title: patient C1P3, before second course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P3-M2-T0-CD4

value: peripheral blood

tag: patient id

tag: mp course

value: second

tag: time point

value: before

tag: cell population

value: CD4+ T cells

tag: clinical evaluation

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

tag: course of disease

tag: disease duration (years)

tag: number of relapses in the past 2 years

tag: duration since last relapse (months)

tag: edss score

tag: disease-modifying therapy

value: peginterferon beta-1a

value: recurring


title: F02689-TCR_Batch6

status: Public on Feb 20 2024

type: SRA

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

country: USA

institute: TGen - Translational Genomics Research Institute

library_source: transcriptomic

data_processing:
*library strategy: CITE-seq,V(D)J
Reads with a read quality <3 were filtered and CellRanger Count v5.0.0 (10x Genomics) was used to align reads to a modified GRCh38 reference genome. V(D)J libraries were processed similarly, but with CellRanger VDJ v5.0.0 (10x Genomics).
Assembly: Modified GRCh38 Ensembl 98 with CAR construct added
Supplementary files format and content: Matrix file containing counts
Supplementary files format and content: Tab-separated values file containing features
Supplementary files format and content: Tab-separated values file containing cell barcodes
Supplementary files format and content: CSV containing filtered contig annotations

molecule: polyA RNA

organism: Homo sapiens

source_name: CAR Product

extract_protocol:
Excess CarT product was cyostored and sent to TGEN for processing. PBMC, Tumor, and CART product sample types were processed in batches of 8 and hashed using (Biolegend™) TotalSeq™-C hashing antibodies for 5' assays and TotalSeq™-A for 3' assays. Cite-Seq was performed using TotalSeq™-C Human Universal Cocktail on 27 samples. Samples were sorted together with Calcien-AM live stain gating(eBioscience™).
10x Genomics 5’ Assays were carried out on 60,000 cell single GEM reaction batches predominantly. Three batches used 10x Genomics 3’ Multiome assays. CarT cells were profiled using either Il13-RA2 antibody spike in Cite-seq libraries, or single transcript enrichment, where a modified V(D)J amplification protocol yielded single CAR transcript libraries.

tag: tissue

value: CAR Product

tag: batch


title: F03264-GEX_F03266-FB_Batch14


title: Ssrp1-2

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

library_source: genomic

data_processing:
Libraries were mapped to mm9 genome using STAR with the options –alignIntronMax and –AlignEndsType set to 1 and EndToEnd respectively.
peaks were called using MACS2 and bigiwg files were produced by deeptools, bamCoverage --normalizeUsing RPGC
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeaks indicating the binding region of the libraries on the Genome
Supplementary_files_format_and_content: bigwig file, indicating the enrichment of the libraries on the Genome

molecule: genomic DNA

organism: Mus musculus

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% defined FBS (Hyclone), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco) and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)). All the EC and ESC cell lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 .

extract_protocol:
10 million cells were cross-linked with 1% formaldehyde for 10 min at room temperature, with the formaldehyde then quenched by the addition of 200 mM glycine and cells then washed once with ice-cold PBS. Cell lysis was carried out with a buffer containing 10 mM Tris-Cl (pH 8), 100 mM NaCl, 10 mM EDTA, 0.25% Triton X-100 and protease inhibitor cocktail (Roche). Cells were then resuspended in 1% SDS lysis buffer containing 50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC and protease inhibitor cocktail. The suspension was nutated for 15 mins at 4°C before spinning down to collect the chromatin pellet. The pellet was then washed twice with 0.1% SDS lysis buffer containing 50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 0.1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC, 1 mM PMSF and protease inhibitor cocktail. Sonication was conducted using the Branson sonifier 250 on ice (11 cycles, power amplitude of 35%, 30s pulses on with 59.9 s pulses off). The chromatin solution was clarified by centrifugation at 20,000 g at 4°C for 45 mins and then pre-cleared with Dynabeads protein A (Life Technologies) for 2 hrs. The pre-cleared chromatin sample was incubated with 50 μl of Dynabeads protein A loaded with 5 μg antibody overnight. The beads were then washed three times with 0.1% SDS lysis buffer, once with 0.1% SDS lysis buffer/0.35 M NaCl, once with 10 mM Tris-Cl (pH 8), 1 mM EDTA, 0.5% NP40, 0.25 LiCl, 0.5% NaDOC, and once with TE buffer (PH8.0). The immunoprecipitated material was eluted from the beads by heating for 45 min at 68°C in 50 mM Tris-Cl (pH 7.5), 10 mM EDTA, 1% SDS. To reverse the crosslinks, samples were incubated with 1.5 μg/ml Pronase at 42°C for 2 hr followed by 67°C for 6 hr. The samples were then extracted with phenol chloroform isoamyl alcohol followed by chloroform, ethanol precipitated in the presence of glycogen, and re-suspended in TE buffer.
The ChIP-Seq libraries were prepared using Illumina TruSeq ChIP Sample Prep Kit (Catalog #: IP-202-1012) as per manufacturer's instructions.

tag: developmental stage

tag: cell type

value: embryonic stem cells

tag: antibody

value: SSRP1 antibody BioLegend #609702


title: patient C1P3, after second course of MP, T cells

type: RNA

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

country: Germany

institute: University of Rostock

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P3-M2-T1-CD4

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Clariom D Arrays (Applied Biosystems). The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in a GeneChip Fluidics Station 450.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0.3 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background reduction, intensity normalization, probe set summarization and log2 transformation. The TAC software was also utilized for the analysis of differential alternative splicing.
Exon-level processed data are available on the Series record.

label: Biotin

molecule: total RNA

source_name: T helper cells from the peripheral blood

label_protocol: According to the GeneChip Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: Up to ~30 ml of peripheral blood were taken from MS patients in relapse immediately before and after high-dose short-term MP therapy.

extract_protocol: The blood was collected in BD Vacutainer Glass Cell Preparation Tubes (Fisher Scientific). The tubes were centrifuged for the isolation of peripheral blood mononuclear cells (PBMC). B cells were positively selected from the PBMC using CD19 MicroBeads. T helper cells were obtained from the negative fraction of the B-cell separation by first removing non-T cells using the Pan T Cell Isolation Kit (Miltenyi Biotec) and then isolating CD4+ T cells using CD4 MicroBeads (Miltenyi Biotec). The RNA was isolated using the miRNeasy Mini Kit and the RNase-Free DNase Set (Qiagen).

treatment_protocol: The patients were treated according to the approved labels and the guidelines and recommendations of the German Society of Neurology.

tag: patient id

tag: mp course

tag: time point

value: after

tag: cell population

tag: clinical evaluation

value: responder

tag: percentage in pbmc

value: female

tag: body weight (in kg)

tag: body size (in cm)

tag: body mass index

tag: current smoker

value: no

tag: study center

value: Berlin

value: CIS/RRMS

tag: number of other medications taken

tag: neurological dysfunction

tag: fs

value: bladder or bowel:unchanged

tag: total dose of mp in mg

tag: days from first to last mp application

tag: side effects to mp


title: Brain 18 - diencephalon, scRNAseq

city: Berlin

first: Nina

last: Mitic

address: Hannoversche Strasse 28

department: Berlin Institute for Medical Systems Biology

institute: Max-Delbrück-Center for Molecular Medicine

description: scRNA-seq library of adult brain for transcriptomic profiling

library_source: transcriptomic single cell

data_processing:
The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect, the gene expression matrices were processed with the SoupX tool (Young & Behjati, 2020) for removing ambient RNA contamination.
A subset of libraries was also mapped with Velocyto (v0.17.17) (La Manno et al, 2018) to create count matrices for unspliced and spliced molecules.
The targeted lineage tracing libraries were aligned using bwa mem3 (v.0.7.12) to individual references of endogenous genes used in the lineage tracing experiment (actb1, actb2, cfl1, cirbpb, rpl39 and ube2e1). The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors.
For custom code and further downstream analysis, see: https://github.com/nimitic/radial-glia.
Assembly: GRCz11
Supplementary files format and content: Tab-separated barcode files and matrix files along with the tab-separated gene file (supplementary file) are the output of CellRanger mapping, further processed by the SoupX package for ambient RNA removal.
Supplementary files format and content: Loom files are the output of velocyto mapping (distinguishing spliced and unspliced mRNAs).
Supplementary files format and content: filtered_scars.csv files contain the output of a custom scar filtering pipeline.

organism: Danio rerio

source_name: adult brain

extract_protocol:
Adult zebrafish brain tissue was extracted, optionally dissected to select a specific region of interest (telencephalon, diencephalon, mesencephalon or rhombencephalon) and then dissociated with a trypsin protocol. Briefly, the samples were incubated in 750 µl of HBSS-glucose solution and dissocated with 15 µl of 0.05% trypsin-EDTA (Gibco) for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA-EBSS-HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter, washed with cold HBSS and resuspended in 100-200 µl HBSS with 0.05% BSA, then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM-seq samples, a papain dissociation protocol (Worthington kit, according to manufecturer's instructions) was used followed by an adapted scSLAM-seq protocol for labeling nascent transcripts (see sample-specific entry).
The standard transcriptome libraries were constructed according to the manufacturer's protocol (10X Genomics). For targeted libraries of scars used for lineage tracing, the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target, specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit, so they could be sequenced on the same platform.

