title: Pool113_RS2_Plate5-6-G19-I11

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.


title: mESC_WT rep2

status: Public on May 04 2023

type: SRA

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

country: China

institute: Huazhong University of Science and Technology

library_source: transcriptomic

data_processing:
Raw reads were processed with Cutadapt v1.16. Trimmed reads were mapped to mouse genome using STAR with default settings.
Assembly: mm10
Supplementary files format and content: DESeq result with normalized and raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: embryonic stem cells (ESCs)

growth_protocol: The mouse ESC line AB2.2 were seeded on mitotically inactivated MEF feeder cells in N2B27 medium with 2i and LIF in tissue culture dishes.

extract_protocol:
For mouse ESCs, total RNA was extracted by TRIzol reagent (Invitrogen, USA) from 5×105 cells for each group.
RNA libraries were prepared for sequencing using standard RNA-seq library preparation (Truseq RNA Sample Preparation Kit, Illumina).

treatment_protocol: ESCs were treated with 50 μM Mdivi-1 for 24h.

tag: strain

tag: cell type

value: ESCs

tag: genotype

value: Control


title: mESC_WT_H3K27me3 rep1

library_source: genomic

data_processing:
Raw reads were processed with cutadapt v1.8.1 to remove adapters and perform quality trimming.
Trimmed reads were mapped to the UCSC mm10 assembly using Bowtie2 with default parameters.
Assembly: mm10
Supplementary files format and content: Bigwig files were generated for data visualization.

molecule: genomic DNA

source_name: embryonic stem cell

extract_protocol:
mESCs were collected and MEF cells were removed after treatment for 24h, followed by ChIP-seq library preparation.
ChIP-seq was performed using a Hyperactive In-Situ ChIP Library Prep Kit for Illumina (pG-Tn5) according to the manufacturer’s procedure

value: embryonic stem cell

tag: treatment

value: Mdivi-1 treatment

tag: antibody

value: anti-H3K27me3, Abcam, ab6002


title: HuhST1KO_IFNa_24h_rep2

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

department: Laboratory of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University

data_processing:
After quality control assessments using FastQC, fastq files were mapped to the Homo sapiens GRCh38/hg38 genome build (release-100) using STAR version 2.7.3a
Read counts were generated using FeatureCounts v1.6.2 with default parameters
Counts normalization and DEG analysis were performed using the DESeq2 v.1.30.1 package in R version 4.0.3
Assembly: hg38
Supplementary files format and content: Raw read counts in .csv format

organism: Homo sapiens

source_name: IFN alpha stimulated HuhST1KO cells, 24h

growth_protocol: Huh7.5 WT and KO cell lines were maintained in DMEM complete medium supplemented with 10% fetal bovine serum (FBS), 1% MEM NEAA and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using TRI-REAGENT (MRC) followed by a column-based Total RNA Zol-Out™ D kit (A&A Biotechnology) following the manufacturer's protocol
RNA-seq libraries were prepared in two biological replicates from 1ug of total RNA using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) together with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext® Multiplex Oligos for Illumina® (NEB) according to manufacturer's protocol

treatment_protocol:
Cells were seeded in full cell culture medium, which was replaced the next day with starving medium containing 1% FBS for 8h before starting the treatment
IFNα (1000 U/ml, IF007, MERCK) or IFNγ (10 ng/ml, IF002, MERCK) was added for indicated time points

tag: cell line

value: human hepatocellular carcinoma cells

value: STAT1 knockout

value: IFN alpha, 1000U/ml

tag: time


title: Pool113_RS2_Plate5-6-G19-H24

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2 & 3

source_name: brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x1012 to 1x1013 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: tissue

value: brain

tag: source

value: RSP

tag: target

value: PTLp

tag: Sex

value: female


title: Pool113_RS2_Plate5-6-G19-J11

value: male


title: KPT, replicate 3, ATAC-seq 2

city: Stanford

first: Laura

middle: D

last: Attardi

address: 269 Campus Drive

institute: Stanford University

description:
ATAC-seq
AK7

data_processing:
ATAC-seq reads were trimmed of adapter sequences using Skewer (version 0.2.2, https://github.com/relipmoc/skewer), aligned to the mouse genome (mm10) using Bowtie2 (version 2.4.0, https://github.com/BenLangmead/bowtie2), and sorted based on genomic location and indexed using Samtools (version 1.3.1, https://github.com/samtools/samtools). Peak calling and differential peak analysis were performed using the ‘ChrAccR’ package in R (version 0.9.17, https://github.com/GreenleafLab/ChrAccR) with the sorted BAM file as input using the default parameters. The setConfigElement “doPeakCalling” was used with “annotationPeakGroupAgreePerc” at 1 to generate the conserved peaks list.
Assembly: mm10
Supplementary files format and content: raw counts for all peaks for all samples

source_name: lung

extract_protocol:
KT, KFT, and KPT mice were transduced with Ad5-SPC-Cre and harvested for cell sorting at 10 weeks post-transduction. Non-transduced lungs were used as a control. Briefly, lungs were perfused with 10 mL of ice-cold PBS and placed in a sterile dish on ice. Lungs were finely minced with sterile scissors and razor blades and resuspended in 6 mL digestion media (RPMI with 2.5 mg of Liberase TL (Sigma-Aldrich) and 25 µg/mL DNase (Sigma Aldrich)). Lungs were rotated for 45 minutes at 37ºC. Tubes were briefly cooled on ice, and then samples were passed through a 40 µM filter. 5 mL of FACS buffer (10% FBS, 2 mM EDTA, 25 µg/mL DNase in DPBS) was added and tubes were spun for 5 minutes at 300g. Cells were resuspended in ACK lysing buffer (Gibco), incubated for 1 minute on ice, and quenched with 8 mL of FACS buffer. Cells were washed 2x with FACS buffer, resuspended with biotinylated primary antibodies (CD45, BioLegend 103104 30-F11; CD31, BioLegend 102404 390; F4/80, BioLegend 123106 BM8; Ter119, BioLegend 116204 TER-119, 1:800 in FACS buffer) and incubated for 20 minutes on ice. After washing 2x, cells were resuspended in streptavidin-APC secondary antibody (BioLegend 405207, 1:800) for 20 minutes on ice. Cells were washed 2x and resuspended in FACS buffer with 1 µg/mL DAPI, filtered through a 40 µM filter, and sorted using a Sony SH800S cell sorter. Data were analyzed using the default Sony SH800S software and FCS Express (Version 7, De Novo Software).
ATAC-sequencing was performed as previously described. Two independent ATAC-sequencing experiments were performed, one with KT and KPT mice and the second with KT and KFT cells. Briefly, 5x105 cells were sorted and washed 2x in FACS buffer without DNase added. Nuclei were then isolated, lysed, and incubated with Tn5 transposase precisely as described. Transposed DNA was then isolated using the MinElute Reaction Cleanup Kit (Qiagen). Libraries were prepared by amplifying DNA for 5 cycles with NEBNext 2x MasterMix (NEB), after which qPCR was run on samples to determine the number of additional cycles needed. After any additional amplifications were performed, libraries were purified using the MinElute Reaction Cleanup Kit (Qiagen). Samples were sequenced on a HiSeq4000 (Illumina) (KT vs. KPT experiment).

value: lung

value: KPT


title: Pool113_RS2_Plate5-6-G19-H23


title: HuhST1KO_IFNa_24h_rep1


title: HuhST1KO_IFNa_8h_rep2

source_name: IFN alpha stimulated HuhST1KO cells, 8h


title: KPT, replicate 2, ATAC-seq 2

description:
ATAC-seq
AK6


title: Pool113_RS2_Plate5-6-G19-H12


title: mESC_WT rep1


title: KPT, replicate 1, ATAC-seq 2

description:
ATAC-seq
AK5


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#1 - totalRNA-seq

city: Rehovot

first: Orly

last: Reiner

address: 234, Herzl Street,

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
ribosomal RNA depleted total RNA
Biological replicate1, clone1

data_processing:
Sequenced reads were trimmed for adaptor sequence using Cutadapt and were aligned with STAR.
Raw counts were processed with qCount from QuasR package, and normalized reads were obtained by DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: raw count quantification files

source_name: mouse embryonic stem cells

growth_protocol: Mouse ES cells were grown in FBS+LIF culture media.

extract_protocol:
Total RNA was extracted from cells, using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
TruSeq Stranded Total RNA Library Prep kit

tag: culture medium

value: FBS+LIF

value: Lis1 Floxed/- (F/-)

value: hybrid


title: Pool113_RS2_Plate5-6-G19-H11


title: HuhST1KO_IFNa_8h_rep1


title: HuhST1KO_IFNa_4h_rep2

source_name: IFN alpha stimulated HuhST1KO cells, 4h


title: Pool113_RS2_Plate5-6-G19-G24


title: KT, replicate 4, ATAC-seq 2

description:
ATAC-seq
AK4

value: KT


title: p53-null-CB5232-Ad-Emp

data_processing:
RNA-seq reads were aligned to the mouse genome (mm10) using HISAT2 (version 2.0.5, https://github.com/DaehwanKimLab/hisat2), sorted based on genomic location and indexed using Samtools (version 1.3.1, https://github.com/samtools/samtools), and counted and mapped to each gene using HTSeq-Count (version 0.6.1, https://github.com/simon-anders/htseq). Differentially expressed genes (DEGs) were identified using DESeq2 with a cutoff of a p-adjusted value of < 0.05 (version 1.24.0, https://github.com/mikelove/DESeq2).
Assembly: mm10
Supplementary files format and content: counts file, each column is a sample

extract_protocol:
For RNA-sequencing, LUAD cells were harvested, pelleted, and flash frozen in liquid directly after sorting.
Once all samples were collected, RNA was harvested and library prepared with TruSeq RNA Library Prep Kit v2 for sequencing on a HiSeq4000 (Illumina).

treatment_protocol: LUAD cell lines were maintained in Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 10% Fetal Bovine Serum (FCS and incubated at 37°C in a carbon dioxide incubator. To reactivate p53, LUAD cell lines were treated with Ad5-CMV-Cre (University of Iowa Viral Vector Core), or cell lines were treated with Ad5-CMV-Empty (University of Iowa Viral Vector Core) to remains p53 null. Cell lines were infected at an MOI of 100. Cells were harvested for immunofluorescence, Western blotting, and RT-qPCR between 24-96 hours after infection.

value: LUAD cancer cells


title: mESC_WT rep3

value: ESCs

value: Control


title: KT, replicate 3, ATAC-seq 2

description:
ATAC-seq
AK3


title: Pool113_RS2_Plate5-6-G19-G23


title: HuhST1KO_IFNa_4h_rep1

value: human hepatocellular carcinoma cells


title: CAR_Emapalumab_Donor#3

type: RNA

city: Rome

first: Marika

last: Guercio

state: RM

address: Viale di San Paolo, 15

department: Oncohematology

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

description: Expression of 780 genes associated to essential pathways of CAR-T cell biology

hyb_protocol: 500 nanograms of total RNA were hybridized overnight with nCounter Reporter (20 μL) probes in hybridization buffer and excess of nCounter Capture probes (5 μL) at 65 °C for over night. After overnight hybridization, the abundance of specific target molecules was then quantified using the nCounter digital analyzer.

scan_protocol: Individual fluorescent barcodes and target molecules present in each sample were recorded with a CCD camera by performing a high-density scan (600 fields of view).

data_processing: Raw data processing, quality control, and normalization were performed using the nSolver™ 4.0 analysis software (NanoString nCounter Technologies, Seattle, WA). Background subtraction from raw transcript counts was performed through negative input controls. Normalization to 10 housekeeping genes and differential expression analysis were completed using the Advanced Analysis software plugin (version 2.0.115). For differential expression analysis, a p‐value of ≤0.05, were applied as cut-offs.

