title: PRDM1_2

description: R2 was used for analysis

data_processing:
Paired-end reads were processed using Cutadapt 3.2, BWA 0.7.17, and SAMtools 1.12 to identify off-target integration events.
Supplementary files format and content: Tab-delimited text files contain off-targets sites and normalized reads.

source_name: CD8 T cell

extract_protocol:
positive CAR-T cell genomic DNA was extracted
The adapter was made by annealing the Miseq common oligo with the sample barcode oligo (A01-A06). Libraries were prepared by doing 2 rounds of PCR.
PCR product library preparation

value: pXD60-PRDM1cr1 AAV& Cpf1 mRNA

tag: individual

value: CD8 T cell


title: PRDM1_3

status: Public on Dec 09 2022

type: SRA

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

country: USA

institute: Yale University

description: R2 was used for analysis

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: treatment

tag: cell type


title: Cocaine Low Cue, 4

city: Galveston

first: Kamil

last: Khanipov

state: TX

address: 301 University Blvd

institute: University of Texas Medical Branch

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v21 (Qiagen Bioinformatics) (Sholler et al., 2020) was used for sequencing quality control and mapping of the RNA-Seq data to the Rattus norvegicus reference genome and the collection of the coding sequences (Sholler et al., 2020). Sequencing data were initially trimmed using CLC's "Trim Reads" module. Reads containing nucleotides below the quality threshold of 0.05 (using the modified Richard Mott algorithm), those with two or more unknown nucleotides or sequencing adapters were trimmed from the dataset.
Filtered sequencing reads were then processed using the "RNA-Seq Analysis" module by mapping using a global alignment strategy against the Rat Rnot_6.0.97 annotated reference genome with 95% length fraction and 80% similarity fraction scores.
Differential gene expression analysis was performed as part of the "RNA-Seq Analysis" module. The gene expression count was modeled by a separate Generalized Linear Model (GLM), and statistical significance was evaluated using the Wald Test.
A volcano plot of differentially expressed genes was rendered using the Volcano Plot tool in Galaxy Version 0.0.5 (Afgan et al., 2018). Functional enrichment analysis was performed separately using Ingenuity Pathway Analysis (IPA) (QIAGEN, Venlo, NL) to determine the biological functions of significantly differentially expressed genes. The most significant functional pathways [?log10(p value)???1.3] were then evaluated. The genes associated with behavioral pathways by IPA were extracted and further evaluated using the Cytoscape (Shannon et al., 2003) application ClueGo (Bindea et al., 2009). As a result, we remapped the significant, differentially expressed genes to a more common open source using Gene Ontology accession numbers (Ashburner et al., 2000;Gene Ontology, 2021) and further dissected into more specific and relevant biological processes specifically related to behavior. The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database (Version 11.5; ELIXER, Cambridgeshire, UK) (Szklarczyk et al., 2019;Szklarczyk et al., 2021) was utilized to determine protein?protein interactions which are predicted based on published experimental data (e.g., co-expression, protein homology) and other bioinformatics databases [(e.g., Kyoto Encyclopedia of Genes and Genomes (KEGG)], Reactome, etc.) to generate the protein-protein interaction (PPI) network [reference genome: Rattus norvegicus, confidence score=0.4 (default).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Gene Expression Abundance Measurements

molecule: total RNA

organism: Rattus norvegicus

source_name: brain

growth_protocol: Animals. Male, Sprague-Dawley rats (n=10; Envigo, Houston, TX) weighing 250-275 g upon arrival were housed two per cage and maintained on a 12-h light-dark cycle with monitored and controlled temperature (21-23°C) and humidity (45-50%). Rats were acclimated to the colony room for seven days prior to handling and experimentation and were allowed ad libitum access to food and water except during daily operant sessions. Experiments were carried out in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals (2011) and with the approval of the University of Texas Medical Branch Institutional Animal Care and Use Committee.

extract_protocol:
RNA isolation from mPFC tissue homogenates. Rats (n=10) were anesthetized with chloral hydrate (400?mg/kg) on experimental day 27, and brains were dissected. The mPFC, comprised of infralimbic, prelimbic, and anterior cingulate cortex regions (Paxinos and Watson, 2005), was microdissected immediately over ice, flash-frozen in liquid nitrogen, and stored at ?80°C for subsequent RNA isolation as previously described (Anastasio et al., 2014a;Anastasio et al., 2014b;Fink et al., 2015;Sholler et al., 2020). The mPFC was homogenized in 10X W/V extraction buffer (20?mM HEPES, 200 mM NaCl,1?mM EDTA, 1?mM DTT, 10??L/mL protease inhibitor cocktail, 10??L/mL phosphatase inhibitor cocktails 2 and 3 (Sigma-Aldrich, St Louis, MO), and 5 ?L/mL RNaseOUT™ Recombinant Ribonuclease Inhibitor (Thermo Fisher Scientific, Waltham, MA). Immediately following homogenization, the sample was transferred to 500??L of TRI Reagent (Life Technologies, Grand Island, NY), and isolated RNA was purified using RNeasy Mini Kit (Qiagen, Germantown, MD). The RNA concentration and quality were analyzed using Cytation 5 Cell Imaging Multi-Mode Reader (BioTek Instruments, Winooski, VT) and preserved at ?80°C until assayed.
Total RNA-sequencing was performed at the University of California Los Angeles Technology Center for Genomics and Bioinformatics. Libraries were prepared using Kapa Stranded RNA-Seq Kit (Kapa Biosystems, Wilmington, MA). During the library preparation step, samples underwent enrichment, cDNA conversion, end repair, A-tailing, multiplexing, and amplification. Next, libraries were sequenced as single-end, 50 base-pair reads using the Illumina Hiseq3000 instrument generating between 12 and 23 million reads per sample.

treatment_protocol: Cocaine self-administration. Rats (n=10) were anesthetized (8.6 mg/kg of xylazine, 1.5 mg/kg of acepromazine, 43 mg/kg of ketamine in bacteriostatic saline) prior to surgical implantation of indwelling jugular catheters with back mounts; rats were allotted seven days to permit postoperative recovery (Cunningham et al., 2011;Cunningham et al., 2013;Anastasio et al., 2014a;Anastasio et al., 2014b). Rats received a 0.1 mL infusion of a bacteriostatic saline solution containing heparin sodium (10 U/mL; American Pharmaceutical Partners, East Schaumburg, IL), streptokinase (0.67 mg/mL; Sigma Chemical, St. Louis, MO), and ticarcillin disodium (66.67 mg/mL; Research Products International, Mt. Prospect, IL) into the catheter immediately following daily self-administration sessions to ensure catheter patency during experimentation.  The cocaine self-administration assay utilized standard operant conditioning chambers (Med Associates, Inc., St. Albans, VT) housed within sound-attenuated, ventilated cubicles equipped with fans (Med Associates, Inc.). Operant chambers were fitted with two retractable response levers, a stimulus light above each response lever, a houselight on the wall opposite the response levers, and an external pellet dispenser. In 180-min sessions, rats were trained to perform a lever press response reinforced by infusions (0.75 mg/kg/0./1 mL) of (-)-cocaine HCl (NIDA Drug Supply Program, Bethesda, MD) dissolved in 0.9% NaCl and delivered through syringes loaded daily into infusion pumps (Med Associates, Inc.) (Cunningham et al., 2011;Anastasio et al., 2014a;Anastasio et al., 2014b;Swinford-Jackson et al., 2016). The infusion pumps were connected to liquid swivels (Instech, Plymouth Meeting, PA) fastened to catheters via polyethylene 20 tubing encased inside a metal spring leash (Plastics One, Roanoke, VA).  Scheduled responses on the active lever resulted in the delivery of a cocaine infusion over a 6-sec period; each infusion was simultaneously paired with the illumination of the house and stimulus lights and activation of the infusion pump (i.e., discrete cue complex paired with cocaine delivery). Inactive lever presses were recorded but had no scheduled consequences. The stimulus light and infusion pump were inactivated following the delivery of cocaine. The house light remained on to signal a timeout period (20 sec); lever presses committed during the timeout period had no scheduled consequences. Rats were trained on a fixed ratio (FR) 1 schedule of reinforcement and progressed to a FR5 schedule until stability as assessed by achieving <10% variation in the number of infusions and lever presses for a minimum of three consecutive sessions (repeated measures, one-way ANOVA; GraphPad Prism 9.2.0) (Cunningham et al., 2013;Anastasio et al., 2014a;Anastasio et al., 2014b;Sholler et al., 2019;Anastasio et al., 2020).  Cue-reinforced cocaine-seeking. Once stable cocaine self-administration was achieved, individual levels of cue-reinforced cocaine-seeking were assessed in a 60-min session (see experimental timeline, Figure 1A). Lever presses on the previously active lever were reinforced by the cocaine-associated discrete cue complex (stimulus light illuminated, infusion pump activated) on a FR1 schedule. Inactive lever presses were recorded with no scheduled consequences. Rats were stratified as HC or LC rats based on a median split analysis of the total number of cue-reinforced lever presses on session 12 (one-tailed Student's t-test) (Anastasio et al., 2014a;Anastasio et al., 2014b;Fink et al., 2015;Sholler et al., 2020).   Self-administration resumed following the cue probe and continued daily for an additional five maintenance sessions, followed by 10 days of abstinence in home cages and daily handling (Figure 1A). Half of the cohort was randomly selected and a second cue-reinforced cocaine-seeking test was conducted to interrogate maintenance of HC and LC phenotypes on session 27 (Pearson's correlation). Total lifetime cocaine consumption [daily intake (mg/kg) = infusions per session * cocaine infusion dose (mg/ml) * infusion volume (0.1 ml/infusion) * body weight (kg)-1] for HC and LC rats was also determined (two-tailed Student’s t-test).

tag: tissue

value: brain

tag: Sex

value: Male

tag: strain

value: Sprague-Dawley

tag: phenotype

value: Low Cue


title: Focal Segmental Glomerulosclerosis [Sample_195]

city: Ann Arbor

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

description: Voom transformed RNAseq profiles from the tubulointerstitium of focal segmental glomeruloscerlosis

data_processing:
fastqScreen 0.11.4
cutadapt 1.14 -m 50 -A CTGTCTCTTATA -a CTGTCTCTTATA
STAR 2.5.2.a --bamRemoveDuplicatesType UniqueIdentical --twopassMode Basic --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
htseq-count --stranded=no --order=pos --mode=union
Assembly: GRCh 38.86
Supplementary files format and content: voom transformation of RNA-seq counts

source_name: Tubulointerstitium from human kidney biopsy

growth_protocol: Not applicable

extract_protocol:
Qiagen Allprep DNA/RNA Micro Kit (cat# 80284)
Takara SMART-Seq v4 Ultra Low Input RNA Kit (cat# 634891)
oligo(dT)

treatment_protocol: Not applicable

tag: disease

value: Focal Segmental Glomerulosclerosis


title: V116-Saliva2_S63

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed using cutadapter.
QIIME2.0 microbiome pipeline.
Centered log-ratio (CLR) transformation.
Assembly: hg38
Supplementary files format and content: *.genus.txt: Genus-level taxon datasets; CLR transformed values.
Library strategy: 16S RNA amplicon sequencing

organism: human oral metagenome

source_name: Oral microbiome

extract_protocol:
DNA was isolated using a Zymo Research Quick-DNA Fecal/Soil Microbe Miniprep Kit (catalog D6010).
DNA libraries were prepared for sequencing using standard Illumina protocols.

