTA and 2% heat-inactivated FBS in calcium/magnesium-free Dulbecco PBS; Thermo Fisher Scientific) and stained with one pooled cocktail containing a custom panel of 197 Total-Seq C antibody–oligonucleotide conjugates (BioLegend) as per standard protocols following pre-incubation with TruStain FcX (Fc Receptor Blocking Solution, Biolegend).
Droplet-based single cell RNA sequencing (scRNAseq) was performed using the 10x Genomics Chromium Single Cell 5ʹ Reagent Kits v2, according to manufacturer instructions. 10X Genomics 5′ v2 Library Construction kits for feature barcoding (protein antibodies) or CITE-seq were used to generate libraries per manufacturer instructions. All sequencing was performed on an Illumina NovaSeq S4 sequencer with paired end 200 base pair read length and 25,000 reads per droplet for gene expression libraries and 5,000 reads per cell for feature barcode libraries.

value: Hepatocellular Carcinoma (HCC)

value: peripheral blood mononuclear cells (PBMCs)

value: HD

value: healthy donor

tag: time


title: PBMC healthy donor CITE-seq replicate 3-9

description: Library name: HC3-09_FB


title: HCC PBMC patient A-36 timepoint C1D1 CITE-seq replicate 2

description: Library name: A-36-01_02_FB

value: durvulamab


title: LNP-Bulk

city: Muraoka-Higashi 2-chome Fujisawa, Kanagawa

first: Taisuke

last: Mochida

institute: Takeda Pharmaceutical Company Limited

data_processing:
Sequenced reads were aligned to the mouse mm10 reference and quantified UMI counts using Cell Ranger v7.0.1 software.
Gene barcode matrices were generated from Cell Ranger software.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skeletal muscle

extract_protocol: Single-cell RNA-seq libraries were generated using the 10x Genomics ChromiumTM controller and Chromium Single Cell 3' kits v3.1 (10x Genomics) according to the manufacturer’s instructions.

value: Skeletal muscle

value: Bulk

value: LNP-CRISPR


title: TM replicate 4

value: Liver


title: TM replicate 1


title: Vehicle-Bulk

value: Vehicle


title: PBMC healthy donor CITE-seq replicate 3-7

description: Library name: HC3-07_FB


title: PBMC healthy donor CITE-seq replicate 3-8

description: Library name: HC3-08_FB


title: HCC PBMC patient A-36 timepoint C1D1 CITE-seq replicate 1

description: Library name: A-36-01_01_FB


title: PBMC healthy donor CITE-seq replicate 3-6

description: Library name: HC3-06_FB


title: M replicate 4


title: HCC PBMC patient A-35 timepoint C1D1 CITE-seq replicate 2

description: Library name: A-35-01_02_FB


title: HCC PBMC patient A-35 timepoint C1D1 CITE-seq replicate 1

description: Library name: A-35-01_01_FB


title: M replicate 1


title: PBMC healthy donor CITE-seq replicate 3-5

description: Library name: HC3-05_FB


title: Vehicle-Satellite cell isolation kit

value: Satellite cells


title: PBMC healthy donor CITE-seq replicate 3-4

description: Library name: HC3-04_FB


title: HCC PBMC patient A-34 timepoint C1D1 CITE-seq replicate 2

description: Library name: A-34-01_02_FB

value: nivolumab


title: PBMC healthy donor CITE-seq replicate 3-3

description: Library name: HC3-03_FB


title: T replicate 4

value: TAF2 overexpression

value: plasmids expressing human TAF2


title: HCC PBMC patient A-34 timepoint C1D1 CITE-seq replicate 1

description: Library name: A-34-01_01_FB


title: PBMC healthy donor CITE-seq replicate 3-2

description: Library name: HC3-02_FB


title: HCC PBMC patient A-33 timepoint C1D1 CITE-seq replicate 3

description: Library name: A-33-01_03_FB

value: durvalumab+tremelimumab


title: HCC PBMC patient A-33 timepoint C1D1 CITE-seq replicate 2

description: Library name: A-33-01_02_FB


title: PBMC healthy donor CITE-seq replicate 3-1

description: Library name: HC3-p1_FB


title: HCC PBMC patient B-15 timepoint C1D1 CITE-seq replicate 2

description: Library name: B-15-01_02_FB

value: sorafenib + nivolumab


title: PBMC healthy donor CITE-seq replicate 2-5

description: Library name: HC2-05_FB


title: S replicate 1

value: Control

value: empty plasmids


title: PBMC healthy donor CITE-seq replicate 2-3

description: Library name: HC2-03_FB

value: Hepatocellular Carcinoma (HCC)