label: NanoString

source_name: PBMCs from Healthy Donor

label_protocol: All sample preparations were performed according to the manufacturer’s instructions (NanoString Technologies).

growth_protocol: PBMCs derived from buffy coats of HDs were isolated, activated, transduced with the retroviral CAR.CD19 construct and expanded in media conaining IL7 and IL 15 cytokines.

extract_protocol: RNA was isolated from samples using the RNeasy mini kit (Qiagen) according to supplier’s instructions.

treatment_protocol: Un-transduced (NT) and CAR.CD19 T-cells were activated with 0.5 μg/ml recombinant human CD19 Fc Chimera Protein for 16 hours in presence or absence of emapalumab (100mg/ml) before the analysis of the gene signature.

value: Emapalumab treated CAR T cells


title: NT_Emapalumab_Donor#3

value: Emapalumab treated NT T cells


title: CAR_Untrated_Donor#3

value: Untreated CAR T cells


title: Pool113_RS2_Plate5-6-G19-G12

value: brain

value: RSP


title: KT, replicate 2, ATAC-seq 2

description:
ATAC-seq
AK2


title: HuhST1KO_IFNa_2h_rep1

source_name: IFN alpha stimulated HuhST1KO cells, 2h

value: STAT1 knockout

value: IFN alpha, 1000U/ml


title: KT, replicate 1, ATAC-seq 2

description:
ATAC-seq
AK1

value: lung


title: Pool113_RS2_Plate5-6-G19-G11

value: PTLp

value: male


title: NT_Untrated_Donor#3

value: Untreated NT T cells


title: HuhST1KO_UN_rep2

source_name: unstimulated HuhST1KO cells

value: unstimulated


title: CAR_Emapalumab_Donor#2


title: 3 Q pos

city: Durham

first: Anthony

last: Filiano

state: NC

address: 701 West Main St.

department: Neurosurgery

institute: Duke University

description: co-cultured with human cord tissue derived MSC for 3 days

data_processing:
Raw FASTQ sequencing reads were chastity filtered to remove clusters having outlying intensity corresponding to bases other than the called base.
Filtered reads were assessed for quality using FastQC.
Transcript-level abundances were calculated using Salmon.
Transcript-level abundances were summarized into gene-level counts with tximport.
Genome_build: mm10

source_name: MSC preconditioned macrophages

growth_protocol: QTracker labeled MSCs were plated on fibronectin coated 6-well plated and 1 day after, T cell-depleted splenocytes were added, centrifuge briefly, and cultured for 3 days in RPMI 1640 containing  10% FBS, 1% penicillin/streptomycin and 25mM HEPES.

extract_protocol:
mRNA of collected cells were purified by RNeasy Mini kit
cDNA libraries were generated using KAPA Stranded RNA-Seq Kits

treatment_protocol: Cells were collected and stained with anti CD11b, Ly6G antibodies. Qtracker positive or negative CD11b+Ly6C- cells were sorted using MoFlo Astrios Cell Sorter and centrifuged (12000rpm, 3 min)

value: Sorted splenic macrophages

tag: engulfed human cord tissue derived mscs  (y/n)

value: Y

tag: surface marker

value: CD11b+ Ly6G-


title: HuhST1KO_UN_rep1


title: Pool113_RS2_Plate5-6-G19-F24

value: female


title: Pool113_RS2_Plate5-6-G19-F12


title: HuhIRF9KO_IFNy_72h_rep2

source_name: IFN gamma stimulated HuhIRF9KO cells, 72h

value: human hepatocellular carcinoma cells

value: IRF9 knockout

value: IFN gamma, 10 ng/ml


title: Pool113_RS2_Plate5-6-G19-F23


title: 2 Q pos


title: NT_Emapalumab_Donor#2

value: Emapalumab treated NT T cells


title: HuhIRF9KO_IFNy_72h_rep1


title: Pool113_RS2_Plate5-6-G19-E24

value: brain


title: CAR_Untrated_Donor#2

value: Untreated CAR T cells


title: HuhST1KO_IFNa_2h_rep2

value: STAT1 knockout


title: 2 Q neg

value: N


title: NT_Untrated_Donor#2


title: HuhIRF9KO_IFNy_24h_rep2

source_name: IFN gamma stimulated HuhIRF9KO cells, 24h


title: HuhIRF9KO_IFNy_24h_rep1


title: CAR_Emapalumab_Donor#1

value: Emapalumab treated CAR T cells


title: Pool113_RS2_Plate5-6-G19-E12

value: RSP

value: PTLp


title: 1 Q pos


title: HuhIRF9KO_IFNy_8h_rep2

source_name: IFN gamma stimulated HuhIRF9KO cells, 8h


title: 1 Q neg


title: Pool113_RS2_Plate5-6-G19-E11

value: male


title: 3 Q neg


title: NT_Emapalumab_Donor#1


title: HuhIRF9KO_IFNy_8h_rep1


title: NT_Untrated_Donor#1

value: Untreated NT T cells


title: L1_GFPminus_rep2

city: Fort Collins

first: Erin

last: Osborne Nishimura

state: CO

address: 1870 Campus Delivery, 200 W. Lake St.

department: Biochemistry and Molecular Biology

institute: Colorado State University

description:
RW055
L1_non-intestine_cells_merged.bw

data_processing:
Samples were assessed for quality and trimmed for adapter, primer, and polyX sequences by fastp (v 0.20.0) (Chen 2017; PMID: 30423086)
Trimmed reads were aligned separately to the ce11 genome using hisat2 (v 2.1.0) (Kim 2017; PMID: 31375807).
The number of reads associated with each gene model was tabulated for the C. elegans WS263 genome annotation using featureCounts (v 1.6.4) (Liao 2014; PMID: 24227677).
samtools (v 1.9) (Li 2009; PMID: 19505943), DeepTools (bamCoverage v 3.2.0) (Ramírez 2016; PMID: 27079975), and UCSC Kent Utilities were used to transform alignments into formats suitable for viewing on UCSC Genome Browser (Kent 2002; PMID: 12045153).
RNA-seq count data were filtered for detected genes (> 10 counts per million across all samples) and analyzed using DESeq2 (v 1.28.1) (Love 2014; PMID: 25516281) with default settings in the R Environment (v 4.0.3, BiocManager, v 1.30.10).
The raw counts (intestine_FACS_RNAseq_raw_counts.txt), normalized counts (intestine_FACS_RNAseq_norm_counts.txt), and normalized/variance-stabilized/log-transformed counts (intestine_FACS_RNAseq_rlog_counts.txt) are provided.
Assembly: C. elegans, ce11
Supplementary files format and content: .gtf file: c_elegans.PRJNA13758.WS263.canonical_geneset.gtf
Supplementary files format and content: .bw files were generated using bamCoverage, part of the DeepTools package
Supplementary files format and content: merged.bw files were merged by replicate using UCSC Kent Utilities
Supplementary files format and content: counts tables were generated from featureCounts tabultion and then processed within DESeq2: intestine_FACS_RNAseq_norm_counts.txt; intestine_FACS_RNAseq_raw_counts.txt; intestine_FACS_RNAseq_rlog_counts.txt

organism: Caenorhabditis elegans

source_name: sorted non-intestine cells

growth_protocol: C. elegans strains were cultered on 150 mm NGM agar plates seeded with 3 ml of OP50 liquid culture. Two rounds of synchronization were performed and then harvested at the approporate stage.

extract_protocol:
Total RNA was extracted using an miRNeasy micro kit (Qiagen 217084).
mRNA was prepared for sequencing using the NEB Next Ultra II RNA Library Prep Kit for Illumina (NEB E7770S) and Poly(A) Magnetic Isolation Module (NEB E7490S).
Libraries of a median 200 - 400 bp length were generated. Libraries RW047-RW055 were sequenced at 2 x 150 bp on a HiSeq X-ten to a read depth of 100 million paired end reads. Libraries RW057-RW089 were sequenced at 2 x 150 bp on NovaSeq 6000 to a read depth of  40 to 100 million paired end reads.

treatment_protocol: Worms were washed 3 times in sterile M9 before cell dissociation to remove excess OP50 E. coli.

value: sorted non-intestine cells

value: non-intestine

tag: Stage

tag: biological replicate

value: 2 min SDS-DTT treatment, 30 min pronase E treatment

value: 100 strokes dounce pestle A


title: L1_GFPplus_rep2

description:
RW054
L1_intestine_cells_merged.bw

source_name: sorted intestine cells

value: sorted intestine cells

value: intestine

value: 300,000 GFP+ cells


title: Kc167_RNApolIIRpb3_Doxorubicin_Rep3_(230301_MW_DmHs_AB8_22223_9)

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: CUT&Tag data profiling Total RNA pol II (Rpb3 subunit) in Drosophila melanogaster cells treated with doxorubicin for 30 minutes

data_processing:
Genome_build: dm6
1. We used cutadapt 2.9 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 2.4.2 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the dm6 Drosophila melanogaster reference sequence obtained from UCSC. 3. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the same paired-end 50bp reads to the masked hg19 Homo sapiens reference sequence obtained from UCSC. 4. We extracted properly paired reads from the D. melanogaster alignments. 5. We counted the properly paired reads from the Homo sapiens alignments. 6. We used bedtools 2.30.0 genomecov to make a normalized count dm6 track which is the fraction of counts at each base pair scaled by the size of the dm6 reference sequence (137567484) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .norm.bw) 7. We used bedtools 2.30.0 genomecov with a scaling factor of (10000/number of fragments mapped to masked hg19) to create a calibrated dm6 track file (Supplementary file .Hs_spike.bw).

organism: Drosophila melanogaster

source_name: CUT&Tag

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v11
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

value: Anti-Rpb3 Bethyl Laboratories Catalog # A303-771A

value: :Kc167 Drosophila melanogaster cell line originally derived from disaggregated 8-12 hour embryos.


title: CAR_Untrated_Donor#1

value: Untreated CAR T cells


title: Pool113_RS2_Plate5-6-G19-D24

value: brain

value: female


title: HuhIRF9KO_IFNy_4h_rep2

source_name: IFN gamma stimulated HuhIRF9KO cells, 4h

value: human hepatocellular carcinoma cells

value: IRF9 knockout

value: IFN gamma, 10 ng/ml


title: Kc167_RNApolIIRpb3_Doxorubicin_Rep2_(230301_MW_DmHs_AB8_22223_2)

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v10
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


title: Pool113_RS2_Plate5-6-G19-D23

value: RSP

value: PTLp

value: male


title: HuhIRF9KO_IFNy_4h_rep1


title: Pool113_RS2_Plate5-6-G19-D11


title: L1_whole_rep2

description:
RW052
L1_whole_merged.bw

source_name: whole worms

value: whole worms

value: all

value: 10ul of packed worm pellet


title: Pool113_RS2_Plate5-6-G19-E23

source_name: brain


title: HuhIRF9KO_IFNy_2h_rep2

source_name: IFN gamma stimulated HuhIRF9KO cells, 2h


title: L1_GFPminus_rep1

description:
RW050
L1_non-intestine_cells_merged.bw

value: sorted non-intestine cells

value: non-intestine

value: 2 min SDS-DTT treatment, 30 min pronase E treatment

value: 100 strokes dounce pestle A


title: Pool113_RS2_Plate5-6-G19-C24


title: HuhIRF9KO_IFNy_2h_rep1


title: Pool113_RS2_Plate5-6-G19-C23


title: Kc167_RNApolIIRpb3_Control_Rep1_(230301_MW_DmHs_AB8_22223_7)

description: CUT&Tag data profiling Total RNA pol II (Rpb3 subunit) in Drosophila melanogaster cells treated with DMSO vehicle for 30 minutes