tag: tissue

value: adult brain

tag: tissue region

value: diencephalon

tag: cell type

value: mixed (tissue dissociation)

tag: genotype

value: wildtype, Tg[ubi:zebrabow-M]


title: Input-1

tag: developmental stage


title: F02621-TCR_Batch4

tag: batch


title: Brain 16 - sorted, scRNAseq

value: sorted


title: patient C1P3, after first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P3-M1-T1-CD4

value: peripheral blood

tag: patient id

tag: mp course

value: first

tag: time point

tag: cell population

value: CD4+ T cells

tag: clinical evaluation

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

tag: body weight (in kg)

tag: course of disease

tag: disease duration (years)

tag: number of relapses in the past 2 years

tag: duration since last relapse (months)

tag: edss score

tag: disease-modifying therapy

value: peginterferon beta-1a


title: Brain 17 - whole, scRNAseq

tag: tissue

tag: tissue region

value: whole

tag: cell type

tag: genotype

value: wildtype


title: patient C1P3, after first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P3-M1-T1-CD19

source_name: B cells from the peripheral blood

tag: patient id

tag: mp course

tag: time point

value: after

tag: cell population

value: CD19+ B cells

tag: clinical evaluation

value: responder

tag: percentage in pbmc

tag: body size (in cm)

tag: body mass index

tag: current smoker

tag: study center

tag: number of other medications taken

tag: neurological dysfunction

value: recurring

tag: fs

tag: total dose of mp in mg

tag: days from first to last mp application

tag: side effects to mp


title: patient C1P3, before first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P3-M1-T0-CD19

tag: tissue

value: before

tag: cells per ml

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

value: female

tag: body weight (in kg)

value: no

value: Berlin

tag: course of disease

value: CIS/RRMS

tag: disease duration (years)

tag: number of relapses in the past 2 years

tag: duration since last relapse (months)

tag: edss score

tag: disease-modifying therapy

value: bladder or bowel:no


title: patient C1P3, before first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P3-M1-T0-CD4

tag: patient id

tag: mp course

tag: time point

tag: cell population

tag: clinical evaluation

tag: percentage in pbmc

tag: body size (in cm)

tag: body mass index

tag: current smoker

tag: study center

tag: number of other medications taken

tag: neurological dysfunction

tag: fs


title: Brain 15 - whole, scRNAseq

tag: tissue

value: adult brain

tag: tissue region

tag: cell type

value: mixed (tissue dissociation)

tag: genotype


title: 5637SH-2.Input

city: zhengzhou

first: Jianjian

last: Yin

state: Henan

address: No. 100 Science Road

country: China

institute: Zhengzhou University

data_processing:
Use hisat2 software (v2.0.4) to compare high-quality reads to the human reference genome (UCSC HG38). Then, under the guidance of the gtf gene annotation file, use HTSeq software (v0.9.1) to obtain the original count, use edgeR to standardize and calculate the fold change and p-value between the two sets of samples to screen for differentially expressed LncRNA And mRNA.
clean reads of input libraries were aligned to reference genome (UCSC HG38) by STAR software. Then circRNAs were identified by DCC software using the STAR alignment results. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software.
Assembly: HG38
Supplementary files format and content: excel format

source_name: 5637 cell line

extract_protocol:
RNA extraction protocol：Total RNA was extracted using the TRIzol reagent (Invitrogen, USA). The RNA concentration of each sample was determined using a NanoDrop 2000 (Thermo Fisher, USA). The quality of the RNAs was subsequently determined by measuring the OD260/OD280 value, and RNA purity was confirmed by measuring the OD260/OD230 value. And the ratio of 260/280 between 1.8–2.0 and the ratio of 260/230 between 2.0–2.2 were considered to be pure RNA. Agarose gel electrophoresis was used for the integrity and quality testing of total RNA.
Briefly, total RNA was used for removing the rRNAs with NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. And m1A RNA immunoprecipitation was performed with the GenSeqTM m1A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input samples without immunoprecipitation and the m1A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: 5637 cell line

tag: cell line

value: 5637 cell

value: bladder cancer cell

value: TRMT61A knockdown

tag: treatment


title: shNT_1

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

institute: IMCB

data_processing:
RNA-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapters and overrepresented sequences have been removed using cutadapt software (https://cutadapt.readthedocs.io/ en/stable/).
Further reads preprocessing was performed by trim_galore with default parameters.
Mapping of RNA-seq reads was done using bowtie2 with default parameters for RNA-seq data.
RSEM software (Li and Dewey, 2011)  were used to quantify the gene-level expression.
Assembly: mm10
Supplementary files format and content: txt format; raw counts for three experimental conditions with 3 replicates each.

source_name: Primary mouse neural stem cells

growth_protocol: Primary mouse neural stem cells (mNSC) were isolated from the brain cortex of E13.5 embryos, and enriched using the neurosphere formation technique. The neurospheres were then expanded by culturing on laminin (5 µg/mL, overnight, 37°C) precoated dishes, in the presence of NeuroCult Proliferation mNSC media (05702, Stem Cell Technologies) that is supplemented with fibroblast growth factor (FGF) (F0291, Sigma) and epidermal growth factor (EGF) (E4127, Sigma) at 10 and 20 ng/mL, respectively.

extract_protocol:
Total RNA from cells was extracted using the RNeasy® Mini or Micro Kit (Qiagen).
The mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: The shRNAs against mouse Rad21 (shRad21 #1, (#TRCN0000174832) and shRad21 #2, (#TRCN0000176084)) were purchased from Sigma. The DePinho laboratory provided non-targeting (NT) or control shRNA plasmid. Plasmid DNA was transfected into cells using Polyethylenimine (Polysciences) and the mNSC was transduced with viral particles.

value: Primary mouse neural stem cells

value: wild type (Phf2flox/flox)

value: wild type (Phf2flox/flox) control, infect shNT

tag: time


title: Lineage tracing rep2, rpl39 scars

description: Targeted library for CRISPR lineage tracing


title: Lineage tracing rep2, cfl1 scars


title: Lineage tracing rep2, ube2e1 scars


title: patient C1P2, after first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P2-M1-T1-CD19

value: peripheral blood

tag: patient id

tag: mp course

value: first

tag: time point

value: after

tag: cell population

value: CD19+ B cells

value: responder

tag: cells per ml

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

value: male

tag: body weight (in kg)

tag: course of disease

tag: disease duration (years)

tag: number of relapses in the past 2 years

tag: duration since last relapse (months)

tag: edss score

tag: disease-modifying therapy

value: teriflunomide

value: bladder or bowel:unchanged

tag: total dose of mp in mg

tag: days from first to last mp application

tag: side effects to mp


title: F02588-GEX_F02589-FB_Batch4

tag: tissue

value: CAR Product

tag: batch


title: patient C1P2, after first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P2-M1-T1-CD4

tag: patient id

tag: mp course

tag: time point

tag: cell population

value: CD4+ T cells

tag: clinical evaluation

tag: percentage in pbmc

tag: cells per ml

tag: body size (in cm)

tag: body mass index

tag: current smoker

value: no

tag: study center

value: Berlin

value: CIS/RRMS

tag: number of other medications taken

tag: neurological dysfunction

value: recurring

tag: fs


title: 5637NC-2.Input

value: 5637 cell line

tag: cell line

value: 5637 cell

tag: cell type

value: bladder cancer cell

tag: genotype

value: WT

tag: treatment


title: Brain 12 - whole, scRNAseq

tag: tissue

value: adult brain

tag: tissue region

value: whole

value: mixed (tissue dissociation)

value: wildtype


title: Brain 13 - whole, scRNAseq


title: F02677-GEX_F02678-FB_Batch6

tag: batch


title: 5637SH-1.Input

value: TRMT61A knockdown


title: patient C1P2, before first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P2-M1-T0-CD4

value: peripheral blood

tag: patient id

tag: mp course

value: first

tag: time point

value: before

tag: cell population

tag: clinical evaluation

value: responder

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

value: male

tag: body weight (in kg)

tag: course of disease

tag: disease duration (years)

tag: number of relapses in the past 2 years

tag: duration since last relapse (months)

tag: edss score

tag: disease-modifying therapy

value: teriflunomide

value: bladder or bowel:no

tag: total dose of mp in mg

tag: days from first to last mp application

tag: side effects to mp


title: Lineage tracing rep2, cirbpb scars

tag: tissue

tag: cell type

tag: genotype


title: Brain 14 - sorted, scRNAseq

tag: tissue region

value: sorted


title: Ssrp1-1

tag: developmental stage

value: embryonic stem cells

tag: antibody

value: SSRP1 antibody BioLegend #609702


title: 5637NC-1.Input

value: 5637 cell line

tag: cell line

value: 5637 cell

value: bladder cancer cell

tag: treatment


title: Brain 23 - telencephalon, Notch inhibition, scSLAMseq

description: scSLAM-seq library (metabolic labeling of nascent transcripts) in a Notch pathway perturbation experiment

data_processing:
The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect, the gene expression matrices were processed with the SoupX tool (Young & Behjati, 2020) for removing ambient RNA contamination.
A subset of libraries was also mapped with Velocyto (v0.17.17) (La Manno et al, 2018) to create count matrices for unspliced and spliced molecules.
The targeted lineage tracing libraries were aligned using bwa mem3 (v.0.7.12) to individual references of endogenous genes used in the lineage tracing experiment (actb1, actb2, cfl1, cirbpb, rpl39 and ube2e1). The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors.
For custom code and further downstream analysis, see: https://github.com/nimitic/radial-glia.
Assembly: GRCz11
Supplementary files format and content: Tab-separated barcode files and matrix files along with the tab-separated gene file (supplementary file) are the output of CellRanger mapping, further processed by the SoupX package for ambient RNA removal.
Supplementary files format and content: Loom files are the output of velocyto mapping (distinguishing spliced and unspliced mRNAs).
Supplementary files format and content: filtered_scars.csv files contain the output of a custom scar filtering pipeline.
Library strategy: scSLAM-seq

extract_protocol:
The samples were prepared according to a scSLAM-seq protocol, adapted from Neuschulz et al (2023). Briefly: in order to label nascent transcripts, 200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected, and a single-cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide (adding 111 µl 100 mM IAA to 800 µl fixed sample) was done overnight. The following day, the reaction was quanched with a quenching buffer (containing 100 mM DTT), after which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA-seq protocol.
Adult zebrafish brain tissue was extracted, optionally dissected to select a specific region of interest (telencephalon, diencephalon, mesencephalon or rhombencephalon) and then dissociated with a trypsin protocol. Briefly, the samples were incubated in 750 µl of HBSS-glucose solution and dissocated with 15 µl of 0.05% trypsin-EDTA (Gibco) for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA-EBSS-HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter, washed with cold HBSS and resuspended in 100-200 µl HBSS with 0.05% BSA, then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM-seq samples, a papain dissociation protocol (Worthington kit, according to manufecturer's instructions) was used followed by an adapted scSLAM-seq protocol for labeling nascent transcripts (see sample-specific entry).
The standard transcriptome libraries were constructed according to the manufacturer's protocol (10X Genomics). For targeted libraries of scars used for lineage tracing, the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target, specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit, so they could be sequenced on the same platform.

treatment_protocol: Notch inhibiton: zebrafish were incubated in a water bath containing system water with 50 µM DAPT (Gamma Secretase Inhibitor, Sigma-Aldrich) for 48 hours.

value: adult brain

value: telencephalon

value: Notch inhibition (DAPT)


title: patient C1P2, before first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P2-M1-T0-CD19

tag: patient id

tag: mp course

tag: time point

tag: cell population

value: CD19+ B cells

tag: clinical evaluation

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

tag: body weight (in kg)

tag: body size (in cm)

tag: body mass index

tag: current smoker

value: no

tag: study center

value: Berlin

tag: course of disease

value: CIS/RRMS

tag: number of other medications taken

tag: neurological dysfunction

value: recurring

tag: fs


title: Brain 11 - whole, scRNAseq

tag: tissue

tag: tissue region

value: whole

tag: cell type

value: mixed (tissue dissociation)

tag: genotype

value: wildtype


title: Brain 22 - telencephalon, control, scSLAMseq

treatment_protocol: Control for Notch inhibition: zebrafish were incubated in a water bath containing system water with 1:200 diluted DMSO for 48 hours.

