title: Whole Blood, ID9, M5, Booster, Baseline

value: female


title: HiC GN, ctrl, FANS, IVE+day8, rep1

status: Public on Jul 21 2026

type: SRA

city: Evanston

first: Yue

last: Yang

state: IL

address: 2200 Campus Dr

department: Neurobiology

country: USA

institute: Northwestern University

description: Library name: Hi-C_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_1

library_source: genomic

data_processing:
Hi-C reads were aligned to the mm10 reference genome with Bowtie2 and HiC-Pro. Uniquely mapped paired-end reads were assigned to MboI restriction fragments and valid pairs with a minimum genomic distance of 1Kb were filtered for PCR duplicates. Interaction matrices were normalized using Knight-Ruiz (KR) matrix balancing and observed divided by expected (o/e) transformation and visualized using hic files in Juicebox
Assembly: mm10
Supplementary files format and content: hic files

molecule: genomic DNA

organism: Mus musculus

source_name: cerebellum

extract_protocol:
The cerebellum from postnatal day 6 or 22 mice or cerebellar vermis from mice at day 1 to 28 after electroporation were removed and microdissected. For electroporated samples, electroporation efficiency was assessed under a stereomicroscope and mCherry+/NeuN+ nuclei were enriched using fluorescence activated nuclei sorting with a SH800S cell sorter (Sony). The genomic DNA was digested with MboI and re-ligated after the biotin fill-in reaction, followed by sonication. The fragmented DNA was then subjected to biotin-IP.
Hi-C libraries were prepared with the NEBNext Ultra™ II DNA Library Prep Kit (#E7645).

treatment_protocol: For in vivo electroporation (IVE), the cerebellum of P6 mouse pups was electroporated with the pCAG-mCherry-NLS plasmid together with a vector encoding U6-sgRNA targeting the indicated genes or control sequences and dissected at day 1 to 28 after electroporation.

tag: tissue

value: cerebellum

tag: cell type

value: granule neurons

tag: genotype

value: ctrl sgRNAs in dCas9-KRAB


title: K562_NPAT_KASCnT_IP_G1_Rep2_(250411_WW_Hs_WW1610)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Library name: K562_NPAT_KASCnT_IP_G1_Rep2
KAS-CUT&Tag IP targeting NPAT in K562 G1 cells

data_processing:
1. We used cutadapt 4.4 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.5.7 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.17 "view" to extract properly paired reads from the alignments.
4. We used bedtools 2.30 "genomecov" to make a normalized count track which is the fraction of counts at each base pair scaled by the size of the reference sequence so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

organism: Homo sapiens

extract_protocol:
CUT&Tag-direct for whole cells with CUTAC  V.4 dx.doi.org/10.17504/protocols.io.x54v9mkmzg3e/v4
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: antibody

value: Invitrogen, PA565419


title: Whole Blood, ID2, D2, Vaccine, 2hour

city: Hamilton

first: Vincent

last: Munster

state: Montana

department: NIAID

institute: NIH

description: Library name: VA0000160029

library_source: transcriptomic

data_processing:
Bulk RNA-seq FASTQ files were processed using the OpenOmics/RNA-seek (https://doi.org/10.5281/zenodo.13312679) v1.9.5 pipeline to run QC and quantify gene transcript counts.
Assembly: GRCh38
Supplementary files format and content: RSEM counts

molecule: polyA RNA

source_name: Whole Blood

extract_protocol:
Whole blood RNA was isolated from PAXgene tubes for 221 study samples using the QIAsymphony PAXgene Blood RNA Kit and the QIAsymphony SP instrument (both Qiagen) according to the manufacturer instructions including DNase I digestion and Proteinase K treatment.  RNA concentration was determined by Quant-iT RiboGreen assay (ThermoFisher) using a Biotek Synergy H1 plate reader (Agilent Technologies) and RINs assessed using Agilent 4200 TapeStation (Agilent).
RNA-seq libraries were prepared from 500 ng of total RNA using Universal Plus mRNA-seq Kit with NuQuant Human Globin AnyDeplete kit (Tecan Genomics) on a Biomek Fx robot (Beckman). First, messenger RNA transcripts were captured, fragmented, and converted to complementary DNA. Following second-strand synthesis and end repair, DNA fragments were ligated with dual-indexed adapters compatible with the Illumina platform. Libraries were subjected to strand selection and removal of globin transcripts, followed by 14 cycles of amplification. Purified libraries were analyzed with the Biotek Synergy H1 plate reader and Agilent 4200 TapeStation (Agilent Technologies) to assess concentration and size distribution, respectively, then normalized and pooled for sequencing. Final molarity of the pool was determined by quantitative polymerase chain reaction using the KAPA library quantification kit (Roche). Paired-end sequencing was performed on the NextSeq 2000 (Illumina) using P3 300 cycles kits in 2 × 150-base pair (bp) format.

value: Whole Blood

tag: individual

tag: Sex

tag: age

tag: treatment

value: Vaccine

tag: time

value: Day 2

tag: timepoint

value: 2 hour

tag: reaction type

tag: reaction type_severity

tag: batch


title: HiC GN, ctrl, FANS, IVE+day7, rep1

description: Library name: Hi-C_ctrl-FANS_IVEd7-dCas9_KRAB-pnd13_1


title: K562_NPAT_KASCnT_IP_G1_Rep1_(250411_WW_Hs_WW1609)

description:
Library name: K562_NPAT_KASCnT_IP_G1_Rep1
KAS-CUT&Tag IP targeting NPAT in K562 G1 cells


title: Whole Blood, ID2, D1/D2, Placebo/Vaccine, 24hour/Baseline

description: Library name: VA0000150029

value: Placebo/Vaccine

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/None

value: Moderate/None


title: HiC GN, ctrl, FANS, IVE+day4, rep2

description: Library name: Hi-C_ctrl-FANS_IVEd4-dCas9_KRAB-pnd10_2


title: Whole Blood, ID9, D2, Vaccine, 6hour

type: protein

hyb_protocol: Hybridization protocol done in accordance with SomaLogic standard operating procedures and best practices.

scan_protocol: The SomaScan Assay was performed on a Tecan Fluent 780 high throughput automation system according to manufacturer’s instructions. Assay data were normalized using SomaLogic’s standard procedure utilizing adaptive normalization by maximum likelihood (Candia, JPR, 2024 (PMID: 39473295)).

data_processing: Protein abundancy was quantified expressed as Relative Fluorescence Units (RFU) and log2 transformed for comparison analysis. Comparison of each timepoint to the baseline for each reaction separately, or comparisons of the groups with reactions to the vaccine to the no-reaction group at each timepoint were completed in R v4.4.2 using R packages lmerTest v3.1-3 and emmeans v1.10.7 to create a linear mixed effects model using the Satterthwaite approximation. Models were set up as an interaction of response and timepoint while blocking on individual group.  Adjusted p-values calculated using Bonferroni correction did not indicate changes with p<0.05 due to the small sample size and thus p-value was used instead of the adjusted p-value.

label: SOMAmer reagents

molecule: protein

source_name: peripheral blood serum

label_protocol: Label protocol done in accordance with SomaLogic standard operating procedures and best practices.

extract_protocol: Blood samples were collected before (baseline or time 0) the second vaccine dose or placebo injections, and 35 min, 2 h, 6 h and 24 h following injections.  For the vaccine booster, samples were obtained before, 35 min and 2 h after the dose. Blood samples were collected using serum separator tubes (BD Biosciences) for high throughput proteomic analysis using the SomaScan platform (SomaLogic).

tag: day

value: 6 hour

tag: reaction type severity


title: K562_NPAT_KASCnT_Input_G1_Rep2_(250411_WW_Hs_WW1634)

description:
Library name: K562_NPAT_KASCnT_Input_G1_Rep2
KAS-CUT&Tag input targeting NPAT in K562 G1 cells


title: Whole Blood, ID2, D1, Placebo, 6hour

description: Library name: VA0000140037

value: Placebo

value: Day 1

value: ISRR

value: Moderate


title: Hydra vulgaris (AEP), siAb1, rep2

city: Innsbruck

first: Birgit

last: Lengerer

address: Technikerstr. 25

country: Austria

institute: University of Innsbruck

description: Library name: siAb1_rep2

data_processing:
Sequencing reads were aligned to the Hydra vulgaris AEP (PMID: 36639202) reference genome using the Minimap2 aligner (version 2.28).
The BAM files were aligned using the Hydra AEP Genome Project Portal assembly provided by the NHGRI Hydra portal (https://research.nhgri.nih.gov/HydraAEP/). This corresponds directly to the NCBI assembly accession GCA_024232925.2.
Read counting and differential gene expression analysis was performed with the Rsubread (version 2.22.1) and edgeR (version 4.6.3) packages in R (version 4.5.0).
Assembly: Hydra vulgaris AEP (PMID: 36639202); GCA_024232925.2
Supplementary files format and content: counts.txt: tab delimited count matrix file with gene identifier in first column.
Supplementary files format and content: The sequence identifiers present in our processed data (e.g., HVAEP1.G000001) are the official gene model identifiers derived from the GFF3 annotation provided by the NHGRI group for the Hydra AEP Genome Project. These identifiers are fully traceable and searchable in a public database. They can be queried directly via the official NHGRI Hydra AEP Gene Wiki search engine at:
Supplementary files format and content: https://research.nhgri.nih.gov/HydraAEP/genewiki/

organism: Hydra vulgaris

source_name: Whole animal

growth_protocol: Hydra vulgaris (AEP) grown asexually at 18°C in Hydra medium and fed with Artemia nauplii.

extract_protocol:
RNA was isolated with Monarch® Total Miniprep Kit (New England BioLabs) according to manufacturers protocoll
Library preparation, sequencing and gene expression analysis were performed at the company XPseq Analytics GmbH (Austria) using their ExpressoSeq rapid 3' RNA-Seq service

treatment_protocol: Budless Hydra vulgaris (AEP) were electroporated with a square pulse of 250 V and 25 ms in a Gene Pulser X cellTM (Biorad). Immediately after electroporation precooled recovery medium was added and the polyps were gently transferred to a Petri dish prefilled with cooled recovery medium. After 24 hours the polyps were transferred from recovery medium to Hydra medium. Electroporation was performed on 0, 2, and 4 days past electroporation (dpe).  Animals were fed four times (7, 8, 9 and 14 dpe). Basal discs were amputated at 10dpe and animals allowed to regenerate. RNA was isolated at 15dpe.

value: Whole animal

value: AEP

value: siRNA against Ab1


title: HiC GN, ctrl, FANS, IVE+day4, rep1

description: Library name: Hi-C_ctrl-FANS_IVEd4-dCas9_KRAB-pnd10_1

value: cerebellum

value: granule neurons

value: ctrl sgRNAs in dCas9-KRAB


title: Whole Blood, ID9, D2, Vaccine, 2hour

value: female

value: Vaccine

value: Day 2

value: 2 hour


title: AB13834

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Sample1528
MARS_v2

data_processing:
bcl2fastq
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used (most samples) i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Samples467 up to Samples733 Pool-barcode used is 5N (random) + 4N (Pool barcode) On R1 1 humming error was allowed. Well-barcode N7 folowed by UMI N8 in read 2.
Samples 259, 295, 297, 299, 232 and 234 Utilized a 9 Nucleotide cell barcode and compose of 768 cells per sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cells_annotation_for_geo_ver_20250306.xlsx

source_name: BM

extract_protocol:
BM aspirates were collected from the posterior iliac crest into EDTA-coated tubes (BD Biosciences), diluted 1:1 with ice-cold FACS buffer (PBS supplemented with 2 mM EDTA, pH 8.0, and 0.5% bovine serum albumin), and maintained on ice. Samples were immediately transported to the laboratory for downstream processing and single-cell analysis.
mRNA from cells sorted into barcoded cell capture plates and converted into cDNA, later pooled by using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina adapters during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration was assessed as described earlier. Overall, barcoding was done in three levels: Cell barcodes allow attribution of each sequence read to its cell of origin, thus enabling pooling; Unique Molecular Identifiers (UMIs) allow tagging each original molecule to avoid amplification bias; and plate barcodes allow elimination of the batch effect.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

value: BM

tag: gate

value: PC


title: HiC GN, ctrl, FANS, IVE+day2, rep2

description: Library name: Hi-C_ctrl-FANS_IVEd2-dCas9_KRAB-pnd8_2


title: Whole Blood, ID9, D2, Vaccine, 35min

value: 35 min


title: Whole Blood, ID2, D1, Placebo, 35min

description: Library name: VA0000120029

value: Whole Blood

value: Placebo


title: K562_RPB1_KASCnT_IP_G2_Rep2_(250411_WW_Hs_WW1564)

description:
Library name: K562_RPB1_KASCnT_IP_G2_Rep2
KAS-CUT&Tag IP targeting RPB1 in K562 G2 cells


title: Hydra vulgaris (AEP), siLb1, rep2

description: Library name: siLb1_rep2

value: siRNA against Lb1


title: Whole Blood, ID9, D1/D2, Placebo/Vaccine, 24hour/Baseline

value: Placebo/Vaccine

value: Day 1/Day 2

value: 24 hour/Baseline

value: None/None


title: HiC GN, ctrl, FANS, IVE+day2, rep1

description: Library name: Hi-C_ctrl-FANS_IVEd2-dCas9_KRAB-pnd8_1

value: cerebellum


title: K562_RPB1_KASCnT_IP_G2_Rep1_(250411_WW_Hs_WW1563)