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v3
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

value: Anti-Rpb3 Bethyl Laboratories Catalog # A303-771A

value: :Kc167 Drosophila melanogaster cell line originally derived from disaggregated 8-12 hour embryos.


title: Pool113_RS2_Plate5-6-G19-C11

value: brain


title: L1_GFPplus_rep1

description:
RW049
L1_intestine_cells_merged.bw

value: sorted intestine cells

value: intestine

value: 300,000 GFP+ cells


title: Kc167_RNApolIIRpb3_Control_Rep3_(230301_MW_DmHs_AB8_22223_12)

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v5
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


title: Kc167_RNApolIIRpb3_ActinomycinD_Rep3_(230301_MW_DmHs_AB8_22223_11)

description: CUT&Tag data profiling Total RNA pol II (Rpb3 subunit) in Drosophila melanogaster cells treated with actinomycin D for 30 minutes

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v14
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


title: Pool113_RS2_Plate5-6-G19-B24

value: female


title: L1_cells_rep2

description:
RW053
L1_dissociated_cells_merged.bw

source_name: dissociated worm cells

value: dissociated worm cells

value: 70ul of cell suspension


title: HuhIRF9KO_IFNa_24h_rep2

source_name: IFN alpha stimulated HuhIRF9KO cells, 24h

value: human hepatocellular carcinoma cells

value: IRF9 knockout

value: IFN alpha, 1000U/ml


title: L1_whole_rep1

description:
RW047
L1_whole_merged.bw

value: whole worms

value: all

value: 10ul of packed worm pellet


title: HuhIRF9KO_IFNa_72h_rep1

source_name: IFN alpha stimulated HuhIRF9KO cells, 72h


title: Kc167_RNApolIIRpb3_Doxorubicin_Rep1_(230301_MW_DmHs_AB8_22223_1)

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v9
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


title: Kc167_RNApolIIRpb3_ActinomycinD_Rep2_(230301_MW_DmHs_AB8_22223_6)

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v13
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


title: Kc167_RNApolIIRpb3_ActinomycinD_Rep1_(230301_MW_DmHs_AB8_22223_5)

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v12
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


title: 15d organoids, ind rep2

city: Berlin

first: Ivano

last: Legnini

address: Hannoversche Strasse 28

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrueck Center for Molecular Medicine in the Helmholtz Association

description: Single-cell RNA-seq

data_processing:
All data obtained from the BIMSB Genomics platform, after basecalling and demultiplexing
Single-cell RNA-seq data were processed with the Spacemake pipeline (https://github.com/rajewsky-lab/spacemake/)
Genome_build: GRCh38
Supplementary_files_format_and_content: Plain text files containing gene counts per cell; cell barcodes as columns and genes as rows

source_name: HiPSC (XMO01)

growth_protocol: HiPSCs were cultured in E8 flex medium (Gibco #A14133-01) with medium replacement every other day until 80% confluency, in the dark. The differentiation protocol was adapted from Zheng et al. (2019). HiPSC colonies were rapidly washed with PBS (Pan Biotech P0436500) and then incubated with accutase (Sigma, #A6964-100ML) for 4 minutes at 37°C. Cells were collected, centrifuged for 3 minutes at 300 g and resuspended in E8 flex medium containing 10 mM Y27632 ROCK inhibitor (VWR, #688000-5). Cells were counted and plated at a density of 500 cells per well in a 96-well ultra-low attachment U-bottom plate (Corning, #CLS7007). On the following day, the medium was replaced with fresh N2-B27 medium (50% Neurobasal (Gibco #A3582901), 50% DMEM/F12 (Gibco, #11320074), 1x N2 (Gibco #17504044), 1x B27 (Gibco, #17504044), 1x MEM non-essential amino acids (Sigma; M7145-100ML), 1x Glutamax (Gibco, #35050038), 0.1 mM b-mercaptoethanol (Merck Millipore #8057400005) supplemented with 2% Geltrex (Gibco, #A1413301), 10 mM TGF-b pathway inhibitor (SB431542, Stem cell technology, #72234 ) and ) 0.1 mM BMP inhibitor (LDN193189, Stem cell technology, #72147). Medium was exchanged daily. From day 4 on, organoids were cultured in 35 mm dishes, medium was additionally supplemented with 1 mM retinoic acid (RA, Sigma, #R2625) until day 8. At day 9, RA was removed, organoids were further cultured in N2B27 medium supplemented with LDN and SB until day 16. For organoids optogenetic stimulations, the same protocol as before was used, but the medium was supplemented with 1mg/ml doxycycline to activate PA-Cre expression at day 3. On the next day, four organoids at once were embedded in a drop of Geltrex on a glass bottom dish (WillCo-dish, #GWSB3522), incubated for 15 min at 37°C and covered with warm N2B27 medium (supplemented with SB, LDN and RA).

extract_protocol:
No RNA extraction was performed for the scRNA-seq data generation (see library construction protocol)
Cells were encapsulated together with barcoded microparticles (Macosko- 2011-10 V+, ChemGenes) using the Dolomite Bio Nadia instrument, using the standard manufacturer’s dropseq-based scRNA-seq protocol. Droplets were broken immediately after collection and cDNA libraries generated as previously described (Wyler et al., 2021). First strand cDNA was amplified by equally distributing beads from one run to 24 Smart PCR reactions (50 μl volume; 4 + 9 to 11 cycles). 20 μl fractions of each PCR reaction were pooled, then double-purified with 0.6 volumes of AMPure XP beads. Amplified cDNA libraries were assessed and quantified on a BioAnalyzer High Sensitivity Chip (Agilent) and the Qubit dsDNA HS Assay. Nine-hundred pg of each cDNA library was fragmented, amplified (13 cycles) and indexed for sequencing with the Nextera XT v2 DNA sample preparation kit (Illumina) using custom primers enabling 3’-targeted amplification. The libraries were purified with AMPure XP Beads, quantified and sequenced on Illumina sequencers (first run: concentration 2pM; Hiseq 3000/4000 SBS kit (150 cycles) paired-end mode; read 1=75 using the custom primer Read1custseqB (8bp) read 2=75. Second run: concentration 2 pM; NextSeq 500/550 High Output v2 kit (75 cycles) in paired-end mode; read 1 = 21 bp using the custom primer Read1CustSeqB (8 bp) read 2 = 63 bp).
Single-cell RNA-seq (Drop-seq)

treatment_protocol: To induce SHH expression in a restricted pole of the organoids, a laser scanning setup was used (Leica Sp8 SMD): a small square ROI of ca. 100-400 mM was selected depending on how the four organoids were positioned with respect to each other, induced for two times 5 seconds at 100Hz with 1% laser power set at 480 nm, every 30 seconds overnight (16 hours). After induction, organoids were retrieved with a pipette and cultured individually until day 16 in an ultra-low attachment 24-well plate (Corning #CLS3473). Control organoids were not induced. Media was exchanged daily with fresh N2B27 supplemented with SB, LDN, 2% Geltrex and RA until day 8. From day 9 onwards, RA was removed as described before.

tag: stable line

value: PA-Cre/Lox, LoxP RFP LoxP SHH NG

tag: time of induction

value: 18h induction, see protocol


title: HuhIRF9KO_IFNa_24h_rep1

tag: cell type


title: Kc167_RNApolIIRpb3_Aclarubicin_Rep3_(230301_MW_DmHs_AB8_22223_10)

description: CUT&Tag data profiling Total RNA pol II (Rpb3 subunit) in Drosophila melanogaster cells treated with aclarubicin for 30 minutes

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v8
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

value: Anti-Rpb3 Bethyl Laboratories Catalog # A303-771A


title: Kc167_RNApolIIRpb3_Aclarubicin_Rep2_(230301_MW_DmHs_AB8_22223_4)

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v7
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

value: :Kc167 Drosophila melanogaster cell line originally derived from disaggregated 8-12 hour embryos.


title: 15d organoids, ind rep1

description: Single-cell RNA-seq


title: 15d organoids, ctr rep2

description: Single-cell RNA-seq

value: non induced (0h), see protocol


title: Kc167_RNApolIIRpb3_Control_Rep2_(230301_MW_DmHs_AB8_22223_8)

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-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


title: 10x Multiome - Control ATAC

city: Montreal

first: Awais

last: Javed

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

description: Tamoxifen at 14 days

data_processing:
scRNA-seq sequencing data were aligned to the mm10 genome using CellRanger version 6.1.2 (Cell Ranger software, 10x Genomics,). Filtered output files were analyzed in Python (Python core team, Python) using Scanpy version 1.9.1 (Wolf et al., 2018). Genes detected in less than 3 cells were removed from the analysis and low-quality cells (less than 200 genes detected, more than 2500 genes detected or more than 5% of mitochondrial genes) were removed from the datasets. To assign individual cell types, scDeepSort version 1.0 (Shao et al., 2021) was used alongside with deep learning trained model grounded on previously published retinal single cell expression data (Clark et al., 2019). Full YFP and mCherry sequences were reconstructed using RNA-Bloom version 1.4.3 (Nip et al., 2020) and Trinity version 2.14.0 (Grabherr et al., 2011), and then remapped to the initial sequencing data. Doublets were identified using Scrublet version 0.2.2 (Wolock et al., 2019) and removed before downstream analysis. Batch correction, data integration, gene expression plotting, differential expression data and further analysis were performed using scVI-tools version 0.19.0 (Gayoso et al., 2022).
Multiome sequencing data were aligned to the mm10 genome using Cell Ranger ARC version 2.0 (Cell Ranger ARC software, 10x Genomics). Filtered output files were analyzed in R (R Core Team, The R project for Statistical Computing) using the Signac package version 1.8.0 (Stuart et al., 2021). Low-quality cells were removed from datasets accordingly to Signac’s standard processing guidelines (cells with less than 1000 ATAC read counts detected, more than 100000 ATAC read counts detected, less than 1000 RNA reads count, more than 25000 RNA reads count, cells with the ratio of mononucleosomal (147–294 bp) to nucleosome-free (<147 bp) fragments higher than 2 or cells the transcription start site enrichment score less than 1. Individual cell types, full YFP and mCherry sequence reconstruction and mapping were performed as described on the section above; scATAC-seq reads were not used to reconstruct the YFP and mCherry sequences, since such reads could potentially be detected irrespective of the excision of the floxed stop cassette. Using the Signac object and the barcoded fragment files, peaks calling were performed using MACS2 (Zhang et al., 2008) under the Signac’s “CallPeaks” function. In order to map Fragments to the peaks and assign them to individual cells, the “FeatureMatrix” function was used. Dataset integration and low dimensional embeddings were done using Signac’s “Merge” and “IntegrateEmbeddings” functions. Data was normalized using the SCTransform, which has been integrated into Signac (Hafemeister & Satija, 2019). In order to get a representing weighted combination of both snRNA-seq and scATAC-seq modalities, Signac’s “RunUMAP” function alongside with its Weighted Nearest Neighbor (WNN) option was used and UMAP embeddings computed. Differential gene expression and differential peaks were accessed by using Signac’s “FindMarkers” function using its logistic regression framework (LR). Differential peaks were assigned to genes using the function “peaks2genes” available on R’s library ChIP-Enrich version 2.14.0 (Welch et al., 2014). Differential gene expression and differential peaks tables were manipulated using PostgreSQL version 14.3 (PostgreSQL Core Team, PostgreSQL) and Python’s library Pandas version 1.5.2 (Pandas Core Team, Pandas).
Raw ATAC-seq fastq reads were aligned using bowtie2 mm9 genome on Galaxy platform. MACS2 was used for peak calling using these parameters: --nomodel --shift -37 --extsize 73 . Bamcoverage was used to generate bigwig files.
Salmon quant function was used to quantify effective length of transcripts and transcript per million value from RNA-seq raw fastq reads using mm10 transcriptome. Salmon quants output files were used to calculate Log2FC and statistical values using DESeq2 for differential analysis. Annotate DESeq2 package on Galaxy platform was used to annotate gene_ids to symbols.
Assembly: mm10, mm9
Supplementary files format and content: Scanpy.loom files containing count matrix, features and barcodes. .h5 files containing cellranger or cellranger-arc output count matrix, features and barcodes whereas .tsv file containing aligned fragment coordinates.
Supplementary files format and content: Bigwig tracks files for ATAC-seq conditions and bed peak files for scored peaks.
Supplementary files format and content: Matrix table with Log2FC and FDR values of comparisons between the two conditions.