value: Saliva

tag: condition

value: not provided

tag: donor id


title: PRDM1_1

description: R2 was used for analysis


title: V114-Saliva2_S126


title: Cocaine Low Cue, 2


title: Cocaine Low Cue, 14


title: V139-Saliva2_S5


title: CAR22_PRDM1_cr3-1

description: Nextera readout

data_processing:
For indel quantification, reads were mapped to expected amplicon sequences using  BWA-MEM with the -M option. 100bp reads from the SAM file that fully mapped within a +/-  75bp window of expected cut site within the amplicon were then identified.
Assembly: Reads were mapped to targeted gene amplicon
Supplementary files format and content: Tab-delimited text files contain each indel position and percentage.

extract_protocol:
positive CAR-T cell genomic DNA was extracted
Nextera XT DNA Library Preparation Kit, Illumina
PCR product library preparation


title: Cocaine Low Cue, 13


title: Minimal Change Disease [Sample_194]

description: Voom transformed RNAseq profiles from the tubulointerstitium of minimal change disease

value: Tubulointerstitium from human kidney biopsy

value: Minimal Change Disease


title: CVX1_C1D01

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

data_processing:
Encoding Sanger/Illumina 1.9 software used for basecalling.
Quality trimming is performed to remove adapter sequences and polyA tails.  Then trimmed reads were aligned to human genome GRCh38/hg38 (Genome Reference Consortium Human Build 38), INSDC Assembly GCA_000001405.28, Dec 2013) using STAR 2.6.1d and featureCounts v2.0.0 was used to generate the raw counts
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Fingerstick

extract_protocol:
RNA was extracted using the Tempus Spin RNA Isolation Kit (ThermoFisher), which was adapted for the handling of small blood volumes. Contaminating DNA was removed using the TurboDNAse kit (ThermoFisher), and RNA was quantitated on a Qubit instrument (ThermoFisher) and QCed using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA).
mRNA-sequencing was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (75 single-end)

tag: patientid

tag: timepoint

value: Turbo Treated

value: PRIME

value: Peripheral blood


title: Focal Segmental Glomerulosclerosis [Sample_193]


title: V104-Saliva2_S103


title: Control_2

description: R2 was used for analysis

value: pXD60-PRDM1cr1 AAV only


title: Focal Segmental Glomerulosclerosis [Sample_192]


title: Control_1

description: R2 was used for analysis


title: Cocaine High Cue, 16

value: High Cue


title: V103-Saliva2_S74


title: V102-Saliva2_S123


title: Minimal Change Disease [Sample_190]


title: Focal Segmental Glomerulosclerosis [Sample_191]


title: Cocaine High Cue, 9


title: healthy volunteer talus 5

city: Qingdao

first: Junjie

last: Wang

address: The Affiliated Hospital of Qingdao University, No.59，Haier Road

country: China

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software（version2.20）. Sample demultiplexing, barcode processing and single-cell 3’gene counting by   using the Cell Ranger pipeline(https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger，version 6.1.1)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: articular cartilage of talus

extract_protocol:
Chondrocytes were dissociated into single cells in dissociation solution (0.35% collagenase IV5,2 mg/ml papain, 120 Units/ml DNase I) in 37 ℃ water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1× PBS containing 10% fetal bovine serum（FBS，V/V）, then pipetting 5-10 times with a Pasteur pipette。The resulting cell suspension was filtered by passing through 70-30um stacked cell strainer and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100ul 1× PBS (0.04% BSA) and added with 1 ml 1× red blood cell lysis buffer（MACS 130-094-183, 10×）and incubated at room temperature or on ice for 2-10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads(MACS 130-090-101) and remove dead cells using Miltenyi ® Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1× PBS(0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C（repeat twice）. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd.,(HangZhou,China) at a minimum depth of 20,000 reads per cell.

tag: disease state

value: healthy volunteer

value: articular cartilage of talus

value: chondrocyte


title: Cocaine High Cue, 11

value: brain


title: Minimal Change Disease [Sample_19]


title: V110-Saliva2_S50


title: healthy volunteer talus 4

institute: The Affiliated Hospital of Qingdao University

description: 10x Genomics


title: V100-Saliva2_S22


title: Cocaine Low Cue, 12

value: Male


title: V380-SalivaRNAL_S275


title: healthy volunteer talus 3

description: 10x Genomics


title: Focal Segmental Glomerulosclerosis [Sample_188]


title: Control_3

description: R2 was used for analysis

value: CD8 T cell


title: healthy volunteer talus 1

description: 10x Genomics


title: Cocaine High Cue, 10

value: Sprague-Dawley


title: Focal Segmental Glomerulosclerosis [Sample_187]

value: Focal Segmental Glomerulosclerosis


title: V376-SalivaRNAL_S20

value: Saliva


title: V375-Subgingival_S159

value: Subgingival sites

value: not provided


title: polyX_8day_2

city: Daejeon

first: Yoonjung

last: Choi

address: 7-12, Daehak-ro 179beon-gil, Yuseong-gu

country: South Korea

institute: Yoonjung

data_processing:
Prepared libraries were sequenced on a Novaseq-6000 with paired-end method (150-bp reads).  The sequenced reads were aligned to the human
genome (version: Hg19) using the STAR aligner (v.2.4.0)
The number of mapped reads was further analyzed using HOMER and DESeq
Genome_build: Hg19
Supplementary_files_format_and_content: RNA-seq : tab-delimited text files include FPKM values for each Sample
Assembly: hg19
Supplementary files format and content: polymerX_RNAseq_FPKM.txt

growth_protocol: Cancer cells (1 × 106) were seeded on polyerX-coated plates and cultured in RPMI-1640, Dulbecco’s Modified Eagle Medium (DMEM) or Minimal Essential Medium (MEM), as appropriate, containing 10% (v/v) serum replacement (SR; Gibco), 1% (v/v) penicillin/streptomycin (P/S; Gibco), and L-glutamine at 37°C in a humidified 5% CO2 atmosphere. For optimum spheroid growth, culture medium was refreshed every 2–3 days.

extract_protocol: DNase-treated mRNA was purified using Magnetic mRNA Isolation Kit (NEB), and subjected to library preparation using NEXTflex™ Rapid Directional mRNA-Seq Kit (BIOO) following the manufacturer’s instructions.  mRNA-seq libraries were made using NEXTflexTM Rapid RNA-Seq kit (cat. 5138) from isolated mRNA.

tag: cell line

value: ovarian cancer cell lines


title: polyX_8day_1


title: healthy volunteer talus 2

description: 10x Genomics


title: Cocaine High Cue, 15


title: V375-SalivaRNAL_S145


title: Minimal Change Disease [Sample_185]

value: Tubulointerstitium from human kidney biopsy

value: Minimal Change Disease


title: Minimal Change Disease [Sample_189]


title: V380-Subgingival_S300


title: TCP0day_2


title: Focal Segmental Glomerulosclerosis [Sample_184]


title: TCP0day_1


title: V372-SalivaRNAL_S293


title: Focal Segmental Glomerulosclerosis [Sample_183]


title: Focal Segmental Glomerulosclerosis [Sample_182]


title: V371-Subgingival_S10


title: Minimal Change Disease [Sample_186]


title: Focal Segmental Glomerulosclerosis [Sample_181]


title: SIIN-1

type: RNA

city: Lebanon

first: Pamela

last: Rosato

state: NH

address: 1 Medical Center Dr, Rubin fl 7-30

institute: Dartmouth College

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

organism: Mus musculus

source_name: T cell

label_protocol: standard Illumina protocol

extract_protocol: none provided by the submitter

value: control


title: V371-SalivaRNAL_S246


title: SETD1AKO_FKBP-SETD1A_DMSO_1h_CTDpS5

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.1.0.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
Duplication reads were removed from aligned file by using picard-tools-1.56.
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: MOLM-13 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
For ChIP-seq, cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: HA-FKBP-hSETD1A expression vector, Cas9 expression vector and SETD1A sgRNA expression vector  were introduced with lentivirus and stable expressing single cell clone was established. Cells were treated with DMSO or 500 nM dTAG-13 for 24 hours.

tag: vector

tag: chip antibody

value: CTDpS5 (#13523, Cell Signaling)

tag: stimulation

value: DMSO

tag: time


title: SETD1AKO_FKBP-SETD1A_dTAG_1h_RNAP2

value: RNAP2 (#14958, Cell Signaling)


title: SIIN-3

tag: treatment


title: SETD1AKO_FKBP-SETD1A_dTAG_1h_CTDpS5


title: GP33-3

value: reactivated


title: Minimal Change Disease [Sample_180]


title: V369-Subgingival_S252


title: GP33-2


title: SETD1AKO_FKBP-SETD1A_DMSO_1h_RNAP2


title: V369-SalivaRNAL_S66


title: V372-Subgingival_S85


title: SK-N-BE2 DMSO_rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al.. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample …

source_name: Neuroblastoma cells

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Neuroblastoma cells


title: V368-Subgingival_S167

tag: tissue


title: Focal Segmental Glomerulosclerosis [Sample_18]


title: Focal Segmental Glomerulosclerosis [Sample_179]


title: V368-SalivaRNAL_S9


title: SK-N-BE2 DMSO_rep1


title: Focal Segmental Glomerulosclerosis [Sample_178]


title: arm skin at baseline, participant 1

first: Luis

middle: Andres

last: Garza

address: 1550 Orleans Street Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins University

description: gene expression data from arm skin at baseline, participant 1

hyb_protocol: 16hrs at 45C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted and their data normalized with the robust mult-array (RMA) algorithm, using the rma() function of the affy package in R.

label: biotin

source_name: arm skin at baseline

label_protocol: biotin

extract_protocol: Face or arm skin was punch biopsied for total RNA isolation from cells using the RNeasy kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: All participants were treated with 1550 nm Er:Glass non-ablative fractional laser on the face and one dorsal forearm (randomly selected) once monthly for 6 months. The following laser settings were used: face, fluence 60-70 mJ, treatment level 8-11, 8 passes; forearm, fluence 60-70 mJ, treatment level 6-9, 8 passes.

tag: participant

tag: Sex

value: female

tag: race

value: white

value: arm skin

value: baseline


description: gene expression data from arm skin at 1 day after first laser session, participant 2

value: 1 day after first laser session


title: SK-N-BE2 dBET57_rep2


title: V367-Subgingival_S107


title: Focal Segmental Glomerulosclerosis [Sample_177]

tag: disease

value: Focal Segmental Glomerulosclerosis


title: face skin at baseline, participant 2

description: gene expression data from face skin at baseline, participant 2

source_name: face skin at baseline

value: face skin


title: V367-SalivaRNAL_S244

value: Saliva

tag: condition

value: not provided


title: SIIN-2

tag: strain


title: face skin at baseline, participant 3

description: gene expression data from face skin at baseline, participant 3


title: SK-N-BE2 dBET57_rep1


title: V363-SalivaRNAL_S303

tag: donor id


title: Minimal Change Disease [Sample_175]

value: Tubulointerstitium from human kidney biopsy


title: Minimal Change Disease [Sample_176]

value: Minimal Change Disease


title: V363-Subgingival_S47

value: Subgingival sites


title: Minimal Change Disease [Sample_174]


description: gene expression data from arm skin at 1 day after first laser session, participant 4

tag: timepoint


title: XDRNA01-CD8T-d0, 2

description:
bulk RNAseq
XDRNA-timecourse_2

data_processing:
FASTQ files from mRNA sequencing were used analyzed using the Kallisto quant algorithm with setting -b 100 for transcript quantification. Differential expression analysis was performed using Sleuth.
Differentially upregulated and downregulated genes were selected for DAVID analysis using a Q value cutoff of 1 × 10−3. Z-scores for time course heatmap were calculated by log2-normalizion of gene counts following by scaling by genes, and differentially expressed genes across the time points were determined by limma with contrasts set up to compare PRDM1 vs vector control CAR-T cells at each time point. Time course cluster analysis was performed with the R package maSigPro using “two.ways.forward” as step method and otherwise default settings. Visualizations of differentially expressed genes such as volcano plots and heatmaps were generated using standard R packages such as ggplot2 and VennDiagram.
Assembly: hg19 reference
Supplementary files format and content: Tab-delimited .tsv files contain Kallisto output (tpm per transcript)

extract_protocol:
CAR-T cells were harvested using TRIzol (Invitrogen) after each round of NALM-6 stimulation. RNA was extracted using RNeasy Plus mini isolation kit (Qiagen).
mRNA library preparations were performed using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina and samples were multiplexed using barcoded primers provided by NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1). Libraries were sequenced with Novaseq systems (Illumina).