description:
Library name: K562_RPB1_KASCnT_IP_G2_Rep1
KAS-CUT&Tag IP targeting RPB1 in K562 G2 cells


title: Whole Blood, ID9, D1, Placebo, 6hour

value: Day 1

value: 6 hour


title: HiC GN, ctrl, FANS, IVE+day1, rep1

description: Library name: Hi-C_ctrl-FANS_IVEd1-dCas9_KRAB-pnd7_1

value: granule neurons

value: ctrl sgRNAs in dCas9-KRAB


title: Patient 063,C3D1, PBMC, RNAseq

city: Los Angeles

first: Lu

last: Sun

state: California

address: 10833 Le Conte Avenue

institute: University of California, LA

description:
Library name: P063-C3D1
RNA-seq of patients' PBMCs

data_processing:
Paired-end, 2 × 100 base pair (bp) transcriptome reads were mapped to the Genome Reference Consortium Human Build 38 (GRCh38) reference genome using HISAT2 (version 2.0.6)
The gene level counts were generated by the HTSeq-count program (version 0.5.4p5)
We utilized the edgeR (version 3.40.2) R package's cpm() function to compute the normalized gene expression values from the raw gene expression counts. These normalized expression values were log2 transformed after adding a pseudo count of 1.
Assembly: GRCh38
Supplementary files format and content: Gene level raw counts of each sample as computed by htseq-count (tab delimited)

molecule: total RNA

source_name: PBMC

extract_protocol:
RNA and genomic DNA were extracted from resected tumor specimens preserved in AllProtect tissue reagent (Qiagen) at the time of surgery. We divided the tumor tissue in half and employed the Qiagen RNeasy Mini Kit (#74104) for RNA isolation and the Qiagen DNeasy Blood and Tissue Kit (#69504) for DNA isolation. Total RNA from PBMCs was extracted using the Qiagen RNeasy Mini Kit.
TruSeq RNA exome kit is used to construct the RNA sequencing libraries

value: PBMC

value: nivolumab+ipilimumab trial

tag: arm

value: Female

tag: ethnicity

value: Non-Hispanic

tag: os


title: Patient 063,C2D1, PBMC, RNAseq

description:
Library name: P063-C2D1
RNA-seq of patients' PBMCs

tag: tissue


title: K562_RPB1_KASCnT_Input_G2_Rep2_(250411_WW_Hs_WW1588)

description:
Library name: K562_RPB1_KASCnT_Input_G2_Rep2
KAS-CUT&Tag input targeting RPB1 in K562 G2 cells

tag: cell type

tag: antibody


title: Whole Blood, ID9, D1, Placebo, 2hour

tag: individual

tag: Sex

value: female

value: 2 hour


title: H3K27ac ChIP-seq GN, ubash3b eKD, FANS, IVE+day8, rep3

description: Library name: H3K27ac_ChIP_ubash3beKD-FANS_IVEd8-dCas9_KRAB-pnd14_3

data_processing:
ChIP-seq reads were aligned to the mm10 reference genome with Bowtie2 using the public server at https://usegalaxy.org/, normalized by library size, and visualized using bigwig files. Peak calling was performed using MACS2 and those overlapping with the ENCODE blacklist were removed. H3K27ac peaks >2 kb distal to H3K4me3-marked TSSs were considered as enhancers.
Assembly: mm10
Supplementary files format and content: bigwig files

extract_protocol:
Cerebella were removed and microdissected. For electroporated samples, electroporation efficiency was assessed under a stereomicroscope and mCherry+/NeuN+ nuclei were enriched using fluorescence activated nuclei sorting with a SH800S cell sorter (Sony). Lysates were sonicated, and protein-DNA complexes were isolated using the indicated antibodies.
Brd4 ChIP-seq libraries were prepared by tagmentation and with the NEB Q5® Hot Start High-Fidelity 2X Master Mix (M0494S). H3K27ac ChIP-seq libraries were prepared with the NEBNext Ultra™ II DNA Library Prep Kit (#E7645).

treatment_protocol: For in vivo electroporation (IVE), the cerebellum of P6 mouse pups was electroporated with the pCAG-mCherry-NLS plasmid together with a vector encoding U6-sgRNA targeting the indicated genes or control sequences and dissected at day 4, 8, or 14 after electroporation

tag: genotype

value: ubash3b enhancer sgRNAs in dCas9-KRAB

tag: chip antibody

value: H3K27ac (Abcam ab4729)


title: K562_RPB1_KASCnT_Input_G2_Rep1_(250411_WW_Hs_WW1587)

description:
Library name: K562_RPB1_KASCnT_Input_G2_Rep1
KAS-CUT&Tag input targeting RPB1 in K562 G2 cells


title: H3K27ac ChIP-seq GN, ubash3b eKD, FANS, IVE+day8, rep2

description: Library name: H3K27ac_ChIP_ubash3beKD-FANS_IVEd8-dCas9_KRAB-pnd14_2


title: Plasma, no Bleeding, Stroke, id188

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

institute: TAmiRNA GmbH

data_processing:
fastQC quality assessment
cutadapt adater trimming
bowtie1 genome alignment
miRDeep2 miRNA quantification (mirbase)
bowtie1 RNAcentral mapping
gtRNAdb based tRNA quantification
Assembly: GRCh38.p12
Assembly: RNAcentral version: v19.0
Assembly: mirBase version: v22.1
Supplementary files format and content: csv with tRNA quantifications (raw count)
Supplementary files format and content: csv with miRNA quantifications (raw count)

source_name: Plasma

extract_protocol:
Total RNA was isolated using the miRNeasy kit (Qiagen)
Small RNA libraries were prepared using the RealSeq Somagenics kit

value: Plasma

tag: major bleeding

tag: stroke

value: Stroke


title: K562_RPB1_KASCnT_IP_S_Rep2_(250411_WW_Hs_WW1558)

description:
Library name: K562_RPB1_KASCnT_IP_S_Rep2
KAS-CUT&Tag IP targeting RPB1 in K562 S cells


title: Whole Blood, ID9, D1, Placebo, Baseline

tag: age

tag: treatment

value: Placebo

tag: timepoint

value: Baseline

tag: reaction type


title: H3K27ac ChIP-seq GN, ubash3b eKD, FANS, IVE+day8, rep1

description: Library name: H3K27ac_ChIP_ubash3beKD-FANS_IVEd8-dCas9_KRAB-pnd14_1

value: cerebellum


title: Whole Blood, ID1, D2, Placebo, 24hour

description: Library name: VA0000090027

value: Whole Blood

tag: time

value: Day 2

value: 24 hour

value: ISRR

tag: reaction type_severity

value: Severe

tag: batch


title: H3K27ac ChIP-seq GN, slc8a1 eKD, FANS, IVE+day8, rep2

description: Library name: H3K27ac_ChIP_slc8a1eKD-FANS_IVEd8-dCas9_KRAB-pnd14_2

value: granule neurons

value: slc8a1 enhancer sgRNAs in dCas9-KRAB


title: Whole Blood, ID8, M5, Booster, 2hour

value: Booster

tag: day

value: Month 5

tag: reaction type severity

value: Mild


title: K562_RPB1_KASCnT_Input_S_Rep2_(250411_WW_Hs_WW1582)

description:
Library name: K562_RPB1_KASCnT_Input_S_Rep2
KAS-CUT&Tag input targeting RPB1 in K562 S cells

tag: cell type


title: Whole Blood, ID1, D2, Placebo, 6hour

description: Library name: VA0000080014

tag: tissue

value: female

value: 6 hour


title: Whole Blood, ID8, M5, Booster, 35min

tag: individual

value: 35 min


title: H3K27ac ChIP-seq GN, slc8a1 eKD, FANS, IVE+day8, rep1

description: Library name: H3K27ac_ChIP_slc8a1eKD-FANS_IVEd8-dCas9_KRAB-pnd14_1

value: H3K27ac (Abcam ab4729)


title: K562_RPB1_KASCnT_Input_S_Rep1_(250411_WW_Hs_WW1581)

description:
Library name: K562_RPB1_KASCnT_Input_S_Rep1
KAS-CUT&Tag input targeting RPB1 in K562 S cells

tag: antibody


title: Whole Blood, ID8, M5, Booster, Baseline

tag: Sex


title: K562_RPB1_KASCnT_IP_G1_Rep2_(250411_WW_Hs_WW1606)

description:
Library name: K562_RPB1_KASCnT_IP_G1_Rep2
KAS-CUT&Tag IP targeting RPB1 in K562 G1 cells


title: Whole Blood, ID1, D2, Placebo, 2hour

description: Library name: VA0000070014

value: Placebo

value: 2 hour


title: H3K27ac ChIP-seq GN, etv1 KD, FANS, IVE+day8, rep3

description: Library name: H3K27ac_ChIP_etv1KD-FANS_IVEd8-dCas9_KRAB-pnd14_3

value: cerebellum

tag: genotype

value: etv1 sgRNAs in dCas9-KRAB

tag: chip antibody


title: Whole Blood, ID8, D2, Placebo, 24hour

value: Day 2

value: VeryMild


title: Whole Blood, ID1, D2, Placebo, 35min

description: Library name: VA0000050014

value: Whole Blood

value: ISRR


title: K562_RPB1_KASCnT_IP_G1_Rep1_(250411_WW_Hs_WW1605)

description:
Library name: K562_RPB1_KASCnT_IP_G1_Rep1
KAS-CUT&Tag IP targeting RPB1 in K562 G1 cells


title: Whole Blood, ID1, D1/D2, Vaccine/Placebo, 24hour/Baseline

description: Library name: VA0000040014

value: Vaccine/Placebo

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/ISRR

value: Mild/Severe


title: K562_NPAT_KASCnT_Input_G1_Rep1_(250411_WW_Hs_WW1633)

description:
Library name: K562_NPAT_KASCnT_Input_G1_Rep1
KAS-CUT&Tag input targeting NPAT in K562 G1 cells

value: Invitrogen, PA565419


title: Whole Blood, ID2, D1, Placebo, 2hour

description: Library name: VA0000130029

value: female

value: Day 1

value: Moderate


title: H3K27ac ChIP-seq GN, etv1 KD, FANS, IVE+day8, rep2

description: Library name: H3K27ac_ChIP_etv1KD-FANS_IVEd8-dCas9_KRAB-pnd14_2

value: granule neurons

value: H3K27ac (Abcam ab4729)


title: H3K27ac ChIP-seq GN, etv1 KD, FANS, IVE+day8, rep1

description: Library name: H3K27ac_ChIP_etv1KD-FANS_IVEd8-dCas9_KRAB-pnd14_1

value: cerebellum


title: Whole Blood, ID8, D2, Placebo, 6hour

value: Placebo

value: 6 hour


title: Whole Blood, ID1, D1, Vaccine, 6hour

description: Library name: VA0000030014

value: Vaccine

value: Mild


title: K562_RPB1_KASCnT_Input_G1_Rep2_(250411_WW_Hs_WW1630)

description:
Library name: K562_RPB1_KASCnT_Input_G1_Rep2
KAS-CUT&Tag input targeting RPB1 in K562 G1 cells


title: H3K27ac ChIP-seq GN, brd4 KD, FANS, IVE+day8, rep2

description: Library name: H3K27ac_ChIP_brd4KD-FANS_IVEd8-dCas9_KRAB-pnd14_2

value: brd4 sgRNAs in dCas9-KRAB


title: K562_RPB1_KASCnT_Input_G1_Rep1_(250411_WW_Hs_WW1629)

description:
Library name: K562_RPB1_KASCnT_Input_G1_Rep1
KAS-CUT&Tag input targeting RPB1 in K562 G1 cells


title: Whole Blood, ID8, D2, Placebo, 2hour

value: Day 2

value: 2 hour

value: ISRR

value: VeryMild


title: Whole Blood, ID1, D1, Vaccine, 2hour

description: Library name: VA0000020014

value: Whole Blood


title: Whole Blood, ID8, D2, Placebo, 35min

value: 35 min


title: H3K27ac ChIP-seq GN, brd4 KD, FANS, IVE+day8, rep1

description: Library name: H3K27ac_ChIP_brd4KD-FANS_IVEd8-dCas9_KRAB-pnd14_1


title: HEK293T_TFIISKO_PolIISer2p_KASCnT_IP_Rep2_(250411_WW_Hs_WW1604)

description:
Library name: HEK293T_TFIISKO_PolIISer2p_KASCnT_IP_Rep2
KAS-CUT&Tag IP targeting PolIISer2p in TFIISKO HEK293T cells

value: Cell Signaling Technology, 13499S


title: Whole Blood, ID1, D1, Vaccine, Baseline

description: Library name: VA0000010032

value: female

value: Day 1

value: Baseline


title: Whole Blood, ID2, D1, Placebo, Baseline

description: Library name: VA0000110058

value: Moderate


title: Whole Blood, ID1, M5, Booster, 2hour

description: Library name: VA0001180023

value: Booster

value: Month 5


title: Whole Blood, ID8, D1/D2, Vaccine/Placebo, 24hour/Baseline

value: Vaccine/Placebo

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/ISRR

value: Mild/VeryMild


title: H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day14, rep3

description: Library name: H3K27ac_ChIP_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_3

value: cerebellum

value: granule neurons

value: ctrl sgRNAs in dCas9-KRAB

value: H3K27ac (Abcam ab4729)


title: HEK293T_TFIISKO_PolIISer2p_KASCnT_IP_Rep1_(250411_WW_Hs_WW1603)

description:
Library name: HEK293T_TFIISKO_PolIISer2p_KASCnT_IP_Rep1
KAS-CUT&Tag IP targeting PolIISer2p in TFIISKO HEK293T cells


title: Kc167, rumpkd cell, bio rep2

city: Bethesda

first: Elissa

middle: P

last: Lei

state: MD

address: 50 south drive, blg50

department: NIDDK

description: Library name: Kc167_rumpkd_HiC_2

data_processing:
FASTQ files were trimmed using fastp (v0.24) with default settings
The trimmed reads were mapped to the FlyBase r6-52 reference genome using the Juicer pipeline (v1.6;(48)) with default parameters.
The Juicer produced *.hic contact map per sample, which were binned to generate contact matrices at resolutions ranging from 5Kb to 25Kb.
Each conditions with biological replicates were merged *.hic and contact matrices were analyzed to investigate chromatin interactions among PcG domains.
Assembly: Flybase r6-52
Supplementary files format and content: hic

organism: Drosophila melanogaster

growth_protocol: Kc167 cells are grown in CCM3 media (Cytiva) at 25°C.