source_name: Retina

extract_protocol: none provided

value: Muller glia

tag: mouse line

value: GLAST-CRE ERT2 ; RosaYFP

tag: strain

tag: condition

value: mCherry


title: 10x Multiome - Ikzf1/4 ATAC

description: Tamoxifen at 14 days

source_name: 10x Multiome - Ikzf1/4

value: 10x Multiome - Ikzf1/4


title: 15d organoids, ctr rep1

description: Single-cell RNA-seq


title: Kc167_RNApolIIRpb3_Aclarubicin_Rep1_(230301_MW_DmHs_AB8_22223_3)

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v6
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


title: L1_cells_rep1

description:
RW048
L1_dissociated_cells_merged.bw

value: dissociated worm cells

tag: genotype

tag: treatment

value: 2 min SDS-DTT treatment, 30 min pronase E treatment

value: 100 strokes dounce pestle A


title: RS Clone 2 scRNA-seq

city: newberry

first: Shane

middle: A

last: Evans

state: Florida

address: 22806 West Newberry Road

department: Bio Med

institute: Brown University

description: Clonal line 2 RS cells. In regular growth media when harvested.

data_processing:
Aligned Using Cell Ranger version 2.1.0
Analysis in Seurat version 3
DE analysis with SCDE
Pathway analysis GSEA
Upstream Regulator Analysis with IPA
Genome_build: hg19
Supplementary_files_format_and_content: CellRanger 2.1.0 outputs

molecule: polyA RNA

source_name: cell culture

extract_protocol:
Cells were lightly trypsinized off of the plate and then processed according to 10x instructions
10x 3 prime Version 2 chemsitry and VDJ chemistry was used for 5' libraries.

treatment_protocol: DDIS: 40uM Etoposide 3 days. OIS: 4OHT 200nM. OIS was achieved after 6 days of hyperprlofieration following the addition of 4OHT. Navitoclax: 1uM for 3 days

value: embryonic lung fibroblast

tag: transgene

value: Infected with 4-OHT HRAS:G12V

tag: clonal line

value: Clonal line 2


title: 10x Multiome - Control GEX

description: Tamoxifen at 14 days

library_source: transcriptomic single cell


title: 10x Multiome - Ikzf1/4 GEX

description: Tamoxifen at 14 days


title: RS Clone 1 scRNA-seq

description: Clonal line 1 RS cells. In regular growth media when harvested.

value: Clonal line 1


title: HuhIRF9KO_IFNa_4h_rep1

source_name: IFN alpha stimulated HuhIRF9KO cells, 4h

extract_protocol:
Total RNA was isolated using TRI-REAGENT (MRC) followed by a column-based Total RNA Zol-Out™ D kit (A&A Biotechnology) following the manufacturer's protocol
RNA-seq libraries were prepared in two biological replicates from 1ug of total RNA using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) together with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext® Multiplex Oligos for Illumina® (NEB) according to manufacturer's protocol

tag: cell line

value: human hepatocellular carcinoma cells

value: IRF9 knockout

value: IFN alpha, 1000U/ml

tag: time


title: DDIS Nav Clone 1 scRNA-seq

description: Clonal line 1 DDIS cells. Used Etoposide to induce DDIS, Kept in Nav for 3 days. Then kept in DMSO for 1 day before harvesting.


title: HuhIRF9KO_IFNa_2h_rep2

source_name: IFN alpha stimulated HuhIRF9KO cells, 2h


title: Brain, O. tsutsugamushi-infected C57BL/6 mice, Day10, replicate 3, RNAseq

city: Galveston

first: Lynn

last: Soong

state: TX

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

data_processing:
Data processing done by LC Sciences (Houston, TX, US). Their methods are described below.
Sequence and filtering of Clean Reads: A cDNA library constructed by technology from the pooled RNA from < sample description > samples of <research species > was sequenced run with Illumina Novaseq  TM 6000 sequence platform. Using the Illuminapaired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-endreads. Reads obtained from the sequencing machines includes raw reads containing adapters or lowqualitybaseswhich will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further  filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). The parameters were as  follows:  1) removing reads containing adapters;  2) removing reads containing polyA and polyG;  3) removing reads containing more than 5% of unknown nucleotides (N);  4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced. The raw sequence data have been submittedto the NCBI Gene Expression Omnibus (GEO) datasets with accession number < GEO accession >  or NCBI Short Read Archive (SRA) with accession number with accession number < SRA accession >.
Alignment with Reference Genome: we aligned reads of all samples to the < research species > reference genome using HISAT2  (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of thereads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch whenmappingthe reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparingthe previously unmapped reads against the database of putative junctions.
Quantification of Gene Abundance: The mapped reads of each sample were assembled using StringTie  (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomesfrom all samples were merged to reconstruct a comprehensive transcriptome using gffcompare  software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown  (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expressionlevels of all transcripts and perform expression abundance for mRNAs by calculating FPKM(fragment per kilobaseof transcript per million mapped reads) value.
Differentially expressed genes (DEGs) Analysis: Genes differential expression analysis was performed by DESeq2 software between two different groups (andbyedgeR between two samples). The genes with the parameter of false discovery rate (FDR) below0.05 andabsolutefold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjectedto enrichment analysis of GO functions and KEGG pathways
The Mus musculus genome build mm10 was used as a reference genome. Quality control analysis was done by using FastQC (Andrews, 2010) and RSeQC6 (Wang, Bioinformatics, 2012). Semi-supervised hierarchical clustering analysis and heatmap generation were performed by using the Morpheus tool. Principal component analysis and volcano plot were done in R using PCAtools and EnhancedVolcano packages.         GSEA analysis    Pathway enrichment analysis using gene set enrichment analysis with GSEA version 3.0 was performed with a ranked gene list (33, 34). Specifically, ranked gene list is prepared from the differential gene expression analysis by using the following metrics: sign of the Log2fold change multiplied by the inverse of the p-value. GSEAPreranked was run with 2000 permutations. Primary gene sets investigated were obtained from the MSigDB and published reports. GSEA FDR Q <0.05 cutoff was applied to examine enriched gene sets in our dataset.         Cytoscape analysis    Enrichment results from the GSEA analysis were visualized using Cytoscape. GSEA output files were uploaded in the EnrichmentMap app of Cytoscape and FDR Q value cut off was set to 0.01. Clusters are automatically defined using AutoAnnotate Cytoscape app.         Statistical Analysis    Data were presented as mean ± standard error of mean (SEM). Differences between individual treatment and control groups were determined by using unpaired Student’s t test, utilizing Welch’s correction when appropriate. One-way ANOVA was used for multiple group comparisons, with a Tukey’s Post Hoc for comparisons between groups. All data were analyzed by using GraphPad Prism software 8.0. Statistically significant values are denoted as *, p < 0.05; **; p < 0.01, ***; p < 0.001, and ****; p < 0.0001, respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Brain

extract_protocol:
Female C57BL/6J mice (6-9 weeks-old, purchased from the Jackson Laboratory #000664) were intravenously inoculated with a lethal dose (6 × 10e4 FFU, 200 µl) of bacteria or PBS (mock). Mice were sacrificed at established timepoints, and spleens were collected in RPMI 1640 medium. Spleen single-cell suspensions were made by passing splenic tissue through a 70-μm cell strainer in RPMI 1640 medium, and these were then treated with Red Blood Cell Lysis Buffer. Untouched B cells were isolated from spleen single-cell suspensions by using the mouse B Cell Isolation Kit (Miltenyi Biotec). B cell samples were then evaluated for purity (~97-98%, based on B220 expression assessed by flow cytometry) and stored in RNALater. Total RNA was extracted by using the RNeasy Mini kit (Qiagen). Total RNA (≥ 1ug) was sent to LC Sciences (Houston, TX) for Poly(A) RNA-Seq Sequencing Service.
The total RNA quantity and purity were analyzed by the Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). High-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. mRNA was purified from total RNA using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat. e6150, USA, under 94℃ 5-7min). Then, the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were then used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat. m0209, USA), RNase H (NEB, cat. m0297, USA) and dUTP Solution (Thermo Fisher, cat. R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat. m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec, and then final extension at 72℃ for 5 min. The average insert sizes for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150 bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC Sciences, Houston, TX, US) following the vendor's recommended protocol.

tag: tissue

value: Brain

tag: age

value: 8-12 weeks

value: O. tsutsugamushi lethal dose

value: Day 10


title: Brain, O. tsutsugamushi-infected C57BL/6 mice, Day10, replicate 2, RNAseq


title: HuhIRF9KO_IFNa_8h_rep2

source_name: IFN alpha stimulated HuhIRF9KO cells, 8h


title: Kc167_RNApolIIser5P_Doxorubicin_Rep6_(220819_BT_DmHs_BT1194_P51)

description: CUT&Tag data profiling paused RNA pol II (ser5P) in Drosophila melanogaster cells treated with doxorubicin for 30 minutes

value: anti-Phospho-Rpb1 CTD (Ser5) (D9N5I) #13523s

value: Kc167 Drosophila melanogaster cell line originally derived from disaggregated 8-12 hour embryos.


title: HuhIRF9KO_IFNa_2h_rep1


title: Brain, O. tsutsugamushi-infected C57BL/6 mice, Day10, replicate 1, RNAseq


title: Brain, O. tsutsugamushi-infected C57BL/6 mice, Day6, replicate 3, RNAseq

value: Day 6


title: HuhIRF9KO_UN_rep2

source_name: unstimulated HuhIRF9KO cells

value: unstimulated


title: DDIS Clone 1 scRNA-seq

description: Clonal line 1 DDIS cells. Used Etoposide to induce DDIS, and were in DMSO when harvested.


title: Kc167_RNApolIIser5P_Doxorubicin_Rep3_(220324_MW_DmHs_AA80_31622_9)

description: CUT&Tag data profiling paused RNA pol II (ser5P) in Drosophila melanogaster cells treated with aclarubicin for 30 minutes

source_name: CUT&Tag


title: OIS Nav Clone 1 5Prime scRNA-seq

description: Clonal line 1 OIS cells. Used 4OHT to induce OIS, Kept in Nav for 3 days. Then kept in DMSO for 1 day before harvesting.  Sequenced from 5' end.


title: HuhIRF9KO_IFNa_4h_rep2


title: HuhIRF9KO_UN_rep1


title: OIS Clone 1 5Prime scRNA-seq

description: Clonal line 1 OIS cells. Used 4OHT to induce OIS, and were in DMSO when harvested. Sequnced from 5' end.


title: HuhIRF1KO_IFNy_72h_rep2

source_name: IFN gamma stimulated HuhIRF1KO cells, 72h

value: IRF1 knockout

value: IFN gamma, 10 ng/ml


title: Kc167_RNApolIIser5P_Doxorubicin_Rep2_(220317_MW_DmHs_AA78_3722_2)


title: Kc167_RNApolIIser5P_Doxorubicin_Rep5_(220819_BT_DmHs_BT1193_P51)


title: OIS Nav Clone 1 scRNA-seq

description: Clonal line 1 OIS cells. Used 4OHT to induce OIS, Kept in Nav for 3 days. Then kept in DMSO for 1 day before harvesting.