value: untreated

value: CD8 T cell

tag: purity

value: Nontreatment

tag: cell species

value: Homo sapiens

value: Day 0

tag: coculture round


title: XDRNA01-CD8T-d0, 3

description:
bulk RNAseq
XDRNA-timecourse_3


title: Donor2-pXD60-round5-d33, 3

description:
bulk RNAseq
XDRNA-timecourse_3

value: CLASH vector

value: in vitro coculture

value: Day 33


title: V359-Subgingival_S63


title: Minimal Change Disease [Sample_173]


title: V359-SalivaRNAL_S80


description: gene expression data from arm skin at 1 day after first laser session, participant 1

value: female

value: white

value: arm skin


title: Minimal Change Disease [Sample_172]


description: gene expression data from face skin at 7 days after first laser session, participant 3

value: face skin

value: 7 days after first laser session


title: arm skin at baseline, participant 3

description: gene expression data from arm skin at baseline, participant 3

value: baseline


title: GP33-1

value: reactivated


title: V358-Subgingival_S308

value: not provided


description: gene expression data from arm skin at 7 days after first laser session, participant 1


description: gene expression data from arm skin at 14 days after first laser session, participant 2

value: 14 days after first laser session


title: Donor2-pXD60-round5-d33, 1

description:
bulk RNAseq
XDRNA-timecourse_1


title: Donor2-pXD60-round3-d19, 3

description:
bulk RNAseq
XDRNA-timecourse_3

value: Day 19


title: Focal Segmental Glomerulosclerosis [Sample_170]

value: Tubulointerstitium from human kidney biopsy

value: Focal Segmental Glomerulosclerosis


title: V356-Subgingival_S234

value: Subgingival sites


title: V356-SalivaRNAL_S272

value: Saliva


description: gene expression data from arm skin at 1 day after first laser session, participant 6

value: 1 day after first laser session


title: Donor2-pXD60-round3-d19, 2

description:
bulk RNAseq
XDRNA-timecourse_2

value: CLASH vector

value: CD8 T cell

value: Homo sapiens

value: in vitro coculture


title: Minimal Change Disease [Sample_171]

value: Minimal Change Disease


title: V358-SalivaRNAL_S42


title: Minimal Change Disease [Sample_17]


title: Donor2-pXD60-round5-d33, 2

description:
bulk RNAseq
XDRNA-timecourse_2

value: Day 33


title: Focal Segmental Glomerulosclerosis [Sample_168]


title: Minimal Change Disease [Sample_167]


description: gene expression data from face skin at 7 days after first laser session, participant 9

value: female

value: white

value: face skin

value: 7 days after first laser session


title: face skin at baseline, participant 4

description: gene expression data from face skin at baseline, participant 4

value: baseline


title: arm skin at baseline, participant 6

description: gene expression data from arm skin at baseline, participant 6

value: arm skin


description: gene expression data from arm skin at 7 days after first laser session, participant 5


title: Donor2-pXD60-round3-d19, 1

description:
bulk RNAseq
XDRNA-timecourse_1

value: Day 19


title: face skin at baseline, participant 6

description: gene expression data from face skin at baseline, participant 6


title: Donor2-pXD60-round1-d8, 2

description:
bulk RNAseq
XDRNA-timecourse_2

value: Day 8


title: Donor2-pXD60-round1-d8, 3

description:
bulk RNAseq
XDRNA-timecourse_3


title: V354-Subgingival_S163

value: Subgingival sites

value: not provided


title: Focal Segmental Glomerulosclerosis [Sample_166]

description: Voom transformed RNAseq profiles from the tubulointerstitium of focal segmental glomeruloscerlosis

value: Tubulointerstitium from human kidney biopsy

value: Focal Segmental Glomerulosclerosis


title: Donor2-pXD60-round1-d8, 1

description:
bulk RNAseq
XDRNA-timecourse_1

value: CLASH vector

value: CD8 T cell


title: V354-SalivaRNAL_S188

value: Saliva


title: arm skin at baseline, participant 9

description: gene expression data from arm skin at baseline, participant 9


title: V353-Subgingival_S187


title: V353-SalivaRNAL_S46


title: Donor2-pXD60-PRDM1sg2-round0-d0, 3

description:
bulk RNAseq
XDRNA-timecourse_3

value: PRDM1-cr2 CAR22 AAV6

value: Unsorted

value: Homo sapiens

value: in vitro coculture

value: Day 0


title: Minimal Change Disease [Sample_169]

description: Voom transformed RNAseq profiles from the tubulointerstitium of minimal change disease

value: Minimal Change Disease


title: V352-Subgingival_S280


title: Minimal Change Disease [Sample_165]


title: Focal Segmental Glomerulosclerosis [Sample_163]


title: Donor2-pXD60-PRDM1sg2-round0-d0, 1

description:
bulk RNAseq
XDRNA-timecourse_1


title: V352-SalivaRNAL_S124


description: gene expression data from face skin at 7 days after first laser session, participant 5

value: female

value: white

value: face skin

value: 7 days after first laser session


title: Donor2-pXD60-PRDM1sg2-round0-d0, 2

description:
bulk RNAseq
XDRNA-timecourse_2


description: gene expression data from face skin at 7 days after first laser session, participant 6


title: Focal Segmental Glomerulosclerosis [Sample_164]


title: V350-SalivaRNAL_S268


title: Donor2-pXD60-PRDM1sg1-round5-d33, 3

description:
bulk RNAseq
XDRNA-timecourse_3

value: PRDM1-cr1 CAR22 AAV6

value: Day 33


title: V347-Subgingival_S68

value: Subgingival sites

value: not provided


title: Focal Segmental Glomerulosclerosis [Sample_160]

value: Tubulointerstitium from human kidney biopsy

value: Focal Segmental Glomerulosclerosis


title: Donor2-pXD60-PRDM1sg1-round5-d33, 2

description:
bulk RNAseq
XDRNA-timecourse_2

value: CD8 T cell


title: Focal Segmental Glomerulosclerosis [Sample_162]


description: gene expression data from arm skin at 14 days after first laser session, participant 1

value: arm skin

value: 14 days after first laser session


title: Donor2-pXD60-PRDM1sg1-round5-d33, 1

description:
bulk RNAseq
XDRNA-timecourse_1

value: Homo sapiens


title: Minimal Change Disease [Sample_161]


title: Donor2-pXD60-PRDM1sg1-round3-d19, 2

description:
bulk RNAseq
XDRNA-timecourse_2

value: in vitro coculture

value: Day 19


description: gene expression data from face skin at 7 days after first laser session, participant 4


title: V346-Subgingival_S25


title: Donor2-pXD60-PRDM1sg1-round3-d19, 3

description:
bulk RNAseq
XDRNA-timecourse_3


title: V347-SalivaRNAL_S197

value: Saliva


title: Minimal Change Disease [Sample_16]

value: Minimal Change Disease


title: V346-SalivaRNAL_S198


description: gene expression data from arm skin at 7 days after first laser session, participant 2

value: female

value: white


description: gene expression data from face skin at 7 days after first laser session, participant 1

value: face skin

value: 7 days after first laser session


description: gene expression data from arm skin at 7 days after first laser session, participant 3


title: face skin at baseline, participant 1

description: gene expression data from face skin at baseline, participant 1

value: baseline


title: Focal Segmental Glomerulosclerosis [Sample_159]


title: Donor2-pXD60-PRDM1sg1-round3-d19, 1

description:
bulk RNAseq
XDRNA-timecourse_1

value: PRDM1-cr1 CAR22 AAV6


title: Focal Segmental Glomerulosclerosis [Sample_158]


title: V344-Subgingival_S8

value: Subgingival sites

value: not provided


title: Focal Segmental Glomerulosclerosis [Sample_157]

value: Tubulointerstitium from human kidney biopsy

value: Focal Segmental Glomerulosclerosis


title: V343-Subgingival_S314


title: arm skin at baseline, participant 2

description: gene expression data from arm skin at baseline, participant 2

value: arm skin


title: Donor2-pXD60-PRDM1cr2, 3

description:
bulk RNAseq
XDRNA-cr1vcr2_3

value: PRDM1-cr2 CAR22 AAV6

value: CD8 T cell

value: in vitro

value: Day 8


title: V343-SalivaRNAL_S96

value: Saliva


title: Minimal Change Disease [Sample_156]

value: Minimal Change Disease


title: Minimal Change Disease [Sample_155]


title: V342-Subgingival_S199


title: Minimal Change Disease [Sample_154]


title: V344-SalivaRNAL_S224


title: Donor2-pXD60-PRDM1cr2, 2

description:
bulk RNAseq
XDRNA-cr1vcr2_2

value: Homo sapiens


title: Minimal Change Disease [Sample_153]


title: Donor2-pXD60-PRDM1sg1-round1-d8, 3

description:
bulk RNAseq
XDRNA-timecourse_3

value: in vitro coculture


title: Donor2-pXD60-PRDM1sg1-round1-d8, 2

description:
bulk RNAseq
XDRNA-timecourse_2


description: gene expression data from arm skin at 1 day after first laser session, participant 3

value: female

value: white

value: 1 day after first laser session


description: gene expression data from arm skin at 14 days after first laser session, participant 9

value: 14 days after first laser session


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 3


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 2


description: gene expression data from arm skin at 14 days after first laser session, participant 3


title: Donor2-pXD60-PRDM1sg1-round1-d8, 1

description:
bulk RNAseq
XDRNA-timecourse_1

value: PRDM1-cr1 CAR22 AAV6


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 1


title: Donor2-pXD60-PRDM1cr1, 3

description:
bulk RNAseq
XDRNA-cr1vcr2_3


title: Donor2-pXD60-PRDM1cr2, 1

description:
bulk RNAseq
XDRNA-cr1vcr2_1


description: gene expression data from arm skin at 1 day after first laser session, participant 5


title: Minimal Change Disease [Sample_151]

description: Voom transformed RNAseq profiles from the tubulointerstitium of minimal change disease


title: V339-Subgingival_S221

value: Subgingival sites

value: not provided


title: Minimal Change Disease [Sample_15]

value: Tubulointerstitium from human kidney biopsy


title: Donor2-pXD60-PRDM1cr1, 1

description:
bulk RNAseq
XDRNA-cr1vcr2_1


title: V340-SalivaRNAL_S258


title: V339-SalivaRNAL_S196


title: V342-SalivaRNAL_S4


title: Minimal Change Disease [Sample_149]


title: Focal Segmental Glomerulosclerosis [Sample_152]

description: Voom transformed RNAseq profiles from the tubulointerstitium of focal segmental glomeruloscerlosis