extract_protocol:
Hi-C libraries were preared following the optimized Hi-C 2.0 protocol (Belaghzal et al., 2017) anad adapted for Drosophila cells. 4-5x10^7 cells per condition were crosslinked with 1% fromaldehyde and quenched with 0.125M glycine. Cells were washed with cold PBS, snap-frozen, and stored at -80C until further processing. Cells were lysed in cold lysis buffer and chromatin from isolated nuclei were permeabilized with 1x NEBuffer 3.1 containing 0.1% SDS and quenched with 1% Triton X-100. DNA was digested with DpnII (NEB) and 5' overhangs were were filled using Klenow DNA polymerase (NEB) and labeled with biotin-14-dATP. Proximity blunt-end ligation was performed in situ using T4 DNA ligase (Invitrogen) followed by Proteinase K treatment to reverse crosslinks. DNA was purified by repeated phenol:chloroform extraction followed by ethanol precipitation and concentration using 30 kDa Amicon columns. Biotin was removed from unligated ends using T4 DNA polymerase (NEB) in the presence of dATP and dGTP (Invitrogen). Free nucleotides including biotin-14-dATP were removed by repetitive concentration with Amicon columns. DNA was then sheared to ~200–300 bp fragments using the Bioruptor (Diagenode). Biotinylated ligation junctions were captured using Dynabeads MyOne Streptavidin C1 (Invitrogen).
Sequencing libraries were prepared using the TruSeq ChIP Library Preparation Kit (Illumina), and AMPure XP beads (Beckman Coulter) selection was used to remove adapter and primer dimers.

treatment_protocol: Cells were transfected with appropriate dsRNA and incubated at 25°C for 5d before harvesting RNA.

tag: cell line

value: hemocyte

value: rump dsRNA


title: Whole Blood, ID1, M5, Booster, 35min

description: Library name: VA0000470056

value: Whole Blood

value: female

tag: age

value: 35 min

value: ISRR


title: H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day14, rep2

description: Library name: H3K27ac_ChIP_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_2


title: Whole Blood, ID9, D1, Placebo, 35min

tag: treatment

value: Placebo

value: Day 1


title: HEK293T_TFIISKO_PolIISer2p_KASCnT_Input_Rep2_(250411_WW_Hs_WW1628)

description:
Library name: HEK293T_TFIISKO_PolIISer2p_KASCnT_Input_Rep2
KAS-CUT&Tag input targeting PolIISer2p in TFIISKO HEK293T cells

value: Cell Signaling Technology, 13499S


title: Whole Blood, ID8, D1, Vaccine, 6hour

value: Vaccine

tag: timepoint

value: 6 hour

value: Mild


title: Kc167, rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_HiC_1


title: Whole Blood, ID8, D1, Vaccine, 2hour

value: 2 hour

tag: reaction type


title: H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day14, rep1

description: Library name: H3K27ac_ChIP_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_1

value: cerebellum


title: HEK293T_TFIISKO_PolIISer2p_KASCnT_Input_Rep1_(250411_WW_Hs_WW1627)

description:
Library name: HEK293T_TFIISKO_PolIISer2p_KASCnT_Input_Rep1
KAS-CUT&Tag input targeting PolIISer2p in TFIISKO HEK293T cells


title: Patient 062,C2D1, PBMC, RNAseq

description:
Library name: P062-C2D1
RNA-seq of patients' PBMCs

value: PBMC

value: nivolumab+ipilimumab trial

tag: arm

value: Male

tag: ethnicity

value: Non-Hispanic

tag: os


title: Whole Blood, ID1, M5, Booster, Baseline

description: Library name: VA0000100027

value: Booster

tag: time

value: Month 5

value: Baseline

tag: reaction type_severity

value: Moderate

tag: batch


title: Kc167, mock cell, bio rep2

description: Library name: Kc167_mock_HiC_2

tag: cell type

value: hemocyte

value: GFP dsRNA


title: H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day8, rep3

description: Library name: H3K27ac_ChIP_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_3

tag: tissue

value: granule neurons

value: ctrl sgRNAs in dCas9-KRAB

value: H3K27ac (Abcam ab4729)


title: HEK293T_WT_PolIISer2p_KASCnT_IP_Rep2_(250411_WW_Hs_WW1598)

description:
Library name: HEK293T_WT_PolIISer2p_KASCnT_IP_Rep2
KAS-CUT&Tag IP targeting PolIISer2p in WT HEK293T cells

tag: antibody

value: Cell Signaling Technology, 13499S


title: Kc167, mock cell, bio rep1

description: Library name: Kc167_mock_HiC_1


title: K562_RPB1_KASCnT_IP_S_Rep1_(250411_WW_Hs_WW1557)

description:
Library name: K562_RPB1_KASCnT_IP_S_Rep1
KAS-CUT&Tag IP targeting RPB1 in K562 S cells


title: Whole Blood, ID8, D1, Vaccine, Baseline

tag: individual

tag: Sex

value: female

value: Vaccine

tag: day

value: Day 1

value: ISRR

tag: reaction type severity

value: Mild


title: H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day8, rep2

description: Library name: H3K27ac_ChIP_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_2

value: cerebellum

tag: genotype

tag: chip antibody


title: H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day8, rep1

description: Library name: H3K27ac_ChIP_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_1


title: HEK293T_WT_PolIISer2p_KASCnT_Input_Rep2_(250411_WW_Hs_WW1622)

description:
Library name: HEK293T_WT_PolIISer2p_KASCnT_Input_Rep2
KAS-CUT&Tag input targeting PolIISer2p in WT HEK293T cells


title: Kc167, H3K27me3 Input in rumpkd cells, bio rep 17

description: Library name: Kc167_rumpkd_input_R17.fastq.gz

data_processing:
All samples were sequenced with Novaseq (Illumina) using 50 bp single-end sequencing at the NHLBI DNA Sequencing and Genomics Core Facility.
All samples were sequenced with Novaseq (Illumina) using 50 bp single-end sequencing at the NHLBI DNA Sequencing and Genomics Core Facility.
FASTQ files of sequenced single-end 50 bp reads were trimmed using Trim Galore (v0.6.7) with default settings.
Bowtie2 v2.5.3 (Langmead and Salzberg, 2012) with default arguments was used to map the trimmed reads to the Flybase r6-52 genome assembly.
Then, multimapping reads were removed using samtools v1.12 (Li et al., 2009) view command with the argument -q 20. Picard MarkDuplicates v2.25.2 (http://broadinstitute.github.io/picard/index.html) was applied to remove duplicates from mapped, uniquely mapping reads.
Assembly: Peaks were called by MACS2 v2.2.7.1 (Zhang et al., 2008) (https://github.com/taoliu/MACS) by providing replicate IPs and inputs as multiple BAMs with arguments ‘-f BAM’, ‘--gsize=dm’ with different q-values for all ChIP samples.
Supplementary files format and content: dm6
Supplementary files format and content: bw, narrowPeak (except for Input samples)

extract_protocol:
2–4×107 cells were fixed by adding 1% formaldehyde directly to cells in culture medium for 10 min at RT with gentle agitation. 0.125 M glycine was used to quench formaldehyde with gentle agitation for 5 min at RT. Cells were centrifugated at 600 x g for 5 min and washed twice with ice-cold PBS. Chromatin preparation and chromatin immunoprecipitation (ChIP) were performed following earlier described methods (Bag et al., 2021), with minor modifications to the chormatin sonication steps. The modifications are as follows, cells were incubated in lysis buffer for 10 min on ice before sonication, which was completed using the Bioruptor (Diagenode) using 15 cycles of 30s on and 30s off.
Libraries were prepared according to the manufacturer’s protocol (NEB; Ultra II for DNA Library Prep Kit; E7645).

treatment_protocol: Cells were transfected with appropriate dsRNA and incubated for 4d at 25°C before harvesting chromatin.

tag: cell line

tag: treatment


title: Kc167, H3K27m3 Input in rumpkd cells, bio rep 16

description: Library name: Kc167_rumpkd_input_R16.fastq.gz


title: Whole Blood, ID7, M5, Booster, 2hour

tag: age

tag: timepoint

value: 2 hour

tag: reaction type


title: H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day4, rep2

description: Library name: H3K27ac_ChIP_ctrl-FANS_IVEd4-dCas9_KRAB-pnd10_2


title: Whole Blood, ID7, M5, Booster, 35min

value: Booster

value: 35 min


title: HEK293T_WT_PolIISer2p_KASCnT_Input_Rep1_(250411_WW_Hs_WW1621)

description:
Library name: HEK293T_WT_PolIISer2p_KASCnT_Input_Rep1
KAS-CUT&Tag input targeting PolIISer2p in WT HEK293T cells


title: HEK293T_WT_PolIISer2p_KASCnT_IP_Rep1_(250411_WW_Hs_WW1597)

description:
Library name: HEK293T_WT_PolIISer2p_KASCnT_IP_Rep1
KAS-CUT&Tag IP targeting PolIISer2p in WT HEK293T cells


title: Kc167, Ph R3, Pho R3, Cg R3 Input in rumpkd cells, bio rep 15

description: Library name: Kc167_rumpkd_input_R15.fastq.gz


title: Whole Blood, ID7, M5, Booster, Baseline

value: Month 5

value: Baseline


title: K562_PolIISer2p_KASCnT_IP_DMSO_Rep2_(241230_WW_HsDm_WW1457)

description:
Library name: K562_PolIISer2p_KASCnT_IP_DMSO_Rep2
KAS-CUT&Tag IP targeting Pol II-Ser2P in K562 cells treated with DMSO


title: H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day4, rep1

description: Library name: H3K27ac_ChIP_ctrl-FANS_IVEd4-dCas9_KRAB-pnd10_1


title: Brd4 ChIP-seq cerebellum, rep4

description: Library name: Brd4_ChIP_P22_CB_4

value: cerebellar cells

value: Brd4 (Bethyl A301-985A)


title: Whole Blood, ID7, D2, Vaccine, 24hour

value: Day 2

value: 24 hour

value: VeryMild


title: Kc167, Ph R1, Pho R1, Cg R1 Input in rumpkd cells, bio rep 14

description: Library name: Kc167_rumpkd_input_R14.fastq.gz

value: hemocyte

value: GFP dsRNA


title: K562_PolIISer2p_KASCnT_IP_DMSO_Rep1_(241230_WW_HsDm_WW1456)

description:
Library name: K562_PolIISer2p_KASCnT_IP_DMSO_Rep1
KAS-CUT&Tag IP targeting Pol II-Ser2P in K562 cells treated with DMSO

value: Cell Signaling Technology, 13499S


title: Brd4 ChIP-seq cerebellum, rep3

description: Library name: Brd4_ChIP_P22_CB_3


title: Kc167, Crol R3 Input in rumpkd cells, bio rep 13

description: Library name: Kc167_rumpkd_input_R13.fastq.gz


title: Whole Blood, ID7, D2, Vaccine, 6hour

value: female

value: Vaccine

value: 6 hour


title: Kc167, Crol R2, Ph R2, Pho R2, Cg R2 Input in rumpkd cells, bio rep 12

description: Library name: Kc167_rumpkd_input_R12.fastq.gz


title: K562_PolIISer2p_KASCnT_Input_DMSO_Rep2_(241230_WW_HsDm_WW1473)

description:
Library name: K562_PolIISer2p_KASCnT_Input_DMSO_Rep2
KAS-CUT&Tag input targeting Pol II-Ser2P in K562 cells treated with DMSO


title: Kc167, Su(z)12 R3, Crol R1 Input in rumpkd cells, bio rep 11

description: Library name: Kc167_rumpkd_input_R11.fastq.gz


title: Brd4 ChIP-seq cerebellum, rep2

description: Library name: Brd4_ChIP_P22_CB_2

value: cerebellum


title: K562_PolIISer2p_KASCnT_Input_DMSO_Rep1_(241230_WW_HsDm_WW1472)

description:
Library name: K562_PolIISer2p_KASCnT_Input_DMSO_Rep1
KAS-CUT&Tag input targeting Pol II-Ser2P in K562 cells treated with DMSO


title: K562_PolIISer2p_KASCnT_IP_C1_plus_biotin_Rep1_(241125_WW_Hs_WW1279)

description:
Library name: K562_PolIISer2p_KASCnT_IP_C1_plus_biotin_Rep1
KAS-CUT&Tag IP targeting Pol II-Ser2P in K562 cells (+biotin+C1 streptavidin beads )