value: embryonic lung fibroblast


title: Brain, O. tsutsugamushi-infected C57BL/6 mice, Day2, replicate 3, RNAseq

value: Day 2


title: Kc167_RNApolIIser5P_Doxorubicin_Rep1_(220317_MW_DmHs_AA78_3722_1)


title: OIS Clone 1 scRNA-seq

description: Clonal line 1 OIS cells. Used 4OHT to induce OIS, and were in DMSO when harvested.

value: Infected with 4-OHT HRAS:G12V


title: Kc167_RNApolIIser5P_Control_Rep5_(220819_BT_DmHs_BT1190_P51)

description: CUT&Tag data profiling paused RNA pol II (ser5P) in Drosophila melanogaster control cells treated with DMSO vehicle.


title: Kc167_RNApolIIser5P_Doxorubicin_Rep4_(220324_MW_DmHs_AA80_31622_10)


title: Kc167_RNApolIIser5P_Control_Rep4_(220819_BT_DmHs_BT1189_P51)


title: OIS 4OHT Clone 1 scRNA-seq

description: Clonal line 1 OIS cells. Were in 4OHT when harvested.

value: Clonal line 1


title: Brain, O. tsutsugamushi-infected C57BL/6 mice, Day2, replicate 1, RNAseq


title: HuhIRF1KO_IFNy_72h_rep1

value: human hepatocellular carcinoma cells


title: Brain, O. tsutsugamushi-infected C57BL/6 mice, Day2, replicate 2, RNAseq


title: Brain, O. tsutsugamushi-infected C57BL/6 mice, Day6, replicate 2, RNAseq


title: HuhIRF1KO_IFNy_24h_rep1

source_name: IFN gamma stimulated HuhIRF1KO cells, 24h


title: Kc167_RNApolIIser5P_Control_Rep3_(220324_MW_DmHs_AA80_31622_16)


title: Brain, PBS mock-infected C57BL/6 mice, Day0, replicate 3, RNAseq

value: PBS

value: Day 0


title: HuhIRF1KO_IFNy_8h_rep2

source_name: IFN gamma stimulated HuhIRF1KO cells, 8h


title: Kc167_RNApolIIser5P_Control_Rep2_(220324_MW_DmHs_AA80_31622_15)


title: Brain, O. tsutsugamushi-infected C57BL/6 mice, Day6, replicate 1, RNAseq

value: Brain


title: Kc167_RNApolIIser5P_Control_Rep1_(220317_MW_DmHs_AA78_3722_7)


title: HuhIRF1KO_IFNy_8h_rep1


title: Brain, PBS mock-infected C57BL/6 mice, Day0, replicate 2, RNAseq

value: 8-12 weeks


title: Proliferating Clone 1 Bio Rep 2 scRNA-seq

description: Clonal line 1 Proliferating cells Bio Rep1.  Kept in Regular Growth Media.


title: Proliferating Clone 2 Bio Rep 2 scRNA-seq

description: Clonal line 2 Proliferating cells Bio Rep2.  Kept in Regular Growth Media.

value: Clonal line 2


title: Brain, PBS mock-infected C57BL/6 mice, Day0, replicate 1, RNAseq


title: Kc167_RNApolIIser5P_ActinomycinD_Rep5_(220819_BT_DmHs_BT1196_P51)

description: CUT&Tag data profiling paused RNA pol II (ser5P) in Drosophila melanogaster cells treated with actinomycin D for 30 minutes


title: Proliferating Clone 2 Bio Rep 1 scRNA-seq


title: HuhIRF1KO_IFNy_4h_rep2

source_name: IFN gamma stimulated HuhIRF1KO cells, 4h


title: HuhIRF1KO_IFNy_24h_rep2


title: mESCs,TT-Ago2-OE:Lis1 F/- ErT2 (+Dox), FBS+LIF condition, Rep#4 - totalRNA-seq

description: Biological replicate4

data_processing:
Sequenced reads were trimmed for adaptor sequence using Cutadapt and were aligned with STAR.
Raw counts were processed with qCount, and normalized reads were obtained by DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: raw count quantification files

source_name: mouse embryonic stem cells

extract_protocol:
Total RNA was extracted from cells, using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
Strand specific mRNA library prep kit

value: mouse embryonic stem cells

tag: culture medium

value: FBS+LIF

value: Lis1 Floxed/- (F/-):Ert2-Cre; Dox. AGO2 overexpression (XLONE-RFP-TT-AGO2)

value: hybrid


title: Proliferating Clone 1 Bio Rep 1 scRNA-seq

description: Clonal line 1 Proliferating cells Bio Rep1. Kept in Regular Growth Media.


title: HuhIRF1KO_IFNy_4h_rep1


title: Kc167_RNApolIIser5P_ActinomycinD_Rep4_(220819_BT_DmHs_BT1195_P51)

value: anti-Phospho-Rpb1 CTD (Ser5) (D9N5I) #13523s

value: Kc167 Drosophila melanogaster cell line originally derived from disaggregated 8-12 hour embryos.


title: Kc167_RNApolIIser5P_ActinomycinD_Rep3_(220324_MW_DmHs_AA80_31622_13)


title: mESCs,TT-Ago2-OE:Lis1 F/- ErT2 (+Dox), FBS+LIF condition, Rep#3 - totalRNA-seq

description: Biological replicate3


title: HuhIRF1KO_IFNy_2h_rep2

source_name: IFN gamma stimulated HuhIRF1KO cells, 2h

value: IRF1 knockout

value: IFN gamma, 10 ng/ml


title: HuhIRF1KO_IFNy_2h_rep1


title: Kc167_RNApolIIser5P_ActinomycinD_Rep2_(220317_MW_DmHs_AA78_3722_6)


title: mESCs,TT-Ago2-OE:Lis1 F/- ErT2 (+Dox), FBS+LIF condition, Rep#1 - totalRNA-seq

description: Biological replicate1


title: mESCs,TT-Ago2-OE:Lis1 F/- ErT2 (+Dox), FBS+LIF condition, Rep#2 - totalRNA-seq

description: Biological replicate2


title: HuhIRF1KO_IFNa_72h_rep2

source_name: IFN alpha stimulated HuhIRF1KO cells, 72h

value: IFN alpha, 1000U/ml


title: mESCs,TT-Ago2-OE:Lis1 F/- ErT2, FBS+LIF condition, Rep#4 - totalRNA-seq

description: Biological replicate4

value: Lis1 Floxed/- (F/-):Ert2-Cre


title: mESCs,TT-Ago2-OE:Lis1 F/- ErT2, FBS+LIF condition, Rep#3 - totalRNA-seq

description: Biological replicate3


title: HuhIRF1KO_IFNa_24h_rep2

source_name: IFN alpha stimulated HuhIRF1KO cells, 24h


title: HuhIRF1KO_IFNa_72h_rep1


title: Kc167_RNApolIIser5P_Aclarubicin_Rep5_(220819_BT_DmHs_BT1191_P51)


title: Kc167_RNApolIIser5P_Aclarubicin_Rep4_(220324_MW_DmHs_AA80_31622_12)


title: mESCs,TT-Ago2-OE:Lis1 F/- ErT2, FBS+LIF condition, Rep#2 - totalRNA-seq

description: Biological replicate2


title: HuhIRF1KO_IFNa_24h_rep1


title: mESCs,TT-Ago2-OE:Lis1 F/- ErT2, FBS+LIF condition, Rep#1 - totalRNA-seq

description: Biological replicate1


title: Kc167_RNApolIIser5P_Aclarubicin_Rep3_(220324_MW_DmHs_AA80_31622_11)


title: Kc167_RNApolIIser5P_Aclarubicin_Rep2_(220317_MW_DmHs_AA78_3722_4)

value: Phospho-Rpb1 CTD (Ser2) (E1Z3G)


title: intestine, NEC, rep3

city: Shanghai

first: Ting

last: Guo

state: Shanghai

address: Shanghai Putuo District,Luding road No.355

department: Department of General surgery

institute: Shanghai Children's Hospital

data_processing:
In RNA sequencing analysis, raw gene count matrix is calculated using RNACocktail pipeline (https://www.nature.com/articles/s41467-017-00050-4)
Assembly: mm10
Supplementary files format and content: csv file representing counts

source_name: intestine

growth_protocol: Con group mice were fed with dam. NEC group mice were fed with  40 μl of 33% Esbilac formula (Pet-Ag, Abbott Laboratories) every 4 h for 96 h.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) and chloroform, and RNA integrity was assessed using an RNA Nano 6000 Assay Kit for the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The library preparations were sequenced on the Illumina NovaSeq platform, and 150 bp paired-end reads were generated.

treatment_protocol:
NEC group mice was induced using formula gavage every 4 h for 96 h using 40 μl of 33% Esbilac formula (Pet-Ag, Abbott Laboratories). Meanwhile, pups were exposed to hypoxia treatments (99.9% N2 for 100 s), followed by cold stress (4 °C for 10 min) every 12 h. The control group were dam-fed without hypoxia and cold stress.
All animals were euthanized after 96 h.

value: intestine

value: WT

tag: group

value: NEC


title: HuhIRF1KO_IFNa_8h_rep2

source_name: IFN alpha stimulated HuhIRF1KO cells, 8h

value: human hepatocellular carcinoma cells


title: Kc167_RNApolIIser5P_ActinomycinD_Rep1_(220317_MW_DmHs_AA78_3722_5)

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v3
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


title: S18

city: BARCELONA

first: Leire

last: Pedrosa

state: Barcelona

address: Carrer del Villarroel 170

country: Spain

institute: IDIBAPS

hyb_protocol: Extracted RNA (150 ng) samples were 210 hybridized (without reverse transcription or amplification) with capture and reporter probes for the selected genes and assay controls according to the manufacturer protocol (MAN-C0021-01).

scan_protocol: nCounter Prep Station using nCounter Analysis System User Manual (MAN-C0035), nSolver software

data_processing: Counts of raw data (taking to account the negative- and positive control) and normalized by HK

source_name: tumour tissue

label_protocol: C (EUS-FNA samples) or S (surgical samples) and # of patient

extract_protocol: RNeasy Mini Kit (QIAGEN; Cat 195 No./ID: 74104)

value: pancreatic ductal adenocarcinoma (PDAC)

tag: sample type

value: Surgical sample


title: RKO-shCtrl-03

first: Jinghu

last: He

address: 168 Changhai Road, Yangpu District, Shanghai

institute: Changhai Hospital Affiliated to Navy Medical University

description: Gene expression from data RKO cells infected with shCtrl

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C

scan_protocol: Affymetrix human GeneChip Clariom S and the outcomes were scanned by Affymetrix Scanner 3000.

data_processing:
The statistical significance of raw data was completed by a Welch t-test with Benjamini-Hochberg FDR.
|Fold Change| ≥ 1.3 and FDR < 0.05 as significant.

label: 3’ IVT Biotin Label

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: RKO cells were cultured in 1640 medium containing 10% fetal bovine serum (FBS) in cell incubator with 5% CO2 at 37°C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: RKO cells in logarithmic growth phase were infected by adding 20 μL 1×108 TU/mL shCtrl or shCNN2 lentivirus, culturing in 1640 medium with 10% FBS in a 6-well dish with 2×105 cells per well.