tag: treatment

value: Control (DMSO)


title: patient C1P1, after second course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P1-M2-T1-CD4

value: peripheral blood

tag: patient id

tag: mp course

value: second

tag: time point

value: after

tag: cell population

value: CD4+ T cells

tag: clinical evaluation

value: responder

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: rna integrity number

value: female

tag: disease duration (years)

tag: number of relapses in the past 2 years

tag: duration since last relapse (months)

tag: edss score

tag: disease-modifying therapy

value: teriflunomide

value: bladder or bowel:unchanged

tag: total dose of mp in mg

tag: days from first to last mp application

tag: side effects to mp

value: headache, diarrhea


title: patient C1P1, before second course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P1-M2-T0-CD4

tag: tissue

tag: patient id

value: before

tag: age (years)

tag: Sex

tag: body weight (in kg)

tag: body size (in cm)

tag: body mass index

tag: current smoker

value: no

tag: study center

tag: course of disease

tag: number of other medications taken

tag: neurological dysfunction

tag: fs

value: bladder or bowel:no


title: Brain 10 - telencephalon, scRNAseq

value: adult brain

tag: tissue region

value: telencephalon

tag: cell type

tag: genotype


title: mod5 knockout mycelium_FC 3 [D3]

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

institute: Leibniz Institute for Natural Product Research and Infection Biology

data_processing:
Pre-processing of raw reads, quality control and gene abundance estimation used GEO2RNaseq pipeline (v0.100.3, (80)) in R (version 3.6.3). Quality analysis was performed with FastQC (v0.11.5) before and after trimming. Read-quality trimming was done with Trimmomatic (v0.36) and reads were rRNA-filtered using SortMeRNA (v2.1) with a single rRNA database combining all rRNA databases shipped with SortMeRNA.
Reference annotation was created by extracting and combining exon features from annotation files. Reads were mapped against reference genome of A. fumigatus (A1163, assembly GCA_000150145.1) using HiSat2 (v2.1.0, paired-end mode). Gene abundance estimation was done with featureCounts (v2.0.1) in paired-end mode with default parameters. MultiQC version 1.7 was used to summarize and assess quality of output from FastQC, Trimmomatic, HiSat, featureCounts and SAMtools. The count matrix with gene abundance data without and with median-of-ratios normalization (MRN, (81)) were extracted.
Assembly: A. fumigatus (A1163, assembly GCA_000150145.1)
Supplementary files format and content: The processed data file is an excel .xlsx file containing four tabs, including read counts for each gene, MRN-normalized counts, RPKM-normalized counts, and TPM-normalized counts.

organism: Aspergillus fumigatus

growth_protocol: A. fumigatus strains were grown on Aspergillus minimal medium (AMM) agar plates (70 mM NaNO3, 11.2 mM KH2PO4, 7 mM KCl, 2 mM MgSO4, 1% (w/v) glucose and 1 μl/ml trace element solution (pH 6.5)). The trace element solution was composed of 1 g FeSO4 • 7 H2O, 8.8 g ZnSO4 • 7 H2O, 0.4 g CuSO4 • 5 H2O, 0.15 g MnSO4 • H2O, 0.1 g NaB4O7 • 10 H2O, 0.05 g (NH4)6Mo7O24 • 4 H2O, and ultra-filtrated water to 1000 ml. Spores were harvested after 5 days with 10 ml of sterile distilled water using a T-shaped inoculation spreader and spore suspensions were filtered through a 30-µm cell strainer (MACS, Miltenyi Biotec GmbH, Germany) to exclude mycelium.

extract_protocol:
Total RNA was isolated from three biological replicates of CEA17ΔakuBKU80 and Δmod5 knockout from 24-h-old mycelium either unstressed, or stressed for the final 8 hours with 5-fluorocytosine. Afterwards, mycelia were harvested using Miracloth (EMD Millipore Corp., USA), rinsed with sterile water and same amounts of mycelium were transferred to 2-mL screw cap tubes for RNA isolation. All centrifugation steps were performed at 4°C and full speed (20,817 x g). 800 µL of TRIzol (Thermo Fischer Scientific, Dreieich) were added to each tube, along with glass beads (1/3 of the tube) and the mycelium was mechanically disrupted by 3 rounds of 30 sec, 4.0 m/sec homogenization using the FastPrep-24™ Homogenizer. Subsequently, the samples were incubated for 5 min on ice, followed by additional 5 min at room temperature. After addition of 160 µL of chloroform, the samples were vigorously vortexed for 10 sec and centrifuged for 5 min. The resulting aqueous phase containing the RNA was carefully transferred to a new RNase-free tube without disturbing the interphase. The RNA phase was then purified using the same amount of phenol/chloroform/isoamyl alcohol and centrifuged for 5 min. The purification step was repeated 2-3 times until the interphase remained clear. In the next step, RNA was further purified with 400 µL of chloroform and centrifugation for 5 min. The aqueous phase was again transferred to a new RNase-free 2-mL tube, precipitated by addition of 500 µL isopropanol for 20 min, and RNA was pelleted by 20 min centrifugation. The RNA pellet was washed with 70% ethanol (v/v) and air-dried at 37°C. Finally, RNA was dissolved in 30-50 µL DEPC water at 65°C. The RNA was purified using the RNA Clean and Concentrator™ kit (Zymo Research, USA) following the manufacturer’s instructions. Up to 10 µg of total RNA was afterwards treated with 2 U of DNase I endonuclease (Thermo Fisher) for 30-60 min at 37°C in a volume of 20 µL. RNA concentration was then quantified with the QubitTM RNA BR Assay kit (Thermo Fisher Scientific) on the Qubit Flex Fluorometer (Thermo Fisher Scientific). Quality was assessed either by agarose gel electrophoresis or QUBITTM Integrity and Quality (IQ) kit (Thermo Fisher).
Poly-(A) selection and directional sequencing of mRNA was performed by Novogene using paired-end 150-bp read sequencing on a NovaSeq 6000.

treatment_protocol: CEA17∆akuBKU80 and CEA17∆akuBKU80∆mod5 fungal samples (5x107 spores) were cultured either for 24 h or for 16 h in AMM followed by an 8-h treatment with 80 ng/µL of 5-fluorocytosine.

value: mycelium

tag: cell line

tag: treatment

tag: replicate

value: Biological Replicate 3


title: 5637SH-2.IP

data_processing:
Use hisat2 software (v2.0.4) to compare high-quality reads to the human reference genome (UCSC HG38). Then, under the guidance of the gtf gene annotation file, use HTSeq software (v0.9.1) to obtain the original count, use edgeR to standardize and calculate the fold change and p-value between the two sets of samples to screen for differentially expressed LncRNA And mRNA.
clean reads of input libraries were aligned to reference genome (UCSC HG38) by STAR software. Then circRNAs were identified by DCC software using the STAR alignment results. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software.
Assembly: HG38
Supplementary files format and content: excel format
Library strategy: MeRIP-seq

tag: tissue

value: 5637 cell line

value: 5637 cell

value: bladder cancer cell

value: TRMT61A knockdown


title: HUVEC-Control-3

city: Boston

first: Alexander

last: Grath

state: MA

address: 360 Huntington Ave

department: Bioengineering

institute: Northeastern University

description: Positive control

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: hg18
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample

source_name: HUVEC

growth_protocol: All cells were maintained in EGM-2 supplemented with growth supplements, 1% P/S, and 1% Glutamax. Cells were incubated at 37C and 5% CO2.

extract_protocol:
RNA was harvested using Rneasy plus mini kit (QIAGEN)
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: To drive reprogramming, ETV2-ECs and rECs (ETV2+SOX17) were treated with 1000ng/mL of doxycycline. NHDF and HUVEC control groups did not receive any doxycycline.

value: HUVEC

value: endothelial cell

value: WT


title: Brain 10 - mesencephalon, scRNAseq

value: mesencephalon

value: mixed (tissue dissociation)

value: wildtype


title: 5637NC-2.IP


title: patient C1P1, after first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P1-M1-T1-CD4

value: peripheral blood

tag: patient id

tag: mp course

value: first

tag: time point

value: after

tag: cell population

value: CD4+ T cells

tag: clinical evaluation

value: non-responder

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

value: female

value: Berlin

value: CIS/RRMS

tag: disease duration (years)

tag: number of relapses in the past 2 years

tag: duration since last relapse (months)

tag: edss score

tag: disease-modifying therapy

value: teriflunomide

value: recurring

value: bladder or bowel:unchanged

tag: total dose of mp in mg

tag: days from first to last mp application

tag: side effects to mp

value: hair loss


title: mod5 knockout mycelium_FC 1 [D1]

tag: tissue

value: mycelium

tag: cell line

tag: genotype

tag: treatment

tag: replicate

value: Biological Replicate 1


title: Wild-type mycelium_FC 3 [C3]

value: Wild type

value: Biological Replicate 3


title: HUVEC-Control-2

description: Positive control

value: HUVEC

tag: cell type

value: endothelial cell

value: WT


title: HUVEC-Control-1

description: Positive control


title: mod5 knockout mycelium_FC 2 [D2]

value: Biological Replicate 2


title: Brain 10 - diencephalon, scRNAseq

value: adult brain

tag: tissue region

value: diencephalon

value: mixed (tissue dissociation)

value: wildtype


title: DF-ETV2-Sox17-3

description: ETV2 and SOX17-driven reprogramming

source_name: NHDF-Ad

value: NHDF-Ad

value: dermal fibroblast

value: ETV2 and SOX17 overexpression

value: NHDF to EC transdifferentiation


title: 5637NC-1.IP

value: 5637 cell line

value: 5637 cell

value: bladder cancer cell


title: Brain 8 - whole, scRNAseq

value: whole


title: Brain 10 - rhombencephalon, scRNAseq

value: rhombencephalon


title: Brain 5 - telencephalon, scRNAseq

value: telencephalon


title: DF-ETV2-Sox17-2

description: ETV2 and SOX17-driven reprogramming


title: 10nM24h_Rep4

city: Chicago

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Reads were mapped to the human genome using STAR version 2.5.2b
Raw read counts were calculated using featureCounts / subread version 1.5.1
Normallization was performed using MAP-Rseq
Differential gene expression was performed using edgeR
Assembly: hg38
Supplementary files format and content: spreadsheet of RPKM values

growth_protocol: Cells were maintained in DMEM/F12 (no phenol red) supplemented with 5% charcoal stripped FBS, 1% Pen/Strep, 20 ng/ml EGF, 10 µg/ml insulin, 0.5 µg/ml hydrocortisone, and 0.1 µg/ml cholera toxin.