title: Whole Blood, ID7, D2, Vaccine, 35min

value: ISRR


title: Kc167, Psc R3, Su(z)12 R2 Input in rumpkd cells, bio rep 10

description: Library name: Kc167_rumpkd_input_R10.fastq.gz


title: Brd4 ChIP-seq cerebellum, rep1

description: Library name: Brd4_ChIP_P22_CB_1


title: Whole Blood, ID7, D2, Vaccine, 2hour

value: 2 hour


title: HEK293T_TFIISKO_RPB1_KASCnT_IP_Rep2_(250411_WW_Hs_WW1600)

description:
Library name: HEK293T_TFIISKO_RPB1_KASCnT_IP_Rep2
KAS-CUT&Tag IP targeting RPB1 in TFIISKO HEK293T cells


title: Whole Blood, ID7, D1/D2, Placebo/Vaccine, 24hour/Baseline

value: Placebo/Vaccine

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/ISRR

value: Severe/VeryMild


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, CD1-P14, rep7

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-CD1-pnd14_7

data_processing:
For FANS-RNA-seq analyses, sequenced reads were aligned to the mm10 reference genome with HISAT2 using the public server at https://usegalaxy.org/ and normalized by library size. Gene annotations were derived using GENCODE version M11. For sync-TRAP-seq analyses, reads from Trio RNA-seq prepared libraries were trimmed 5bp from the 5’ end according to the manufacturer’s instructions (TECAN) and aligned to the mm10 reference genome. Transcripts considered for analyses were selected based on the presence of H3K4me3 and H3K27ac peaks at the TSS and on higher normalized counts following GFP immunoprecipitation in Rpl10a-GFP electroporated samples compared to non-electroporated control samples.
Assembly: mm10
Supplementary files format and content: bigwig files

molecule: cytoplasmic RNA

extract_protocol:
Cerebella were removed and microdissected. For electroporated samples, electroporation efficiency was assessed under a stereomicroscope and mCherry+/NeuN+ nuclei were enriched using fluorescence activated nuclei sorting with a SH800S cell sorter (Sony).
For FANS-RNA-seq, half the amount of purified RNA was treated with a NEBNext rRNA Depletion Kit (New England Biolabs) and libraries were prepared with the NEBNext® Ultra™ Directional RNA Library Prep Kit (#E7420). For sync-TRAP-seq, half the amount of immunopurified RNA was subjected to library preparation using the Trio RNA-seq kit with ribo-depletion (TECAN) according to the manufacturer’s instructions.

treatment_protocol: For in vivo electroporation (IVE), the cerebellum of P6 mouse pups was electroporated with the pCAG-mCherry-NLS plasmid together with a vector encoding U6-sgRNA targeting the indicated genes or control sequences and dissected at day 4 or 8 after electroporation.

value: granule neurons

value: ctrl sgRNAs in CD1


title: HEK293T_TFIISKO_RPB1_KASCnT_IP_Rep1_(250411_WW_Hs_WW1599)

description:
Library name: HEK293T_TFIISKO_RPB1_KASCnT_IP_Rep1
KAS-CUT&Tag IP targeting RPB1 in TFIISKO HEK293T cells


title: Whole Blood, ID7, D1, Placebo, 6hour

value: Placebo

value: Day 1

value: Severe


title: Kc167, E(z) R2 Input in rumpkd cells, bio rep 8

description: Library name: Kc167_rumpkd_input_R8.fastq.gz

value: hemocyte

value: GFP dsRNA


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, CD1-P14, rep6

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-CD1-pnd14_6


title: Kc167, E(z) R3, Psc R2, Su(z)12 R1 Input in rumpkd cells, bio rep 9

description: Library name: Kc167_rumpkd_input_R9.fastq.gz


title: HEK293T_TFIISKO_RPB1_KASCnT_Input_Rep2_(250411_WW_Hs_WW1624)

description:
Library name: HEK293T_TFIISKO_RPB1_KASCnT_Input_Rep2
KAS-CUT&Tag input targeting RPB1 in TFIISKO HEK293T cells


title: HEK293T_TFIISKO_RPB1_KASCnT_Input_Rep1_(250411_WW_Hs_WW1623)

description:
Library name: HEK293T_TFIISKO_RPB1_KASCnT_Input_Rep1
KAS-CUT&Tag input targeting RPB1 in TFIISKO HEK293T cells


title: Whole Blood, ID7, D1, Placebo, 2hour

value: female


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, CD1-P14, rep5

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-CD1-pnd14_5


title: Kc167, E(z) R1, Psc R1 Input in rumpkd cells, bio rep 7

description: Library name: Kc167_rumpkd_input_R7.fastq.gz


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, CD1-P14, rep4

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-CD1-pnd14_4


title: Whole Blood, ID7, D1, Placebo, 35min

value: 35 min


title: HEK293T_WT_RPB1_KASCnT_IP_Rep2_(250411_WW_Hs_WW1594)

description:
Library name: HEK293T_WT_RPB1_KASCnT_IP_Rep2
KAS-CUT&Tag IP targeting RPB1 in WT HEK293T cells


title: Kc167, Su(Hw) R3, Mod(mdg4) R3 Input in rumpkd cells, bio rep 6

description: Library name: Kc167_rumpkd_input_R6.fastq.gz


title: HEK293T_WT_RPB1_KASCnT_IP_Rep1_(250411_WW_Hs_WW1593)

description:
Library name: HEK293T_WT_RPB1_KASCnT_IP_Rep1
KAS-CUT&Tag IP targeting RPB1 in WT HEK293T cells


title: Kc167, Su(Hw) R2, Mod(mdg4) R2 Input in rumpkd cells, bio rep 5

description: Library name: Kc167_rumpkd_input_R5.fastq.gz


title: HiC GN, brd4_KD, FANS, IVE+day8, rep1

description: Library name: Hi-C_brd4_KD-FANS_IVEd8-dCas9_KRAB-pnd14_1

value: cerebellum

value: brd4 sgRNAs in dCas9-KRAB


title: Whole Blood, ID7, D1, Placebo, Baseline

value: Baseline

value: ISRR


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, CD1-P14, rep2

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-CD1-pnd14_2


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, CD1-P14, rep3

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-CD1-pnd14_3


title: HEK293T_WT_RPB1_KASCnT_Input_Rep2_(250411_WW_Hs_WW1618)

description:
Library name: HEK293T_WT_RPB1_KASCnT_Input_Rep2
KAS-CUT&Tag input targeting RPB1 in WT HEK293T cells


title: Whole Blood, ID13, M5, Booster, 2hour

value: Booster

value: Month 5

value: 2 hour

value: Mild


title: Kc167, Su(Hw) R1, Mod(mdg4) R1 Input in rumpkd cells, bio rep 4

description: Library name: Kc167_rumpkd_input_R4.fastq.gz


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, CD1-P14, rep1

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-CD1-pnd14_1

value: granule neurons


title: HEK293T_WT_RPB1_KASCnT_Input_Rep1_(250411_WW_Hs_WW1617)

description:
Library name: HEK293T_WT_RPB1_KASCnT_Input_Rep1
KAS-CUT&Tag input targeting RPB1 in WT HEK293T cells


title: Whole Blood, ID13, M5, Booster, 35min


title: Kc167, CP190 R3, CTCF R3, Pc R3 Input in rumpkd cells, bio rep 3

description: Library name: Kc167_rumpkd_input_R3.fastq.gz


title: K562_RPB1_KASCnT_IP_ActinomycinD_Rep2_(241230_WW_HsDm_WW1467)

description:
Library name: K562_RPB1_KASCnT_IP_ActinomycinD_Rep2
KAS-CUT&Tag IP targeting RPB1 in K562 cells treated with ActinomycinD


title: Whole Blood, ID13, M5, Booster, Baseline


title: RNA-seq cerebellum, IP, CD1-P14, rep3

description: Library name: RNA-seq_IP-CD1-pnd14_3

library_source: other

molecule: other

value: cerebellar cells


title: Kc167, CP190 R2, CTCF R2, Pc R2 Input in rumpkd cells, bio rep 2

description: Library name: Kc167_rumpkd_input_R2.fastq.gz


title: Whole Blood, ID13, D2, Placebo, 24hour

value: Placebo

value: Day 2

value: 24 hour


title: K562_RPB1_KASCnT_IP_ActinomycinD_Rep1_(241230_WW_HsDm_WW1466)

description:
Library name: K562_RPB1_KASCnT_IP_ActinomycinD_Rep1
KAS-CUT&Tag IP targeting RPB1 in K562 cells treated with ActinomycinD


title: RNA-seq cerebellum, IP, CD1-P14, rep2

description: Library name: RNA-seq_IP-CD1-pnd14_2


title: Kc167, CP190 R1, CTCF R1, Pc R1 Input in rumpkd cells, bio rep 1

description: Library name: Kc167_rumpkd_input_R1.fastq.gz

value: hemocyte


title: RNA-seq cerebellum, IP, CD1-P14, rep1

description: Library name: RNA-seq_IP-CD1-pnd14_1


title: K562_RPB1_KASCnT_Input_ActinomycinD_Rep2_(241230_WW_HsDm_WW1483)

description:
Library name: K562_RPB1_KASCnT_Input_ActinomycinD_Rep2
KAS-CUT&Tag IP targeting RPB1 in K562 cells treated with ActinomycinD


title: HiC GN, ctrl, FANS, IVE+day14, rep6

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_6

value: ctrl sgRNAs in dCas9-KRAB


title: Whole Blood, ID13, D2, Placebo, 6hour

value: female

value: 6 hour


title: Kc167, H3K27me3 Input in mock cells, bio rep 17

description: Library name: Kc167_mock_input_R17.fastq.gz

value: GFP dsRNA


title: Whole Blood, ID13, D2, Placebo, 2hour


title: RNA-seq GN, ctrl, IVE+day8, CD1-P14, rep1

description: Library name: RNA-seq_ctrl_IVEd8-CD1-pnd14_1

value: cerebellum

value: ctrl sgRNAs in CD1


title: RNA-seq cerebellum, CD1-P14, rep3

description: Library name: RNA-seq_CD1-pnd14_3


title: K562_RPB1_KASCnT_Input_ActinomycinD_Rep1_(241230_WW_HsDm_WW1482)

description:
Library name: K562_RPB1_KASCnT_Input_ActinomycinD_Rep1
KAS-CUT&Tag IP targeting RPB1 in K562 cells treated with ActinomycinD


title: Whole Blood, ID13, D2, Placebo, 35min

value: 35 min

value: ISRR


title: Kc167, H3K27m3 Input in mock cells, bio rep 16

description: Library name: Kc167_mock_input_R16.fastq.gz


title: Kc167, Ph R3, Pho R3, Cg R3 Input in mock cells, bio rep 15

description: Library name: Kc167_mock_input_R15.fastq.gz


title: K562_RPB1_KASCnT_IP_Flavopiridol_Rep2_(241230_WW_HsDm_WW1463)

description:
Library name: K562_RPB1_KASCnT_IP_Flavopiridol_Rep2
KAS-CUT&Tag input targeting RPB1 in K562 cells treated with Flavopiridol


title: Kc167, Ph R1, Pho R1, Cg R1 Input in mock cells, bio rep 14

description: Library name: Kc167_mock_input_R14.fastq.gz


title: K562_RPB1_KASCnT_IP_Flavopiridol_Rep1_(241230_WW_HsDm_WW1462)

description:
Library name: K562_RPB1_KASCnT_IP_Flavopiridol_Rep1
KAS-CUT&Tag input targeting RPB1 in K562 cells treated with Flavopiridol


title: RNA-seq cerebellum, CD1-P14, rep2

description: Library name: RNA-seq_CD1-pnd14_2


title: Whole Blood, ID13, D1/D2, Vaccine/Placebo, 24hour/Baseline

value: Vaccine/Placebo

value: Day 1/Day 2

value: 24 hour/Baseline

value: None/ISRR

value: None/Mild


title: Whole Blood, ID13, D1, Vaccine, 6hour

value: Vaccine

value: Day 1


title: RNA-seq cerebellum, CD1-P14, rep1

description: Library name: RNA-seq_CD1-pnd14_1

value: cerebellar cells


title: Kc167, Crol R3 Input in mock cells, bio rep 13

description: Library name: Kc167_mock_input_R13.fastq.gz

value: hemocyte


title: RNA-seq GN, ctrl, syncTRAP, IVE+day4, CD1-P10, rep6

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd4-CD1-pnd10_6

value: granule neurons


title: K562_RPB1_KASCnT_Input_Flavopiridol_Rep2_(241230_WW_HsDm_WW1479)

description:
Library name: K562_RPB1_KASCnT_Input_Flavopiridol_Rep2
KAS-CUT&Tag input targeting RPB1 in K562 cells treated with Flavopiridol


title: Kc167, Crol R2, Ph R2, Pho R2, Cg R2 Input in mock cells, bio rep 12

description: Library name: Kc167_mock_input_R12.fastq.gz


title: Whole Blood, ID13, D1, Vaccine, 2hour

value: female

value: 2 hour


title: K562_RPB1_KASCnT_Input_Flavopiridol_Rep1_(241230_WW_HsDm_WW1478)

description:
Library name: K562_RPB1_KASCnT_Input_Flavopiridol_Rep1
KAS-CUT&Tag input targeting RPB1 in K562 cells treated with Flavopiridol