value: Focal Segmental Glomerulosclerosis


title: Donor2-pXD60-CTRL, 3

description:
bulk RNAseq
XDRNA-cr1vcr2_3

value: CLASH vector


title: Donor2-pXD60-PRDM1cr1, 2

description:
bulk RNAseq
XDRNA-cr1vcr2_2

value: CD8 T cell


title: V337-SalivaRNAL_S105


title: Donor2-pXD60-CTRL, 2

description:
bulk RNAseq
XDRNA-cr1vcr2_2

value: in vitro


title: Focal Segmental Glomerulosclerosis [Sample_150]


title: V337-Subgingival_S216


title: Minimal Change Disease [Sample_148]


title: Donor2-pXD60-CTRL, 1

description:
bulk RNAseq
XDRNA-cr1vcr2_1

value: Day 8


description: gene expression data from arm skin at 14 days after first laser session, participant 5

value: arm skin


description: gene expression data from arm skin at 7 days after first laser session, participant 6

value: 7 days after first laser session


title: V335-Subgingival_S181


description: gene expression data from face skin at 7 days after first laser session, participant 11

value: face skin


title: V335-SalivaRNAL_S38

value: Saliva


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 16

value: female


title: Focal Segmental Glomerulosclerosis [Sample_147]


description: gene expression data from arm skin at 7 days after first laser session, participant 11

value: white


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 17


title: Minimal Change Disease [Sample_146]

value: Minimal Change Disease


title: Focal Segmental Glomerulosclerosis [Sample_145]


title: V334-SalivaRNAL_S150


title: CLASH-CD8-invivo-marrow-d14-rep6

description:
Screen Readout
rawcounts_processed_deca04.txt
CLASH-Deca04

data_processing:
Data were paired-end but only the forward read was used for analysis. Raw single-end fastq read files were filtered and demultiplexed using Cutadapt. Reads were demultiplexed for the barcodes included in the forward readout PCR primers. To identify and remove extra sequences immediately upstream of the crRNAs, the following settings were used: cutadapt -g TAATTTCTACTAAGTGTAGAT -e 0.1 -m 19 --discard-untrimmed. The 20 bp crRNA sequences were then mapped the designed Descartes library sequences using a bowtie index generated using the bowtie8 build command in Bowtie 1.2.2. Mapping used the following settings: bowtie -v 1 -m 1, and the number of reads that had mapped to each crRNA within the library was quantified. This processing was used across multiple different in vitro and in vivo CLASH crRNA library readouts, as well as for the MIPs crRNA representation readout. Subsequent data cleaning to generate the procssed data files were performed in R.
Assembly: Reads were mapped to the designed library
Supplementary files format and content: Tab-delimited text files ("rawcounts_processed_deca0X") contain read counts for each crRNA across multiple time points for each set of screens.

source_name: marrow

extract_protocol:
For in vitro experiments, T cells cocultured with NALM-6 cells were harvested at multiple time points after clearance of NALM-6, and genomic DNA was isolated by QIAGEN's DNA purification kit. For in vivo experiments, NSG mice were euthanized, and spleen and bone marrow were collected immediately. Red blood cells were lysed by ACK Lysis Buffer (Thermofisher) for 2 mins. After a wash, cells were analyzed and sorted by BD Facs Aria for CAR+ cells, and then genomic DNA was harvested using QuickExtract DNA extraction solution (Lucigen).
The crRNA library readout was performed using a two-step PCR strategy, where the first In-Out PCR was used to amplify out the integrated fragments from gDNA and the second PCR adds appropriate sequencing adapters to the products from the first PCR. For the first round PCR, the thermocycling parameters were 98 °C for 1 min, 20 cycles of (98 °C for 1s, 60 °C for 5s, 72 °C for 25 s), and 72 °C for 2 min. In each PCR reaction, we used 2 µg of total gDNA for in vitro and used 5ul DNA extraction solution for in vivo. A total of 3-4 reactions was used to capture the full representation of the library. PCR products for each biological sample were pooled and used for amplification with barcoded second PCR primers. For the second round PCR, the thermocycling parameters were 98 °C for 1 min, 28 cycles of (98 °C for 1s, 61 °C for 5s, 72 °C for 10s), and 72 °C for 2 min. Second PCR products were pooled and then normalized for each biological sample before combining uniquely barcoded separate biological samples. The pooled product was then gel purified from a 2% E-gel EX (Life Technologies) using the QIAquick Gel Extraction Kit (Qiagen).
genome-integrated crRNA readout

value: Descartes

value: Homo sapiens

value: in vivo

tag: in vivo_model

value: mouse

value: marrow

tag: cancer model

value: Day 14


title: V334-Subgingival_S266

value: Subgingival sites

value: not provided


title: Minimal Change Disease [Sample_144]

value: Tubulointerstitium from human kidney biopsy


title: CLASH-CD8-invivo-marrow-d14-rep5

value: CD8 T cell

tag: time


title: V331-Subgingival_S87


description: gene expression data from arm skin at 7 days after first laser session, participant 17

value: arm skin


title: CLASH-CD8-invivo-marrow-d14-rep3

tag: treatment


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 15


title: CLASH-CD8-invivo-marrow-d14-rep4

tag: cell type


title: Focal Segmental Glomerulosclerosis [Sample_143]

tag: tissue

value: Focal Segmental Glomerulosclerosis


title: V331-SalivaRNAL_S48


title: Focal Segmental Glomerulosclerosis [Sample_142]


title: XDRNA01-CD8T-d0, 1

description:
bulk RNAseq
XDRNA-timecourse_1

value: untreated

value: Nontreatment

value: Day 0


title: CLASH-CD8-invivo-marrow-d14-rep2


title: V330-Subgingival_S229


title: Minimal Change Disease [Sample_141]


title: V330-SalivaRNAL_S239

value: Saliva


title: CLASH-CD8-invivo-marrow-d14-rep1


title: Focal Segmental Glomerulosclerosis [Sample_140]


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 11

tag: participant

value: female

value: white


description: gene expression data from arm skin at 14 days after first laser session, participant 17

tag: Sex

value: 14 days after first laser session


description: gene expression data from face skin at 7 days after first laser session, participant 17

tag: race

value: face skin

value: 7 days after first laser session


title: CLASH-CD8-invivo-spleen-d14-rep6

source_name: spleen

value: Descartes

value: Homo sapiens

value: in vivo

value: mouse

value: spleen


title: Minimal Change Disease [Sample_14]

value: Tubulointerstitium from human kidney biopsy

tag: disease

value: Minimal Change Disease


title: CLASH-CD8-invivo-spleen-d14-rep5

value: CD8 T cell

tag: condition

value: Day 14


title: Focal Segmental Glomerulosclerosis [Sample_139]

value: Focal Segmental Glomerulosclerosis


title: V329-SalivaRNAL_S40

value: not provided


title: CLASH-CD8-invivo-spleen-d14-rep4


description: gene expression data from arm skin at 1 day after first laser session, participant 17

value: arm skin

value: 1 day after first laser session


title: Minimal Change Disease [Sample_138]


title: V328-SalivaRNAL_S242

value: Saliva


description: gene expression data from arm skin at 14 days after first laser session, participant 11

value: female

value: white

value: 14 days after first laser session


title: V328-Subgingival_S140

value: Subgingival sites


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 14


title: Minimal Change Disease [Sample_137]

description: Voom transformed RNAseq profiles from the tubulointerstitium of minimal change disease


title: CLASH-CD8-invivo-spleen-d14-rep3

value: Descartes

value: Homo sapiens


title: Focal Segmental Glomerulosclerosis [Sample_136]

description: Voom transformed RNAseq profiles from the tubulointerstitium of focal segmental glomeruloscerlosis


title: CLASH-CD8-invivo-spleen-d14-rep2

value: in vivo

value: mouse


title: V327-Subgingival_S207


title: CLASH-CD8-invivo-spleen-d14-rep1

value: spleen


title: V327-SalivaRNAL_S113


title: V329-Subgingival_S225


title: Minimal Change Disease [Sample_135]

value: Tubulointerstitium from human kidney biopsy

value: Minimal Change Disease


description: gene expression data from face skin at 7 days after first laser session, participant 2

value: face skin

value: 7 days after first laser session


title: arm skin at baseline, participant 17

description: gene expression data from arm skin at baseline, participant 17

value: baseline


title: CLASH-CD8-invivo-marrow-d11-rep5

value: CD8 T cell

value: marrow

value: Day 11


title: face skin at baseline, participant 17

description: gene expression data from face skin at baseline, participant 17

value: female


title: V326-Subgingival_S118

value: not provided


description: gene expression data from face skin at 7 days after first laser session, participant 15

value: white


description: gene expression data from arm skin at 14 days after first laser session, participant 16

value: arm skin

value: 14 days after first laser session


title: Minimal Change Disease [Sample_134]


title: V326-SalivaRNAL_S228

value: Saliva


title: Focal Segmental Glomerulosclerosis [Sample_132]

value: Focal Segmental Glomerulosclerosis


title: CLASH-CD8-invivo-marrow-d11-rep2

value: Descartes

value: Homo sapiens

value: in vivo

value: mouse


title: Focal Segmental Glomerulosclerosis [Sample_131]

value: Tubulointerstitium from human kidney biopsy


title: face skin at baseline, participant 11

description: gene expression data from face skin at baseline, participant 11

value: face skin


title: CLASH-CD8-invivo-marrow-d11-rep3

description:
Screen Readout
rawcounts_processed_deca04.txt
CLASH-Deca04


title: V325-SalivaRNAL_S279


title: CLASH-CD8-invivo-marrow-d11-rep4


title: V321-Subgingival_S248

value: Subgingival sites


title: CLASH-CD8-invivo-marrow-d11-rep1

value: CD8 T cell


description: gene expression data from arm skin at 14 days after first laser session, participant 15


title: Minimal Change Disease [Sample_130]

value: Minimal Change Disease


title: V321-SalivaRNAL_S54


title: CLASH-CD8-invivo-spleen-d11-rep5

value: spleen

value: Day 11


title: Minimal Change Disease [Sample_13]


title: Focal Segmental Glomerulosclerosis [Sample_129]


title: CLASH-CD8-invivo-spleen-d11-rep4


title: V319-SalivaRNAL_S218

value: not provided


title: CLASH-CD8-invivo-spleen-d11-rep3


title: V325-Subgingival_S44


title: V319-Subgingival_S309


description: gene expression data from arm skin at 14 days after first laser session, participant 14

value: female

value: white


title: Focal Segmental Glomerulosclerosis [Sample_128]


description: gene expression data from arm skin at 7 days after first laser session, participant 15

value: arm skin

value: 7 days after first laser session


title: Focal Segmental Glomerulosclerosis [Sample_127]

value: Focal Segmental Glomerulosclerosis


title: CLASH-CD8-invivo-spleen-d11-rep2

value: Descartes


title: V316-Subgingival_S178


title: V318-SalivaRNAL_S45

value: Saliva


title: Focal Segmental Glomerulosclerosis [Sample_126]


title: CLASH-CD8-invivo-marrow-d7-rep5

value: Homo sapiens

value: in vivo

value: marrow

value: Day 7


title: Focal Segmental Glomerulosclerosis [Sample_125]

value: Tubulointerstitium from human kidney biopsy


title: CLASH-CD8-invivo-spleen-d11-rep1

value: CD8 T cell

value: mouse


title: V315-Subgingival_S205

value: Subgingival sites


title: arm skin at baseline, participant 15

description: gene expression data from arm skin at baseline, participant 15

value: baseline


description: gene expression data from arm skin at 1 day after first laser session, participant 11

value: 1 day after first laser session


title: Focal Segmental Glomerulosclerosis [Sample_124]