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep following manufacturer's protocols.

treatment_protocol: Cells were treated with 10 nM D-Alanine and mRNA was collected 4h or 24h after tratment.

value: 24h after 10nM D-Alanine


title: 10nM24h_Rep5

value: WT


title: Wild-type mycelium_FC 2 [C2]

value: mycelium

value: Wild type

value: Biological Replicate 2


title: patient C1P1, before first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P1-M1-T0-CD4

value: peripheral blood

tag: patient id

tag: mp course

value: first

tag: time point

value: before

tag: cell population

value: CD4+ T cells

tag: clinical evaluation

value: non-responder

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: rna integrity number

tag: age (years)

value: female

tag: body weight (in kg)

tag: body size (in cm)

tag: body mass index

tag: current smoker

value: no

tag: study center

value: Berlin

tag: course of disease

value: CIS/RRMS

value: teriflunomide

tag: number of other medications taken

tag: neurological dysfunction

value: recurring

tag: fs

value: bladder or bowel:no

value: hair loss


title: 5637SH-1.IP

tag: tissue

value: 5637 cell line

tag: cell line

value: 5637 cell

tag: cell type

value: bladder cancer cell

tag: genotype

value: TRMT61A knockdown

tag: treatment


title: DF-ETV2-Sox17-1

description: ETV2 and SOX17-driven reprogramming

value: NHDF-Ad

value: dermal fibroblast

value: ETV2 and SOX17 overexpression

value: NHDF to EC transdifferentiation


title: mod5 knockout mycelium 3 [B3]

value: mycelium

value: Untreated

tag: replicate

value: Biological Replicate 3


title: 10nM24h_Rep3

value: WT

value: 24h after 10nM D-Alanine


title: Brain 3 - telencephalon, scRNAseq

value: adult brain

tag: tissue region

value: telencephalon

value: mixed (tissue dissociation)


title: DF-ETV2-3

description: ETV2-driven reprogramming

value: ETV2 overexpression


title: mod5 knockout mycelium 2 [B2]

value: Biological Replicate 2


title: Brain 2 - telencephalon, scRNAseq


title: Wild-type mycelium_FC 1 [C1]

value: Wild type

value: Biological Replicate 1


title: 10nM24h_Rep1


title: DF-ETV2-1

description: ETV2-driven reprogramming


title: DF-ETV2-2

description: ETV2-driven reprogramming


title: Brain 1 - telencephalon, scRNAseq


title: mod5 knockout mycelium 1 [B1]


title: DF-Control-3

description: Negative control


title: 10nM4h_Rep5

value: 4h after 10nM D-Alanine


title: Wild-type mycelium 3 [A3]


title: Wild-type mycelium 1 [A1]


title: DF-Control-1

description: Negative control

value: NHDF-Ad


title: Wild-type mycelium 2 [A2]


title: lung, WT 3

city: Los Angeles

first: Benjamin

last: Hurrell

state: CA

address: 1450 Biggy Street

institute: USC

data_processing:
Image analysis andbase calling was carried out usingRTA 1.13.48.0. Final file formatting,demultiplexing andfastq generation were carried out usingCASAVA v 1.8.2.
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genomemm10 usingSTAR (v3.5.3) with default parameter settings
Gencode M20 annotation was used to quantify the aligned reads to genes/transcripts usingPartek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression usingPartek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Assembly: mm10
Supplementary files format and content: .txt file with aligned gene counts

source_name: lung

growth_protocol: Freshly isolated ILC2s after 3 i.n. injections of 1µg rm-IL33 were stimulated with rm-IL-2 (10ng/mL) and rm-IL-7 (10ng/mL) at 37°C

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen, Valencia, California). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were incubated for 24h

value: lung


title: lung, Piezo1 KO 3


title: lung, Piezo1 KO 2


title: lung, Piezo1 KO 1


title: 10nM4h_Rep1


title: 10nM4h_Rep2


title: 8-cell embryos, atg5 mutants expressing proTPE8:8-cell embryos, atg5-GFP replicate 3

city: Wuhan

first: Peng

last: Zhao

address: Luojia Hill

department: College of Life Sciences

institute: Wuhan University

description: atg5 Com-3

data_processing:
Raw reads were filtered by fastp with "--detect_adapter_for_pe" to remove low quality reads and adapter
Clean reads were aligned to Nicotiana tabacum reference genome by STAR (2.7.11a) with "--outSAMtype BAM SortedByCoordinate"
Reads count and FPKM of genes was generated with RSEM (1.3.3) with "--paired-end --no-bam-output"
Supplementary files format and content: table-delimited test file includes raw counts for each samples

organism: Nicotiana tabacum

source_name: 8-cell embryo

extract_protocol:
mRNA was isolated using the Dynabeads mRNA DIRECTTM Micro Kit (Life Technologies) according to the manufacturer’s instructions.
cDNA synthesis and amplification were performed using a SMARTerUltra Low RNA Kit for Illumina Sequencing (Clontech, USA).

value: 8-cell embryo

value: atg5 mutants expressing proTPE8:ATG5-GFP


title: 10nM24h_Rep2


title: SAS, sham, replicate 3

city: Dresden

first: Claudia

last: Peitzsch

address: Fetscherstr. 105

institute: Center for Regenerative Therapies Dresden (CRTD)

data_processing:
RNA sequencing data were processed by the DKFZ One Touch Pipeline (OTP) (https://doi.org/10.1016/j.jbiotec.2017.08.006), using the RNA-seq workflow version 1.3.0, which is available athttps://github.com/DKFZ-ODCF/RNAseqWorkflowin combination with the workflow management system Roddy version 3.5.4 (https://github.com/TheRoddyWMS/Roddy).
alignment was performed against 1KGRef_PhiX (generated from the 1000 Genomes assembly, based on hs37d5 and including decoy sequences merged with PhiX contigs to be able to align spike in reads) using the STAR aligner version 2.5.3a (https://academic.oup.com/bioinformatics/article/29/1/15/272537).
duplicate marking using Sambamba version 0.6.5 (https://pubmed.ncbi.nlm.nih.gov/25697820/)
quality control using Samtools version 1.6 flagstat (https://doi.org/10.1093/bioinformatics/btp352) as well as rnaseqc version 1.1.8 (https://www.ncbi.nlm.nih.gov/pubmed/22539670)
gene specific quantification of reads using FeatureCounts of the Subread package version 1.5.1 (https://www.ncbi.nlm.nih.gov/pubmed/24227677) on gene annotation GENCODE version 19[in the strand-specific counting mode].
Assembly: 1KGRef_PhiX (generated from the 1000 Genomes assembly, based on hs37d5 and including decoy sequences merged with PhiX contigs to be able to align spike in reads)
Supplementary files format and content: tab-separated values file containing number of reads (feature counts), FPKM and TPM for both forward and reverse strands for each sample are provided. Column number 9 from each sample was used for downstream analysis (DESeq2 input)

source_name: tongue

growth_protocol: The cell lines were cultured in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% L-Glutamine, 1% 2-(4-(2-Hydroxyethyl)-1-piperazinyl)-ethansulfonacid (HEPES), 1% minimum essential medium (MEM), 1% non-essential amino acid (NEAA), and 1% sodium pyruvate. All cell lines were used for experiments until passage 15, tested for mycoplasma infection and SNP-based cell authentication on a regular basis.

extract_protocol:
RNA was isolated using the RNeasy mini kit (Qiagen; #74104) according to the manufacturer’s recommendation, in triplicates. RNA concentrations were measured with the NanoDrop ND-1000 (Peqlab).
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit following the manufacturer’s instructions.

treatment_protocol: The HNSCC cell lines SAS and Cal33 were treated with GSK-J1 (IC5, 4.5 µM) with or without a single 4 Gy x-ray irradiation. After 24 hours treatment, RNA was isolated.

value: tongue

value: SAS

value: Head and Neck Squamous Cell Carcinoma

value: sham


title: SAS, sham, replicate 2

value: WT


title: 8-cell embryos, atg5 mutants expressing proTPE8:8-cell embryos, atg5-GFP replicate 2

description: atg5 Com-2


title: Control_Rep5

value: Control


title: 8-cell embryos, atg5 mutants expressing proTPE8:8-cell embryos, atg5-GFP replicate 1

description: atg5 Com-1


title: lung, WT 1


title: SAS, sham, replicate 1


title: DF-Control-2

description: Negative control

value: dermal fibroblast


title: 10nM4h_Rep3


title: 10nM4h_Rep4


title: Control_Rep4


title: 8-cell embryos, atg5 mutant replicate 3

value: atg5 mutant


title: Control_Rep3


title: lung, Yoda1 5

treatment_protocol: 10µM Yoda1 or DMSO was added for 24h

tag: strain

value: BALB/c


title: 8-cell embryos, atg5 mutant replicate 2


title: SAS, 4 Gy x-ray irradiation, replicate 2

value: 4 Gy x-ray irradiation


title: Control_Rep2


title: lung, Yoda1 4


title: Control_Rep1


title: lung, DMSO 3

value: DMSO


title: SAS, 4 Gy x-ray irradiation, replicate 1


title: SAS, GSK-J1, replicate 3


title: lung 491 CD44/SSEA4+ cells with lactate treatment

city: minneappolis

first: LiBang

last: yang

state: MN

address: 420 delaware st

department: medicine

institute: University of minnesota

description:
LC491Lac
IPFlac4
stemlike

data_processing:
Trimmomatic v 0.39: Reads were trimmed from 3-prime end to remove sequencing adapters and until base quality was >15, discarding reads shorter than 18nt.
BWA-MEM 0.7.17: Reads were mapped to the GRCh38.p13 reference assembly (repeat masked) with default parameters.
Picard-3.0.0: BAM files were cleaned of duplicates.
Samtools 1.14: BAM files were cleaned of read pairs with MAPQ<30, reads mapping to sequences other than the autosomes and X and Y, and non-primary alignments.
MACS2 v 2.2.7.1: Peaks were called with MACS2 in paired-end mode, treating the IPF library as a control and IPFlac library as a ChIP.
MSPC: Per-sample peaks were merged with MSPC in R, requiring at least 1 sample with a P value of less than 1E-3.
featureCounts 2.0.5: Reads in peaks were quantified from filtered BAM files and consensus peak set.
Assembly: GRCh38.p13
Supplementary files format and content: narrowPeak: Per-sample peak calls.
Supplementary files format and content: BED: Consensus merged peak calls.
Supplementary files format and content: TSV: Tab-separated matrix of raw peak quantification.
Supplementary files format and content: CSV: Comma-separated matrix of log2-transformed normalized peak quantification.