title: RNA-seq GN, ctrl, syncTRAP, IVE+day4, CD1-P10, rep4

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd4-CD1-pnd10_4


title: Whole Blood, ID13, D1, Vaccine, Baseline

value: Baseline


title: Kc167, Su(z)12 R3, Crol R1 Input in mock cells, bio rep 11

description: Library name: Kc167_mock_input_R11.fastq.gz

value: GFP dsRNA


title: Whole Blood, ID13, D1, Vaccine, 35min


title: RNA-seq GN, ctrl, syncTRAP, IVE+day4, CD1-P10, rep5

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd4-CD1-pnd10_5

value: cerebellum

value: ctrl sgRNAs in CD1


title: K562_RPB1_KASCnT_IP_Triptolide_Rep2_(241230_WW_HsDm_WW1459)

description:
Library name: K562_RPB1_KASCnT_IP_Triptolide_Rep2
KAS-CUT&Tag input targeting RPB1 in K562 cells treated with Triptolide


title: K562_RPB1_KASCnT_IP_Triptolide_Rep1_(241230_WW_HsDm_WW1458)

description:
Library name: K562_RPB1_KASCnT_IP_Triptolide_Rep1
KAS-CUT&Tag input targeting RPB1 in K562 cells treated with Triptolide


title: Kc167, Psc R3, Su(z)12 R2 Input in mock cells, bio rep 10

description: Library name: Kc167_mock_input_R10.fastq.gz


title: RNA-seq GN, ctrl, syncTRAP, IVE+day4, CD1-P10, rep3

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd4-CD1-pnd10_3


title: Whole Blood, ID5, M5, Booster, 2hour

value: Booster

value: Month 5

value: ISRR

value: VeryMild


title: K562_RPB1_KASCnT_Input_Triptolide_Rep2_(241230_WW_HsDm_WW1475)

description:
Library name: K562_RPB1_KASCnT_Input_Triptolide_Rep2
KAS-CUT&Tag input targeting RPB1 in K562 cells treated with Triptolide


title: Kc167, E(z) R3, Psc R2, Su(z)12 R1 Input in mock cells, bio rep 9

description: Library name: Kc167_mock_input_R9.fastq.gz


title: Whole Blood, ID5, M5, Booster, 35min

value: 35 min


title: RNA-seq GN, ctrl, syncTRAP, IVE+day4, CD1-P10, rep2

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd4-CD1-pnd10_2


title: Kc167, E(z) R2 Input in mock cells, bio rep 8

description: Library name: Kc167_mock_input_R8.fastq.gz


title: Whole Blood, ID5, M5, Booster, Baseline


title: Kc167, E(z) R1, Psc R1 Input in mock cells, bio rep 7

description: Library name: Kc167_mock_input_R7.fastq.gz


title: RNA-seq cerebellum, IP, CD1-P10, rep3

description: Library name: RNA-seq_IP-CD1-pnd10_3


title: K562_RPB1_KASCnT_Input_Triptolide_Rep1_(241230_WW_HsDm_WW1474)

description:
Library name: K562_RPB1_KASCnT_Input_Triptolide_Rep1
KAS-CUT&Tag input targeting RPB1 in K562 cells treated with Triptolide


title: HiC GN, ctrl, FANS, IVE+day8, rep3

description: Library name: Hi-C_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_3

value: ctrl sgRNAs in dCas9-KRAB


title: K562_RPB1_KASCnT_IP_DMSO_Rep2_(241230_WW_HsDm_WW1455)

description:
Library name: K562_RPB1_KASCnT_IP_DMSO_Rep2
KAS-CUT&Tag IP targeting RPB1 in K562 cells treated with DMSO


title: K562_RPB1_KASCnT_IP_DMSO_Rep1_(241230_WW_HsDm_WW1454)

description:
Library name: K562_RPB1_KASCnT_IP_DMSO_Rep1
KAS-CUT&Tag IP targeting RPB1 in K562 cells treated with DMSO


title: Whole Blood, ID5, D2, Placebo, 24hour

value: Placebo

value: Day 2

value: 24 hour


title: RNA-seq GN, ctrl, syncTRAP, IVE+day4, CD1-P10, rep1

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd4-CD1-pnd10_1


title: RNA-seq cerebellum, IP, CD1-P10, rep2

description: Library name: RNA-seq_IP-CD1-pnd10_2

value: cerebellar cells


title: Kc167, Su(Hw) R3, Mod(mdg4) R3 Input in mock cells, bio rep 6

description: Library name: Kc167_mock_input_R6.fastq.gz

value: hemocyte


title: K562_RPB1_KASCnT_Input_DMSO_Rep2_(241230_WW_HsDm_WW1471)

description:
Library name: K562_RPB1_KASCnT_Input_DMSO_Rep2
KAS-CUT&Tag input targeting RPB1 in K562 cells treated with DMSO


title: Kc167, Su(Hw) R2, Mod(mdg4) R2 Input in mock cells, bio rep 5

description: Library name: Kc167_mock_input_R5.fastq.gz


title: Whole Blood, ID5, D2, Placebo, 6hour

value: female

value: 6 hour


title: K562_RPB1_KASCnT_Input_DMSO_Rep1_(241230_WW_HsDm_WW1470)

description:
Library name: K562_RPB1_KASCnT_Input_DMSO_Rep1
KAS-CUT&Tag input targeting RPB1 in K562 cells treated with DMSO


title: Kc167, Su(Hw) R1, Mod(mdg4) R1 Input in mock cells, bio rep 4

description: Library name: Kc167_mock_input_R4.fastq.gz


title: Whole Blood, ID5, D2, Placebo, 2hour

value: 2 hour


title: RNA-seq cerebellum, IP, CD1-P10, rep1

description: Library name: RNA-seq_IP-CD1-pnd10_1


title: RNA-seq GN, ctrl, IVE+day4, CD1-P10, rep1

description: Library name: RNA-seq_ctrl_IVEd4-CD1-pnd10_1


title: DX_HS_P2S5_K562-60k_(240709_DX_HS_P2S5_K562-60k)

description:
Library name: DX_HS_P2S5_K562-60k
CUT&Tag targeting Pol II-Ser5P in K562 cells (-kethoxal)

value: Cell Signaling Technology, 13523S


title: Whole Blood, ID5, D2, Placebo, 35min


title: Kc167, CP190 R3, CTCF R3, Pc R3 Input in mock cells, bio rep 3

description: Library name: Kc167_mock_input_R3.fastq.gz

value: GFP dsRNA


title: RNA-seq cerebellum, CD1-P10, rep3

description: Library name: RNA-seq_CD1-pnd10_3

value: cerebellum


title: Whole Blood, ID5, D1/D2, Vaccine/Placebo, 24hour/Baseline

value: Vaccine/Placebo

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/None

value: VeryMild/None


title: K562_PolIISer5p_KASCnT_Input_Rep2_(250411_WW_Hs_WW1640)

description:
Library name: K562_PolIISer5p_KASCnT_Input_Rep2
KAS-CUT&Tag input targeting Pol II-Ser5P in K562 cells (+kethoxal)


title: Kc167, CP190 R2, CTCF R2, Pc R2 Input in mock cells, bio rep 2

description: Library name: Kc167_mock_input_R2.fastq.gz


title: RNA-seq cerebellum, CD1-P10, rep2

description: Library name: RNA-seq_CD1-pnd10_2


title: K562_PolIISer5p_KASCnT_Input_Rep1_(250411_WW_Hs_WW1639)

description:
Library name: K562_PolIISer5p_KASCnT_Input_Rep1
KAS-CUT&Tag input targeting Pol II-Ser5P in K562 cells (+kethoxal)


title: Whole Blood, ID5, D1, Vaccine, 6hour

value: Vaccine

value: Day 1

value: ISRR

value: VeryMild


title: RNA-seq cerebellum, CD1-P10, rep1

description: Library name: RNA-seq_CD1-pnd10_1

value: cerebellar cells


title: PBMC anti-CD20

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: Library name: DA4745_PBMC

library_source: transcriptomic single cell

data_processing:
The Cell Ranger v7.2.0 software (10x Genomics) with default parameters was used to demultiplex and align the barcoded reads to the human reference GRCh38 (GENCODE v32/Ensembl 98) version 2020-A (July 7, 2020) for gene expression data and human V(D)J reference GRCh38 v7.1.0 for immune receptors (BCR).
Assembly: GRCh38 (GENCODE v32/Ensembl 98) version 2020-A (July 7, 2020)
Supplementary files format and content: annotated_bcells_celltypist.h5ad: h5ad file of scRNA counts and metadata
Supplementary files format and content: bcr_calls.csv.gz: comma seperated file with clone level annotation

source_name: Blood

extract_protocol:
From blood: Peripheral blood mononuclear cells (PBMCs) have been purified from fresh human blood samples by density gradient sedimentation using Lymphoprep (Progen). Negative B cell enrichment was performed using the human Pan B cell Isolation kit by Miltenyi. Either direct scRNA-seq of isolated immune cells were performed or isolated PBMCs were cryopreserved in 10% DMSO/hi-FCS and stored in liquid nitrogen until use. From gut-mucosal biopsies: Samples were obtained during screening gastro- and colonoscopy. Two times double biopsies sampled with standard forceps were immediately transferred into chilled Roswell Park Memorial Institute Medium (RPMI, Sigma-Aldrich), supplemented with 10% heat-inactivated (hi-)FCS and 1% Penicillin-Streptomycin (cRPMI). Samples were incubated in Hank’s balanced salt solution (HBSS Ca- Mg-, Gibco) supplemented with 1 mM dithiothreitol (DTT) and 5 mM Ethylenediaminetetraacetic acid (EDTA) at 37°C for 10 minutes with a total of two digestion steps. Samples were washed with HBSS, minced, and digested in HBSS containing 1 mg/ml Collagenase A (Roche) and 5 U/ml DNase I (Roche) at 37 °C for 60 min. After filtering the digest, cell pellets were stained with Zombie Violet followed by anti-CD45–PE (1:20). Cells were resuspended in FACS buffer (1% FCS/PBS) and sorted into CD45⁺ and CD45⁻ cells using a BD FACSMelody, Cytoflex SRT, or FACS Aria. Sorted cells were centrifuged and resuspended in RPMI-10 for subsequent scRNA-seq.
The Chromium Next GEM Single Cell 5' HT Kit v2 with a maximum target recovery rate of 20,000 cells was used. The recommended number of cells per compartment, as specified by the manufacturer’s protocol, was loaded. RPMI-10 (RPMI with 10% filtered hi-FCS) was used in the master mix for GEM generation instead of nuclease-free water. RNA from individual cells in droplets was reverse-transcribed into cDNA by incubating the emulsion at 53°C for 45 min and 85°C for 5 min, incorporating UMIs and cell-specific barcodes for single-cell identification. Samples were stored at 4°C for up to 24h or at -20°C for longer periods before cDNA clean-up and amplifications were performed following the manufacturer’s protocol. PCR cell cycle number for amplification was selected according to the estimated targeted cell recovery per GEM well (≤ 4,000: 16 cycles; 4,000-12,000: 14 cycles; > 12,000: 13 cycles). Quality control and quantification was performed with Agilent bioanalyzer and Agilent TapeStation. Subsequently, amplified cDNA was used to construct sequencing libraries, including steps for fragmentation, adapter ligation, and index addition. Sequencing libraries for gene expression and B cell receptors were generated using the primers from the respective 10x Genomics kits. Samples were sequenced with the Illumina NovaSeqX system with 50,000 reads for gene expression and 5,000 reads for V(D)J libraries.

value: Blood


title: Kc167, CP190 R1, CTCF R1, Pc R1 Input in mock cells, bio rep 1

description: Library name: Kc167_mock_input_R1.fastq.gz

value: hemocyte


title: Whole Blood, ID5, D1, Vaccine, 35min

value: female

value: 35 min


title: ILEUM anti-CD20

description: Library name: DA4745_ILEUM

source_name: Ileum

value: Ileum


title: RNA-seq GN, brd4 KD, syncTRAP, IVE+day8, rep11

description: Library name: RNA-seq_brd4_KD-syncTRAP_IVEd8-dCas9_KRAB-pnd14_11

value: granule neurons

value: brd4 sgRNAs in dCas9-KRAB


title: Whole Blood, ID5, D1, Vaccine, 2hour

value: 2 hour


title: RNA-seq GN, brd4 KD, syncTRAP, IVE+day8, rep10

description: Library name: RNA-seq_brd4_KD-syncTRAP_IVEd8-dCas9_KRAB-pnd14_10

value: cerebellum


title: Kc167, H3K27me3, ChIP in rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_H3K27me3_R1.fastq.gz

value: rump dsRNA


title: Whole Blood, ID9, D2, Vaccine, 24hour

value: Day 2

value: 24 hour


title: DUDO anti-CD20

description: Library name: DA4745_DUOD

source_name: Duodenum

value: Duodenum


title: Whole Blood, ID5, D1, Vaccine, Baseline

value: Vaccine

value: Day 1

value: Baseline


title: Kc167, H3K27me3, ChIP in rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_H3K27me3_R2.fastq.gz