title: arm skin at baseline, participant 11

description: gene expression data from arm skin at baseline, participant 11

value: female


description: gene expression data from arm skin at 1 day after first laser session, participant 15

value: white


title: V340-Subgingival_S138

value: not provided


description: gene expression data from arm skin at 7 days after first laser session, participant 16

value: arm skin

value: 7 days after first laser session


title: Minimal Change Disease [Sample_123]

description: Voom transformed RNAseq profiles from the tubulointerstitium of minimal change disease

value: Minimal Change Disease


title: CLASH-CD8-invivo-marrow-d7-rep3

value: Descartes


title: face skin at baseline, participant 15

description: gene expression data from face skin at baseline, participant 15

value: face skin


title: face skin at baseline, participant 14

description: gene expression data from face skin at baseline, participant 14


title: CLASH-CD8-invivo-marrow-d7-rep2

value: Homo sapiens

value: in vivo


title: Minimal Change Disease [Sample_133]


title: V314-SalivaRNAL_S31

value: Saliva


title: V316-SalivaRNAL_S284


title: Minimal Change Disease [Sample_122]

value: Tubulointerstitium from human kidney biopsy


title: Minimal Change Disease [Sample_121]


title: CLASH-CD8-invivo-marrow-d7-rep4

value: CD8 T cell

value: marrow

value: Day 7


title: CLASH-CD8-invivo-spleen-d7-rep5

value: mouse

value: spleen


description: gene expression data from arm skin at 7 days after first laser session, participant 14

value: female


title: V311-Subgingival_S190

value: Subgingival sites


title: V315-SalivaRNAL_S291

value: not provided


title: Focal Segmental Glomerulosclerosis [Sample_120]

description: Voom transformed RNAseq profiles from the tubulointerstitium of focal segmental glomeruloscerlosis

value: Focal Segmental Glomerulosclerosis


title: CLASH-CD8-invivo-spleen-d7-rep4


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 13

value: white

value: arm skin


title: V311-SalivaRNAL_S307


title: arm skin at baseline, participant 14

description: gene expression data from arm skin at baseline, participant 14

value: baseline


title: V314-Subgingival_S116


title: Focal Segmental Glomerulosclerosis [Sample_12]


description: gene expression data from face skin at 7 days after first laser session, participant 14

value: face skin

value: 7 days after first laser session


title: arm skin at baseline, participant 13

description: gene expression data from arm skin at baseline, participant 13


title: CLASH-CD8-invivo-marrow-d7-rep1

description:
Screen Readout
rawcounts_processed_deca04.txt
CLASH-Deca04

value: Descartes

value: Homo sapiens

value: in vivo


title: V310-Subgingival_S297


title: CLASH-CD8-invivo-spleen-d7-rep3

value: CD8 T cell


title: V310-SalivaRNAL_S92

value: Saliva


description: gene expression data from arm skin at 7 days after first laser session, participant 13


title: CLASH-CD8-invivo-spleen-d7-rep1

value: Day 7


title: Minimal Change Disease [Sample_117]

value: Tubulointerstitium from human kidney biopsy

value: Minimal Change Disease


title: CLASH-CD8-invivo-d0-rep3

value: in vitro

value: Day 0


title: V306-SalivaRNAL_S274

value: not provided


title: V306-Subgingival_S77

value: Subgingival sites


title: Focal Segmental Glomerulosclerosis [Sample_116]

value: Focal Segmental Glomerulosclerosis


title: CLASH-CD8-invivo-d0-rep2


title: V305-Subgingival_S106


title: Minimal Change Disease [Sample_115]


title: CLASH-CD8-invivo-d0-rep1


title: arm skin at baseline, participant 16

description: gene expression data from arm skin at baseline, participant 16

value: female

value: white

value: arm skin


title: V305-SalivaRNAL_S19


title: Focal Segmental Glomerulosclerosis [Sample_119]


description: gene expression data from arm skin at 14 days after first laser session, participant 13

value: 14 days after first laser session


title: face skin at baseline, participant 16

description: gene expression data from face skin at baseline, participant 16

value: face skin

value: baseline


title: Minimal Change Disease [Sample_114]


title: CLASH-CD8-invivo-spleen-d7-rep2

value: Descartes

value: Homo sapiens

value: in vivo

value: mouse

value: spleen


description: gene expression data from face skin at 7 days after first laser session, participant 13

value: 7 days after first laser session


title: Focal Segmental Glomerulosclerosis [Sample_118]

value: Tubulointerstitium from human kidney biopsy


description: gene expression data from arm skin at 1 day after first laser session, participant 16

value: 1 day after first laser session


description: gene expression data from arm skin at 1 day after first laser session, participant 14


title: CLASH-CD4-invitro-d48_3

description:
Screen Readout
rawcounts_processed_deca05.txt
CLASH-Deca05

value: CD4 T cell

value: in vitro coculture

value: Day 48


title: Minimal Change Disease [Sample_113]

description: Voom transformed RNAseq profiles from the tubulointerstitium of minimal change disease

value: Minimal Change Disease


title: CLASH-CD4-invitro-d41_3

value: Day 41


title: V302-Subgingival_S238

value: Subgingival sites

value: not provided


title: V302-SalivaRNAL_S21

value: Saliva


title: Minimal Change Disease [Sample_111]


title: V298-Subgingival_S43


title: V299-SalivaRNAL_S151


title: CLASH-CD4-invitro-d20_3

value: Day 20


title: CLASH-CD4-invitro-d27_3

value: Descartes

value: Day 27


description: gene expression data from face skin at 7 days after first laser session, participant 16

value: female

value: white

value: face skin


title: Focal Segmental Glomerulosclerosis [Sample_110]

value: Focal Segmental Glomerulosclerosis


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 12

value: arm skin


title: Minimal Change Disease [Sample_11]

value: Tubulointerstitium from human kidney biopsy


title: Minimal Change Disease [Sample_112]


title: CLASH-CD4-invitro-d34_3

value: CD4 T cell

value: Homo sapiens

value: Day 34


title: V298-SalivaRNAL_S295


title: V297-Subgingival_S56


description: gene expression data from arm skin at 14 days after first laser session, participant 10

value: 14 days after first laser session


title: face skin at baseline, participant 13

description: gene expression data from face skin at baseline, participant 13

value: baseline


description: gene expression data from arm skin at 1 day after first laser session, participant 13

value: 1 day after first laser session


title: CLASH-CD4-invitro-d13_3

value: in vitro coculture

value: Day 13


title: CLASH-CD4-invitro-d06_3

value: Day 06


title: Focal Segmental Glomerulosclerosis [Sample_107]

description: Voom transformed RNAseq profiles from the tubulointerstitium of focal segmental glomeruloscerlosis


title: CLASH-CD4-invitro-d0_3

value: Descartes

value: Day 0


title: V295-Subgingival_S134

value: Subgingival sites

value: not provided


title: Focal Segmental Glomerulosclerosis [Sample_109]


title: CLASH-CD4-invitro-d48_2

value: Day 48


title: Focal Segmental Glomerulosclerosis [Sample_106]

value: Focal Segmental Glomerulosclerosis


title: CLASH-CD4-invitro-d41_2

value: Day 41


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 10

value: female

value: white

value: arm skin


title: V293-Subgingival_S51


title: V295-SalivaRNAL_S152

value: Saliva


title: Focal Segmental Glomerulosclerosis [Sample_105]

value: Tubulointerstitium from human kidney biopsy


title: Minimal Change Disease [Sample_104]

value: Minimal Change Disease


description: gene expression data from arm skin at 7 days after first laser session, participant 10

value: 7 days after first laser session


description: gene expression data from face skin at 7 days after first laser session, participant 10

value: face skin


title: V297-SalivaRNAL_S236


title: V293-SalivaRNAL_S15


title: Minimal Change Disease [Sample_108]


title: V289-Subgingival_S114


title: Minimal Change Disease [Sample_103]


title: Minimal Change Disease [Sample_102]

description: Voom transformed RNAseq profiles from the tubulointerstitium of human minimal change disease


title: V289-SalivaRNAL_S81


title: CLASH-CD4-invitro-d34_2

value: CD4 T cell

value: Homo sapiens

value: in vitro coculture

value: Day 34


title: CLASH-CD4-invitro-d27_2

value: Descartes

value: Day 27


title: CLASH-CD4-invitro-d20_2

value: Day 20


description: gene expression data from arm skin at 14 days after first laser session, participant 12

value: 14 days after first laser session


description: gene expression data from arm skin at 1 day after first laser session, participant 10

value: 1 day after first laser session


title: CLASH-CD4-invitro-d13_2

value: Day 13


title: arm skin at baseline, participant 10

description: gene expression data from arm skin at baseline, participant 10

value: female

value: white

value: baseline


title: V285-Subgingival_S37

value: Subgingival sites

value: not provided


description: gene expression data from arm skin at 7 days after first laser session, participant 12

value: arm skin

value: 7 days after first laser session


title: Focal Segmental Glomerulosclerosis [Sample_101]

value: Tubulointerstitium from human kidney biopsy

value: Focal Segmental Glomerulosclerosis


title: Minimal Change Disease [Sample_100]

value: Minimal Change Disease


description: gene expression data from face skin at 7 days after first laser session, participant 12

value: face skin


description: gene expression data from arm skin at 1 day after first laser session, participant 12


title: CLASH-CD4-invitro-d06_2

description:
Screen Readout
rawcounts_processed_deca05.txt
CLASH-Deca05

value: Descartes

value: CD4 T cell

value: Homo sapiens

value: in vitro coculture

value: Day 06


title: CLASH-CD4-invitro-d0_2

value: Day 0


title: V285-SalivaRNAL_S120

value: Saliva


title: V282-Subgingival_S97


title: CLASH-CD4-invitro-d48_1

value: Day 48


title: CLASH-CD4-invitro-d41_1

value: Day 41


title: Focal Segmental Glomerulosclerosis [Sample_10]

description: Not applicable


title: V278-Subgingival_S177

value: Subgingival sites


title: Focal Segmental Glomerulosclerosis [Sample_1]

description: Not applicable


title: face skin at baseline, participant 8

description: gene expression data from face skin at baseline, participant 8

value: female

value: white

value: baseline


title: V282-SalivaRNAL_S215

value: not provided


title: face skin at baseline, participant 12

description: gene expression data from face skin at baseline, participant 12


title: WT_wIAA_R2

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description: add IAA for 24hrs that CTCF were acute degraded

data_processing:
Paired-end 100-cycle sequencing was performed on NovaSeq6000 sequencer following the manufacturer’s instructions (Illumina). Raw reads were first trimmed using TrimGalore (v0.6.3) with parameters ‘--paired --retain_unpaired’
Filtered reads were then mapped to the Homo sapiens reference genome GRCm37.p13 using STAR (v2.7.9a). Gene-level read quantification was done using RSEM (v1.3.1)on the Gencode annotation v19
To identify the differentially expressed genes, normalization factors are first estimated using the trimmed mean of M values (TMM) and genes with CPM < 1 in all samples were removed
Next, the TMM normalization factors and raw counts were then used for the Limma-voom analysis using the “voom”, “lmFit” and “eBayes” functtions from the limma R package
Assembly: hg19
Supplementary files format and content: tsv

source_name: cell line

growth_protocol: CTCFAID2 cells were maintained in RPMI-1640 medium (Lonza) containing 10% fetal bovine serum (Hyclone), 2 mM glutamine (Sigma), and 1% penicillin/streptomycin (Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted from cells using Trizol (Thermo Fisher Scientific, 15596026) with the zymo RNA clean and concentrator kit 5 kit.
The QuantSeq 3’ RNA-Seq Library Prep Kit for Illumina (Lexogen) was used for library construction