value: RKO

value: shCtrl


title: intestine, NEC, rep2


title: RKO-shCNN2-03

description: Gene expression from data RKO cells infected with shCNN2


title: Kc167_RNApolIIser5P_Aclarubicin_Rep1_(220317_MW_DmHs_AA78_3722_3)


title: intestine, NEC, rep1


title: Kc167_RNApolIIser2P_Doxorubicin_Rep6_(220819_BT_DmHs_BT1202_P72)

description: CUT&Tag data profiling elongating RNA pol II (ser2P) in Drosophila melanogaster cells treated with doxorubicin for 30 minutes


title: S17


title: S16


title: HuhIRF1KO_IFNa_4h_rep2

data_processing:
After quality control assessments using FastQC, fastq files were mapped to the Homo sapiens GRCh38/hg38 genome build (release-100) using STAR version 2.7.3a
Read counts were generated using FeatureCounts v1.6.2 with default parameters
Counts normalization and DEG analysis were performed using the DESeq2 v.1.30.1 package in R version 4.0.3
Assembly: hg38
Supplementary files format and content: Raw read counts in .csv format

source_name: IFN alpha stimulated HuhIRF1KO cells, 4h


title: HuhIRF1KO_IFNa_8h_rep1


title: RKO-shCNN2-02


title: RKO-shCtrl-02


title: RKO-shCtrl-01


title: HuhIRF1KO_IFNa_4h_rep1


title: intestine, Control, rep3

value: control


title: S15


title: Kc167_RNApolIIser2P_Doxorubicin_Rep5_(220819_BT_DmHs_BT1201_P72)


title: HuhIRF1KO_IFNa_2h_rep2

source_name: IFN alpha stimulated HuhIRF1KO cells, 2h


title: Kc167_RNApolIIser2P_Doxorubicin_Rep4_(220317_MW_DmHs_AA79_3922_10)


title: S14


title: intestine, Control, rep2


title: S13


title: intestine, Control, rep1


title: HuhIRF1KO_UN_rep2

source_name: unstimulated HuhIRF1KO cells

value: unstimulated


title: Kc167_RNApolIIser2P_Doxorubicin_Rep1_(220317_MW_DmHs_AA78_3722_9)


title: Kc167_RNApolIIser2P_Doxorubicin_Rep3_(220317_MW_DmHs_AA79_3922_9)


title: Kc167_RNApolIIser2P_Doxorubicin_Rep2_(220317_MW_DmHs_AA78_3722_10)


title: RNA-seq 48hours BM/Ikzf1/4 rep3

description: Raw salmon counts/DESeq2

data_processing:
Raw ATAC-seq fastq reads were aligned using bowtie2 mm9 genome on Galaxy platform. MACS2 was used for peak calling using these parameters: --nomodel --shift -37 --extsize 73 . Bamcoverage was used to generate bigwig files.
Salmon quant function was used to quantify effective length of transcripts and transcript per million value from RNA-seq raw fastq reads using mm10 transcriptome. Salmon quants output files were used to calculate Log2FC and statistical values using DESeq2 for differential analysis. Annotate DESeq2 package on Galaxy platform was used to annotate gene_ids to symbols.
Genome_build: mm10, mm9
Supplementary_files_format_and_content: Bigwig tracks files for ATAC-seq conditions and bed peak files for scored peaks.
Supplementary_files_format_and_content: Matrix table with Log2FC and FDR values of comparisons between the two conditions.

source_name: MEFs

extract_protocol:
RNA extraction from MEF cultures was performed using the RNeasy Plus Micro Kit (Qiagen).
mRNA was isolated by Poly(A) mRNA magnetic isolation (NEBNext; E7490S), and cDNA libraries were generated with KAPA RNA HyperPrep kits (Roche; 08098197702).

treatment_protocol: MEFs infected with doxycycline-inducible lentiviral vectors for Brn2, Myt1l, Ikzf1, and Ikzf4 were culture with doxycycline for 2 days.

value: Mouse embryonic fibroblasts


title: RKO-shCNN2-01


title: S12


title: Kc167_RNApolIIser2P_Control_Rep5_(220819_BT_DmHs_BT1198_P72)

description: CUT&Tag data profiling elongating RNA pol II (ser2P) in Drosophila melanogaster control cells treated with DMSO vehicle.

value: Kc167 Drosophila melanogaster cell line originally derived from disaggregated 8-12 hour embryos.


title: S11


title: HuhIRF1KO_UN_rep1

value: IRF1 knockout


title: S10


title: RNA-seq 48hours BM/Ikzf1/4 rep1

description: Raw salmon counts/DESeq2


title: Huh-dKO_IFNy_72h_rep1

source_name: IFN gamma stimulated Huh-dKO cells, 72h

value: IRF9/IRF1 double knockout


title: RNA-seq 48hours BM/Ikzf1/4 rep2

description: Raw salmon counts/DESeq2


title: S9


title: Kc167_RNApolIIser2P_Control_Rep3_(220317_MW_DmHs_AA79_3922_16)

source_name: CUT&Tag


title: Kc167_RNApolIIser2P_Control_Rep4_(220819_BT_DmHs_BT1197_P72)


title: Huh-dKO_IFNy_24h_rep2

source_name: IFN gamma stimulated Huh-dKO cells, 24h

value: IFN alpha, 1000U/ml


title: HuhIRF1KO_IFNa_2h_rep1


title: RNA-seq 48hours BM rep2

description: Raw salmon counts/DESeq2

treatment_protocol: MEFs infected with doxycycline-inducible lentiviral vectors for Brn2 and Myt1l were culture with doxycycline for 2 days.


title: S8


title: RNA-seq 48hours BM rep3

description: Raw salmon counts/DESeq2


title: S7


title: Huh-dKO_IFNy_24h_rep1


title: Kc167_RNApolIIser2P_Control_Rep2_(220317_MW_DmHs_AA79_3922_15)


title: RNA-seq 48hours BM rep1

description: Raw salmon counts/DESeq2


title: Kc167_RNApolIIser2P_Control_Rep1_(220317_MW_DmHs_AA78_3722_15)


title: Huh-dKO_IFNy_72h_rep2


title: Huh-dKO_IFNy_8h_rep2

source_name: IFN gamma stimulated Huh-dKO cells, 8h


title: ATAC-seq 48hours BM/Ikzf1/4 rep3

description: Bamcoverage .bigwig file/MACS2 peak calling .bed file

extract_protocol:
48 hours after doxycycline addition, 50000 MEF nuclei were isolated as previously reported (Buenrostro et al., 2015), with modifications described in (Mayran et al., 2018).
Isolated nuclei underwent transposase reaction: 2.5μl of 10x TD buffer, 10μl of water, and 12.5μl of enzyme (Illumina Nextera kit; FC-121–1031). DNA was purified with GeneRead Purification columns (Qiagen), enriched by PCR, and purified again with GeneRead Purification columns before being sequenced.


title: Kc167_RNApolIIser2P_ActinomycinD_Rep6_(220819_BT_DmHs_BT1204_P72)

description: CUT&Tag data profiling elongating RNA pol II (ser2P) in Drosophila melanogaster cells treated with actinomycin D for 30 minutes


title: ATAC-seq 48hours BM/Ikzf1/4 rep2


title: Kc167_RNApolIIser2P_ActinomycinD_Rep5_(220819_BT_DmHs_BT1203_P72)


title: Huh-dKO_IFNy_4h_rep2

source_name: IFN gamma stimulated Huh-dKO cells, 4h


title: HuhIRF9KO_IFNa_8h_rep1

source_name: IFN alpha stimulated HuhIRF9KO cells, 8h

value: IRF9 knockout


title: ATAC-seq 48hours BM/Ikzf1/4 rep1


title: Huh-dKO_IFNy_4h_rep1


title: Kc167_RNApolIIser2P_ActinomycinD_Rep4_(220317_MW_DmHs_AA79_3922_14)

value: Phospho-Rpb1 CTD (Ser2) (E1Z3G)


title: HuhIRF9KO_IFNa_72h_rep2

source_name: IFN alpha stimulated HuhIRF9KO cells, 72h


title: ATAC-seq 48hours BM rep3


title: Kc167_RNApolIIser2P_ActinomycinD_Rep3_(220317_MW_DmHs_AA79_3922_13)


title: Huh-dKO_IFNy_2h_rep1

source_name: IFN gamma stimulated Huh-dKO cells, 2h


title: Kc167_RNApolIIser2P_ActinomycinD_Rep2_(220317_MW_DmHs_AA78_3722_14)


title: ATAC-seq 48hours BM rep2


title: S3


title: ATAC-seq 48hours BM rep1


title: Huh-dKO_IFNa_72h_rep2

source_name: IFN alpha stimulated Huh-dKO cells, 72h


title: Kc167_RNApolIIser2P_ActinomycinD_Rep1_(220317_MW_DmHs_AA78_3722_13)


title: Huh-dKO_IFNy_8h_rep1


title: S1


title: S6


title: scRNA-seq - Control

description: Scanpy.loom files containing count matrix, features and barcodes. .h5 files containing cellranger or cellranger-arc output count matrix, features and barcodes whereas .tsv file containing aligned fragment coordinates.

data_processing:
scRNA-seq sequencing data were aligned to the mm10 genome using CellRanger version 6.1.2 (Cell Ranger software, 10x Genomics,). Filtered output files were analyzed in Python (Python core team, Python) using Scanpy version 1.9.1 (Wolf et al., 2018). Genes detected in less than 3 cells were removed from the analysis and low-quality cells (less than 200 genes detected, more than 2500 genes detected or more than 5% of mitochondrial genes) were removed from the datasets. To assign individual cell types, scDeepSort version 1.0 (Shao et al., 2021) was used alongside with deep learning trained model grounded on previously published retinal single cell expression data (Clark et al., 2019). Full YFP and mCherry sequences were reconstructed using RNA-Bloom version 1.4.3 (Nip et al., 2020) and Trinity version 2.14.0 (Grabherr et al., 2011), and then remapped to the initial sequencing data. Doublets were identified using Scrublet version 0.2.2 (Wolock et al., 2019) and removed before downstream analysis. Batch correction, data integration, gene expression plotting, differential expression data and further analysis were performed using scVI-tools version 0.19.0 (Gayoso et al., 2022).
Raw ATAC-seq fastq reads were aligned using bowtie2 mm9 genome on Galaxy platform. MACS2 was used for peak calling using these parameters: --nomodel --shift -37 --extsize 73 . Bamcoverage was used to generate bigwig files.
Salmon quant function was used to quantify effective length of transcripts and transcript per million value from RNA-seq raw fastq reads using mm10 transcriptome. Salmon quants output files were used to calculate Log2FC and statistical values using DESeq2 for differential analysis. Annotate DESeq2 package on Galaxy platform was used to annotate gene_ids to symbols.
Genome_build: mm10, mm9
Supplementary_files_format_and_content: Bigwig tracks files for ATAC-seq conditions and bed peak files for scored peaks.
Supplementary_files_format_and_content: Matrix table with Log2FC and FDR values of comparisons between the two conditions.

source_name: Retina

extract_protocol:
Electroporated retina pieces were dissociated in papain (Worthington). YFP+ cells from both mCherry+ (n=4 retinas) or mCherry- (n=5 retinas) regions were pooled. Fluorescent cells were sorted with a FACSAria III Cell Sorter (BD Biosciences). Viable YFP+ cells (single cells) were collected in PBS with 0.15% BSA (Millipore). Cells were then spun at 300g for 10 minutes at 4°C and re-suspended in 0.15% BSA/PBS.
Cells were loaded on a 10xGenomics Single Cell 3’ chip and processed according to manufacturer V3 pipeline 3.1.0 kit.

treatment_protocol: Animals were electroporated with a Cre-dependent control construct, received tamoxifen at P21 or older, and were sacrificed 3 weeks post-tamoxifen.