title: Kc167, H3K27me3, ChIP in mock cell, bio rep2

description: Library name: Kc167_mock_H3K27me3_R2.fastq.gz

value: GFP dsRNA


title: RNA-seq GN, brd4 KD, syncTRAP, IVE+day8, rep9

description: Library name: RNA-seq_brd4_KD-syncTRAP_IVEd8-dCas9_KRAB-pnd14_9


title: Whole Blood, ID4, M5, Booster, 2hour

value: Booster

value: Month 5

value: Allergic


title: Whole Blood, ID8, D1, Vaccine, 35min

value: female

value: 35 min

value: ISRR

value: Mild


title: RNA-seq GN, brd4 KD, syncTRAP, IVE+day8, rep8

description: Library name: RNA-seq_brd4_KD-syncTRAP_IVEd8-dCas9_KRAB-pnd14_8

value: granule neurons

value: brd4 sgRNAs in dCas9-KRAB


title: Kc167, SuHw, ChIP in rumpkd cell, bio rep3

description: Library name: Kc167_rumpkd_SuHw_R3.fastq.gz

value: hemocyte

value: rump dsRNA


title: COLASC anti-CD20

description: Library name: DA4745_COLASC

source_name: Colon ascendens

value: Colon ascendens


title: RNA-seq GN, brd4 KD, syncTRAP, IVE+day8, rep7

description: Library name: RNA-seq_brd4_KD-syncTRAP_IVEd8-dCas9_KRAB-pnd14_7

value: cerebellum


title: COLDESC anti-CD20

description: Library name: DA4745_COLDESC

source_name: Colon descendens

value: Colon descendens


title: Whole Blood, ID4, M5, Booster, 35min


title: Kc167, H3K27me3, ChIP in mock cell, bio rep1

description: Library name: Kc167_mock_H3K27me3_R1.fastq.gz


title: BCELLS anti-CD20

description: Library name: DA4745_BCELLS

value: Blood


title: Kc167, SuHw, ChIP in rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_SuHw_R2.fastq.gz


title: RNA-seq GN, brd4 KD, syncTRAP, IVE+day8, rep6

description: Library name: RNA-seq_brd4_KD-syncTRAP_IVEd8-dCas9_KRAB-pnd14_6


title: Whole Blood, ID4, M5, Booster, Baseline

value: Baseline


title: ILEUM control

description: Library name: DA4664_ILEUM

value: Ileum

value: control


title: Whole Blood, ID4, D2, Placebo, 6hour

value: Placebo

value: Day 2

value: 6 hour

value: Moderate


title: RNA-seq GN, brd4 KD, syncTRAP, IVE+day8, rep5

description: Library name: RNA-seq_brd4_KD-syncTRAP_IVEd8-dCas9_KRAB-pnd14_5


title: Whole Blood, ID4, D2, Placebo, 24hour

value: female

value: 24 hour

value: ISRR


title: Kc167, SuHw, ChIP in mock cell, bio rep3

description: Library name: Kc167_mock_SuHw_R3.fastq.gz

value: GFP dsRNA


title: RNA-seq GN, brd4 KD, syncTRAP, IVE+day8, rep4

description: Library name: RNA-seq_brd4_KD-syncTRAP_IVEd8-dCas9_KRAB-pnd14_4

value: granule neurons

value: brd4 sgRNAs in dCas9-KRAB


title: Whole Blood, ID4, D2, Placebo, 2hour

value: 2 hour


title: DUOD control

description: Library name: DA4664_DUOD

value: Duodenum


title: RNA-seq GN, brd4 KD, syncTRAP, IVE+day8, rep3

description: Library name: RNA-seq_brd4_KD-syncTRAP_IVEd8-dCas9_KRAB-pnd14_3

value: cerebellum


title: COLDESC control

description: Library name: DA4664_COLDESC

value: Colon descendens


title: Kc167, SuHw, ChIP in mock cell, bio rep2

description: Library name: Kc167_mock_SuHw_R2.fastq.gz

value: hemocyte


title: Whole Blood, ID4, D2, Placebo, 35min

value: 35 min


title: Kc167, SuHw, ChIP in mock cell, bio rep1

description: Library name: Kc167_mock_SuHw_R1.fastq.gz


title: Whole Blood, ID4, D1/D2, Vaccine/Placebo, 24hour/Baseline

value: Vaccine/Placebo

value: Day 1/Day 2

value: 24 hour/Baseline

value: Allergic/ISRR

value: None/Moderate


title: RNA-seq GN, brd4 KD, syncTRAP, IVE+day8, rep2

description: Library name: RNA-seq_brd4_KD-syncTRAP_IVEd8-dCas9_KRAB-pnd14_2


title: Kc167, Suz12, ChIP in rumpkd cell, bio rep3

description: Library name: Kc167_rumpkd_Suz12_R3.fastq.gz

value: rump dsRNA


title: COLASC control

description: Library name: DA4664_COLASC

value: Colon ascendens

value: control


title: Whole Blood, ID4, D1, Vaccine, 6hour

value: female

value: Vaccine

value: Day 1

value: 6 hour

value: Allergic


title: RNA-seq GN, brd4 KD, syncTRAP, IVE+day8, rep1

description: Library name: RNA-seq_brd4_KD-syncTRAP_IVEd8-dCas9_KRAB-pnd14_1

value: cerebellum

value: granule neurons

value: brd4 sgRNAs in dCas9-KRAB


title: BCELLS control

description: Library name: DA4664_BCELLS

value: Blood


title: Kc167, Suz12, ChIP in rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_Suz12_R2.fastq.gz

value: hemocyte


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, rep7

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-dCas9_KRAB-pnd14_7

value: ctrl sgRNAs in dCas9-KRAB


title: Kc167, Suz12, ChIP in rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_Suz12_R1.fastq.gz


title: AB13488

description: Library name: Sample88

data_processing:
RNA sequencing data were processed starting with the Cell Ranger software (10x Genomics) to perform quality control, read alignment to the human reference genome (GRCh38), and quantification of gene expression levels. Unique Molecular Identifiers (UMIs) were used to count individual mRNA molecules, ensuring accurate expression levels.
The resultant data were then normalized to account for variations in sequencing depth and cell count discrepancies. Differential expression analysis was conducted using the Seurat package in R, which included scaling, principal component analysis, and clustering to identify cell populations and marker genes.
Assembly: refdata-cellranger-GRCh38-1.2.0
Supplementary files format and content: SPID_metadata_annotated.txt

source_name: CSF

extract_protocol:
Human CSF samples were obtained from 14 patients diagnosed with MS, and from 2 CSF inflammatory and 2 peripheral inflammatory donors at Rabin Medical Center hospital, Israel. CSF samples were collected via lumbar puncture by trained medical personnel and were processed within 2-4 hours from collection. CSF samples were diluted with sterile PBS and centrifuged at 350 x g for 5 minutes at 4°C to pellet cells. The supernatant was washed, counted, and used immediately for FACS staining. Sorting gate was immune cells CD45+.
Next Gem single-cell 3′ with Feature Barcode technology for Cell Surface Protein v3.1.

value: CSF

tag: diagnosis

value: RRMS

tag: patient

tag: category

value: MS


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, rep6

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-dCas9_KRAB-pnd14_6

tag: cell type


title: Whole Blood, ID4, D1, Vaccine, 2hour

value: 2 hour

tag: batch


title: AB13487

description: Library name: Sample87

tag: tissue


title: Kc167, Suz12, ChIP in mock cell, bio rep3

description: Library name: Kc167_mock_Suz12_R3.fastq.gz

value: GFP dsRNA


title: Whole Blood, ID4, D1, Vaccine, Baseline

tag: individual

value: Baseline


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, rep5

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-dCas9_KRAB-pnd14_5


title: AB13486

description: Library name: Sample86


title: Kc167, Suz12, ChIP in mock cell, bio rep2

description: Library name: Kc167_mock_Suz12_R2.fastq.gz


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, rep4

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-dCas9_KRAB-pnd14_4


title: AB13485

description: Library name: Sample85


title: Kc167, Suz12, ChIP in mock cell, bio rep1

description: Library name: Kc167_mock_Suz12_R1.fastq.gz


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, rep3

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-dCas9_KRAB-pnd14_3


title: AB13484

description: Library name: Sample84


title: Whole Blood, ID3, M5, Booster, 35min

tag: Sex

value: female

value: Booster

value: Month 5

value: 35 min

value: ISRR

value: VeryMild


title: Whole Blood, ID3, M5, Booster, Baseline

tag: day


title: Kc167, Psc, ChIP in rumpkd cell, bio rep3

description: Library name: Kc167_rumpkd_Psc_R3.fastq.gz

value: rump dsRNA


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, rep2

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-dCas9_KRAB-pnd14_2

value: cerebellum

value: granule neurons


title: AB13483

description: Library name: Sample83


title: Kc167, Psc, ChIP in rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_Psc_R2.fastq.gz

value: hemocyte


title: RNA-seq GN, ctrl, syncTRAP, IVE+day8, rep1

description: Library name: RNA-seq_ctrl-syncTRAP_IVEd8-dCas9_KRAB-pnd14_1

value: ctrl sgRNAs in dCas9-KRAB


title: Whole Blood, ID3, D2, Vaccine, 24hour

value: Vaccine

value: Day 2

value: 24 hour

tag: reaction type severity

value: Moderate


title: AB13480

description: Library name: Sample82

value: CSF

value: RRMS

value: MS


title: Kc167, Psc, ChIP in rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_Psc_R1.fastq.gz


title: RNA-seq GN, slc8a1 eKD, FANS, IVE+day8, rep2

description: Library name: RNA-seq_slc8a1_eKD-FANS_IVEd8-dCas9_KRAB-pnd14_2

molecule: nuclear RNA

tag: genotype

value: slc8a1 enhancer sgRNAs in dCas9-KRAB


title: PBMC control

description: Library name: DA4664_PBMC

value: Blood

value: control


title: Kc167, Psc, ChIP in mock cell, bio rep3

description: Library name: Kc167_mock_Psc_R3.fastq.gz

value: GFP dsRNA


title: Whole Blood, ID3, D2, Vaccine, 6hour

value: female

value: 6 hour

value: ISRR


title: AB13479

description: Library name: Sample81


title: RNA-seq GN, slc8a1 eKD, FANS, IVE+day8, rep1

description: Library name: RNA-seq_slc8a1_eKD-FANS_IVEd8-dCas9_KRAB-pnd14_1

value: cerebellum

value: granule neurons


title: AB13478

description: Library name: Sample80


title: Whole Blood, ID3, D2, Vaccine, 2hour

value: 2 hour


title: Whole Blood, ID4, D1, Vaccine, 35min

value: Vaccine

value: Day 1

value: 35 min

value: Allergic


title: Kc167, Psc, ChIP in mock cell, bio rep2

description: Library name: Kc167_mock_Psc_R2.fastq.gz

value: hemocyte


title: Whole Blood, ID3, M5, Booster, 2hour

value: Booster

value: Month 5

value: VeryMild


title: RNA-seq GN, ctrl, FANS, IVE+day8, rep12

description: Library name: RNA-seq_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_12

value: ctrl sgRNAs in dCas9-KRAB


title: AB13477

description: Library name: Sample79

value: CSF

value: Inflammatory disease NOS

value: CNS inflammatory


title: Whole Blood, ID3, D2, Vaccine, 35min

value: female

value: Day 2

value: Moderate


title: Kc167, SuHw, ChIP in rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_SuHw_R1.fastq.gz

value: rump dsRNA


title: Kc167, Psc, ChIP in mock cell, bio rep1

description: Library name: Kc167_mock_Psc_R1.fastq.gz

value: GFP dsRNA


title: Whole Blood, ID3, D1/D2, Placebo/Vaccine, 24hour/Baseline

value: Placebo/Vaccine

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/ISRR

value: Mild/Moderate


title: RNA-seq GN, ctrl, FANS, IVE+day8, rep11

description: Library name: RNA-seq_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_11

value: cerebellum

value: granule neurons


title: AB13476

description: Library name: Sample78


title: RNA-seq GN, top1-2b KD, FANS, IVE+day8, rep6

description: Library name: RNA-seq_top1_2b_KD-FANS_IVEd8-dCas9_KRAB-pnd14_6

value: top1/2b sgRNAs in dCas9-KRAB


title: Whole Blood, ID3, D1, Placebo, 6hour

value: Placebo

value: Day 1

value: 6 hour

value: ISRR

value: Mild


title: AB13475

description: Library name: Sample77

value: CSF

value: Inflammatory disease NOS

value: CNS inflammatory


title: Kc167, Pc, ChIP in rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_Pc_R2.fastq.gz

value: hemocyte

value: rump dsRNA


title: Whole Blood, ID3, D1, Placebo, 2hour

value: female

value: 2 hour


title: RNA-seq GN, top1-2b KD, FANS, IVE+day8, rep5

description: Library name: RNA-seq_top1_2b_KD-FANS_IVEd8-dCas9_KRAB-pnd14_5


title: AB13474

description: Library name: Sample76


title: Kc167, Pc, ChIP in rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_Pc_R1.fastq.gz