value: peripheral blood mononuclear cells (PBMCs)


title: HCC PBMC patient B-07 timepoint C2D1 CITE-seq replicate 2

description: Library name: B-07-04_02_FB


title: PBMC healthy donor CITE-seq replicate 2-2

description: Library name: HC2-02_FB

value: HD

value: healthy donor


title: HCC PBMC patient B-06 timepoint C3D1 CITE-seq

description: Library name: B-06-06_FB


title: HCC PBMC patient B-11 timepoint baseline CITE-seq replicate 2

description: Library name: B-11-01_02_FB

value: no treatment

value: baseline


title: HCC PBMC patient A-05 timepoint C4D1 CITE-seq replicate 2

description: Library name: A-05-01_02_FB


title: HCC PBMC patient A-31 timepoint C2D1 CITE-seq

description: Library name: A-31-02_FB


title: HCC PBMC patient B-14 timepoint C2D1 CITE-seq replicate 2

description: Library name: B-14-03_02_FB


title: HCC PBMC patient B-07 timepoint C1D1 CITE-seq

description: Library name: B-07-02_FB


title: HCC PBMC patient B-08 timepoint C2D1 CITE-seq

description: Library name: B-08-04_FB


title: HCC PBMC patient A-33 timepoint C1D1 CITE-seq replicate 1

description: Library name: A-33-01_01_FB


title: HCC PBMC patient B-03 timepoint C2D1 CITE-seq

description: Library name: B-03-04_FB


title: HCC PBMC patient B-04 timepoint baseline CITE-seq

description: Library name: B-04-01_FB


title: PBMC healthy donor CITE-seq replicate 2-1

description: Library name: HC2-01_FB


title: PBMC healthy donor CITE-seq replicate 1-8

description: Library name: HC1-08_FB


title: HCC PBMC patient B-18 timepoint baseline CITE-seq

description: Library name: B-18-01_FB


title: HCC PBMC patient B-06 timepoint C2D1 CITE-seq

description: Library name: B-06-04_FB


title: HCC PBMC patient B-21 timepoint C3D1 CITE-seq

description: Library name: B-21-05_FB


title: HCC PBMC patient B-14 timepoint C1D1 CITE-seq replicate 1

description: Library name: B-14-01_01_FB


title: HCC PBMC patient B-07 timepoint C2D1 CITE-seq replicate 1

description: Library name: B-07-04_01_FB


title: HCC PBMC patient A-02 timepoint C2D1 CITE-seq

description: Library name: A-02-02_FB


title: HCC PBMC patient B-08 timepoint Safety follow up CITE-seq

description: Library name: B-08-08_FB

value: Safety follow up


title: HCC PBMC patient A-03 timepoint Long term follow up CITE-seq replicate 2

description: Library name: A-03-01_02_FB

value: temsirolimus + sorafenib

value: Long term follow up


title: PBMC healthy donor CITE-seq replicate 2-4

description: Library name: HC2-04_FB


title: HCC PBMC patient B-14 timepoint C1D1 CITE-seq replicate 2

description: Library name: B-14-01_02_FB


title: HCC PBMC patient B-01 timepoint baseline CITE-seq

description: Library name: B-01-01_FB


title: HCC PBMC patient B-21 timepoint C2D1 CITE-seq

description: Library name: B-21-03_FB


title: HCC PBMC patient B-05 timepoint C2D1 CITE-seq

description: Library name: B-05-04_FB


title: HCC PBMC patient A-03 timepoint Long term follow up CITE-seq replicate 1

description: Library name: A-03-01_01_FB


title: PBMC healthy donor CITE-seq replicate 1-7

description: Library name: HC1-07_FB


title: HCC PBMC patient A-30 timepoint C1D1 CITE-seq replicate 2

description: Library name: A-30-01_02_FB

value: atezolizumab + bevacizumab


title: HCC PBMC patient A-02 timepoint C1D1 CITE-seq

description: Library name: A-02-01_FB

value: nivolumab


title: HCC PBMC patient B-23 timepoint C1D1 CITE-seq

description: Library name: B-23-02_FB