source_name: primary

growth_protocol: DMEM with 10% FBS.

extract_protocol:
Qiagen mRNA extraction kit and protocol.
Illumina kit and protocol.

treatment_protocol: 4 mM lactate.

value: primary

value: lung cancer cells

value: IPF+Lactate

tag: chip antibody


title: lung, WT 2

value: lung


title: lung, DMSO 2


title: SAS, GSK-J1, replicate 2


title: lung, DMSO 1


title: lung 848 CD44/SSEA4+ cells with lactate treatment

description:
LC848Lac
IPFlac3
stemlike


title: 8-cell embryos, WT replicate 1

value: 8-cell embryo

value: wild type


title: lung 661 CD44/SSEA4+ cells with lactate treatment

description:
LC661Lac
IPFlac2
stemlike


title: lung, Yoda1 6


title: SAS, GSK-J1, replicate 1

value: tongue


title: iMyb MyPL1, Day 4, Dox, rep4

city: Ghent

first: Bruno

last: Palhais

address: Corneel Heymanslaan 10

department: Department of Biomolecular Medicine

country: Belgium

institute: Ghent University

data_processing:
alignment by STAR 2.4.2a
quantified on Gencode v25
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes the raw counts for each sample (column name specified matches the library name).

source_name: Thymus

growth_protocol: A primary murine T-ALL cell line, named MyPL1, was derived from a leukemia-burdened R26-Mybtg/tg; Ptenfl/fl; Lck-Cretg/+ (Myb/PtenLck) mouse. In brief, thymomas were dissected, cut into small tumor fragments using two needles, collected in RPMI 1640 medium (Thermo Fisher) containing 15% heat-inactivated fetal bovine serum (FBS), 0.1 mM non-essential amino-acids (Thermo Fisher), 2 mM L-glutamine (Gibco), 10 mM β-mercaptoethanol (Thermo Fisher), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco), and 5 ng/mL recombinant murine interleukin-7 (mIL-7; PeproTech), and cultured at 37°C in a humidified atmosphere with 5% CO2. Cells in suspension were split regularly and became independent of mIL-7 after 4 to 8 weeks.

extract_protocol:
RNA was extracted from the samples by using the RNeasy Plus Micro Kit (Qiagen, 74034) according to the manufacturer’s instructions.
RNAseq libraries were prepared with the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 015.96) according to the manufacturer’s instructions.

treatment_protocol: For MYB silencing, we used a pLVTSH lentiviral construct with a dox-inducible Myb shRNA48 that was generated by Prof. Dr. Tom Gonda (Brisbane, Australia). For induction of Myb knockdown, 1 µg/mL of doxycycline (DOX) was added to the culture medium and refreshed daily, for 4 consecutive days.

value: Thymus

value: T-ALL

tag: condition


title: Experiment 8, tg(her4:RFP), tg(mcm5:gfp)

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
Reads were mapped to zebrafish genome using STAR
Gene counts were computed using featureCounts
Differential expression analysis was performed with DESeq2
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text file generated by featureCounts

source_name: brain/telencephali

extract_protocol:
PicoPure Isolation kit (Life technologies), RNase-free DNase Set (Qiagen®)
SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian kit (Clontech Laboratories)

value: brain/telencephali

value: tg(her4:RFP), tg(mcm5:gfp)

tag: nsc status

value: Activated

value: RG

tag: region

value: tel

tag: age


title: Experiment 8, tg(her4:RFP)

value: Quiescent

value: R


title: SAS, GSK-J1 plus 4 Gy x-ray irradiation, replicate 3

value: SAS

value: Head and Neck Squamous Cell Carcinoma

value: WT

value: GSK-J1 plus 4 Gy x-ray irradiation


title: SAS, 4 Gy x-ray irradiation, replicate 3

value: 4 Gy x-ray irradiation


title: lung 549 CD44/SSEA4+ cells with lactate treatment

description:
LC549Lac
IPFlac1
stemlike

value: primary

value: lung cancer cells

value: IPF+Lactate


title: iMyb MyPL1, Day 4, Control, rep4

value: Thymus


title: lung 491 CD44/SSEA4+ cells

description:
LC491
IPF4
stemlike

value: IPF-Lactate


title: SAS, GSK-J1 plus 4 Gy x-ray irradiation, replicate 2

value: tongue


title: iMyb MyPL1, Day 3, Dox, rep4

value: T-ALL


title: SAS, GSK-J1 plus 4 Gy x-ray irradiation, replicate 1


title: 8-cell embryos, WT replicate 3

value: 8-cell embryo

value: wild type


title: Experiment 6, tg(her4:RFP), tg(mcm5:gfp)

value: brain/telencephali

value: tg(her4:RFP), tg(mcm5:gfp)

value: Activated

value: RG

value: tel


title: Cal33, sham, replicate 3

value: Head and Neck Squamous Cell Carcinoma

value: WT

value: sham


title: Experiment 6, tg(her4:RFP)

value: Quiescent

value: R


title: lung 848 CD44/SSEA4+ cells

description:
LC848
IPF3
stemlike

value: primary

value: lung cancer cells


title: Experiment 4, tg(her4:RFP), tg(mcm5:gfp)


title: 8-cell embryos, WT replicate 2


title: lung 661 CD44/SSEA4+ cells

description:
LC661
IPF2
stemlike

value: IPF-Lactate


title: iMyb MyPL1, Day 2, Dox, rep4

value: Thymus


title: iMyb MyPL1, Day 3, Control, rep4

value: T-ALL


title: 8-cell embryos, atg5 mutant replicate 1

value: 8-cell embryo

value: atg5 mutant


title: lung 549 CD44/SSEA4+ cells

description:
LC549
IPF1
stemlike


title: iMyb MyPL1, Day 2, Control, rep4


title: Experiment 4, tg(her4:RFP)

value: brain/telencephali


title: Cal33, sham, replicate 1

value: tongue


title: iMyb MyPL1, Day 1, Dox, rep4


title: Experiment 3, tg(her4:RFP), tg(mcm5:gfp)

value: tg(her4:RFP), tg(mcm5:gfp)

value: Activated


title: Cal33, sham, replicate 2


title: Cal33, 4 Gy x-ray irradiation, replicate 3

value: 4 Gy x-ray irradiation


title: RAO55 xenograft, Pax-Met

city: Callaghan

first: Dylan

last: Kiltschewskij

state: NSW

address: Room MS616, Level 6, Medical Sciences Building, University Drive

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: The University of Newcastle

data_processing:
Raw base calls were demultiplexed and converted into fastq format using bcl2fastq2 (v2.20)
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Assembly: UCSC hg38, UCSC mm10
Supplementary files format and content: Excel spreadsheets (1x for hg38, 1x for mm10) containing all detected ATAC-Seq peaks, annotated with genomic features, fragment densities for each sample, and log2 fold changes between all pairwise comparisons

growth_protocol: A single cell suspension of SU-DIPG-XIII-P*, HSJD-DIPG-007, RA-055, or UON-VIBE5 neurospheres were injected into the pontine region of 6-8 week old, female, NSG mice under isoflurane anesthesia. Stereotactic coordinates were 0.8 mm to the right of midline, 0.5 mm posterior to lambda and 5 mm deep using 500,000 cells (SU-DIPG-XIII-P*), 300,000 cells (HSJD-DIPG-007), 200,000 cells (RA-055) or 300,000 cells (UON-VIBE5) in 2 µL HBSS. For all animal studies, animals were randomly allocated to treatment group.

extract_protocol: Flash-frozen tissues were sent to Active Motif to perform the ATAC-seq assay. The tissues were manually disassociated, isolated nuclei were quantified using a hemocytometer, and 100,000 nuclei were tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017) using the enzyme and buffer provided in the ATAC-Seq Kit (Active Motif). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified by Nanodrop and sequenced with PE42 sequencing on the NovaSeq 6000 sequencer (Illumina).

treatment_protocol: RAO55 xenograft mice commenced treatment 21 days post xenograft. To assess the combination effects of paxalisib and targeted therapies, 5 mg/kg twice daily dosing of paxalisib was combined with metformin (175 mg/kg, day, gavage) and enzastaurin (100 mg/kg, daily, gavage), in 1% methylcellulose cp15/0.2% Tween 80 for 4 weeks.

value: Diffuse intrinsic pontine glioma (DIPG)

tag: protocol

value: RA055 injected into the pontine region of 6-8 week old, female, NSG mice

value: Paxalisib (5 mg/kg twice daily) + metformin (175 mg/kg, day, gavage) in 1% methylcellulose cp15/0.2% Tween 80

tag: time

value: 4 weeks


title: Experiment 3, tg(her4:RFP)

value: Quiescent

value: R

value: tel


title: Cal33, 4 Gy x-ray irradiation, replicate 2

value: Head and Neck Squamous Cell Carcinoma

value: WT


title: RAO55 xenograft, Pax-Enz

value: Paxalisib (5 mg/kg twice daily) + enzastaurin (100 mg/kg, daily, gavage) in 1% methylcellulose cp15/0.2% Tween 80


title: iMyb MyPL1, Day 4, Dox, rep3

value: Thymus

value: T-ALL


title: Experiment 2, tg(her4:RFP), tg(mcm5:gfp)

value: brain/telencephali

value: RG


title: RAO55 xenograft, Enzastaurin

value: Enzastaurin (100 mg/kg, daily, gavage) in 1% methylcellulose cp15/0.2% Tween 80


title: iMyb MyPL1, Day 4, Control, rep3


title: Cal33, 4 Gy x-ray irradiation, replicate 1

value: tongue


title: Experiment 2, tg(her4:RFP)


title: Experiment 1, tg(her4:RFP), tg(mcm5:gfp)

value: tg(her4:RFP), tg(mcm5:gfp)

value: Activated


title: iMyb MyPL1, Day 3, Dox, rep3


title: Cal33, GSK-J1, replicate 3


title: Cal33, GSK-J1, replicate 2


title: RAO55 xenograft, Paxalisib

value: Diffuse intrinsic pontine glioma (DIPG)

value: RA055 injected into the pontine region of 6-8 week old, female, NSG mice

value: Paxalisib (5 mg/kg twice daily) in 1% methylcellulose cp15/0.2% Tween 80


title: Experiment 1, tg(her4:RFP)