title: RNA-seq GN, top1-2b KD, FANS, IVE+day8, rep4

description: Library name: RNA-seq_top1_2b_KD-FANS_IVEd8-dCas9_KRAB-pnd14_4


title: AB13455

description: Library name: Sample75

value: Peripheral neuropathy

value: Peripheral inflammatory


title: Kc167, Pc, ChIP in mock cell, bio rep3

description: Library name: Kc167_mock_Pc_R3.fastq.gz

value: GFP dsRNA


title: RNA-seq GN, top1-2b KD, FANS, IVE+day8, rep3

description: Library name: RNA-seq_top1_2b_KD-FANS_IVEd8-dCas9_KRAB-pnd14_3

value: cerebellum

value: granule neurons


title: Whole Blood, ID2, M5, Booster, 2hour

value: Booster

value: Month 5


title: Whole Blood, ID3, D1, Placebo, Baseline

value: Placebo

value: Day 1

value: Baseline


title: Kc167, Pc, ChIP in mock cell, bio rep2

description: Library name: Kc167_mock_Pc_R2.fastq.gz


title: AB13454

description: Library name: Sample74

value: CSF


title: AB13453

description: Library name: Sample73


title: RNA-seq GN, top1-2b KD, FANS, IVE+day8, rep1

description: Library name: RNA-seq_top1_2b_KD-FANS_IVEd8-dCas9_KRAB-pnd14_1

value: top1/2b sgRNAs in dCas9-KRAB


title: Whole Blood, ID2, M5, Booster, Baseline

value: ISRR

value: Mild


title: Kc167, Pc, ChIP in mock cell, bio rep1

description: Library name: Kc167_mock_Pc_R1.fastq.gz

value: hemocyte


title: Kc167, MOD, ChIP in rumpkd cell, bio rep3

description: Library name: Kc167_rumpkd_MOD_R3.fastq.gz

value: rump dsRNA


title: Whole Blood, ID2, D2, Vaccine, 24hour

value: female

value: Vaccine

value: Day 2

value: 24 hour


title: AB13452

description: Library name: Sample72

value: Peripheral neuropathy

value: Peripheral inflammatory


title: AB13450

description: Library name: Sample70

value: RRMS

value: MS


title: RNA-seq GN, ctrl, FANS, IVE+day8, rep9

description: Library name: RNA-seq_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_9

value: cerebellum

value: granule neurons

value: ctrl sgRNAs in dCas9-KRAB


title: RNA-seq GN, ctrl, FANS, IVE+day8, rep10

description: Library name: RNA-seq_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_10


title: AB13451

description: Library name: Sample71

value: CSF


title: Kc167, MOD, ChIP in rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_MOD_R1.fastq.gz


title: Whole Blood, ID2, D2, Vaccine, 2hour

value: 2 hour


title: Whole Blood, ID2, M5, Booster, 35min

value: Booster

value: Month 5

value: 35 min

value: ISRR


title: RNA-seq GN, ctrl, FANS, IVE+day8, rep8

description: Library name: RNA-seq_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_8


title: Whole Blood, ID2, D2, Vaccine, 6hour

value: female

value: 6 hour


title: RNA-seq GN, top1-2b KD, FANS, IVE+day8, rep2

description: Library name: RNA-seq_top1_2b_KD-FANS_IVEd8-dCas9_KRAB-pnd14_2

value: top1/2b sgRNAs in dCas9-KRAB


title: AB13449

description: Library name: Sample69


title: Kc167, MOD, ChIP in rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_MOD_R2.fastq.gz

value: hemocyte

value: rump dsRNA


title: Kc167, Pc, ChIP in rumpkd cell, bio rep3

description: Library name: Kc167_rumpkd_Pc_R3.fastq.gz


title: Kc167, MOD, ChIP in mock cell, bio rep2

description: Library name: Kc167_mock_MOD_R2.fastq.gz

value: GFP dsRNA


title: Kc167, MOD, ChIP in mock cell, bio rep3

description: Library name: Kc167_mock_MOD_R3.fastq.gz


title: RNA-seq GN, ctrl, FANS, IVE+day8, rep7

description: Library name: RNA-seq_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_7


title: Whole Blood, ID2, D1, Placebo, 6hour

value: Placebo

value: Day 1

value: Moderate


title: Whole Blood, ID2, D1/D2, Placebo/Vaccine, 24hour/Baseline

value: Placebo/Vaccine

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/None

value: Moderate/None


title: AB13447

description: Library name: Sample67

value: CSF

value: RRMS

value: MS


title: AB13446

description: Library name: Sample66


title: AB13448

description: Library name: Sample68


title: RNA-seq GN, etv1 KD, FANS, IVE+day8, rep5

description: Library name: RNA-seq_etv1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_5

value: cerebellum

value: granule neurons

value: etv1 sgRNAs in dCas9-KRAB


title: AB13445

description: Library name: Sample65


title: RNA-seq GN, etv1 KD, FANS, IVE+day8, rep4

description: Library name: RNA-seq_etv1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_4


title: Kc167, Ez, ChIP in rumpkd cell, bio rep3

description: Library name: Kc167_rumpkd_Ez_R3.fastq.gz

value: hemocyte


title: Kc167, MOD, ChIP in mock cell, bio rep1

description: Library name: Kc167_mock_MOD_R1.fastq.gz


title: RNA-seq GN, etv1 KD, FANS, IVE+day8, rep6

description: Library name: RNA-seq_etv1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_6


title: Whole Blood, ID2, D1, Placebo, 35min

value: female

value: 35 min

value: ISRR


title: Kc167, Ez, ChIP in rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_Ez_R2.fastq.gz

value: rump dsRNA


title: Whole Blood, ID2, D1, Placebo, 2hour

value: Placebo

value: Day 1

value: 2 hour

value: Moderate


title: RNA-seq GN, etv1 KD, FANS, IVE+day8, rep3

description: Library name: RNA-seq_etv1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_3


title: Whole Blood, ID2, D1, Placebo, Baseline

value: Baseline


title: AB13444

description: Library name: Sample64


title: Kc167, Ez, ChIP in rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_Ez_R1.fastq.gz


title: AB13439

description: Library name: Sample63

value: PPMS


title: AB13438

description: Library name: Sample62

value: CSF


title: Kc167, Ez, ChIP in mock cell, bio rep2

description: Library name: Kc167_mock_Ez_R2.fastq.gz

value: GFP dsRNA


title: RNA-seq GN, etv1 KD, FANS, IVE+day8, rep2

description: Library name: RNA-seq_etv1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_2


title: AB13437

description: Library name: Sample61

value: MS


title: RNA-seq GN, ctrl, FANS, IVE+day8, rep6

description: Library name: RNA-seq_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_6

value: cerebellum

value: ctrl sgRNAs in dCas9-KRAB


title: Kc167, Ez, ChIP in mock cell, bio rep3

description: Library name: Kc167_mock_Ez_R3.fastq.gz


title: Whole Blood, ID1, M5, Booster, 2hour

value: Booster

value: Month 5


title: Kc167, Ez, ChIP in mock cell, bio rep1

description: Library name: Kc167_mock_Ez_R1.fastq.gz

value: hemocyte


title: RNA-seq GN, etv1 KD, FANS, IVE+day8, rep1

description: Library name: RNA-seq_etv1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_1

value: granule neurons

value: etv1 sgRNAs in dCas9-KRAB


title: Whole Blood, ID1, M5, Booster, 35min

value: female

value: 35 min

value: ISRR


title: Whole Blood, ID1, M5, Booster, Baseline


title: Whole Blood, ID1, D2, Placebo, 24hour

value: Placebo

value: Day 2

value: 24 hour

value: Severe


title: RNA-seq GN, ctrl, FANS, IVE+day8, rep5

description: Library name: RNA-seq_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_5


title: AB13436

description: Library name: Sample60

value: CSF

value: PPMS


title: Kc167, CTCF, ChIP in rumpkd cell, bio rep3

description: Library name: Kc167_rumpkd_CTCF_R3.fastq.gz

value: rump dsRNA


title: Whole Blood, ID1, D2, Placebo, 6hour

value: 6 hour


title: RNA-seq GN, ctrl, FANS, IVE+day8, rep4

description: Library name: RNA-seq_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_4

value: cerebellum

value: ctrl sgRNAs in dCas9-KRAB


title: Kc167, CTCF, ChIP in rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_CTCF_R2.fastq.gz


title: AB13435

description: Library name: Sample59

value: MS


title: AB13434

description: Library name: Sample58


title: Whole Blood, ID1, D2, Placebo, 2hour

value: 2 hour


title: Kc167, CTCF, ChIP in rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_CTCF_R1.fastq.gz

value: hemocyte


title: RNA-seq GN, ctrl, FANS, IVE+day8, rep2

description: Library name: RNA-seq_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_2

value: granule neurons


title: Kc167, CTCF, ChIP in mock cell, bio rep3

description: Library name: Kc167_mock_CTCF_R3.fastq.gz

value: GFP dsRNA


title: RNA-seq GN, ctrl, FANS, IVE+day8, rep3

description: Library name: RNA-seq_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_3


title: AB13433

description: Library name: Sample57


title: Whole Blood, ID1, D1/D2, Vaccine/Placebo, 24hour/Baseline

value: female

value: Vaccine/Placebo

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/ISRR

value: Mild/Severe


title: Whole Blood, ID1, D2, Placebo, 35min

value: Placebo

value: Day 2

value: 35 min

value: ISRR

value: Severe


title: RNA-seq GN, ctrl, FANS, IVE+day8, rep1

description: Library name: RNA-seq_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_1

value: cerebellum

value: ctrl sgRNAs in dCas9-KRAB


title: Kc167, CTCF, ChIP in mock cell, bio rep2

description: Library name: Kc167_mock_CTCF_R2.fastq.gz


title: AB13432

description: Library name: Sample56

value: CSF

value: PPMS

value: MS


title: HiC GN, brd2_cKO, FANS, IVE+day28, rep3

description: Library name: Hi-C_brd2_cKO-FANS_IVEd28-G6Cre_LSLCas9-pnd34_3

value: granule neurons

value: brd2 sgRNAs in Cas9


title: Whole Blood, ID1, D1, Vaccine, 6hour

value: female

value: Vaccine

value: Day 1

value: 6 hour

value: Mild


title: AB13431

description: Library name: Sample55

value: CIDP

value: Peripheral inflammatory


title: HiC GN, brd2_cKO, FANS, IVE+day28, rep2

description: Library name: Hi-C_brd2_cKO-FANS_IVEd28-G6Cre_LSLCas9-pnd34_2


title: AB13430

description: Library name: Sample54

value: APLA

value: CNS inflammatory


title: Whole Blood, ID1, D1, Vaccine, 2hour

value: 2 hour

value: ISRR


title: Kc167, Ph, ChIP in rumpkd cell, bio rep3

description: Library name: Kc167_rumpkd_Ph_R3.fastq.gz

value: hemocyte

value: rump dsRNA


title: Kc167, CTCF, ChIP in mock cell, bio rep1

description: Library name: Kc167_mock_CTCF_R1.fastq.gz

value: GFP dsRNA


title: AB13429

description: Library name: Sample53

value: CSF


title: HiC GN, brd2_cKO, FANS, IVE+day28, rep1

description: Library name: Hi-C_brd2_cKO-FANS_IVEd28-G6Cre_LSLCas9-pnd34_1

value: cerebellum

value: granule neurons


title: Whole Blood, ID1, D1, Vaccine, Baseline

value: female

value: Baseline


title: Kc167, Ph, ChIP in rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_Ph_R2.fastq.gz


title: HiC GN, ubash3b_eKD, FANS, IVE+day14, Novaseq, rep5

description: Library name: Hi-C_ubash3b_eKD-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_5

value: ubash3b enhancer sgRNAs in dCas9-KRAB


title: HiC GN, ubash3b_eKD, FANS, IVE+day14, rep6

description: Library name: Hi-C_ubash3b_eKD-FANS_IVEd14-dCas9_KRAB-pnd20_6


title: AB12628

description: Library name: Sample52

value: RRMS

value: MS


title: Kc167, Ph, ChIP in rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_Ph_R1.fastq.gz


title: HiC GN, etv1_KD, FANS, IVE+day14, Novaseq, rep5

description: Library name: Hi-C_etv1_KD-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_5

value: etv1 sgRNAs in dCas9-KRAB


title: HiC GN, ubash3b_eKD, FANS, IVE+day14, rep5

description: Library name: Hi-C_ubash3b_eKD-FANS_IVEd14-dCas9_KRAB-pnd20_5


title: AB12627

description: Library name: Sample51


title: Kc167, Ph, ChIP in mock cell, bio rep3

description: Library name: Kc167_mock_Ph_R3.fastq.gz


title: HiC GN, etv1_KD, FANS, IVE+day14, Novaseq, rep4

description: Library name: Hi-C_etv1_KD-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_4


title: AB12626

description: Library name: Sample50


title: HiC GN, ubash3b_eKD, FANS, IVE+day14, rep4

description: Library name: Hi-C_ubash3b_eKD-FANS_IVEd14-dCas9_KRAB-pnd20_4


title: HiC GN, ubash3b_eKD, FANS, IVE+day14, rep3

description: Library name: Hi-C_ubash3b_eKD-FANS_IVEd14-dCas9_KRAB-pnd20_3


title: HiC GN, etv1_KD, FANS, IVE+day14, Novaseq, rep3

description: Library name: Hi-C_etv1_KD-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_3


title: Kc167, Ph, ChIP in mock cell, bio rep2

description: Library name: Kc167_mock_Ph_R2.fastq.gz


title: AB12624

description: Library name: Sample49


title: Kc167, Ph, ChIP in mock cell, bio rep1

description: Library name: Kc167_mock_Ph_R1.fastq.gz


title: HiC GN, etv1_KD, FANS, IVE+day14, Novaseq, rep2

description: Library name: Hi-C_etv1_KD-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_2


title: HiC GN, ubash3b_eKD, FANS, IVE+day14, rep2

description: Library name: Hi-C_ubash3b_eKD-FANS_IVEd14-dCas9_KRAB-pnd20_2


title: AB12623

description: Library name: Sample48


title: Kc167, Pho, ChIP in rumpkd cell, bio rep3

description: Library name: Kc167_rumpkd_Pho_R3.fastq.gz


title: HiC GN, etv1_KD, FANS, IVE+day14, Novaseq, rep1

description: Library name: Hi-C_etv1_KD-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_1