title: HCC PBMC patient A-08 timepoint C1D1 CITE-seq replicate 2

description: Library name: A-08-01_02_FB


title: HCC PBMC patient B-06 timepoint Safety follow up CITE-seq

description: Library name: B-06-07_FB


title: HCC PBMC patient B-15 timepoint C1D1 CITE-seq replicate 1

description: Library name: B-15-01_01_FB


title: HCC PBMC patient B-13 timepoint C1D1 CITE-seq

description: Library name: B-13-01_FB


title: LNP-Satellite cell isolation kit

value: Skeletal muscle

value: Satellite cells

value: LNP-CRISPR


title: HCC PBMC patient B-08 timepoint C7D1 CITE-seq

description: Library name: B-08-07_FB

value: sorafenib + nivolumab


title: HCC PBMC patient B-02 timepoint C2D1 CITE-seq

description: Library name: B-02-04_FB


title: PBMC healthy donor CITE-seq replicate 1-6

description: Library name: HC1-06_FB


title: HCC PBMC patient B-11 timepoint baseline CITE-seq replicate 1

description: Library name: B-11-01_01_FB


title: HCC PBMC patient B-17 timepoint Safety follow up CITE-seq

description: Library name: B-17-07_FB


title: HCC PBMC patient B-06 timepoint C1D1 CITE-seq

description: Library name: B-06-02_FB


title: HCC PBMC patient B-22 timepoint C1D1 CITE-seq

description: Library name: B-22-02_FB


title: HCC PBMC patient B-12 timepoint C1D1 CITE-seq

description: Library name: B-12-01_FB


title: HCC PBMC patient A-30 timepoint C1D1 CITE-seq replicate 1

description: Library name: A-30-01_01_FB


title: HCC PBMC patient B-17 timepoint C2D1 CITE-seq

description: Library name: B-17-04_FB


title: PBMC healthy donor CITE-seq replicate 1-5

description: Library name: HC1-05_FB


title: HCC PBMC patient B-10 timepoint C1D1 CITE-seq

description: Library name: B-10-01_FB


title: HCC PBMC patient B-23 timepoint C1D15 CITE-seq

description: Library name: B-23-03_FB


title: HCC PBMC patient B-05 timepoint C1D1 CITE-seq

description: Library name: B-05-02_FB


title: HCC PBMC patient B-14 timepoint C2D1 CITE-seq replicate 1

description: Library name: B-14-03_01_FB


title: HCC PBMC patient B-03 timepoint C7D1 CITE-seq

description: Library name: B-03-07_FB


title: HCC PBMC patient A-05 timepoint C4D1 CITE-seq replicate 1

description: Library name: A-05-01_01_FB


title: HCC PBMC patient A-07 timepoint C2D1 CITE-seq replicate 2

description: Library name: A-07-02_FB


title: HCC PBMC patient B-09 timepoint baseline CITE-seq

description: Library name: B-09-01_FB


title: HCC PBMC patient A-08 timepoint C1D1 CITE-seq replicate 1

description: Library name: A-08-01_01_FB


title: HCC PBMC patient B-22 timepoint C2D15 CITE-seq

description: Library name: B-22-04_FB


title: HCC PBMC patient B-12 timepoint C2D1 CITE-seq

description: Library name: B-12-03_FB


title: HCC PBMC patient B-02 timepoint C1D1 CITE-seq

description: Library name: B-02-02_FB


title: HCC PBMC patient B-13 timepoint C2D1 CITE-seq

description: Library name: B-13-03_FB


title: PBMC healthy donor CITE-seq replicate 1-3

description: Library name: HC1-03_FB


title: HCC PBMC patient B-08 timepoint C1D1 CITE-seq

description: Library name: B-08-02_FB


title: HCC PBMC patient A-12 timepoint baseline CITE-seq replicate 2

description: Library name: A-12-01_02_FB


title: HCC PBMC patient A-04 timepoint C2D1 CITE-seq replicate 2

description: Library name: A-04-01_02_FB


title: HCC PBMC patient A-32 timepoint C1D1 CITE-seq

description: Library name: A-32-01_FB