treatment_protocol: CTCFAID2 cells were treated with 10uM 5-Ph-IAA (Med Chem Express) for 24 hours or 1uM 5-Ph-IAA for 4 and 7 days. SEMWT and CTCFAID1 cells treated with either DMSO or 500 mM IAA; 1 mg/ml Dox for 1 day, and CTCFAID2

value: SEM

value: IAA 24hrs


title: CLASH-CD4-invitro-d34_1

value: Day 34


title: V276-Subgingival_S126


title: WT_wIAA_R1


title: WT_noIAA_R2

description: no IAA

value: no IAA 24hrs


title: CLASH-CD4-invitro-d20_1

value: Descartes

value: CD4 T cell

value: Day 20


title: V278-SalivaRNAL_S5


title: face skin at baseline, participant 5

description: gene expression data from face skin at baseline, participant 5

value: face skin


title: V276-SalivaRNAL_S129


title: WT_noIAA_R1

description: no IAA


title: V275-Subgingival_S121


title: CTCFAID2-24hr-noIAA-R4

description: no IAA


title: V275-SalivaRNAL_S18


description: gene expression data from arm skin at 1 day after first laser session, participant 9

value: arm skin

value: 1 day after first laser session


title: CTCFAID2-24hr-noIAA-R3

description: no IAA


title: CLASH-CD4-invitro-d06_1

value: Homo sapiens

value: in vitro coculture

value: Day 06


title: CLASH-CD4-invitro-d0_1

value: Day 0


title: arm skin at baseline, participant 5

description: gene expression data from arm skin at baseline, participant 5

value: female

value: white


title: face skin at baseline, participant 10

description: gene expression data from face skin at baseline, participant 10

value: baseline


title: V273-Subgingival_S33

value: Subgingival sites

value: not provided


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 8


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 7


title: deca3_Plasmid

description:
Screen Readout
rawcounts_processed_deca0103.txt
CLASH-Deca0103

value: CD8 T cell


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 4


title: CTCFAID2-24hr-noIAA-R2

description: no IAA

value: SEM

value: no IAA 24hrs


title: CLASH-CD4-invitro-d27_1

value: Descartes

value: CD4 T cell

value: Day 27


title: V273-SalivaRNAL_S82

value: Saliva


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 5

value: arm skin


title: CLASH-CD4-invitro-d13_1

value: Homo sapiens

value: Day 13


title: V266-SalivaRNAL_S146


title: CTCFAID2-24hr-noIAA-R1

description: no IAA


title: deca3_day54_coculture_3

value: in vitro coculture

value: Day 54


title: V266-Subgingival_S59


title: CTCFAID2-24hr-1uM-5PHIAA-R4

value: IAA 24hrs


title: deca3_day41_coculture_3

value: Day 41


title: deca3_day32_coculture_3

value: Day 32


title: CTCFAID2-24hr-1uM-5PHIAA-R3


title: face skin at baseline, participant 9

description: gene expression data from face skin at baseline, participant 9

value: female

value: white

value: face skin

value: baseline


title: V265-Subgingival_S148

value: Subgingival sites

value: not provided


title: deca3_day20_coculture_3

value: Descartes

value: CD8 T cell

value: Day 20


description: gene expression data from arm skin at 7 days after first laser session, participant 4

value: arm skin

value: 7 days after first laser session


title: V265-SalivaRNAL_S60

value: Saliva


title: CTCFAID2-24hr-1uM-5PHIAA-R1

value: SEM


title: arm skin at baseline, participant 4

description: gene expression data from arm skin at baseline, participant 4


title: deca3_day16_coculture_3

value: Homo sapiens

value: in vitro coculture

value: Day 16


description: gene expression data from arm skin at 7 days after first laser session, participant 9


title: V263-Subgingival_S104


title: DeltaRBR_IAA_Rep2

description:
DeltaRBR_plus_Rep2
add IAA for 6hrs that CTCF were acute degraded

treatment_protocol: CTCFAID2 cells were treated with 10uM 5-Ph-IAA (Med Chem Express) for 24 hours or 1uM 5-Ph-IAA for 4 and 7 days.

value: IAA 6hrs


title: V263-SalivaRNAL_S139


title: DeltaRBR_noIAA_Rep2

description:
DeltaRBR_minus_Rep2
no IAA

value: no IAA


title: deca3_day13_coculture_3

value: Day 13


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 6

value: female

value: white


title: deca3_day9_coculture_3

value: Day 09


title: V262-Subgingival_S192

value: Subgingival sites

value: not provided


title: V262-SalivaRNAL_S230


title: deca3_day5_coculture_3

value: Descartes

value: CD8 T cell

value: Day 05


title: deca3_day54_coculture_2

value: Day 54


title: DeltaZ10_IAA_Rep2

description:
DeltaZ10_plus_Rep2
add IAA for 6hrs that CTCF were acute degraded


title: CTCFAID2-24hr-1uM-5PHIAA-R2

description: add IAA for 24hrs that CTCF were acute degraded

value: IAA 24hrs


title: V259-Subgingival_S287


title: DeltaZ1_IAA_Rep2

description:
DeltaZ1_plus_Rep2
add IAA for 6hrs that CTCF were acute degraded

value: SEM


description: gene expression data from arm skin at 14 days after first laser session, participant 7

value: arm skin

value: 14 days after first laser session


description: gene expression data from face skin at 7 days after first laser session, participant 7

value: face skin

value: 7 days after first laser session


title: DeltaZ1_noIAA_Rep2

description:
DeltaZ1_minus_Rep2
no IAA

value: no IAA


title: V259-SalivaRNAL_S283

value: Saliva


description: gene expression data from arm skin at 7 days after first laser session, participant 7

value: female


title: deca3_day32_coculture_2

value: Homo sapiens

value: in vitro coculture

value: Day 32


description: gene expression data from arm skin at 29 days after first laser session & 1 day after second laser session, participant 9

value: white


title: arm skin at baseline, participant 12

description: gene expression data from arm skin at baseline, participant 12

value: baseline


title: V258-Subgingival_S24

value: Subgingival sites

value: not provided


description: gene expression data from face skin at 7 days after first laser session, participant 8


description: gene expression data from arm skin at 14 days after first laser session, participant 8


title: WT_IAA_Rep2

description:
WT_plus_Rep2
add IAA for 6hrs that CTCF were acute degraded

value: IAA 6hrs


title: V258-SalivaRNAL_S255


title: DeltaZ10_noIAA_Rep2

description:
DeltaZ10_minus_Rep2
no IAA


title: deca3_day20_coculture_2

description:
Screen Readout
rawcounts_processed_deca0103.txt
CLASH-Deca0103

value: Descartes

value: CD8 T cell

value: Day 20


title: WT_noIAA_Rep2

description:
WT_minus_Rep2
no IAA

value: SEM


title: V257-Subgingival_S154


title: deca3_day16_coculture_2

value: Day 16


title: deca3_day13_coculture_2

value: Day 13


title: deca3_day41_coculture_2

value: Day 41


title: V257-SalivaRNAL_S26

value: Saliva


title: DeltaRBR_noIAA_Rep1

description:
DeltaRBR_minus_Rep1
no IAA

value: no IAA


title: DeltaRBR_IAA_Rep1

description:
DeltaRBR_plus_Rep1
add IAA for 6hrs that CTCF were acute degraded


title: face skin at baseline, participant 7

description: gene expression data from face skin at baseline, participant 7

value: female

value: face skin


title: deca3_day9_coculture_2

value: Homo sapiens

value: in vitro coculture

value: Day 09


title: V256-Subgingival_S86

value: Subgingival sites


description: gene expression data from arm skin at 14 days after first laser session, participant 6

value: white

value: arm skin

value: 14 days after first laser session


title: deca3_day0_coculture_2

value: Descartes

value: CD8 T cell

value: Day 0


description: gene expression data from arm skin at 14 days after first laser session, participant 4


title: V256-SalivaRNAL_S101

value: not provided


title: V253-Subgingival_S292


title: DeltaZ1_IAA_Rep1

description:
DeltaZ1_plus_Rep1
add IAA for 6hrs that CTCF were acute degraded

value: SEM

value: IAA 6hrs


title: V253-SalivaRNAL_S141

value: Saliva


title: DeltaZ1_noIAA_Rep1

description:
DeltaZ1_minus_Rep1
no IAA

value: no IAA


title: arm skin at baseline, participant 7

description: gene expression data from arm skin at baseline, participant 7

value: female

value: baseline


title: V251-Subgingival_S208


title: deca3_day54_coculture_1

value: Homo sapiens

value: Day 54


description: gene expression data from arm skin at 7 days after first laser session, participant 8

value: 7 days after first laser session


title: deca3_day41_coculture_1

value: in vitro coculture

value: Day 41


description: gene expression data from arm skin at 1 day after first laser session, participant 7

value: white

value: arm skin

value: 1 day after first laser session


title: WT_IAA_Rep1

description:
WT_plus_Rep1
add IAA for 6hrs that CTCF were acute degraded


title: WT_P2_8

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Assembly: ENCODE VM9
Supplementary files format and content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

organism: Danio rerio

source_name: whole kidney marrow (WKM)

growth_protocol: Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.

extract_protocol:
Three months old wild-type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral, midline incision was made and kidney were dissected and placed into ice-cold 0.9× PBS containing 5% FCS. Single-cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40-μm nylon mesh filter with a plunger from a 1-ml syringe.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: No Treatment was performed.

value: whole kidney marrow (WKM)

tag: age

value: 3 months

tag: genotype/variation

value: Wildtype WKM cells


title: V251-SalivaRNAL_S55

value: not provided

tag: donor id


title: arm skin at baseline, participant 8

description: gene expression data from arm skin at baseline, participant 8

tag: timepoint


description: gene expression data from arm skin at 1 day after first laser session, participant 8


title: WT_P2_7


title: DeltaZ10_IAA_Rep1

description:
DeltaZ10_plus_Rep1
add IAA for 6hrs that CTCF were acute degraded

value: SEM

value: IAA 6hrs


title: deca3_day20_coculture_1

value: Descartes

value: CD8 T cell

tag: cell species

value: Day 20


title: WT_P2_6


title: V250-Subgingival_S133

value: Subgingival sites


title: V250-SalivaRNAL_S294

value: Saliva


title: deca3_day5_coculture_2

value: Homo sapiens

value: Day 05


title: deca3_day16_coculture_1

value: in vitro coculture

value: Day 16


title: WT_P2_5


title: DeltaZ10_noIAA_Rep1

description:
DeltaZ10_minus_Rep1
no IAA

value: no IAA


title: deca3_day13_coculture_1

value: Day 13


title: CTCF-HiCHIP-IAA-6hrs-Replicate 2

description:
Rep.HiChIP_plusIAA6hr.bedpe.gz
add IAA for 6hrs that CTCF were acute degraded

data_processing:
For HiChIP, paired-end reads of 150bp were confirmed for enrichment of MboI ligation sites(GATCGATC) and trimmed for adapters by fastp (version 0.20.0, paired-end mode, parameter as “--detect_adapter_for_pe --trim_poly_x --cut_by_quality5 --cut_by_quality3 --cut_mean_quality 15 --length_required 20 --low_complexity_filter --complexity_threshold 30 ”). Then trimmed reads were processed by HiC-Pro (version 2.11.4) using human genome hg19 (GRC37 from GENCODE) and MboI fragment file(cut site GATC).
Bowtie2-2.2.4, samtools-1.2, R-3.4.0, Python-2.7.12 were configured for HiC-Pro. allValidPairs files from HiC-Pro pipeline were then used to generate .hic file for visualization.
Both our samples have 2 biological replicates with good depth (~150M pairs) and comparable metrics with the published data (GEO id:GSE80820) such as valid interaction rate (95.6% to 97.8% compared to GEO 78.65% to 80.53%).
After confirmation of reproducibility, contacts from replicates were merged and call loops using FitHiChIP(Stringent mode using Coverage for normalization) based on CTCF peaks from GSM3312803.
Assembly: hg19
Supplementary files format and content: bedpe for loops
Library strategy: HIChIP-Seq

growth_protocol: SEM (ACC-546, DSMZ) cells were maintained in RPMI-1640 medium (Lonza) containing 10% fetal bovine serum (FBS) (HyClone) and 1% penicillin/streptomycin (Thermo Fisher Scientific).