value: Muller glia

value: mCherry


title: S2


title: C18

value: EUS-FNA


title: S5


title: scRNA-seq - Ikzf1/4

data_processing:
scRNA-seq sequencing data were aligned to the mm10 genome using CellRanger version 6.1.2 (Cell Ranger software, 10x Genomics,). Filtered output files were analyzed in Python (Python core team, Python) using Scanpy version 1.9.1 (Wolf et al., 2018). Genes detected in less than 3 cells were removed from the analysis and low-quality cells (less than 200 genes detected, more than 2500 genes detected or more than 5% of mitochondrial genes) were removed from the datasets. To assign individual cell types, scDeepSort version 1.0 (Shao et al., 2021) was used alongside with deep learning trained model grounded on previously published retinal single cell expression data (Clark et al., 2019). Full YFP and mCherry sequences were reconstructed using RNA-Bloom version 1.4.3 (Nip et al., 2020) and Trinity version 2.14.0 (Grabherr et al., 2011), and then remapped to the initial sequencing data. Doublets were identified using Scrublet version 0.2.2 (Wolock et al., 2019) and removed before downstream analysis. Batch correction, data integration, gene expression plotting, differential expression data and further analysis were performed using scVI-tools version 0.19.0 (Gayoso et al., 2022).
Raw ATAC-seq fastq reads were aligned using bowtie2 mm9 genome on Galaxy platform. MACS2 was used for peak calling using these parameters: --nomodel --shift -37 --extsize 73 . Bamcoverage was used to generate bigwig files.
Salmon quant function was used to quantify effective length of transcripts and transcript per million value from RNA-seq raw fastq reads using mm10 transcriptome. Salmon quants output files were used to calculate Log2FC and statistical values using DESeq2 for differential analysis. Annotate DESeq2 package on Galaxy platform was used to annotate gene_ids to symbols.
Genome_build: mm10, mm9
Supplementary_files_format_and_content: Scanpy.loom files containing count matrix, features and barcodes. Scope.loom files containing processed count matrix, features and barcodes including the AUC regulons. Reg.csv files containing regulon data for downstream analysis.
Supplementary_files_format_and_content: Bigwig tracks files for ATAC-seq conditions and bed peak files for scored peaks.
Supplementary_files_format_and_content: Matrix table with Log2FC and FDR values of comparisons between the two conditions.

extract_protocol:
Electroporated retina pieces were dissociated in papain (Worthington). YFP+ cells from mCherry+ regions of 7 retinas (n=7) were pooled. Fluorescent cells were sorted with a FACSAria III Cell Sorter (BD Biosciences). Viable YFP+ cells (single cells) were collected in PBS with 0.15% BSA (Millipore). Cells were then spun at 300g for 10 minutes at 4°C and re-suspended in 0.15% BSA/PBS.
Cells were loaded on a 10xGenomics Single Cell 3’ chip and processed according to manufacturer V3 pipeline 3.1.0 kit.

treatment_protocol: Animals were electroporated with Cre-dependent Ikzf1/4 constructs, received tamoxifen at P21 or older, and were sacrificed 3 weeks post-tamoxifen.

value: mCherry + Ikzf1+Ikzf4


title: Kc167_RNApolIIser2P_Aclarubicin_Rep6_(220819_BT_DmHs_BT1200_P72)

description: CUT&Tag data profiling elongating RNA pol II (ser2P) in Drosophila melanogaster cells treated with aclarubicin for 30 minutes


title: Huh-dKO_IFNa_72h_rep1

value: human hepatocellular carcinoma cells


title: C17

value: pancreatic ductal adenocarcinoma (PDAC)


title: Huh-dKO_IFNa_24h_rep2

source_name: IFN alpha stimulated Huh-dKO cells, 24h


title: S4

value: Surgical sample


title: Huh-dKO_IFNy_2h_rep2


title: Kc167_RNApolIIser2P_Aclarubicin_Rep5_(220819_BT_DmHs_BT1199_P72)


title: Kc167_RNApolIIser2P_Aclarubicin_Rep3_(220317_MW_DmHs_AA79_3922_11)


title: C16


title: mESCs,TT-FHAgo2:LIS1-GFP-OE (+Dox), FBS+LIF condition, Rep#2 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate2

source_name: mouse embryonic stem cells

extract_protocol:
Total RNA was extracted from cells, using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
Lexogen SENSE mRNA-Seq Library Prep Kit

value: FBS+LIF

value: Ago1/2/3/4 -/- ; LIS1 overexpression (LIS1 GFP OE); Dox. AGO2

value: hybrid


title: Huh-dKO_IFNa_8h_rep2

source_name: IFN alpha stimulated Huh-dKO cells, 8h


title: Huh-dKO_IFNa_8h_rep1


title: mESCs,TT-FHAgo2:LIS1-GFP-OE (+Dox), FBS+LIF condition, Rep#3 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate3


title: Huh-dKO_IFNa_24h_rep1


title: C15

source_name: tumour tissue


title: Kc167_RNApolIIser2P_Aclarubicin_Rep4_(220317_MW_DmHs_AA79_3922_12)


title: C14


title: mESCs,TT-FHAgo2:LIS1-GFP-OE (+Dox), FBS+LIF condition, Rep#1 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate1


title: C13


title: Kc167_RNApolIIser2P_Aclarubicin_Rep2_(220317_MW_DmHs_AA78_3722_12)


title: Kc167_RNApolIIser2P_Aclarubicin_Rep1_(220317_MW_DmHs_AA78_3722_11)


title: Huh-dKO_IFNa_4h_rep2

source_name: IFN alpha stimulated Huh-dKO cells, 4h


title: mESCs,TT-FHAgo2 (+Dox), FBS+LIF condition, Rep#4 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate4


title: mESCs,TT-FHAgo2:LIS1-GFP-OE (+Dox), FBS+LIF condition, Rep#4 - totalRNA-seq


title: Huh-dKO_IFNa_4h_rep1


title: C11


title: Kc167_RNApolIIser2PCUTAC_Doxorubicin_Rep2_(220414_MW_DmHs_AA81_4322_10)

description: CUTAC data profiling elongating RNA pol II (ser2P) in Drosophila melanogaster cells treated with aclarubicin for 30 minutes

source_name: CUTAC


title: Huh-dKO_IFNa_2h_rep2

source_name: IFN alpha stimulated Huh-dKO cells, 2h


title: mESCs,TT-FHAgo2 (+Dox), FBS+LIF condition, Rep#3 - totalRNA-seq


title: Kc167_RNApolIIser2PCUTAC_Doxorubicin_Rep1_(220414_MW_DmHs_AA81_4322_9)


title: mESCs,TT-FHAgo2 (+Dox), FBS+LIF condition, Rep#1 - totalRNA-seq


title: C10


title: Huh-dKO_IFNa_2h_rep1


title: C9


title: Huh-dKO_UN_rep2

source_name: unstimulated Huh-dKO cells


title: Kc167_RNApolIIser2PCUTAC_Control_Rep2_(220927_MW_DmHs_AA91_91522_1)


title: C8


title: Kc167_RNApolIIser2PCUTAC_Control_Rep1_(220414_MW_DmHs_AA81_4322_15)


title: mESCs,TT-FHAgo2:LIS1-GFP-OE, FBS+LIF condition, Rep#3 - totalRNA-seq

value: Ago1/2/3/4 -/- ; LIS1 overexpression (LIS1 GFP OE)


title: Huh-dKO_UN_rep1


title: C12


title: SC175

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

data_processing:
For scRNA, FASTQ generation, demultiplexing, barcode assignment, and gene counting were performed using 10X Genomics' Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). For scATAC, FASTQ generation, demultiplexing, barcode assignment, and peak calling were performed using 10X Genomics' Cell Ranger-ATAC software v1.2.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac)
Downstream data analysis was performed using R packages Signac (v1.3.0) , Seurat (v4.0.3), harmony (v1.0),  and chromVAR (v1.12.0) [38]. Peak calling was performed by cluster using macs2.
Wilcoxon rank sum test with Bonferroni FDR correction was used for DEG testing.
Assembly: GRCh38 for scRNA and hg19 for scATAC
Supplementary files format and content: 10x Genomics output scRNA files: raw_feature_bc_matrix.h5
Supplementary files format and content: 10x Genomics output scATAC files: fragments.tsv.gz, fragments.tsv.gz.tbi, singlecell.csv, summary.csv, raw_peak_bc_matrix.h5, filtered_peak_bc_matrix.h5, filtered_tf_bc_matrix.h5, peaks.bed, peak_annotation.tsv

source_name: lung

extract_protocol:
Explanted subpleural peripheral lung tissue was finely diced and digested for 1 hour in a mix of either Collagenase A/DNase I or Liberase DL/DNase I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA.  For some lungs, CD45+ and EPCAM+ cell populations were partially depleted with Miltenyi magnetic bead separation.  For scATAC, cells were lysed according to 10X Genomics' Nuclei Isolation for Single Cell ATAC Sequencing protocol (CG000169 ).  Cells or nuclei were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed per the manufacturer’s instructions (Single Cell 3' v2, Single Cell 5' v1, scATACv1 protocols, 10x Genomics). In short, for the scRNA protocols, lung cells were added to the master mix and loaded into the chip; subsequently, gel beads and partitioning oil were added into the chip which was then loaded into the Chromium instrument, generating the gel bead-in-emulsion (GEM). Once emulsified, cells were lysed and poly-A RNA transcribed to cDNA, adding an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and 10x Barcode. Silane DynaBeads were then used to clean up the pooled and barcoded cDNA which was then amplified by PCR.  SPRIselect reagent was used to select the appropriately sized fragments for library construction. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added during the library construction protocol.  For scATAC, nuclei were incubated for one hour with the transposase then loaded into the Chromium instrument with barcoding reagents, gel beads, and partitioning oil.  Once emulsified, the P5 sequence and 10X barcode were added during the PCR GEM generation and barcoding steps.  The resulting 10x barcoded single-stranded DNA was then cleaned up with Silane Dynabeads and size selected with SPRIselect reagent.  Finally, a P7 sequence and a sample index were added during library construction via PCR.

value: lung

tag: disease state

value: IPF

tag: Sex

value: Male

tag: corecode

tag: samplename

value: IPF 10

tag: lungsection

value: Upper Lobe

tag: depletions

tag: protocol

value: 10X Genomics 3PrimeV2


title: mESCs,TT-FHAgo2:LIS1-GFP-OE, FBS+LIF condition, Rep#2 - totalRNA-seq

tag: genotype

tag: strain


title: Kc167_RNApolIIser2PCUTAC_ActinomycinD_Rep3_(220927_MW_DmHs_AA91_91522_3)

tag: antibody

value: Phospho-Rpb1 CTD (Ser2) (E1Z3G)

tag: cell type

value: Kc167 Drosophila melanogaster cell line originally derived from disaggregated 8-12 hour embryos.