value: Quiescent


title: Cal33, GSK-J1, replicate 1


title: RAO55 xenograft, Untreated

value: Untreated

value: 4 weeks


title: iMyb MyPL1, Day 2, Dox, rep3


title: RAO55 xenograft, Pax-Met-Enz

value: Paxalisib (5 mg/kg twice daily) + metformin (175 mg/kg, day, gavage) + enzastaurin (100 mg/kg, daily, gavage) in 1% methylcellulose cp15/0.2% Tween 80


title: iMyb MyPL1, Day 3, Control, rep3


title: MicroC_HSPC_rep2

city: San Antonio

first: Pinpin

last: Sui

state: TX

address: 8403 Floyd Curl Dr., STRF

department: Molecular Medicine

institute: UT health San Antonio

data_processing:
The fastq files were quality controlled by fastqc and trimmed by trim_galore(v0.6.7)
Clean reads were aligned to the reference genome using BWA(v0.7.17-r1188)
Pairtools (v1.0.2) was used to generate final valid pairs bam file
Juicer (v1.22.01) and cooler (v0.9.1) was used to generate .cool and .hic file respectively
FAN-C(v0.9.25), Juicer arrowhead (v1.22.01) and mustache (v1.3.1) was used to identify compartment, TAD and loop respectively
Assembly: GRCh38
Supplementary files format and content: .mcool file for each sample
Library strategy: Micro-C

source_name: HSPCs

growth_protocol: Human CD34+ HSPCs and CRISPR-Cas9 engineered MLL-AF9 leukemia cells were cultured in StemSpan SFEM II medium with SCF (50 ng/mL), thrombopoietin (100 ng/mL), Flt3 ligand (100 ng/mL), IL-6 (100 ng/mL), IL-3 (50 ng/mL), G-CSF (50 ng/mL), UM729 (0.75 µM), StemRegenin 1 (0.75 µM), and 20% FBS at 37°C, 5% CO2

extract_protocol:
1x106 leukemia and healthy donor cells were resuspended in 1xPBS and crosslinked with 3mM DSG and 1% formaldehyde. Treated cells were then washed and digested with 0.5 uL MNase in 100 uL of Nuclease digest buffer. Digested chromatin was thawed by addition of 3µl of 20% SDS and capture on chromatin capture beads.
Micro-C libraries were performed following Dovetail Micro-C Kit protocol (Cat # 21006, Dovetail Genomics, Scotts Valley, CA, USA)

value: HSPCs

value: WT


title: MicroC_HSPC_rep1


title: Cal33, GSK-J1 plus 4 Gy x-ray irradiation, replicate 3

value: Head and Neck Squamous Cell Carcinoma

value: GSK-J1 plus 4 Gy x-ray irradiation


title: Experiment 13, tg(her4:RFP-high)

data_processing:
Reads were mapped to zebrafish genome using STAR
Gene counts were computed using featureCounts
Differential expression analysis was performed with DESeq2
Assembly: GRCz10
Supplementary files format and content: Tab-delimited text file with gene Ids and their respective counts

value: brain/telencephali

value: 3 mpf

value: Quiescent, highly expressing her4.3

value: H


title: Experiment 13, tg(her4:RFP-low)

value: Quiescent, low expression of her4.3

value: L


title: Cal33, GSK-J1 plus 4 Gy x-ray irradiation, replicate 2

value: tongue


title: iMyb MyPL1, Day 1, Control, rep4

value: Thymus

value: T-ALL


title: iMyb MyPL1, Day 1, Dox, rep3


title: Cal33, GSK-J1 plus 4 Gy x-ray irradiation, replicate 1


title: iMyb MyPL1, Day 2, Control, rep3


title: MicroC_AML_MA9_rep1

source_name: AML cells

value: AML cells


title: MicroC_AML_MA9_rep2


title: Experiment 13, tg(her4:RFP), tg(mcm5:gfp)

value: tg(her4:RFP), tg(mcm5:gfp)

value: Activated

value: G


title: iMyb MyPL1, Day 1, Control, rep3


title: RNA_HSPC_rep2

data_processing:
The fastq files were quality controlled by fastqc and trimmed by trim_galore(v0.6.7)
Clean reads were aligned to the reference genome using STAR(v2.7.10b)
The raw read counts of each gene were calculated using HTSeq(v2.0.2)
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was extracted from control and leukemia cells with RNeasy Plus Mini Kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: HSPCs


title: iMyb MyPL1, Day 4, Dox, rep2


title: Experiment 12, tg(her4:RFP-low)


title: Experiment 12, tg(her4:RFP-high)


title: RNA_HSPC_rep1

value: WT


title: iMyb MyPL1, Day 4, Control, rep2


title: Experiment 12, tg(her4:RFP), tg(mcm5:gfp)


title: ADAR eCLIP IP rep2

city: LA JOLLA

first: Hsuan-Lin

last: Her

address: 9500 Gilman Dr,

institute: UCSD

description:
4137_CLIP1_rep1.vs.4137_CLIP2_rep2.bed
encode4_batch23.4137_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.bed

data_processing:
Processed Using https://github.com/YeoLab/eclip 0.7.0
After standard HiSeq demultiplexing, eCLIP libraries with distinct in-line barcodes were demultiplexed using custom scripts, and the random-mer was appended to the read name for later usage. Reads were then adapter trimmed (cutadapt v1.9.dev1) and reads less than 18 bp were discarded
Mapping was then first performed against human elements in RepBase (v18.05) with STAR (v2.4.0i), repeat-mapping reads were segregated for separate analysis, and all others were then mapped against the full human genome (hg19) including a database of splice junctions with STAR (v 2.4.0i) (Dobin et al., 2013). Uniquely mapping reads were then run through a custom-built PCR duplicate removal script, removing duplicate reads based on sharing identical Read1 start position, Read2 start position, and random-mer sequence to leave 'Usable' reads.
eCLIP data sets with multiple in-line barcodes were merged at the usable read stage, and cluster identification was performed on usable reads using CLIPper (Yeo et al., 2009) (available at https://github.com/YeoLab/clipper/releases/tag/1.0) with options –s GRCh38 –o –bonferroni –superlocal–threshold-method binomial–save-pickle
data are further downsampled to roughly equal number per replicate
Assembly: hg38
Supplementary files format and content: wig files represent read covergae for plus and minus strands
Supplementary files format and content: peak files

growth_protocol: While plated, HepG2 cells were crosslinked with UV (254 nm, 400 mJ/cm2). HepG2 cells were then isolated with cell scrapers, pelleted at 200g, and snap frozen. K562 suspension cells were pelleted at 200g and resuspended in 1X PBS to 20 million cells per mL. 60 million cells in 3 mL were UV crosslinked (254 nm, 400 mJ/cm2) per 10 cm dish, pelleted, and snap frozen.

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.
seCLIP

treatment_protocol: HepG2 cells were grown under standard conditions (DMEM + 10% FBS + Pen/Strep (100U / mL)). K562 cells were grown in suspension in standard media (RPMI + 10% FBS + Pen/Strep (100U / mL)).

value: human  lymphoblast cell

value: ADAR1 antibody (CST #14175)


title: ADAR eCLIP IN rep1

description:
4137_CLIP1_rep1.vs.4137_CLIP2_rep2.bed
encode4_batch23.4137_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.bed


title: RNA_AML_MA9_rep2


title: RNA_AML_MA9_rep1


title: Experiment 11, tg(her4:RFP-low)

value: brain/telencephali


title: iMyb MyPL1, Day 3, Dox, rep2


title: iMyb MyPL1, Day 3, Control, rep2


title: Experiment 11, tg(her4:RFP-high)

value: 3 mpf


title: Experiment 11, tg(her4:RFP), tg(mcm5:gfp)


title: ADAR eCLIP IP rep1


title: iMyb MyPL1, Day 2, Control, rep2


title: 37degC, scRNAseq

city: Shanghai

first: Yuxiao

last: Ma

address: No. 1630 Pujian Road

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

description: singlecellRNA-Seq

data_processing:
The feature-barcode matrices were obtained by aligning reads to the human genome (GRCh38 Ensemble: version 91) using CellRanger v3.1.0.
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 20%;   Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized counts for each cell
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Primary cells

growth_protocol: For the process of neural induction, the neurospheres were meticulously dissociated into a single-cell suspension and plated on coverslips that had been previously coated with 0.01% poly-L-lysine at a density of 2×104 cells/cm2. Subsequently, the cells were cultured in expansion medium for 48 hours, to allow for adequate recovery from passage. Once the recovery period had elapsed, the cultured medium was changed to a neural differentiation medium, which comprised of neurobasal medium (Gbico, 21103049), 2% B27 supplement, 1% penicillin/streptomycin, and 1% L-GlutaMAX (Gbcio, 35050079). Following 14 days of culture, the cells were collected for sc-RNA.

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

treatment_protocol: After cells was cultutred with differentiation condition, the cells was treated with 35degC and 37degC temperature in different culture incubator.

value: Primary cells

value: human  neural stem cell


title: SOX2 knockdown bulk RNA-seq G.i1_clone3 -Dox biol_rep2

city: Planegg

first: Wolfgang

last: Enard

address: Großhadernerstr. 2

institute: Ludwig-Maximilians-Universität München

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone3_6
BC:  TCGGTTCGCTCA

data_processing:
Fastq data file quality assessment was conducted using fastqc (Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data. Available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
polyA trimming was performed with cutadapt (Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal, 17(1), 10-12.).
Quality filtering, mapping and counting was done using the zUMIs pipeline (Parekh, S., Ziegenhain, C., Vieth, B., Enard, W., & Hellmann, I. (2018). zUMIs—A fast and flexible pipeline to process RNA sequencing data with UMIs. GigaScience, 7(6), giy059).
Assembly: hg38, gorGor6, macFas6, all extended by the KRAB-dCas9 encoding sequence that was integrated in the genomes of the cell lines
Supplementary files format and content: We provide a separate count table per species as rds files
Supplementary files format and content: The sample conditions are noted in the additional sample_annotation_data_submission file.

organism: Gorilla gorilla

source_name: KRAB-dCas9 iPSCs

growth_protocol: Cell were grown in SF03 +Dox (1 µg/mL) or -Dox for 4 days.