extract_protocol:
10 million SEM Cells were resuspended in 10mL fresh cell media, and crosslinked by 2% formaldhyde for 10 min with rotating at room temperature. Crosslinking  were quenched by glycine to a final concentration of 0.2M and incubating for 5 min with rotating at room temperature. Cells were washed once by 1 mL of cold PBS, flash-froze cell pellets in dry ice/ethanol bath and store at -80°C
HIChIP was performed as previously described in (Mumbach et. al. 2017) with the following modifications. 15 μl of 25U/μl MboI restriction enzyme (New England Biolabs, R0147M) was used for digesting chromatin from 10 million cells at 37°C for 2 hours with shaking. Proximity ligation was performed overnight at 16°C on Eppendorf thermomixer with 900rpm shaking speed. Post proximity ligated products were washed once by 1 mL of Covaris shearing buffer (10mM Tris-HCl pH8.0, 1mM EDTA, 0.1% SDS, 1x cOmplete EDTA-free protease inhibitor) and resuspended in 1mL Covaris shearing buffer then transfer to Covaris milliTUBE. Sonication was performed with Covaris LE220-plus with the following settings: Duty Cycle = 30%, PIP = 400, Cycles/Burst = 200, Dithering = x +- 0.5mm, Y +- 0.5mm, z +- 0.0mm, speed 10mm/s, pause duration 0.0 and time = 10min. 120 μl DiaMag protein G beads (diagenode, C03010021) were pre-blocked in ChIP dilution buffer plus 0.1% BSA overnight at 4°C. After Covaris shearing, add 3 mL ChIP dilution buffer plus protease inhibitor to 1 mL of sheared chromatin, then precleared with 60ul pre-blocked DiaMag protein G beads at 4°C for 1 hour. 8 μg of Diagenode CTCF antibody (C15410210-50, 2.3 μg/μl) was used for 10 million cells and rotated at 4 °C overnight. Another pre-blocked 60 μl DiaMag protein G beads were added next day and incubate at 4 °C for 3 hours. Post ChIP DNA was purified by Qiagen MinElute PCR Purification Kit, typically yield 2-11ng. HiChIP libraries were prepared using Kapa HyperPrep Kit (Roche, KK8502). 15 μl of Dynabeads MyOne Streptavidin T1 (Thermo Fisher, 65602) were used for biotin pull down. After end repair and A-tailing, 5 μl of Illumina TruSeq DNA UD Indexes were used for adaptor ligation at 20°C for 15min. Libraries were amplified for 12 to 13 PCR cycles (DNA>5ng: 12 cycles, DNA<5ng: 13 cycles).

treatment_protocol: CTCF-AID knockin SEM cells were treated with DMSO or 1uM 5-Ph-IAA (HY-134653, MedChemExpress)  for 6 hours.


title: CTCF-HiCHIP-IAA-6hrs-Replicate 1


title: V248-Subgingival_S251


title: deca3_day32_coculture_1

value: Day 32


title: WT_P1_4

value: whole kidney marrow (WKM)

value: 3 months


title: WT_noIAA_Rep1

description:
WT_minus_Rep1
no IAA


title: deca3_day9_coculture_1

value: Day 09


title: V248-SalivaRNAL_S160

value: not provided


title: CTCF-HiCHIP-noIAA-Replicate 2

description:
Rep.HiChIP_noIAA.bedpe.gz
no IAA

value: SEM

value: noIAA


title: WT_P1_3

value: Wildtype WKM cells


title: deca3_day5_coculture_1

value: Descartes

value: CD8 T cell


title: V241-Subgingival_S122

value: Subgingival sites


title: Kasumi1_Cinobufagin_100nM_2

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: HL60 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum. Kasumi-1 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 20% fetal bovine serum

extract_protocol:
Total RNA was collected using RNeasy Mini Kit (Qiagen)
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA)

treatment_protocol: HL60 cells were cultured with or without 100nM Cinobufagin. Kasumi-1 cells were cultured with or without 100nM Cinobufagin. Drug treatment duration is 24 hours

tag: cell line


title: WT_P1_2


title: CTCF-HiCHIP-noIAA-Replicate 1

description:
Rep.HiChIP_noIAA.bedpe.gz
no IAA


title: deca3_day0_coculture_1

value: Homo sapiens

tag: in vivo_model

value: Day 0


title: V241-SalivaRNAL_S250

value: Saliva


title: V240-Subgingival_S50


title: SEM_CTCF-AIDV2.0_24hr-R2

data_processing:
reads were processed using fastp v0.19.6 with optional parameters -l 51 --disable_trim_poly_g
De-indexed reads (fastq) were trimmed, mapped and processed with slamdunk v0.4.2, producing converted read counts and total read counts at the 3' UTR level (slamdunk all, with parameters -5 12 -m -rl 51 --skip-sam)
Counts were collapsed to gene level using slamdunk v0.4.2 command alleyoop collapse, with default parameters.
Converted read counts and total read counts were normalized using edgeR v3.24.3 (calcNormFactors, method = "TMM"), CPM<10 were filtered.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text file includes TMM normalized log2 counts per million
Library strategy: SLAM-Seq

source_name: SEM

growth_protocol: CTCFAID1 and CTCFAID2 cells were maintained in RPMI-1640 medium (Lonza) containing 10% fetal bovine serum (Hyclone), 2 mM glutamine (Sigma), and 1% penicillin/streptomycin (Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted from cells in a dark room using Trizol (Thermo Fisher Scientific, 15596026).  3ug RNA was used for thiol modification and then purified using the zymo RNA clean and concentrator kit.
The QuantSeq 3’ RNA-Seq Library Prep Kit for Illumina (Lexogen) was used for library construction

treatment_protocol: CTCFAID1 cells were treated with 500uM IAA (Sigma) and 1ug/ml Dox for 0, 2, 6, 12 and 24hrs.  CTCFAID2 cells were treated with 10uM 5-Ph-IAA (Med Chem Express) for 0, 2, 4, 6, 12 and 24 hours.  For all samples, 250uM 4SU was added to the medium 1hr before collection. After addition of 4SU, all handling was performed in the dark.

value: B-ALL

tag: genotype

value: WT


title: Kasumi1_Cinobufagin_100nM_1


title: WT_P1_1


title: IT325_P2_4

value: IT325 Mutant WKM cells


title: Kasumi1_Cinobufagin_0nM_2


title: V240-SalivaRNAL_S90


title: SEM_CTCF-AIDV2.0_24hr-R1

tag: time


title: IT325_P2_3


title: Kasumi1_Cinobufagin_0nM_1


title: SEM_CTCF-AIDV2.0_12hr-R2

tag: treatment


title: V238-Subgingival_S302


title: HL60_Cinobufagin_100nM_2


title: SEM_CTCF-AIDV2.0_12hr-R1

tag: cell type


title: V238-SalivaRNAL_S64

tag: tissue


title: IT325_P2_1


title: HL60_Cinobufagin_100nM_1


title: V237-Subgingival_S132


title: SEM_CTCF-AIDV2.0_6hr-R2


title: IT325_P1_9


title: HL60_Cinobufagin_0nM_2


title: V237-SalivaRNAL_S240


title: SEM_CTCF-AIDV2.0_6hr-R1


title: IT325_P1_12


title: SEM_CTCF-AIDV2.0_4hr-R2


title: HL60_Cinobufagin_0nM_1


title: IT325_P2_2


title: V236-Subgingival_S261


title: IT325_P1_11


title: V236-SalivaRNAL_S213


title: ChIP_Cinobufagin_100nM_K4me3

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.1.0.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
Duplication reads were removed from aligned file by using picard-tools-1.56.
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: HL60 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol: ChIP assay were performed using approximately 107 HL60 cells. Procedures were taken as reported previously[ A. Kaneda et al, PLoS Genet, 2011]. Antibodies against H3K4me3 (#ab8580, Abcam), H3K27ac (#39135, Active Motif) and Protein G-sepharose beads (GE Healthcare) were used. Chromatin-immunoprecipitated DNA was dissolved in EB buffer (Qiagen, Hilden, Germany). ChIP-seq Libraries were constructed using the KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer’s instructions and sequenced at a concentration of 1.5 pM on Illumina Nextseq500 platform (Illumina, San Diego, CA, USA).

treatment_protocol: HL60 cells were cultured with or without 100nM Cinobufagin.

value: acute myeloid leukemia


title: SEM_CTCF-AIDV2.0_2hr-R2


title: V235-Subgingival_S11

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed using cutadapter.
QIIME2.0 microbiome pipeline.
Centered log-ratio (CLR) transformation.
Assembly: hg38
Supplementary files format and content: *.genus.txt: Genus-level taxon datasets; CLR transformed values.
Library strategy: 16S RNA amplicon sequencing

extract_protocol:
DNA was isolated using a Zymo Research Quick-DNA Fecal/Soil Microbe Miniprep Kit (catalog D6010).
DNA libraries were prepared for sequencing using standard Illumina protocols.


title: IT325_P1_10

value: whole kidney marrow (WKM)


title: ChIP_Cinobufagin_100nM_K27ac


title: SEM_CTCF-AIDV2.0_4hr-R1


title: FR105_P2_8

value: 3 months

value: FR105 Mutant WKM cells


title: V235-SalivaRNAL_S22

value: not provided


title: SEM_CTCF-AIDV2.0_2hr-R1

value: SEM


title: ChIP_Cinobufagin_0nM_K4me3


title: FR105_P2_7


title: ChIP_Cinobufagin_0nM_K27ac


title: SEM_CTCF-AIDV2.0_0hr-R2

value: DMSO


title: V234-Subgingival_S217


title: FR105_P2_6


title: V234-SalivaRNAL_S74


title: MOLM13iCas9_sgCCNK_2_H3K36me3 ChIP-Seq

tag: vector

value: iCas9-puro;CCNK_2 sgRNA-tRFP657

tag: chip antibody

tag: stimulation

value: Doxycycline


title: FR105_P2_5


title: SEM_CTCF-AIDV1.0_24hr-R2


title: SEM_CTCF-AIDV2.0_0hr-R1


title: V233-Subgingival_S227


title: SEM_CTCF-AIDV1.0_12hr-R2


title: MOLM13iCas9_sgEmpty_H3K36me3 ChIP-Seq

value: iCas9-puro;Empty sgRNA-tRFP657


title: SETD1AKO_FKBP-SETD1A_dSET_dTAG_K36me3 ChIP-Seq


title: V233-SalivaRNAL_S128


title: FR105_P1_3


title: MOLM13iCas9_sgCCNK_1_H3K36me3 ChIP-Seq

value: iCas9-puro;CCNK_1 sgRNA-tRFP657


title: SEM_CTCF-AIDV1.0_6hr-R2


title: FR105_P1_2


title: SETD1AKO_FKBP-SETD1A_dSET_DMSO_K36me3 ChIP-Seq


title: V228-Subgingival_S179

value: Subgingival sites


title: SEM_CTCF-AIDV1.0_0hr-R2


title: SETD1AKO_FKBP-SETD1A_WT_dTAG_K36me3 ChIP-Seq


title: FR105_P1_1


title: FR105_P1_4


title: V227-Subgingival_S202


title: V227-SalivaRNAL_S76


title: SEM_CTCF-AIDV1.0_24hr-R1


title: SETD1AKO_FKBP-SETD1A_WT_DMSO_K36me3 ChIP-Seq


title: SEM_CTCF-AIDV1.0_12hr-R1


title: V228-SalivaRNAL_S277


title: SETD1AKO_FKBP-SETD1A_Empty_DMSO_K36me3 ChIP-Seq


title: Pou4f2_HA Rep2 Cut&Tag

city: Buffalo

first: Xiuqian

last: Mu

state: NY

address: 701 Ellicott Street

department: Ophthalmology

institute: University at Buffalo

description: Pou4f2_mergepeak_BAMPE2271_peaks.narrowPeak

data_processing:
Illumina RTA 2.2.68 Basecaller
Cellranger 3  mkoutput with Bcl2Fastq 2.20.0.422 and Cellranger-ATAC 1.1
Cellranger 3 and Cellranger-Atac 1.1 Count against mm10 genome to produce count matrix (h.5 format files, fragment tsv files, bam)
Seurat 4.0.1 used for marker gene analysis and visualization
Cut&Tag MACS2 Peak Calling -g mm using treatment and control (IgGRabbit) options
Feature Counts to DESeq2 for BULK-RNA analysis
Assembly: mm10
Supplementary files format and content: h5 File containing UMI corrected read counts, ATAC Fragment Files, narrowPeak peak calls from Cut&Tag
Library strategy: CUT&Tag