title: AB12622

description: Library name: Sample47


title: HiC GN, brd4_KD, FANS, IVE+day14, Novaseq, rep4

description: Library name: Hi-C_brd4_KD-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_4

value: brd4 sgRNAs in dCas9-KRAB


title: Kc167, Pho, ChIP in rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_Pho_R2.fastq.gz


title: HiC GN, ubash3b_eKD, FANS, IVE+day14, rep1

description: Library name: Hi-C_ubash3b_eKD-FANS_IVEd14-dCas9_KRAB-pnd20_1


title: HiC GN, etv1_KD, FANS, IVE+day14, rep5

description: Library name: Hi-C_etv1_KD-FANS_IVEd14-dCas9_KRAB-pnd20_5


title: HiC GN, etv1_KD, FANS, IVE+day14, rep4

description: Library name: Hi-C_etv1_KD-FANS_IVEd14-dCas9_KRAB-pnd20_4


title: Kc167, Pho, ChIP in rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_Pho_R1.fastq.gz


title: AB12620

description: Library name: Sample45


title: HiC GN, brd4_KD, FANS, IVE+day14, Novaseq, rep3

description: Library name: Hi-C_brd4_KD-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_3


title: Kc167, Pho, ChIP in mock cell, bio rep3

description: Library name: Kc167_mock_Pho_R3.fastq.gz


title: AB12621

description: Library name: Sample46


title: HiC GN, brd4_KD, FANS, IVE+day14, Novaseq, rep2

description: Library name: Hi-C_brd4_KD-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_2


title: HiC GN, brd4_KD, FANS, IVE+day14, Novaseq, rep1

description: Library name: Hi-C_brd4_KD-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_1


title: HiC GN, etv1_KD, FANS, IVE+day14, rep3

description: Library name: Hi-C_etv1_KD-FANS_IVEd14-dCas9_KRAB-pnd20_3


title: Kc167, Pho, ChIP in mock cell, bio rep2

description: Library name: Kc167_mock_Pho_R2.fastq.gz


title: AB12619

description: Library name: Sample44


title: HiC GN, etv1_KD, FANS, IVE+day14, rep2

description: Library name: Hi-C_etv1_KD-FANS_IVEd14-dCas9_KRAB-pnd20_2


title: AB12618

description: Library name: Sample43


title: HiC GN, ctrl, FANS, IVE+day14, Novaseq, rep7

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_7

value: ctrl sgRNAs in dCas9-KRAB


title: HiC GN, etv1_KD, FANS, IVE+day14, rep1

description: Library name: Hi-C_etv1_KD-FANS_IVEd14-dCas9_KRAB-pnd20_1


title: Kc167, Pho, ChIP in mock cell, bio rep1

description: Library name: Kc167_mock_Pho_R1.fastq.gz


title: HiC GN, ctrl, FANS, IVE+day14, Novaseq, rep6

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_6


title: AB12617

description: Library name: Sample42


title: AB12616

description: Library name: Sample41


title: Kc167, Cg, ChIP in rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_Cg_R2.fastq.gz


title: HiC GN, ctrl, FANS, IVE+day14, Novaseq, rep5

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_5


title: Kc167, Cg, ChIP in rumpkd cell, bio rep3

description: Library name: Kc167_rumpkd_Cg_R3.fastq.gz


title: HiC GN, brd4_KD, FANS, IVE+day14, rep3

description: Library name: Hi-C_brd4_KD-FANS_IVEd14-dCas9_KRAB-pnd20_3


title: Kc167, Cg, ChIP in rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_Cg_R1.fastq.gz


title: HiC GN, ctrl, FANS, IVE+day14, Novaseq, rep4

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_4


title: HiC GN, brd4_KD, FANS, IVE+day14, rep4

description: Library name: Hi-C_brd4_KD-FANS_IVEd14-dCas9_KRAB-pnd20_4


title: AB12615

description: Library name: Sample40


title: HiC GN, brd4_KD, FANS, IVE+day14, rep2

description: Library name: Hi-C_brd4_KD-FANS_IVEd14-dCas9_KRAB-pnd20_2


title: AB12177

description: Library name: Sample39


title: Kc167, Cg, ChIP in mock cell, bio rep3

description: Library name: Kc167_mock_Cg_R3.fastq.gz


title: AB12176

description: Library name: Sample38


title: HiC GN, brd4_KD, FANS, IVE+day14, rep1

description: Library name: Hi-C_brd4_KD-FANS_IVEd14-dCas9_KRAB-pnd20_1


title: Kc167, Cg, ChIP in mock cell, bio rep2

description: Library name: Kc167_mock_Cg_R2.fastq.gz


title: AB12174

description: Library name: Sample36


title: Kidney_low_salt_4

city: New York

first: Evan

middle: C

last: Palmer-Young

state: NY

address: 525 E 68th St

institute: Cornell University

description: Library name: 7_9_R4

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
We used the PreProcSEQ  pipeline to prepare raw sequencing files for further  analysis. Library read quality was visualized using MultiQC .  Reads were trimmed using Trimmomatic to remove Illumina adapter sequences and the first and last 3 bp of each read. Reads less than 36 bp in length or with average per-base quality scores below 15 were excluded. Reads were mapped to transcripts of the NCBI reference genome for Rattus norvegicus (GCF_036323735.1 (Refseq)) using Salmon  followed by construction of the gene expression matrix with tximeta.
Assembly: GCF_036323735.1
Supplementary files format and content: Read count matrix with one row per gene locus and one column per sample . Separate files for heart and kidney for low salt experiment; and for aldosterone-treated kidneys.

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
Papilla dissected from one kidney or piece of ventricle removed from heart. Tissue incubated overnight at 4 oC[EP12.1] in RNAlater (Invitrogen AM7020). Tissue was transferred to lysis buffer, stored at -70 oC, lysed with two freeze-thaw cycles and disrupted manually with forceps. Samples were centrifuged (12.1 rcf, 2 min) and the supernatant passed through an 18-gauge needle.   Total RNA was isolated using a PureLink RNA Mini kit (Invitrogen #12183018A).   For RNAseq the samples were treated with DNase I.
RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), and concentrations were measured using the NanoDrop system (Thermo Fisher Scientific, Inc., Waltham, MA). Preparation of RNA sample library and RNA-seq were performed by the Genomics Core Laboratory at Weill Cornell Medicine. Messenger RNA was prepared using TruSeq Stranded mRNA Sample Library Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions. The normalized cDNA libraries were pooled and sequenced on Illumina NovaSeq X plus sequencer with single-end 50 cycles.

treatment_protocol: Female Sprague-Dawley rats (120-200 g) were maintained on synthetic diets (Harlan Teklad) containing control Na (Na content 0.4%) or low Na (Na content 0.01 – 0.02%) for 7 d.  Some animals on control-Na diet were implanted with osmotic minipumps (Alzet model 2002) infusing aldosterone at a rate of 12 ug/day.

value: Kidney

value: L


title: HiC GN, wapl_KD, FANS, IVE+day8, rep3

description: Library name: Hi-C_wapl_KD-FANS_IVEd8-dCas9_KRAB-pnd14_3

value: wapl sgRNAs in dCas9-KRAB


title: HiC GN, ctrl, FANS, IVE+day14, Novaseq, rep3

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_3


title: HiC GN, wapl_KD, FANS, IVE+day8, rep1

description: Library name: Hi-C_wapl_KD-FANS_IVEd8-dCas9_KRAB-pnd14_1


title: HiC GN, ctrl, FANS, IVE+day14, Novaseq, rep1

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_1


title: Kc167, Cg, ChIP in mock cell, bio rep1

description: Library name: Kc167_mock_Cg_R1.fastq.gz

value: hemocyte


title: HiC GN, ctrl, FANS, IVE+day14, Novaseq, rep2

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_Novaseq_2


title: Kc167, Crol, ChIP in rumpkd cell, bio rep3

description: Library name: Kc167_rumpkd_Crol_R3.fastq.gz

value: rump dsRNA


title: AB12175

description: Library name: Sample37


title: HiC GN, wapl_KD, FANS, IVE+day8, rep2

description: Library name: Hi-C_wapl_KD-FANS_IVEd8-dCas9_KRAB-pnd14_2


title: AB12173

description: Library name: Sample35


title: Kidney_low_salt_3

description: Library name: 7_9_R3


title: HiC GN, top2b_KD, FANS, IVE+day8, rep3

description: Library name: Hi-C_top2b_KD-FANS_IVEd8-dCas9_KRAB-pnd14_3

value: top2b sgRNAs in dCas9-KRAB


title: Kc167, Crol, ChIP in rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_Crol_R2.fastq.gz


title: Kc167, Crol, ChIP in rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_Crol_R1.fastq.gz


title: Kidney_high_salt_4

description: Library name: 7_9_R2

value: H


title: AB12172

description: Library name: Sample34

value: CSF


title: Kidney_high_salt_3

description: Library name: 7_9_R1


title: AB12171

description: Library name: Sample33


title: AB12170

description: Library name: Sample32


title: HiC GN, top2b_KD, FANS, IVE+day8, rep2

description: Library name: Hi-C_top2b_KD-FANS_IVEd8-dCas9_KRAB-pnd14_2

value: cerebellum

value: granule neurons


title: HiC GN, top1_KD, FANS, IVE+day8, rep3

description: Library name: Hi-C_top1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_3

value: top1 sgRNAs in dCas9-KRAB


title: Kc167, Crol, ChIP in mock cell, bio rep3

description: Library name: Kc167_mock_Crol_R3.fastq.gz

value: GFP dsRNA


title: HiC GN, top2b_KD, FANS, IVE+day8, rep1

description: Library name: Hi-C_top2b_KD-FANS_IVEd8-dCas9_KRAB-pnd14_1


title: Kc167, Crol, ChIP in mock cell, bio rep2

description: Library name: Kc167_mock_Crol_R2.fastq.gz


title: Kidney_low_salt_2

description: Library name: 6_25_R4


title: Kc167, Crol, ChIP in mock cell, bio rep1

description: Library name: Kc167_mock_Crol_R1.fastq.gz


title: Kidney_low_salt_1

description: Library name: 6_25_R3


title: AB12169

description: Library name: Sample31

value: RRMS


title: AB12168

description: Library name: Sample30

value: MS


title: HiC GN, top1_KD, FANS, IVE+day8, rep2

description: Library name: Hi-C_top1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_2


title: HiC GN, top1_KD, FANS, IVE+day8, rep1

description: Library name: Hi-C_top1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_1


title: Kc167, CP190, ChIP in rumpkd cell, bio rep3

description: Library name: Kc167_rumpkd_Cp190_R3.fastq.gz


title: Kc167, CP190, ChIP in rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_Cp190_R2.fastq.gz


title: Kidney_high_salt_1

description: Library name: 6_25_R1


title: AB12166

description: Library name: Sample28


title: AB12167

description: Library name: Sample29


title: Kidney_high_salt_2

description: Library name: 6_25_R2


title: Kc167, CP190, ChIP in mock cell, bio rep3

description: Library name: Kc167_mock_Cp190_R3.fastq.gz


title: Kc167, rumpkd cell, bio rep3

description: Library name: Kc167_rumpkd_RNAseq_R3.fastq.gz

data_processing:
FASTQ files were trimmed using Trim Galore (v0.6.10) with default settings
The resulting reads were mapped to the FlyBase r6-52 reference genome using HISAT2 v2.2.1 with default parameters.
Aligned reads were counted using subread featureCounts v2.0.6 with optimized parameters, “-t exon” option was used to quantify for RNA-seq, and “-s1” option specifically for this sense-stranded library.
Counts tables were used as input files for the downstream differential analysis.
Counts tables from independent nascent RNA-seq experiments were independently imported into DESeq2 v1.40.1 in R4.3.0 version and normalized by design “~treatment” and with otherwise default parameters. DEGs were those with FDR < 0.05.
Assembly: Flybase r6-52
Supplementary files format and content: bigwg

extract_protocol:
RNA was extracted from transfected Kc167 cells using the RNeasy Mini Kit (Qiagen).
Unfragmented RNA-seq libraries were created from 60-100ng of RNA using the Ovation RNA-seq Systems 1-16 for Model Organisms (Nugen), as described in Chen et al., 2018.

treatment_protocol: Cells were transfected with appropriate dsRNA and incubated at 25°C for 3d before harvesting RNA.


title: Kc167, CP190, ChIP in rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_Cp190_R1.fastq.gz


title: Heart_low_salt_4

description: Library name: R8

source_name: Heart

value: Heart


title: Kc167, rumpkd cell, bio rep2

description: Library name: Kc167_rumpkd_RNAseq_R2.fastq.gz


title: AB12165

description: Library name: Sample27


title: AB12164

description: Library name: Sample26


title: Kc167, rumpkd cell, bio rep1

description: Library name: Kc167_rumpkd_RNAseq_R1.fastq.gz


title: Heart_low_salt_3

description: Library name: R7


title: Kc167, mock cell, bio rep3

description: Library name: Kc167_mock_RNAseq_R3.fastq.gz


title: Kc167, CP190, ChIP in mock cell, bio rep2

description: Library name: Kc167_mock_Cp190_R2.fastq.gz


title: Heart_high_salt_4

description: Library name: R6


title: AB12163

description: Library name: Sample25


title: Kc167, CP190, ChIP in mock cell, bio rep1

description: Library name: Kc167_mock_Cp190_R1.fastq.gz


title: Kc167, mock cell, bio rep2

description: Library name: Kc167_mock_RNAseq_R2.fastq.gz


title: Heart_high_salt_3

description: Library name: R5