title: HCC PBMC patient A-12 timepoint baseline CITE-seq replicate 1

description: Library name: A-12-01_01_FB


title: HCC PBMC patient B-10 timepoint C2D1 CITE-seq

description: Library name: B-10-03_FB


title: PBMC healthy donor CITE-seq replicate 1-1

description: Library name: HC1-01_FB


title: HCC PBMC patient B-22 timepoint C3D1 CITE-seq

description: Library name: B-22-05_FB


title: HCC PBMC patient A-07 timepoint C2D1 CITE-seq replicate 1

description: Library name: A-07-01_FB


title: HCC PBMC patient B-21 timepoint C1D1 CITE-seq

description: Library name: B-21-01_FB


title: PBMC healthy donor scRNA-seq replicate 3-10

description: Library name: HC3-10_GEX

data_processing:
Cell Ranger version 7.0.0 (10x Genomics, Genome Build: GRCh38 3.0.0) was used to align the raw sequencing data. The feature barcoding library sequences were aligned to a customized reference genome provided by Biolegend containing the oligonucleotide sequences corresponding to each antibody. Cell Ranger generated a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
Assembly: GRCm38
Supplementary files format and content: Cell Ranger output filtered matrix files for both scRNA-seq libraries and CITE-seq (feature barcoding) libraries: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.


title: PBMC healthy donor scRNA-seq replicate 3-9

description: Library name: HC3-09_GEX


title: HCC PBMC patient B-23 timepoint C3D1 CITE-seq

description: Library name: B-23-04_FB


title: HCC PBMC patient A-21 timepoint baseline CITE-seq

description: Library name: A-21-01_FB


title: HCC PBMC patient A-04 timepoint C2D1 CITE-seq replicate 1

description: Library name: A-04-01_01_FB


title: PBMC healthy donor scRNA-seq replicate 3-8

description: Library name: HC3-08_GEX


title: PBMC healthy donor scRNA-seq replicate 3-7

description: Library name: HC3-07_GEX


title: HCC PBMC patient A-36 timepoint C1D1 scRNA-seq replicate 2

description: Library name: A-36-01_02_GEX

value: durvulamab


title: HCC PBMC patient A-35 timepoint C1D1 scRNA-seq replicate 1

description: Library name: A-35-01_01_GEX


title: HCC PBMC patient A-36 timepoint C1D1 scRNA-seq replicate 1

description: Library name: A-36-01_01_GEX


title: PBMC healthy donor scRNA-seq replicate 3-3

description: Library name: HC3-03_GEX


title: HCC PBMC patient A-34 timepoint C1D1 scRNA-seq replicate 1

description: Library name: A-34-01_01_GEX


title: HCC PBMC patient A-33 timepoint C1D1 scRNA-seq replicate 3

description: Library name: A-33-01_03_GEX

value: durvalumab+tremelimumab


title: HCC PBMC patient A-35 timepoint C1D1 scRNA-seq replicate 2

description: Library name: A-35-01_02_GEX

value: Hepatocellular Carcinoma (HCC)


title: HCC PBMC patient A-33 timepoint C1D1 scRNA-seq replicate 2

description: Library name: A-33-01_02_GEX

value: peripheral blood mononuclear cells (PBMCs)


title: PBMC healthy donor scRNA-seq replicate 3-6

description: Library name: HC3-06_GEX

value: HD


title: PBMC healthy donor scRNA-seq replicate 3-2

description: Library name: HC3-02_GEX

value: healthy donor


title: PBMC healthy donor scRNA-seq replicate 3-1

description: Library name: HC3-p1_GEX


title: HCC PBMC patient A-34 timepoint C1D1 scRNA-seq replicate 2

description: Library name: A-34-01_02_GEX


title: PBMC healthy donor scRNA-seq replicate 3-5

description: Library name: HC3-05_GEX


title: HCC PBMC patient B-03 timepoint C1D1 CITE-seq

description: Library name: B-03-02_FB