source_name: Mouse Retina

growth_protocol: Retinas with the desired genotypes at different developmental stages (E14.5, and E17.5) were collected in cold phosphate buffered solution (PBS) after timed mating. retinas were incubated in PBS with 100 μg/mL trypsin for 5 minutes at 37ºC and then triturated five times with a pipette. The soybean trypsin inhibitor was added to a final concentration of 100 μg/mL to stop digestion. Cells were collected by centrifugation at 500 g for 5 minutes, washed twice with PBS, and re-suspended in PBS. Cell sorting was performed on a BD FACS Fusion Cell Sorter. The viable and single cell events were selected for sorting through the forward and side scatter gates. The zsGreen signal was collected by a 488 laser with a 530/30 detector, and a 561 laser with a 582/15 detector was used to collect tdTomato expressing cells. The gating threshold for the fluorescence was set to relatively low levels to isolate cells that had just begun to express the two fluorescent proteins. The viability of purified cells was tested by trypan blue staining, and each sample had at least 80% of cells viable.

extract_protocol:
Nuclei isolation was performed following the protocol from 10X Genomics (CG000169). Briefly, 100,000-1,000,000 cells were collected by FACS and centrifuged at 300 g for 5 min at 4°C. Cell pellets were resuspended in 100 μl cold Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, 1%BSA), mixed by gently by pipetting then incubated for 2 min on ice. One milliliter of cold Wash Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1%BSA) was then added immediately and mixed by gentle pipetting. The cells were then spun down at 500 g for 5 min at 4°C, and resuspended in cold 1X Nuclei Buffer (10x Genomics, PN-2000153). The nuclei concentration and quality were determined with a hemocytometer.
scRNA-seq:  scRNA-seq was performed on 10X Chromium single cell platform using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1, in keeping with the manufacturer’s instructions (10X Genomics, CG000204). The sorted cells were loaded onto the 10X Genomics Chromium Controller targeting >5,000 cells per sample to generate scRNA-seq libraries. The quantity and quality of the libraries were evaluated by the Qubit Fluorometer and Agilent Fragment Analyzer. High-quality libraries were subsequently sequenced on a NovaSeq6000 sequencer (PE 26X100).
snATAC-seq:  scATAC-seq library preparation was performed following the protocol from 10X Genomics (CG000168 Rev B) using the Chromium Single Cell ATAC Reagent Kits (10X Genomics). The libraries were cleaned using SPRIselect reagent (Beckman Coulter). The quantity and quality of the libraries were evaluated by the Qubit Fluorometer and Agilent Fragment Analyzer. The libraries were subsequently sequenced on a NovaSeq6000 (PE50).
CUT&Tag:  The Cleavage Under Targets & Tagmentation (CUT&Tag) experiments were performed using reagents and following a protocol from EpiCypher.
scRNA-Seq (10 Genomics), snATAC-Seq (10 Genomics), CUT & Tag (Epicypher)

tag: antibody

value: rabbit, 3724, Cell Signaling

tag: strain

value: Mouse Retina

tag: developmental stage


title: SEM_CTCF-AIDV1.0_2hr-R2

value: B-ALL


title: Rabbit IgG Rep1 Cut&Tag (1st sequencing)

value: rabbit, SC-2027, Santa Cruz


title: Rabbit IgG Rep1 Cut&Tag (2nd sequencing)


title: SEM_CTCF-AIDV1.0_2hr-R1

value: WT


title: SETD1AKO_FKBP-SETD1A_dTAG_NELFe ChIP-Seq

value: NELFe (#ab170104, Abcam)


title: V224-Subgingival_S67

tag: condition


title: SETD1AKO_FKBP-SETD1A_DMSO_NELFe ChIP-Seq


title: Otx2 Rep1 Cut&Tag

description: Otx2_mergepeak_BAMPE2271_peaks.narrowPeak

value: rabbit, HPA000633, Sigma


title: V224-SalivaRNAL_S235

value: Saliva

tag: donor id


title: SETD1AKO_FKBP-SETD1A_dTAG_SPT5 ChIP-Seq

value: SPT5 (#65689, Active Motif)


title: SETD1AKO_FKBP-SETD1A_Empty_dTAG_K36me3 ChIP-Seq


title: V223-Subgingival_S241

value: not provided


title: SETD1AKO_FKBP-SETD1A_DMSO_SPT5 ChIP-Seq


title: V225-Subgingival_S310


title: SETD1AKO_FKBP-SETD1A_dTAG_CTDpY1

value: CTDpY1 (#61383, Active Motif)


title: SETD1AKO_FKBP-SETD1A_DMSO_CTDpY1

value: DMSO


title: SETD1AKO_FKBP-SETD1A_dTAG_PAF1 ChIP-Seq

value: PAF1 (#ab20662, Abcam)


title: Isl1 Rep2 Cut&Tag (1st sequencing)

description: Isl1_mergepeak_qval0.2_BAMPE2271_peaks.narrowPeak

value: rabbit, AB4326, Millipore


title: SEM_CTCF-AIDV1.0_6hr-R1

value: SEM


title: V225-SalivaRNAL_S95


title: anti-PRDM1, exon3 skip PRDM1, replicate 2

first: Ryan

middle: D

last: Chow

description: Cut&Run with PRDM1 antibody (CST), on CD22-CAR-T cells with PRDM1cr1 (exon3 skip mutant)

data_processing:
CUT & RUN fastq sequencing data were analyzed according to a previously published protocol, with some modifications. Raw fastq files were first trimmed and cleaned using Trimmomatic  and Kseq. Cleaned fastq reads were then separately aligned to the human genome (hg38.p13) and the E. coli genome (GCF_000005845.2) using BWA mem with settings -M -t 8 -K 10000000.
Peaks were called from the hg38 BAM alignment files using MACS2 callpeak, comparing each experimental sample to each IgG control. The resulting peaks for a given sample were then merged with BEDTools. These peaks were then further merged, combining the peaks  from each biological condition (vector or PRDM1-cr1).
To define genes that are bound by PRDM1, we annotated the peak calls from the vector-treated samples using HOMER, assigning  each peak to the closest TSS (<=2.5kb). Overlaps between PRDM1-bound genes and DEGs were assessed by hypergeometric test, assuming 20,465 total human genes.
The number of aligned reads to each genome were then determined in order to calculate library scaling factors, as described in the EpiCypher CUTANA user manual. Specifically, the hg38- aligned read counts were scaled such that the reads aligned to the spike-in E. coli genome would be normalized across samples. The scaling factors were used to generate normalized bedgraph files, which were then converted into bigWig files. Replicate IgG control bigWig files were averaged by wiggleTools to create a single IgG control sample. Finally, signal visualization was performed using deepTools and Gviz.
Assembly: hg38.p13
Supplementary files format and content: .bw: bigWig normalized signal tracks. XDCut_Run01.mergedControl.bw contains the average signal for all 3 IgG replicates
Supplementary files format and content: .bed: *.200flank.bed has the MACS2 peak summits with surrounding 200bp. Sample5_7.MACS.merged.bed and Sample12_13.MACS.merged.bed are the merged peaks from Sample5+7 and Sample12+13, respectively.
Library strategy: Cut & Run

source_name: primary CD8 T cells

extract_protocol:
Vector CAR-T cells and PRDM1cr1 exon3-skip mutant CAR-T cells were FACS isolated, and CUT & RUN was performed following the EpiCypher CUTANA user manual. Briefly, 1 × 106 CAR-T cells were washed with cold PBS and resuspended in nuclei isolation buffer (100mM Hepes-KOH PH7.6, 100mM KCl, 5mM Mgcl2, 0.5% NP40 supplemented with Roche complete protease inhibitor) and incubated on ice for 10 min. Nuclei were washed twice with CUT & RUN wash buffer and incubated with activated concanavalin-A (ConA) beads for 10 min at RT. ConAbead- bound nuclei were incubated overnight at 4°C in CUT & RUN antibody buffer and antibodies including anti-Blimp1/PRDM1 (CST#9115), anti-H3K4me3 (positive control) and Rabbit IgG (negative control) antibodies. After antibody incubation, ConA-bead-bound nuclei were washed once with Cell Permeabilization Buffer then incubated with 2.5μL pAG-MNase for 10 min at RT. ConA-bound-nuclei were then washed twice with Cell Permeabilization Buffer. Targeted chromatin was digested and released by adding 1ul 100mM CaCl2 and incubated on ice for 2h. The reaction was stopped by addition of 33μl stop buffer.
1ul E. coli Spike-in DNA was added to each sample as internal control. DNA fragments were purified by using DNA cleanup columns. CUT & RUN sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primer Set 1 and 2). Library fragment size was analyzed by TapeStation (Agilent). The pass-QC libraries were sequenced on Illumina NovaSeq 150-bp paired-end reads.

value: primary CD8 T cells

value: pXD60-PRDM1cr1 AAV& Cpf1 mRNA


title: Otx2 Rep2 Cut&Tag


title: anti-PRDM1, exon3 skip PRDM1, replicate 1


title: SEM_CTCF-AIDV1.0_0hr-R1


title: V222-SalivaRNAL_S271


title: SETD1AKO_FKBP-SETD1A_dTAG_CTDpS2 ChIP-Seq

value: CTDpS2 (Cell Signaling)


title: Atoh7_HA Rep1 Cut&Tag

description: Atoh7HA_mergepeak_BAMPE2271_peaks.narrowPeak

value: rabbit, 3724, Cell Signaling

value: Mouse Retina


title: Isl1 Rep1 Cut&Tag


title: Atoh7_HA Rep2 Cut&Tag


title: V219-Subgingival_S123

value: Subgingival sites


title: SETD1AKO_FKBP-SETD1A_DMSO_CTDpS2 ChIP-Seq


title: SETD1AKO_FKBP-SETD1A_DMSO_PAF1 ChIP-Seq


title: V222-Subgingival_S189


title: Isl1 Rep2 Cut&Tag (2nd sequencing)