extract_protocol:
Cells that were cultured in 24-wells, were lysed in 200 µL Buffer RLT Plus supplemented with 1 % 2-Mercaptoethanol and then stored at -80 °C until processing.
Libraries were constructed following the published prime-seq protocol. (Janjic, A., Wange, L.E., Bagnoli, J.W. et al. Prime-seq, efficient and powerful bulk RNA sequencing. Genome Biol 23, 88 (2022). https://doi.org/10.1186/s13059-022-02660-8); https://www.protocols.io/view/prime-seqs9veh66
polyA-capture bulk RNA-seq

value: KRAB-dCas9 iPSCs

value: iPSCs

value: -Dox


title: Experiment 10, tg(her4:RFP-low)

value: Quiescent, low expression of her4.3

value: L


title: iMyb MyPL1, Day 2, Dox, rep2

value: Thymus

value: T-ALL


title: 35degC, scRNAseq

description: singlecellRNA-Seq


title: SOX2 knockdown bulk RNA-seq G.i1_clone3 -Dox biol_rep3

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone3_7
BC:  CGTATGAAGAGG


title: iMyb MyPL1, Day 1, Dox, rep2


title: Experiment 10, tg(her4:RFP-high)

value: Quiescent, highly expressing her4.3

value: H


title: ADAR eCLIP IN rep2


title: Experiment 10, tg(her4:RFP), tg(mcm5:gfp)

value: tg(her4:RFP), tg(mcm5:gfp)

value: Activated

value: G


title: SOX2 knockdown bulk RNA-seq G.i1_clone3 +Dox biol_rep4

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone3_4
BC:  TTGTACCTACGG

value: +Dox


title: hNSCs 37C, RBM3, Proteintech

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads. We used Hisat2 (version:2.0.4) to map the cleaned reads to the human GRCh38 reference genome with two mismatches. After genome mapping, Stringtie (ersion:1.3.0) was run with a reference annotation to generate FPKM.txt values for known gene models. Differentially expressed genes were identified using edgeR. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR) . The fold-changes were also estimated according to the FPKM.txt in each sample.
The differentially expressed genes were selected using the following filter criteria: FDR ≤0.05 and fold-change ≥2.
Assembly: GRCh38
Supplementary files format and content: Text files include FPKM.txt values for each Sample

extract_protocol:
The hNSCs were treated with 4-SU at a final concentration of 100 μM, 24 hours prior to cells collection. Subsequently, the hNSCs cultured in a 6 cm plate for 14 days of differentiation were carefully washed twice with ice-cold PBS and subjected to cross-linkage using 4000 joules of UV irradiation for three times. Following this process, the cells were gently scraped off using 1 ml PBS and centrifuged at 300 g × 5 min, after which they were re-suspended in 300 μl of complete IP cell lysis buffer (20 μM of Tris-HCl pH 7.5, 10 μM of KCl, 5 μM of MgCl2, 0.5% NP-40, 1 μM of DTT (ThermoFisher, R0862), 40 units/ml of RNase inhibitor (Sangon Biotech, B600478), and EDTA-Free Protease Inhibitor Cocktail (Bimake, B14001)). Besides, after centrifugation, 100 ml of scraped cells were added with TRIzol (Vazyme, R401-01) labelled as “Input” for RNA analysis. The cells were then incubated on ice for 15 minutes and centrifuged at 12000 g for 15 minutes at 4C. After centrifugation, 30 ml of cell lysate supernatant were transferred to a new tube labelled as “Input” for protein analysis. The remaining supernatant was then treated with or without Rnase T1 (Thermo Scientific, EN0601), at a final concentration of 1 unit/ml, for 10 minutes at room temperature. Subsequently, the lysate supernatant was mixed with 10 ml of antibody-coupling agarose beads and incubated overnight at 4C with rotation. The next day, the samples were centrifuged at 3000 g for 5 minutes and the supernatant was carefully discarded. The samples were then washed thrice with 1 millilitre of ice-cold PBS. After the third centrifugation, the beads were resuspended with 200 microliters of IP buffer, and 20 microliters of the sample was taken for protein testing. Subsequently, protease K was added to a concentration of 100 micrograms/millilitre and incubated at 55 degrees Celsius for 2 hours. Finally, 1 millilitre of TRIzol was added to one sample to extract RNA for further sequence and qRT-PCR analysis.
Bounded RNA was isolated from sample using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Purified libraries were quantified by Qubit® 2.0Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced. The library construction and sequencing was performed at Shanghai Biotechnology Corporation.

value: human neural stem cells

tag: rip antibody

value: RBM3 (Proteintech, 14363-1-AP)


title: iMyb MyPL1, Day 4, Dox, rep1


title: hNSCs 35C, RBM3, Proteintech

value: Primary cells


title: SOX2 knockdown bulk RNA-seq G.i1_clone3 +Dox biol_rep3

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone3_3
BC:  AAGAGCTGGTCT


title: 116 – HC3

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

description: Healthy Control samples from the trunk area 112 – HC1, 115 – HC2, 116 – HC3 and 121 – HC4 used in this manuscript, which are already publicly available via Gene Expression Omnibus GSE173205, were updated using the newer Cell Ranger version (v. 6.1.2; 10x Genomics) for consistency reasons.

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38) and counted using Cell Ranger (version 6.1.2; 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

source_name: Skin Biopsy

extract_protocol:
Single cell suspensions from full thickness skin punch biopsies were generated using the Skin Dissociation Kit by Miltenyi Biotech (Bergisch Gladbach, Germany).
These cells were immediately processed for scRNA-seq by using the Chromium Single Cell Controller and Single Cell 5’ Library & Gel Bead Kit v1.1 (10X Genomics, Pleasanton, CA), following the manufacturer’s suggestions. T-cell receptor (TCR) sequences were enriched from cDNA using the respective reagents, and according to the instructions of the VDJ Kit workflow by 10X Genomics. Sequencing was performed using the Illumina NovaSeq platform and the 150bp paired-end configuration.

value: Skin Biopsy

tag: subject id

tag: serum ige (kiu/l)

tag: diagnosis

value: Healthy control skin

tag: chemistry

value: Single Cell 5' PE


title: 121 – HC4

tag: tissue


title: iMyb MyPL1, Day 4, Control, rep1

tag: cell type

tag: genotype


title: SOX2 knockdown bulk RNA-seq G.i1_clone3 -Dox biol_rep4

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone3_8
BC:  TCTTGCGTTCAA

tag: cell line

value: KRAB-dCas9 iPSCs

value: iPSCs

tag: treatment

value: -Dox


title: n2l3_snu66x_sz371_az012

city: Santa Cruz

first: Alan

middle: M

last: Zahler

address: 1156 High St.

department: MCD Biology

institute: UC Santa Cruz

data_processing:
150 x 150 paired end reads. Sequencing libraries were strand-specific (read2 is the coding strand).
Reads were mapped with Bowtie2 to the RepeatMasker library of C.elegans repeat elements.
After removing reads with both ends mapped to repeat elements, the remaining reads were mapped to the ce10 genome assembly using STAR.
Potential PCR duplicates were removed with samtools rmdup.
Splice junctions were extracted from the bam files by examining the CIGAR string, resulting in a non-redundant set of introns spanned by these splice junctions.
Alternative splicing events of types A5,A3 were identified from the splice junctions found in sequencing libraries.
A5 events: A custom script was employed to identify junctions that define alternative 5' ss separated by <50bp across the libraries mapped to the indicated genome assembly.
A3 events: A custom script was employed to identify junctions that define alternative 3' ss separated by <50bp across the libraries mapped to the indicated genome assembly.
Alternative splicing events of types SE, RI, MS, MX, AF, AL were extracted from the ce10 EnsemblArchive65 transcript annotation using junctionCounts:infer_pairwise_events (github ajw2329/junctionCounts)
The program junctionCounts (github ajw2329/junctionCounts) was used to determine PSI (percent spliced in) for all events in all samples. The option "suppress_eij_use" was used for the A5,A3 events.
The junctionCounts PSI estimates for a sample were merged into a gtf with the scores for the 2 alternative transcripts of an event representing (1000 times) its PSI (and 1-PSI) values. If junctionCounts reported a non-zero span of the PSI estimate, these scores were reduced by a factor of (1-spanPSI).
Assembly: Oct. 2010 (WS220/ce10)
Supplementary files format and content: The ensArch65 gtf file for a sample contains the 2 alternative transcripts for each event of type SE, RI, MS, MX, AF, AL derived from the ce10 EnsembleArchive65 annotation. The score field of a transcript is 1000 times the PSI (1-PSI) value for the "included" ("excluded") transcript. This score is modified by a factor of (1-spanPSI) if there is a non-zero span in the estimate of PSI.
Supplementary files format and content: The libIntrons gtf file for a sample contains the 2 alternative transcripts for each event of type A3, A5 derived from the introns found in all sample sequencing libraries. The score field of a transcript is 1000 times the PSI (1-PSI) value for the "included" ("excluded") transcript. For these event types the span in the estimate of PSI is always zero.

organism: Caenorhabditis elegans

source_name: whole worm - L3

growth_protocol: Indicated strains were grown at 20C on NGM agar plates fed OP50 E. coli

extract_protocol:
Worms were lysed in Trizol and total RNA was cleaned by Zymo RNA Clean and Concentrator according to manufacturer's protocol.
mRNA libraries for high throughput sequencing were prepared by polyA selection by Azenta. Paired 150 nt reads, Illumina

treatment_protocol: Embryos were isolated by bleach treatment, grown for 34hours to the L3 larval stage, at which time RNA was extracted

value: whole worm - L3

value: SZ371 (snu-66(az161)V) H765L allele


title: n2l3_snu66x_sz371_az011


title: 115 – HC2


title: SOX2 knockdown bulk RNA-seq G.i1_clone3 +Dox biol_rep2

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone3_2
BC:  GTGCGATAGTCC


title: iMyb MyPL1, Day 3, Control, rep1

value: Thymus

value: T-ALL


title: SOX2 knockdown bulk RNA-seq G.i1_clone3 -Dox biol_rep1

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone3_5
BC:  GCGCCTTCTCTA


title: SOX2 knockdown bulk RNA-seq G.i1_clone2 -Dox biol_rep4

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone2_8
BC:  TCCTCCGCTTGT


title: SOX2 knockdown bulk RNA-seq G.i1_clone3 +Dox biol_rep1

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone3_1
BC:  AAGCTTACCGGA


title: n2l3_snu66x_sz371_az010


title: 112 – HC1


title: 96 – Trunk AD5

description: Trunk AD samples 74 – (Trunk) AD1, 75 – (Trunk) AD2, 77 – (Trunk) AD3, 81 – (Trunk) AD4  and 96 – (Trunk) AD5 used in this manuscript are about to become publicly available, since the manuscript "Single-cell RNA sequencing defines disease-specific differences between chronic nodular prurigo and atopic dermatitis" where these samples first appear has just been accepted and currently undergoes the preprint processing (Gene Expression Omnibus is GSE222840):