title: Kc167_RNApolIIser2PCUTAC_Doxorubicin_Rep3_(220927_MW_DmHs_AA91_91522_4)


title: SC174

value: IPF 9

value: Lower Lobe


title: SC156

value: Normal

value: Female

value: CONTROL 8


title: Kc167_RNApolIIser2PCUTAC_ActinomycinD_Rep2_(220414_MW_DmHs_AA81_4322_14)


title: mESCs,TT-FHAgo2 (+Dox), FBS+LIF condition, Rep#2 - totalRNA-seq

value: FBS+LIF


title: mESCs,TT-FHAgo2, FBS+LIF condition, Rep#4 - totalRNA-seq


title: SC154

value: IPF 8


title: mESCs,TT-FHAgo2:LIS1-GFP-OE, FBS+LIF condition, Rep#4 - totalRNA-seq

value: hybrid


title: Kc167_RNApolIIser2PCUTAC_Aclarubicin_Rep2_(220927_MW_DmHs_AA91_91522_2)


title: C5

value: pancreatic ductal adenocarcinoma (PDAC)

value: EUS-FNA


title: mESCs,TT-FHAgo2, FBS+LIF condition, Rep#3 - totalRNA-seq


title: C3


title: C2


title: mESCs,TT-FHAgo2, FBS+LIF condition, Rep#2 - totalRNA-seq


title: C4


title: Kc167_RNApolIIser2PCUTAC_Aclarubicin_Rep1_(220414_MW_DmHs_AA81_4322_12)


title: Kc167_GQuadruplex_Doxorubicin_Rep3_(220523_MW_DmHs_AA85_51322_9)

description: CUT&Tag data profiling G-quadruplex in Drosophila melanogaster cells treated with doxorubicin for 30 minutes

source_name: CUT&Tag

value: Anti-DNA G-quadruplex structures clone BG4 Sigma-Aldrich MABE917


title: C7


title: mESCs,TT-FHAgo2, FBS+LIF condition, Rep#1 - totalRNA-seq


title: C6


title: Kc167_GQuadruplex_Doxorubicin_Rep2_(220414_MW_DmHs_AA81_4322_2)


title: Kc167_RNApolIIser2PCUTAC_ActinomycinD_Rep1_(220414_MW_DmHs_AA81_4322_13)


title: SC93

value: lung

value: IPF

value: Male

value: IPF 5


title: SC94

value: IPF 6

value: Upper Lobe

value: 10X Genomics 3PrimeV2


title: mESCs, Lis1 WT, 2i+LIF condition, Rep#1 - ATACseq, technical replcate2

description:
Biological replicate1, technical replcate2
b1_WT_2IL_enc_atac_scalefactor_normalized.bdg

data_processing:
Paired ATAC-seq reads were first trimmed to remove adaptor sequences using cutadapt.
Trimmed reads were aligned with Bowtie2, filtering out secondary alignments, and converted to bam format.
Primary alignments were processed with qCount from QuasR package, and normalized using DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: Bedgraph files were generated with Deeptools and were normalized with scaleFactors. For calculating scaleFactors, reciprocals of DESeq2 size factors were estimated using calcNormFactors from edgeR Bioconductor package with RLE method.

growth_protocol: Mouse ES cells were grown in FBS+LIF, 2i+LIF and FGF+Activin culture media.

extract_protocol: ATAC-seq was performed according to the previously described protocol (Buenrostro et al., 2015) with modifications. Briefly, 50,000 cells were washed with cold PBS and resuspended in lysis buffer to extract nuclei. The nuclei were cold-centrifuged at 500 x g for 10 min. The nuclei pellet was incubated with transposition reaction buffer for 30 min. at 37 °C. The DNA was purified using the PCR Purification Kit (Qiagen).The eluted transposed DNA was submitted to the PCR using Q5 High-Fidelity Polymerase (NEB). DNA was amplified with 11-12 cycles of PCR.

value: Wild type


title: SC87

value: IPF 4

value: Lower Lobe


title: C1


title: Kc167_GQuadruplex_Doxorubicin_Rep1_(220414_MW_DmHs_AA81_4322_1)

value: Kc167 Drosophila melanogaster cell line originally derived from disaggregated 8-12 hour embryos.


title: Kc167_GQuadruplex_Control_Rep3_(220523_MW_DmHs_AA85_51322_12)

description: CUT&Tag data profiling G-quadruplex in Drosophila melanogaster control cells treated with DMSO vehicle


title: 87010 CART Emapalumab

description:
Expression of 770 genes related to components of glial biology
nCounter Human Glial Profiling panel
hGM-CSF/hIL3 NOG mice

hyb_protocol: 300 nanograms of total RNA were hybridized overnight with nCounter Reporter (20 μL) probes in hybridization buffer and excess of nCounter Capture probes (5 μL) at 65 °C for over night. After overnight hybridization, the abundance of specific target molecules was then quantified using the nCounter digital analyzer.

data_processing: Raw data processing, quality control, and normalization were performed using the nSolver™ 4.0 analysis software (NanoString nCounter Technologies, Seattle, WA). Background subtraction from raw transcript counts was performed through negative input controls. Normalization to 10 housekeeping genes and differential expression analysis were completed using the Advanced Analysis software plugin (version 2.0.115). For differential expression analysis, a p‐value of ≤0.05, were applied as cut-offs.

source_name: FFPE mouse brain tissues

extract_protocol: Total RNA was extracted from 5 FFPE slides (10 μm thickness) using QUIAGEN FFPE RNA extraction kit.

treatment_protocol: hGM-CSF/hIL3 NOG mice (n=10) were infused with irradiated FF-Luciferase positive Daudi cells at Day-2 and treated with 10x106 CAR.CD19 T-cells/mouse either in the presence of 100mg/Kg/day emapalumab (n=5) or of the vehicle (n=5). Two mice were considered as for negative control, being infused only with DAUDI cells. Mice were sacrified 3 days after CAR T-cell infusion to evaluate the brain damage occurrence in this murine model of acute CAR T-cell toxicity.

tag: treatment

value: Emapalumab


title: 87009 CART Untreated

value: CART Untreated


title: SC56

tag: tissue

value: Normal

value: Female

value: CONTROL 7


title: SC153

tag: age

value: IPF 7


title: 87012 CART Emapalumab


title: mESCs, Lis1 OE, FBS+LIF condition, Rep#2 - ATACseq

description:
Biological replicate2
b2_OE_SL_enc_atac_scalefactor_normalized.bdg

tag: culture medium

value: FBS+LIF

value: LIS1 overexpression (LIS1 dsRED-OE)

value: hybrid


title: Kc167_GQuadruplex_Control_Rep2_(220414_MW_DmHs_AA81_4322_8)

description: CUT&Tag data profiling G-quadruplex in Drosophila melanogaster control cells treated with DMSO vehicle.

value: Anti-DNA G-quadruplex structures clone BG4 Sigma-Aldrich MABE917


title: mESCs,TT-FHAgo2:LIS1-GFP-OE, FBS+LIF condition, Rep#1 - totalRNA-seq

value: Ago1/2/3/4 -/- ; LIS1 overexpression (LIS1 GFP OE)


title: 87008 CART Untreated


title: mESCs, Lis1 F/-, FGF+Activin condition, Rep#2 - ATACseq

description:
Biological replicate2
b2_FLX_FA_enc_atac_scalefactor_normalized.bdg

value: FGF+Activin

value: Lis1 Floxed/- (F/-)


title: Kc167_GQuadruplex_ActinomycinD_Rep1_(220414_MW_DmHs_AA81_4322_5)

description: CUT&Tag data profiling G-quadruplex in Drosophila melanogaster cells treated with actinomycin D for 30 minutes


title: mESCs, Lis1 OE, 2i+LIF condition, Rep#2 - ATACseq

description:
Biological replicate2
b2_OE_2IL_enc_atac_scalefactor_normalized.bdg


title: CasRx_PS18_Rep1_totRNA

description: Ribodepleted RNA-seq

data_processing:
All data obtained from the BIMSB Genomics platform, after basecalling and demultiplexing
RNA-seq data processed with the PiGx pipeine (http://bioinformatics.mdc-berlin.de/pigx/), default settings; additional analyses reported in the associated publication
10X Visium processed with Spaceranger v.1.2.0 (default settings); additional analyses reported in the associated publication
Genome_build: GRCh38
Supplementary_files_format_and_content: analysis1.star.deseq_results.tsv: results from the PiGx pipeline, STAR/featurecounts/deseq2 normalized counts
Supplementary_files_format_and_content: deseq_normalized_counts.tsv: results from the PiGx pipeline, STAR/deseq2 output

growth_protocol: HEK cells were cultured 10%FBS DMEM. For the RNA-seq experiment. HiPSCs expresing a light-inducible Cre cassette and a LoxP-RFP-LoxP-SHH-NeonGreen cassette were cultured in E8 flex media on PET membranes.

extract_protocol:
RNA extraction was performed with a standard trizol protocol. No extraction was performed for the spatial transcriptimics experiment.
For RNA-seq, libraries were prepared according to the Illumina Truseq mRNA stranded kit. For the Visium, samples were treated according to the 10X Visium protocol.
RNA-seq / Other: 10X Visium

treatment_protocol: Cells were transfected with Lipofectamine 3000, with 1 microgram CasRx plasmid, 1 microgram guide RNA plasmid and 800 ng RFP reporter plasmid. Cells were harvested 36 hours post-transfection. Induced with blue light as described in the associated publication, collected after the indicated time points. Membranes were then transferred onto a Visium Slide for spatial transcriptomic profiling.

tag: plasmid

value: CasRx plasmid, TagRFP plasmid, RFP-targeting guide RNA plasmid


title: Hybrid clone of A375 and macrophage

city: Sapporo

first: Tomoyuki

last: Minowa

state: Hokkaido

address: west 17, south 1, Chuo-ku

department: Pathology

country: Japan

institute: Sapporo medical university school of medicine

data_processing:
CAGE libraries were sequenced using single end reads of 75nt on a NextSeq 500 instrument (Illumina). Obtained reads (CAGE tags) were mapped to the human hg38 genome using BWA (version 0.5.9). Unmapped reads were then mapped by HISAT2 (version 2.0.5). CAGE tag count data were clustered using the CAGEr using Paraclu algorithm with default parameters. Differentially expressed genes were detected using the DESeq2 package (version 1.20.0). For motif analysis, the genomic DNA sequence of the region from 200bp upstream to 50bp downstream of differentially expressed CAGE peaks were subjected to de novo motif discovery tools: AMD, GLAM2, DREME and Weeder. The occurrences of the motifs were examined by FIMO. The similarity of consensus motifs and the motifs in database JASPAR CORE 2016 vertebrates were evaluated by Tomtom. The list of differentially expressed genes detected by CAGEr (CPM > 1 and fold-change < 0.25, or CPM > 1 and fold-change > 4) were used for GO enrichment analysis by clusterProfiler package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include CPM values for each samples

source_name: skin

extract_protocol:
Total RNA was isolated from A375 cell line and hybrid cells using the RNeasy Mini Kit (Qiagen, Valencia, CA).
The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed.

value: skin

value: co-culture with macrophage


title: 87007 CART Untreated


title: Kc167_GQuadruplex_ActinomycinD_Rep2_(220523_MW_DmHs_AA85_51322_11)

data_processing:
Genome_build: dm6
1. We used cutadapt 2.9 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 2.4.2 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the dm6 Drosophila melanogaster reference sequence obtained from UCSC. 3. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the same paired-end 50bp reads to the masked hg19 Homo sapiens reference sequence obtained from UCSC. 4. We extracted properly paired reads from the D. melanogaster alignments. 5. We counted the properly paired reads from the Homo sapiens alignments. 6. We used bedtools 2.30.0 genomecov to make a normalized count dm6 track which is the fraction of counts at each base pair scaled by the size of the dm6 reference sequence (137567484) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .norm.bw) 7. We used bedtools 2.30.0 genomecov with a scaling factor of (10000/number of fragments mapped to masked hg19) to create a calibrated dm6 track file (Supplementary file .Hs_spike.bw).

value: Kc167 Drosophila melanogaster cell line originally derived from disaggregated 8-12 hour embryos.


title: CasRx_PS18_Rep2_totRNA

description: Ribodepleted RNA-seq


title: SC45

value: lung

value: Male

value: CONTROL 6

value: 10X Genomics 3PrimeV2


title: mESCs, Lis1 OE, 2i+LIF condition, Rep#1 - ATACseq, technical replcate2

description:
Biological replicate1, technical replcate2
b1_OE_2IL_enc_atac_scalefactor_normalized.bdg


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#2 - ATACseq

description:
Biological replicate2
b2_FLX_SL_enc_atac_scalefactor_normalized.bdg


title: A375, melanoma cell line

tag: cell line


title: Kc167_GQuadruplex_Aclarubicin_Rep2_(220414_MW_DmHs_AA81_4322_4)

description: CUT&Tag data profiling G-quadruplex in Drosophila melanogaster cells treated with aclarubicin for 30 minutes


title: Kc167_GQuadruplex_Aclarubicin_Rep3_(220523_MW_DmHs_AA85_51322_10)


title: 87006 CART Emapalumab

value: Emapalumab