value: 96 – Trunk AD2

value: Atopic dermatitis


title: iMyb MyPL1, Day 2, Dox, rep1


title: n2l3_snu66x_sz370_az008

value: SZ370  (snu-66(az160)V) H765G allele


title: SOX2 knockdown bulk RNA-seq G.i1_clone2 -Dox biol_rep3

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone2_7
BC:  GACTATGAGCAA


title: iMyb MyPL1, Day 1, Control, rep2


title: 81 – Trunk AD4

value: 81 – Trunk AD2


title: iMyb MyPL1, Day 2, Control, rep1


title: n2l3_snu66x_sz370_az007


title: 77 – Trunk AD3

value: 77 – Trunk AD2


title: iMyb MyPL1, Day 1, Dox, rep1


title: iMyb MyPL1, Day 1, Control, rep1


title: SOX2 knockdown bulk RNA-seq G.i1_clone2 -Dox biol_rep1

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone2_5
BC:  ACCAGCCACCTA


title: iMyb MyPL1, Day 3, Dox, rep1


title: SOX2 knockdown bulk RNA-seq G.i1_clone2 +Dox biol_rep4

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone2_4
BC:  GATTCATTCGGA

value: +Dox


title: tdTomato+, wt, E15, rep2

city: Lyon

first: Guillaume

last: Marcy

address: 8 avenue Rockefeller

institute: Universite Lyon 1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt
Trimmed sequence reads were mapped to GRCm38 using STAR
Read count extraction and normalization were performed using Subread R package
Assembly: GRCm38
Supplementary files format and content: comma-delimited text files include raw values for each sample

source_name: brain

growth_protocol: P3 Mice were placed in a hypoxic rearing chamber maintaining at 10 ± 0.5% O2 concentration by displacement with N2 as described previously. Hypoxia began at P3, for 8 days, until P11. A separate group was maintained in a normal atmosphere (normoxic group; Nx). Foster mother was used to conserve milk quality under a hypoxic environment, control mother and hypoxic mother were exchanged at P6 and P9

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen). 400 pg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs)

value: brain

value: progenitor cells

tag: development stage

value: wt


title: 74 – Trunk AD1

value: Skin Biopsy

value: 74 – Trunk AD1

value: Single Cell 5' PE


title: n2l3_snrp27_sz211_az004

value: SZ211 (snrp-27(az56)I) M141T allele


title: n2l3_snrp27_sz211_az005

value: whole worm - L3


title: 180 – Head/neckAD5

value: 180 – Head/neckAD5


title: SOX2 knockdown bulk RNA-seq G.i1_clone2 +Dox biol_rep3

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone2_3
BC:  TCCATACGCGAA

value: KRAB-dCas9 iPSCs

value: iPSCs


title: n2l3_snu66x_sz370_az009


title: tdTomato+, wt, E15, rep1


title: 176 – Head/neckAD3

value: 176 – Head/neckAD3


title: SOX2 knockdown bulk RNA-seq G.i1_clone2 +Dox biol_rep2

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone2_2
BC:  TTCCGCCACTCA


title: tdTomato+, wt, E13, rep1


title: SOX2 knockdown bulk RNA-seq G.i1_clone2 +Dox biol_rep1

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone2_1
BC:  ATCTCGATACGA


title: SOX2 knockdown bulk RNA-seq G.i1_clone1 -Dox biol_rep4

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone1_8
BC:  AATGCATCAGCA

value: -Dox


title: n2l3_wldtyp_xxxxx_az003

value: N2  wildype strain


title: tdTomato+, wt, E13, rep2


title: tdTomato+, Nx, P12, rep2

value: normoxia


title: n2l3_wldtyp_xxxxx_az002


title: 151 – Head/neckAD2

value: 151 – Head/neckAD2

value: Atopic dermatitis


title: n2l3_snrp27_sz211_az006


title: SOX2 knockdown bulk RNA-seq G.i1_clone2 -Dox biol_rep2

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone2_6
BC:  AGAGTAATGCCA


title: SOX2 knockdown bulk RNA-seq G.i1_clone1 -Dox biol_rep3

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone1_7
BC:  ACGTATTGTCCA


title: 75 – Trunk AD2

value: 75 – Trunk AD2


title: 148 – Head/neckAD1

value: 148 – Head/neckAD1


title: SOX2 knockdown bulk RNA-seq G.i1_clone1 -Dox biol_rep2

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone1_6
BC:  TTATCTAACCGG


title: tdTomato+, Nx, P12, rep1

value: brain

value: progenitor cells


title: 161 – DAHND6

value: Skin Biopsy

value: 161 – DAHND6

value: Dupilumab-associated head neck dermatitis


title: SOX2 knockdown bulk RNA-seq G.i1_clone1 -Dox biol_rep1

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone1_5
BC:  CGATTCCTTCAA


title: 147 – DAHND5

value: 147 – DAHND5

value: Single Cell 5' PE


title: tdTomato+, Hx, P12, rep2

value: hypoxia


title: MG1655 recovery2h -2

city: Giessen

first: Bork

middle: A.

last: Berghoff

address: Heinrich-Buff-Ring 26-32

institute: University of Giessen

data_processing:
Quality and adapter trimming was performed with Trim Galore (Version 0.6.5) with Cutadapt Version 2.7 using the parameters ‘--quality 20 --length 20’ and default adapter detection and trimming.
MultiQC (Version 1.8) and FastQC (Version 0.11.8) were used for quality control.
The preprocessed reads were aligned with Bowtie2 (Version 2.3.5)  using the ‘--mm’ and ‘--very-sensitive’ settings and GCF_000005845.2 (NCBI; downloaded 25.11.2019) as a reference genome.
For postprocessing of the alignments, gene counting and data analysis, Samtools (Version 1.9), featureCounts (Version 1.6.4) and DESeq2 (Version 1.26) were applied, respectively.
All bioinformatic calculations were performed using Curare (Version 0.1.1)  and R statistical language.
Assembly: GCF_000005845.2
Supplementary files format and content: Excel file containing normalized read counts of each sample and DESeq2 comparison between conditions.

organism: Escherichia coli

growth_protocol: Cells were grown in LB medium at 37°C and shaking at 180 rpm.

extract_protocol:
RNA was isolated according to the hot acid-penol method. DNA was removed with TURBO DNA-freeTM kit (Invitrogen) according to "rigorous treatment" instructions. The final clean-up was performed using phenol/chloroform/isoamyl alcohol (25:24:1) mixed with the sample in a 1:1 ratio, followed by chloroform treatment and precipitation.
For cDNA synthesis, all RNA samples were first fragmented using ultrasound (4 pulses of 30 seconds, each at 4°C). Then, an oligonucleotide adapter was ligated to the 3’ end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5’ Illumina TruSeq sequencing adapter was ligated to the 3’ end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/µl using a high-fidelity DNA polymerase for 12 cycles. The TruSeq barcode sequences, which are part of the 5’ and 3’ TruSeq sequencing adapters, were used. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis.

treatment_protocol:
tisB was induced with L-arabinose (0.2%) for 30 min.
L-arabinose was removed by washing with 0.9% NaCl and cells were resuspended in LB medium for recovery.

tag: strain

value: K-12 F-lambda-

value: bacterial cell

tag: treatment 1

value: L-arabinose (0,2%)

tag: treatment 2

value: recovery after washing

value: 30 min + 120 min


title: MG1655 recovery2h -1


title: MG1655 recovery1h -3

value: 30 min + 60 min


title: MG1655 recovery2h -3


title: 177 – Head/neckAD4

value: 177 – Head/neckAD4

value: Atopic dermatitis


title: tdTomato+, Hx, P12, rep1


title: n2l3_wldtyp_xxxxx_az001

value: whole worm - L3

value: N2  wildype strain


title: SOX2 knockdown bulk RNA-seq G.i1_clone1 +Dox biol_rep4

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone1_4
BC:  CGCGGTCAAGAA

value: KRAB-dCas9 iPSCs

value: iPSCs

value: +Dox


title: 137 – DAHND4

value: Skin Biopsy

value: 137 – DAHND4

value: Dupilumab-associated head neck dermatitis


title: MG1655 recovery1h -2


title: 133 – DAHND3

value: 133 – DAHND3

value: Single Cell 5' PE


title: MG1655 recovery1h -1

value: K-12 F-lambda-

value: bacterial cell


title: SOX2 knockdown bulk RNA-seq G.i1_clone1 +Dox biol_rep2

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone1_2
BC:  CAGCGGAACTTA


title: BM-cDC1 IFNaA+anti-CD40 rep2

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

institute: University of Melbourne

data_processing:
Reads were aligned to the GRCm39 reference genome using bwa mem (version 0.7.17)
BAM files were coordinate sorted using samtools (version 1.16.1)
Duplicates were removed using Picard Tools' MarkDuplciates (version 2.25.0)
Peaks were called using MACS2 (version 2.2.7.1)
Peaks were annotated using homer
Assembly: Ensemblgene GRCm39 build 105
Supplementary files format and content: Tab separated peak files (annotated)
Library strategy: CUT&Tag

source_name: BM-derived cDC1

growth_protocol: BM-cDC1 were sorted from BM-derived DCs that were generated from bone marrow precursors cutlured for 8 days with Flt3L (150 ng/mL).

extract_protocol:
Isolated nuclei bound to activated Concanavalin A-coated magnetic beads before immunoprecipitation with 0.5ug of primary Ab (anti-IRF1 or rabbit anti-mous IgG control)
CUT&Tag libraries were prepared using hyperactive in situ ChIP Library Prep Kit purchased from Epicypher (CUTANA™ CUT&Tag Assays) following manufacturer's protocols.

treatment_protocol: Following sort, BM-cDC1 were washed and were stimulated with IFNaA (1000 U/mL) and/or anti-CD40 (10 ug/mL) for 4h. Following stimulation, samples were washed and frozen down.

value: BM-derived cDC1

value: IFNaA + anti-CD40 for 4h


title: 126 – DAHND2

value: 126 – DAHND2


title: MG1655 30min -3

value: L-arabinose (0,2%)

value: 30 min


title: SOX2 knockdown bulk RNA-seq G.i1_clone1 +Dox biol_rep3

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone1_3
BC:  GCCTCAAGATAA


title: 120 – DAHND1

value: 120 – DAHND1


title: SOX2 knockdown bulk RNA-seq G.i1_clone1 +Dox biol_rep1

description:
sample_annotation_data_submission.xlsx
Sox2_gorilla.dgecounts.rds
SOX2_KD_bulkRNA-seq_G.i1_clone1_1
BC:  TTAGCACACCTT


title: BM-cDC1 Unstimulated rep2

value: Untreated


title: MG1655 30min -2


title: BM-cDC1 IFNaA rep2

value: IFNaA for 4h